TMPRSS6 iRNA COMPOSITIONS AND METHODS OF USE THEREOF

Abstract
The invention relates to RNAi agents, e.g, double-stranded RNAi agents, targeting the TMPRSS6 gene, and methods of using such RNAi agents to inhibit expression of TMPRSS6 and methods of treating subjects having a TMPRSS6 associated disorder, e.g., an iron overload associated disorder, such as β-thalassemia or hemochromatosis.
Description
SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Dec. 7, 2020, is named 121301_00707_SL.txt and is 449,779 bytes in size.


BACKGROUND OF THE INVENTION

TMPRSS6 (Transmembrane Protease, Serine 6) gene encodes TMPRSS6, also known as matriptase-2, a type II serine protease. It is primarily expressed in the liver, although high levels of TMPRSS6 mRNA are also found in the kidney, with lower levels in the uterus and much smaller amounts detected in many other tissues (Ramsay et al., Haematologica (2009), 94(6), 840-849). TMPRSS6 plays a role in iron homeostatis by binding and proteolytically degrading the hepcidin activator and BMP co-receptor HJV (hemojuvelin), which causes down-regulation of hepcidin levels.


TMPRSS6 consists of a short N-terminal intracytoplasmic tail, a type II transmembrane domain, a stem region composed of two extracellular CUB (complement factor Cls/Clr, urchin embryonic growth factor and BMP (bone morphogenetic protein)) domains, three LDLR (low-density-lipoprotein receptor class A) domains, and a C-terminal trypsin-like serine protease domain. There are also consensus sites for N-glycosylation in the extracellular domain, and a potential phosphorylation site in the intracytoplasmic tail region.


Numberous disorders can be associated with iron overload, a condition characterized by increased levels of iron. Iron overload can result in excess iron deposition in various tissues and can lead to tissue and organ damage. Accordingly, methods for effective treatment of disorders associated with iron overload are currently needed.


SUMMARY OF THE INVENTION

The present invention provides compositions comprising RNAi agents, e.g, double-stranded iRNA agents, targeting TMPRSS6. The present invention also provides methods using the compositions of the invention for inhibiting TMPRSS6 expression and for treating TMPRSS6 associated disorders, e.g., iron overload associated disorders, such as thalassemia, e.g., β-thalassemia, or hemochromatosis.


Accordingly, in one aspect, the present invention provides RNAi agents, e.g., double-stranded RNAi agents, capable of inhibiting the expression of TMPRSS6 (matriptase-2) in a cell, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double-stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO:5, and the antisense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO: 10,


wherein substantially all of the nucleotides of the sense strand and substantially all of the nucleotides of the antisense strand are modified nucleotides, and


wherein the sense strand is conjugated to a ligand attached at the 3′-terminus.


In one embodiment, all of the nucleotides of said sense strand and all of the nucleotides of said antisense strand are modified nucleotides.


In one embodiment, the sense strand and the antisense strand comprise a region of complementarity which comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the antisense sequences listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12.


In one embodiment, at least one of the modified nucleotides is selected from the group consisting of a 3′-terminal deoxy-thymine (dT) nucleotide, a 2′-O-methyl modified nucleotide, a 2′-fluoro modified nucleotide, a 2′-deoxy-modified nucleotide, a locked nucleotide, an abasic nucleotide, a 2′-amino-modified nucleotide, a 2′-alkyl-modified nucleotide, a morpholino nucleotide, a phosphoramidate, a non-natural base comprising nucleotide, a nucleotide comprising a 5′-phosphorothioate group, a nucleotide comprising a 5′ phosphate or 5′ phosphate mimic (see, e.g, PCT Publication No. WO 2011/005860), and a terminal nucleotide linked to a cholesteryl derivative or a dodecanoic acid bisdecylamide group.


In one embodiment, at least one strand comprises a 3′ overhang of at least 1 nucleotide. In another embodiment, at least one strand comprises a 3′ overhang of at least 2 nucleotides.


In another aspect, the present invention provides RNAi agents, e.g., double-stranded RNAi agents, capable of inhibiting the expression of TMPRSS6 (matriptase-2) in a cell, wherein the double stranded RNAi agent comprises a sense strand complementary to an antisense strand, wherein the antisense strand comprises a region complementary to part of an mRNA encoding TMPRSS6, wherein each strand is about 14 to about 30 nucleotides in length, wherein the double stranded RNAi agent is represented by formula (III):





sense: 5′np-Na—(XXX)i—Nb—YYY—Nb—(ZZZ)j—Na-nq3′





antisense: 3′np′—Na′—(X′X′X′)k—Nb′—Y′Y′Y′—Nb′−(Z′Z′Z′)l—Na′-nq′5′  (III)


wherein:


i, j, k, and l are each independently 0 or 1;


p, p′, q, and q′ are each independently 0-6;


each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;


each Nb and Nb′ independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;


each np, np′, nq, and nq′, each of which may or may not be present, independently represents an overhang nucleotide;


XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides;


modifications on Nb differ from the modification on Y and modifications on Nb′ differ from the modification on Y′; and


wherein the sense strand is conjugated to at least one ligand.


In one embodiment, i is 0; j is 0; i is 1; j is 1; both i and j are 0; or both i and j are 1. In another embodiment, k is 0; 1 is 0; k is 1; 1 is 1; both k and l are 0; or both k and l are 1.


In one embodiment, XXX is complementary to X′X′X′, YYY is complementary to Y′Y′Y′, and ZZZ is complementary to Z′Z′Z′.


In one embodiment, YYY motif occurs at or near the cleavage site of the sense strand.


In one embodiment, Y′Y′Y′ motif occurs at the 11, 12 and 13 positions of the antisense strand from the 5′-end.


In one embodiment, Y′ is 2′-O-methyl.


In one embodiment, formula (III) is represented by formula (IIIa):





sense: 5′np-Na—YYY—Na-nq3′





antisense: 3′np′—Na′—Y′Y′Y′—Na′-nq′5′  (IIIa).


In another embodiment, formula (III) is represented by formula (IIIb):





sense: 5′np-Na—YYY—Nb—ZZZ—Na-nq3′





antisense: 3′np′—Na′—Y′Y′Y′—Nb′—Z′Z′Z′—Na′-nq′5′  (IIIb)


wherein each Nb and Nb′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides.


In yet another embodiment, formula (III) is represented by formula (IIIc):





sense: 5′np-Na—XXX—Nb—YYY—Na-nq3′





antisense: 3′np′—Na′—X′X′X′—Nb′—Y′Y′Y′—Na′-nq′5′  (IIIc)


wherein each Nb and Nb′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides.


In one embodiment, formula (III) is represented by formula (IIId):





sense: 5′np-Na—XXX—Nb—YYY—Nb—ZZZ—Na-nq3′





antisense: 3′np′—Na′—X′X′X′—Nb′—Y′Y′Y′—Nb′—Z′Z′Z′—Na′-nq′5′  (IIId)


wherein each Nb and Nb′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides and each Na and Na′ independently represents an oligonucleotide sequence comprising 2-10 modified nucleotides.


In one embodiment, the double-stranded region is 15-30 nucleotide pairs in length. In another embodiment, the double-stranded region is 17-23 nucleotide pairs in length. In yet another embodiment, the double-stranded region is 17-25 nucleotide pairs in length. In one embodiment, the double-stranded region is 23-27 nucleotide pairs in length. In another embodiment, the double-stranded region is 19-21 nucleotide pairs in length. In another embodiment, the double-stranded region is 21-23 nucleotide pairs in length. In one embodiment, each strand has 15-30 nucleotides. In another embodiment, each strand has 19-30 nucleotides.


In one embodiment, the modifications on the nucleotides are selected from the group consisting of LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O-alkyl, 2′-O-allyl, 2′-C-allyl, 2′-fluoro, 2′-deoxy, 2′-hydroxyl, and combinations thereof. In another embodiment, the modifications on the nucleotides are 2′-O-methyl or 2′-fluoro modifications.


In one embodiment, the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker. In another embodiment, the ligand is




embedded image


In one embodiment, the ligand is attached to the 3′ end of the sense strand.


In one embodiment, the RNAi agent is conjugated to the ligand as shown in the following schematic




embedded image


wherein X is O or S. In a specific embodiment, X is O.


In one embodiment, the agent further comprises at least one phosphorothioate or methylphosphonate internucleotide linkage.


In one embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at the 3′-terminus of one strand. In one embodiment, the strand is the antisense strand. In another embodiment, the strand is the sense strand.


In one embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at the 5′-terminus of one strand. In one embodiment, the strand is the antisense strand. In another embodiment, the strand is the sense strand.


In one embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at the both the 5′- and 3′-terminus of one strand. In one embodiment, the strand is the antisense strand.


In one embodiment, the RNAi agent comprises 6-8 phosphorothioate internucleotide linkages.


In one embodiment, the antisense strand comprises two phosphorothioate internucleotide linkages at the 5′-terminus and two phosphorothioate internucleotide linkages at the 3′-terminus, and the sense strand comprises at least two phosphorothioate internucleotide linkages at either the 5′-terminus or the 3′-terminus.


In one embodiment, the base pair at the 1 position of the 5′-end of the antisense strand of the duplex is an AU base pair.


In one embodiment, the Y nucleotides contain a 2′-fluoro modification.


In one embodiment, the Y′ nucleotides contain a 2′-O-methyl modification.


In one embodiment, p′>0. In another embodiment, p′=2.


In one embodiment, q′=0, p=0, q=0, and p′ overhang nucleotides are complementary to the target mRNA. In another embodiment, q′=0, p=0, q=0, and p′ overhang nucleotides are non-complementary to the target mRNA.


In one embodiment, the sense strand has a total of 21 nucleotides and the antisense strand has a total of 23 nucleotides.


In one embodiment, at least one np′ is linked to a neighboring nucleotide via a phosphorothioate linkage.


In one embodiment, all np′ are linked to neighboring nucleotides via phosphorothioate linkages.


In one embodiment, the RNAi agent is selected from the group of RNAi agents listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12.


In one embodiment, the RNAi agent is AD-59743. In another embodiment, the RNAi agent is AD-60940.


In one aspect, the present invention provides double stranded RNAi agents for inhibiting expression of TMPRSS6 in a cell,


wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region,


wherein the sense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO:5, and the antisense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO: 10,


wherein substantially all of the nucleotides of the sense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification,


wherein the sense strand comprises two phosphorothioate internucleotide linkages at the 5′-terminus,


wherein substantially all of the nucleotides of the antisense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification,


wherein the antisense strand comprises two phosphorothioate internucleotide linkages at the 5′-terminus and two phosphorothioate internucleotide linkages at the 3′-terminus, and


wherein the sense strand is conjugated to one or more GalNAc derivatives attached through a branched bivalent or trivalent linker at the 3′-terminus.


In one embodiment, all of the nucleotides of the sense strand and all of the nucleotides of the antisense strand comprise a modification.


In another aspect, the present invention provides RNAi agents, e.g., double stranded RNAi agents, capable of inhibiting the expression of TMPRSS6 (matriptase-2) in a cell, wherein the double stranded RNAi agent comprises a sense strand complementary to an antisense strand, wherein the antisense strand comprises a region complementary to part of an mRNA encoding TMPRSS6, wherein each strand is about 14 to about 30 nucleotides in length, wherein the double stranded RNAi agent is represented by formula (III):





sense: 5′np-Na—(XXX)i—Nb—YYY—Nb—(ZZZ)j—Na-nq3′





antisense: 3′np′—Na′—(X′X′X′)k—Nb′—Y′Y′Y′—Nb′—(Z′Z′Z′)l—Na′-nq′5′  (III)


wherein:


i, j, k, and l are each independently 0 or 1;


p, p′, q, and q′ are each independently 0-6;


each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;


each Nb and Nb′ independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;


each np, np′, nq, and nq′, each of which may or may not be present independently represents an overhang nucleotide;


XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides, and wherein the modifications are 2′-O-methyl or 2′-fluoro modifications;


modifications on Nb differ from the modification on Y and modifications on Nb′ differ from the modification on Y′; and


wherein the sense strand is conjugated to at least one ligand.


In yet another aspect, the present invention provides RNAi agents, e.g, double stranded RNAi agents, capable of inhibiting the expression of TMPRSS6 (matriptase-2) in a cell, wherein the double stranded RNAi agent comprises a sense strand complementary to an antisense strand, wherein the antisense strand comprises a region complementary to part of an mRNA encoding TMPRSS6, wherein each strand is about 14 to about 30 nucleotides in length, wherein the double stranded RNAi agent is represented by formula (III):





sense: 5′np-Na—(XXX)i—Nb—YYY—Nb—(ZZZ)j—Na-nq3′





antisense: 3′np′—Na′—(X′X′X′)k—Nb′—Y′Y′Y′—Nb′—(Z′Z′Z′)l—Na′-nq′5′  (III)


wherein:


i, j, k, and l are each independently 0 or 1;


each np, nq, and nq′, each of which may or may not be present, independently represents an overhang nucleotide;


p, q, and q′ are each independently 0-6;


np′>0 and at least one np′ is linked to a neighboring nucleotide via a phosphorothioate linkage;


each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;


each Nb and Nb′ independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;

    • XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides, and wherein the modifications are 2′-O-methyl or 2′-fluoro modifications;


modifications on Nb differ from the modification on Y and modifications on Nb′ differ from the modification on Y′; and


wherein the sense strand is conjugated to at least one ligand.


In a further aspect, the present invention provides RNAi agents, e.g., double stranded RNAi agents, capable of inhibiting the expression of TMPRSS6 (matriptase-2) in a cell, wherein the double stranded RNAi agent comprises a sense strand complementary to an antisense strand, wherein the antisense strand comprises a region complementary to part of an mRNA encoding TMPRSS6, wherein each strand is about 14 to about 30 nucleotides in length, wherein the double stranded RNAi agent is represented by formula (III):





sense: 5′np-Na—(XXX)i—Nb—YYY—Nb—(ZZZ)j—Na-nq3′





antisense: 3′np′—Na′—(X′X′X′)k—Nb′—Y′Y′Y′—Nb′—(Z′Z′Z′)l—Na′-nq′5′  (III)


wherein:


i, j, k, and l are each independently 0 or 1;


each np, nq, and nq′, each of which may or may not be present, independently represents an overhang nucleotide;


p, q, and q′ are each independently 0-6;


np′>0 and at least one np′ is linked to a neighboring nucleotide via a phosphorothioate linkage;


each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;


each Nb and Nb′ independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;


XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides, and wherein the modifications are 2′-O-methyl or 2′-fluoro modifications;


modifications on Nb differ from the modification on Y and modifications on Nb′ differ from the modification on Y′; and


wherein the sense strand is conjugated to at least one ligand, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.


In another aspect, the present invention provides RNAi agents, e.g., double stranded RNAi agents capable of inhibiting the expression of TMPRSS6 (matriptase-2) in a cell, wherein the double stranded RNAi agent comprises a sense strand complementary to an antisense strand, wherein the antisense strand comprises a region complementary to part of an mRNA encoding TMPRSS6, wherein each strand is about 14 to about 30 nucleotides in length, wherein the double stranded RNAi agent is represented by formula (III):





sense: 5′np-Na—(XXX)i—Nb—YYY—Nb—(ZZZ)j—Na-nq3′





antisense:3′np′—Na′—(X′X′X′)k—Nb′—Y′Y′Y′—Nb′—(Z′Z′Z′)l—Na′-nq′5′  (III)


wherein:


i, j, k, and l are each independently 0 or 1;


each np, nq, and nq′, each of which may or may not be present, independently represents an overhang nucleotide;


p, q, and q′ are each independently 0-6;


np′>0 and at least one np′ is linked to a neighboring nucleotide via a phosphorothioate linkage;


each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;


each Nb and Nb′ independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;


XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides, and wherein the modifications are 2′-O-methyl or 2′-fluoro modifications;


modifications on Nb differ from the modification on Y and modifications on Nb′ differ from the modification on Y′;


wherein the sense strand comprises at least one phosphorothioate linkage; and


wherein the sense strand is conjugated to at least one ligand, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.


In yet another aspect, the present invention provides RNAi agents, e.g, double stranded RNAi agents, capable of inhibiting the expression of TMPRSS6 (matriptase-2) in a cell, wherein the double stranded RNAi agent comprises a sense strand complementary to an antisense strand, wherein the antisense strand comprises a region complementary to part of an mRNA encoding TMPRSS6, wherein each strand is about 14 to about 30 nucleotides in length, wherein the double stranded RNAi agent is represented by formula (III):





sense: 5′np-Na—YYY—Na-nq3′





antisense: 3′np′—Na′—Y′Y′Y′—Na′-nq′5′  (IIIa)


wherein:


each np, nq, and nq′, each of which may or may not be present, independently represents an overhang nucleotide;


p, q, and q′ are each independently 0-6;


np′>0 and at least one np′ is linked to a neighboring nucleotide via a phosphorothioate linkage;


each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;


YYY and Y′Y′Y′ each independently represent one motif of three identical modifications on three consecutive nucleotides, and wherein the modifications are 2′-O-methyl or 2′-fluoro modifications;


wherein the sense strand comprises at least one phosphorothioate linkage; and


wherein the sense strand is conjugated to at least one ligand, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.


In one embodiment, the present invention provides RNAi agent selected from the group of RNAi agents listed in any one of Tables 1, 2, 4, 5, 8, 19, and 12.


In one aspect, the present invention provides compositions comprising a modified antisense polynucleotide agent, wherein the agent is capable of inhibiting the expression of TMPRSS6 in a cell, and comprises a sequence complementary to a sense sequence selected from the group of the sequences listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12, wherein the polynucleotide is about 14 to about 30 nucleotides in length.


The present invention also provides cells, vectors, host cells, and pharmaceutical compositions comprising, e.g., the double stranded RNAi agents of the invention.


In some embodiments, the RNAi agent is administered using a pharmaceutical composition.


In preferred embodiments, the RNAi agent is administered in a solution. In some such embodiments, the siRNA is administered in an unbuffered solution. In one embodiment, the siRNA is administered in water. In other embodiments, the siRNA is administered with a buffer solution, such as an acetate buffer, a citrate buffer, a prolamine buffer, a carbonate buffer, or a phosphate buffer or any combination thereof. In some embodiments, the buffer solution is phosphate buffered saline (PBS).


In one embodiment, the pharmaceutical compositions further comprise a lipid formulation. In one embodiment, the lipid formulation comprises a LNP, or XTC. In another embodiment, the lipid formulation comprises a MC3.


In one aspect, the present invention provides methods of inhibiting TMPRSS6 expression in a cell. The methods include contacting the cell with an RNAi agent, e.g., a double stranded RNAi agent, or a modified antisense polynucleotide agent of the invention, or vector of the invention, or a pharmaceutical composition of the invention; and maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of a TMPRSS6 gene, thereby inhibiting expression of the TMPRSS6 gene in the cell.


In one embodiment, the cell is within a subject.


In one embodiment, the subject is a human.


In one embodiment, the TMPRSS6 expression is inhibited by at least about 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100%.


In another embodiment, hepcidin gene expression is increased by at least about 1.5-fold, about 2-fold, about 3-fold, about 4-fold, or about 5-fold.


In yet another embodiment, serum hepcidin concentration is increased by at least about 10%, about 25%, about 50%, about 100%, about 150%, about 200%, about 250%, or about 300%.


In one embodiment, serum iron concentration is decreased by at least about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 98% or about 100%.


In another embodiment, a percent transferrin saturation is decreased by at least about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 98% or about 100%.


In another aspect, the present invention provides methods of treating a subject having a disorder mediated by, or associated with, TMPRSS6 expression. The methods include administering to the subject a therapeutically effective amount of an RNAi agent, e.g., a double stranded RNAi agent, of the invention, or a modified antisense polynucleotide agent of the invention, or a vector of the invention, or a pharmaceutical composition of the invention, thereby treating the subject.


In one aspect, the present invention provides methods of treating a subject having a TMPRSS6-associated disorder. The methods include subcutaneously administering to the subject a therapeutically effective amount of a double stranded RNAi agent,


wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region,


wherein the sense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO:5, and the antisense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO: 10,


wherein substantially all of the nucleotides of the antisense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification,


wherein the antisense strand comprises two phosphorothioate internucleotide linkages at the 5′-terminus and two phosphorothioate internucleotide linkages at the 3′-terminus,


wherein substantially all of the nucleotides of the sense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification,


wherein the sense strand comprises two phosphorothioate internucleotide linkages at the 5′-terminus and,


wherein the sense strand is conjugated to one or more GalNAc derivatives attached through a branched bivalent or trivalent linker at the 3′-terminus, thereby treating the subject.


In one embodiment, all of the nucleotides of the sense strand and all of the nucleotides of the antisense strand comprise a modification.


In one embodiment, the subject is a human.


In one embodiment, the subject has a disorder associated with iron overload, e.g., hereditary hemochromatosis, β-thalassemia (e.g., β-thalassemia major and β-thalassemia intermedia) erythropoietic porphyria, Parkinson's Disease, Alzheimer's Disease or Friedreich's Ataxia.


In one embodiment, the RNAi agent, e.g., double stranded RNAi agent, is administered at a dose of about 0.01 mg/kg to about 10 mg/kg, about 1 mg/kg to about 10 mg/kg, about 2 mg/kg to about 10 mg/kg, about 3 mg/kg to about 10 mg/kg, about 4 mg/kg to about 10 mg/kg, about 5 mg/kg to about 15 mg/kg, about 6 mg/kg to about 15 mg/kg, about 7 mg/kg to about 15 mg/kg, about 8 mg/kg to about 15 mg/kg, about 9 mg/kg to about 15 mg/kg, about 10 mg/kg to about 20 mg/kg, about 12 mg/kg to about 20 mg/kg, about 13 mg/kg to about 20 mg/kg, about 14 mg/kg to about 20 mg/kg, about 15 mg/kg to about 20 mg/kg, about 16 mg/kg to about 20 mg/kg or about 18 mg/kg to about 20 mg/kg. In particular embodiments, the double stranded RNAi agent is administered at a dose of about 0.1 mg/kg, about 1.0 mg/kg, or about 3.0 mg/kg.


In one embodiment, the RNAi agent, e.g., double stranded RNAi agent, is administered subcutaneously or intravenously.


In one embodiment, the RNAi agent is administered in two or more doses. In a specific embodiment, the RNAi agent is administered at intervals selected from the group consisting of once every about 12 hours, once every about 24 hours, once every about 48 hours, once every about 72 hours, once every about 96 hours, once about every 7 days, or once about every 14 days. In particular embodiments, the RNAi agent is administered once a week for up to 2 weeks, up to 3 weeks, up to 4 weeks, up to 5 weeks, or longer.


In yet another aspect, the present invention provides methods of treating an iron overload associated disorder in a subject. The methods include administering to the subject a therapeutically effective amount of an RNAi agent, e.g., a double stranded RNAi agent, or the vector of the invention, thereby treating the subject.


In one embodiment, the iron overload associated disorder is hemochromatosis. In another embodiment, the iron overload associated disorder is a thalassemia, e.g., β-thalassemia (e.g, β-thalassemia major and β-thalassemia intermedia), or erythropoietic porphyria. In yet another embodiment, the iron overload associated disorder is a neurological disease, e.g., Parkinson's Disease, Alzheimer's Disease or Friedreich's Ataxia.


In one embodiment, the subject is a primate or rodent. In another embodiment, the subject is a human.


In one embodiment, the RNAi agent, e.g, double stranded RNAi agent, is administered at a dose of about 0.01 mg/kg to about 10 mg/kg, about 0.5 mg/kg to about 50 mg/kg, about 10 mg/kg to about 30 mg/kg, about 10 mg/kg to about 20 mg/kg, about 15 mg/kg to about 20 mg/kg, about 15 mg/kg to about 25 mg/kg, about 15 mg/kg to about 30 mg/kg, or about 20 mg/kg to about 30 mg/kg.


In one embodiment, the RNAi agent, e.g., double stranded RNAi agent, is administered subcutaneously or intravenously.


In one embodiment, the RNAi agent is administered in two or more doses. In a specific embodiment, the RNAi agent is administered at intervals selected from the group consisting of once every about 12 hours, once every about 24 hours, once every about 48 hours, once every about 72 hours, once every about 96 hours, once about every 7 days, or once about every 14 days.


In one embodiment, administering results in a decrease in iron levels, ferritin level and/or transferrin saturation level in the subject.


In one embodiment, the methods further comprise determining the iron level in the subject.


In one embodiment, the methods of the invention which include administering an iRNA agent of the invention (or pharmaceutical composition of the invention) to a subject are practiced in combination with administration of additional pharmaceuticals and/or other therapeutic methods. In one embodiment, the methods of the invention further comprise administering an iron chelator, e.g, deferiprone, deferoxamine, and deferasirox, to a subject.


The present invention is further illustrated by the following detailed description and drawings.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 is a graph showing relative levels of TMPRSS6 mRNA in the liver of wild-type mice following administration of a single dose of 1 mg/kg, 3 mg/kg or 10 mg/kg of the iRNA agent AD-59743.



FIG. 2 is a graph showing relative levels of hepcidin mRNA in the liver of wild-type mice following administration of a single dose of 1 mg/kg, 3 mg/kg or 10 mg/kg of the iRNA agent AD-59743.



FIG. 3A is a graph showing the levels of hepatic TMPRSS6 mRNA in C57BL/6 mice at various time points following a single subcutaneous injection of AD-60940 at a dose of 0.3 mg/kg, 1.0 mg/kg or 3.0 mg/kg, or PBS alone (control). Each data point represents the mean value from three mice. The standard deviation of the mean is represented by error bars.



FIG. 3B is a graph showing the levels of hepatic hepcidin mRNA in C57BL/6 mice at various time points following a single subcutaneous injection of AD-60940 at a dose of 0.3 mg/kg, 1.0 mg/kg or 3.0 mg/kg, or PBS alone (control). Each data point represents the mean value from three mice. The standard deviation of the mean is represented by error bars.



FIG. 3C is a graph showing the levels of serum hepcidin in C57BL/6 mice at various time points following a single subcutaneous injection of AD-60940 at a dose of 0.3 mg/kg, 1.0 mg/kg or 3.0 mg/kg, or PBS alone (control). Each data point represents the mean value from three mice. The standard deviation of the mean is represented by error bars.



FIG. 3D is a graph showing the levels of total serum iron in C57BL/6 mice at various time points following a single subcutaneous injection of AD-60940 at a dose of 0.3 mg/kg, 1.0 mg/kg or 3.0 mg/kg, or PBS alone (control). Each data point represents the mean value from three mice. The standard deviation of the mean is represented by error bars.



FIG. 3E is a graph showing the percent transferrin saturation (FIG. 3E) in C57BL/6 mice at various time points following a single subcutaneous injection of AD-60940 at a dose of 0.3 mg/kg, 1.0 mg/kg or 3.0 mg/kg, or PBS alone (control). Each data point represents the mean value from three mice. The standard deviation of the mean is represented by error bars.



FIG. 3F is a graph demonstrating the relative hepatic TMPRSS6 mRNA concentration as a function of AD-60940 dose at 11 days following administration. Each data point represents the maximum suppression of TMPRSS6 mRNA concentration observed at each dose level. The data were fit to the Hill equation.



FIG. 4A is a schematic depicting the administration regimen of one dose per week for three weeks followed by sacrifice of the mice at day 21. FIG. 4B is a graph showing the levels of hepatic TMPRSS6 mRNA, hepatic hepcidin mRNA, and percent transferrin saturation in C57BL/6 mice administered a subcutaneous injection of AD-60940 at a dose of 0.3 mg/kg, 1.0 mg/kg, or PBS (control) according to the regimen shown in FIG. 4A. Each bar represents the mean value from three mice. The standard deviation of the mean is represented by error bars.



FIG. 4C demonstrates the relative hepatic TMPRSS6 mRNA concentration as a function of AD-60940 dose. The data were fit to the Hill equation.



FIG. 5A is a graph showing the relationship between serum hepcidin concentration and relative TMPRSS6 mRNA levels.



FIG. 5B is a graph showing the relationship between percent transferrin saturation and relative TMPRSS6 mRNA levels.



FIG. 5C is a graph showing the relationship between serum hepcidin concentration and relative hepcidin mRNA levels.



FIG. 5D is a graph showing the relationship between percent transferrin saturation and serum hepcidin concentration.



FIG. 6 is a graph showing relative levels of TMPRSS6 mRNA in the liver of C57BL/6 mice following administration of a single subcutaneous dose of 3 mg/kg of the indicated iRNA agent or PBS (control). The bars represent the mean from three mice and the error bars represent the standard deviation of the mean.



FIG. 7 is a graph showing relative levels of TMPRSS6 mRNA in the liver of C57BL/6 mice following a subcutaneous dose of 0.3 mg/kg or 1.0 mg/kg of the indicated iRNA agent, or PBS (control), once a week for three weeks. The bars represent the mean from three mice and the error bars represent the standard deviation of the mean.



FIG. 8 shows the nucleotide sequence of Homo sapiens TMPRSS6 (SEQ ID NO: 1).



FIG. 9 shows the nucleotide sequence of Mus musculus TMPRSS6 (SEQ ID NO:2).



FIG. 10 shows the nucleotide sequence of Rattus norvegicus TMPRSS6 (SEQ ID NO:3).



FIG. 11 shows the nucleotide sequence of Macaca mulatta TMPRSS6 (SEQ ID NO:4).



FIG. 12 shows the nucleotide sequence of Macaca mulatta TMPRSS6 (SEQ ID NO:5).



FIG. 13 shows the reverse complement of SEQ ID NO: 1 (SEQ ID NO:6).



FIG. 14 shows the reverse complement of SEQ ID NO:2 (SEQ ID NO:7).



FIG. 15 shows the reverse complement of SEQ ID NO:3 (SEQ ID NO:8).



FIG. 16 shows the reverse complement of SEQ ID NO:4 (SEQ ID NO:9).



FIG. 17 shows the reverse complement of SEQ ID NO:5 (SEQ ID NO: 10).





DETAILED DESCRIPTION OF THE INVENTION

The present invention provides compositions comprising RNAi agents, e.g, double-stranded iRNA agents, targeting TMPRSS6. The present invention also provides methods using the compositions of the invention for inhibiting TMPRSS6 expression and for treating TMPRSS6 associated disorders, e.g., β-thalassemia or hemochromatosis.


TMPRSS6 plays an important role in iron homeostasis as an inhibitor of HAMP gene expression. The HAMP gene encodes the liver hormone hepcidin, which is a central regulator of iron homeostasis. Hepcidin binds to the iron exporter protein ferroportin (FPN1), which is localized mainly on absorptive enterocytes, hepatocytes and macrophages. Hepcidin binding to the extracellular domain of ferroportin leads to the internalization and degradation of ferroportin, thus decreasing the absorption of dietary iron from the intestine, and the release of iron from macrophages and hepatocytes. HAMP gene expression can be stimulated in response to iron through Bone Morphogenetic Protein (BMP)/Sons of Mothers Against Decapentaplegic (SMAD)-dependent signal transduction cascade mediated by the BMP-co-receptor hemojuvelin (HJV). The key role of TMPRSS6 in HAMP regulation is in the inhibition of BMP-mediated HAMP upregulation. TMPRSS6 inhibits BMP-mediated HAMP upregulation by cleaving the BMP co-receptor HJV, which is essential for BMP-mediated HAMP upregulation; thus preventing BMP signaling, SMAD translocation to the nucleus, and HAMP transcriptional activation.


Several human and mouse studies have confirmed the role of TMPRSS6 in HAMP regulation and iron homeostasis (Du et al. Science 2008, Vol. 320, pp 1088-1092; Folgueras et al. Blood 2008, Vol. 112, pp 2539-45). Studies have shown that loss of function mutations in TMPRSS6 can lead to the upregulation of hepcidin expression, causing an inherited iron deficiency anemia called iron refractory iron deficiency anemia (IRIDA) (Finberg. Seminars in Hematology 2009, Vol. 46, pp 378-86), which is characterized by elevated hepcidin levels, hypochromic microcytic anemia, low mean corpuscular volume (MCV), low transferrin saturation, poor absorption of oral iron, and incomplete response to parenteral iron. However, loss of function mutations in positive regulators of HAMP (e.g., BMP1, BMP4, and HFE) have been shown to downregulate hepcidin expression and cause iron overload disorders (Milet et al. Am J Hum Gen 2007, Vol. 81, pp 799-807; Finberg et al. Blood 2011, Vol. 117, pp 4590-9). In the primary iron overload disorders, collectively called hereditary hemochromatosis (HH), in anemias characterized by massive ineffective hematopoiesis, and in iron overload (secondary hemochromatosis), such as β-thalassemia intermedia (TI), hepcidin levels are low despite elevated serum iron concentrations and iron stores. A mouse model of β-thalassemia intermedia has demonstrated that the loss of TMPRSS6 expression leads to elevated levels of hepcidin (Finberg 2010 Oral Presentation: “TMPRSS6, an inhibitor of Hepatic BMP/Smad Signaling, is required for Hepcidin Suppression and Iron Loading in a Mouse Model of β-Thalassemia.” American Society of Hematology Annual Meeting 2010, Abstract No.: 164).


The present invention describes iRNA agents, compositions and methods for modulating the expression of a TMPRSS6 gene. In certain embodiments, expression of TMPRSS6 is reduced or inhibited using a TMPRSS6-specific iRNA agent, thereby leading to increase HAMP expression, and decreased serum iron levels. Thus, inhibition of TMPRSS6 gene expression or activity using the iRNA compositions featured in the invention can be a useful approach to therapies aimed at reducing the iron levels in a subject. Such inhibition can be useful for treating iron overload associated disorders, such as hemochromatosis or thalassemia, e.g., β-thalassemia (e.g, β-thalassemia major and β-thalassemia intermedia).


I. Definitions

In order that the present invention may be more readily understood, certain terms are first defined. In addition, it should be noted that whenever a value or range of values of a parameter are recited, it is intended that values and ranges intermediate to the recited values are also intended to be part of this invention.


The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element, e.g., a plurality of elements.


The term “including” is used herein to mean, and is used interchangeably with, the phrase “including but not limited to”.


The term “or” is used herein to mean, and is used interchangeably with, the term “and/or,” unless context clearly indicates otherwise.


As used herein, “TMPRSS6” refers to the type II plasma membrane serine protease (TTSP) gene or protein. TMPRSS6 is also known as matriptase-2, IRIDA (iron refractory iron-deficiency anemia), transmembrane protease serine 6, type II transmembrane serine protease 6, and membrane-bound mosaic serine proteinase matriptase-2. TMPRSS6 is a serine protease Type II transmembrane protein of approximately 899 amino acids in length. TMPRSS6 contains multiple domains, e.g., a short endo domain, a transmembrane domain, a sea urchin sperm protein/enteropeptidase domain/agrin (SEA) domain, two complement factor/urchin embryonic growth factor/BMP domains (CUB), three LDL-R class a domains (LDLa), and a trypsin-like serine protease domain with conserved His-Asp-Ser triad (HDS). The term “TMPRSS6” includes human TMPRSS6, the amino acid and nucleotide sequence of which may be found in, for example, GenBank Accession No. GI: 56682967; mouse TMPRSS6, the amino acid and nucleotide sequence of which may be found in, for example, GenBank Accession No. GT125656151; rat TMPRSS6, the amino acid and nucleotide sequence of which may be found in, for example, GenBank Accession No. GI: 194474097; rhesus TMPRSS6, the amino acid and nucleotide sequence of which may be found in, for example, GenBank Accession No. XM_001085203.2 (GT297260989) and XM_001085319.1 (GI: 109094061). Additional examples of AGT mRNA sequences are readily available using publicly available databases, e.g., GenBank, UniProt, OMIM, and the Macaca genome project web site.


The term “TMPRSS6,” as used herein, also refers to naturally occurring DNA sequence variations of the TMPRSS6 gene, such as a single nucleotide polymorphism (SNP) in the TMPRSS6 gene. Exemplary SNPs may be found in the dbSNP database available at www.ncbi.nlm.nih.gov/projects/SNP.


As used herein, “target sequence” refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a TMPRSS6 gene, including mRNA that is a product of RNA processing of a primary transcription product.


As used herein, the term “strand comprising a sequence” refers to an oligonucleotide comprising a chain of nucleotides that is described by the sequence referred to using the standard nucleotide nomenclature.


“G,” “C,” “A” and “U” each generally stand for a nucleotide that contains guanine, cytosine, adenine, and uracil as a base, respectively. “T” and “dT” are used interchangeably herein and refer to a deoxyribonucleotide wherein the nucleobase is thymine, e.g., deoxyribothymine, 2′-deoxythymidine or thymidine. However, it will be understood that the term “ribonucleotide” or “nucleotide” or “deoxyribonucleotide” can also refer to a modified nucleotide, as further detailed below, or a surrogate replacement moiety. The skilled person is well aware that guanine, cytosine, adenine, and uracil may be replaced by other moieties without substantially altering the base pairing properties of an oligonucleotide comprising a nucleotide bearing such replacement moiety. For example, without limitation, a nucleotide comprising inosine as its base may base pair with nucleotides containing adenine, cytosine, or uracil. Hence, nucleotides containing uracil, guanine, or adenine may be replaced in the nucleotide sequences of the invention by a nucleotide containing, for example, inosine. Sequences comprising such replacement moieties are embodiments of the invention.


The terms “iRNA”, “RNAi agent,” “iRNA agent,”, “RNA interference agent” as used interchangeably herein, refer to an agent that contains RNA as that term is defined herein, and which mediates the targeted cleavage of an RNA transcript via an RNA-induced silencing complex (RISC) pathway. iRNA directs the sequence-specific degradation of mRNA through a process known as RNA interference (RNAi). The iRNA modulates, e.g., inhibits, the expression of TMPRSS6 in a cell, e.g, a cell within a subject, such as a mammalian subject.


In one embodiment, an RNAi agent of the invention includes a single stranded RNA that interacts with a target RNA sequence, e.g, a TMPRSS6 target mRNA sequence, to direct the cleavage of the target RNA. Without wishing to be bound by theory, it is believed that long double stranded RNA introduced into cells is broken down into siRNA by a Type III endonuclease known as Dicer (Sharp et al. (2001) Genes Dev. 15:485). Dicer, a ribonuclease-III-like enzyme, processes the dsRNA into 19-23 base pair short interfering RNAs with characteristic two base 3′ overhangs (Bernstein, et al., (2001) Nature 409:363). The siRNAs are then incorporated into an RNA-induced silencing complex (RISC) where one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition (Nykanen, et al., (2001) Cell 107:309). Upon binding to the appropriate target mRNA, one or more endonucleases within the RISC cleave the target to induce silencing (Elbashir, et al., (2001) Genes Dev. 15:188). Thus, in one aspect the invention relates to a single stranded RNA (siRNA) generated within a cell and which promotes the formation of a RISC complex to effect silencing of the target gene, i.e., a TMPRSS6 gene. Accordingly, the term “siRNA” is also used herein to refer to an RNAi as described above.


In another embodiment, the RNAi agent may be a single-stranded siRNA that is introduced into a cell or organism to inhibit a target mRNA. Single-stranded RNAi agents bind to the RISC endonuclease Argonaute 2, which then cleaves the target mRNA. The single-stranded siRNAs are generally 15-30 nucleotides and are chemically modified. The design and testing of single-stranded siRNAs are described in U.S. Pat. No. 8,101,348 and in Lima et al., (2012) Cell 150: 883-894, the entire contents of each of which are hereby incorporated herein by reference. Any of the antisense nucleotide sequences described herein may be used as a single-stranded siRNA as described herein or as chemically modified by the methods described in Lima et al., (2012) Cell 150;:883-894.


In yet another embodiment, the present invention provides single-stranded antisense oligonucleotide molecules targeting TMPRSS6. A “single-stranded antisense oligonucleotide molecule” is complementary to a sequence within the target mRNA (i.e., TMPRSS6). Single-stranded antisense oligonucleotide molecules can inhibit translation in a stoichiometric manner by base pairing to the mRNA and physically obstructing the translation machinery, see Dias, N. et al., (2002) Mol Cancer Ther 1:347-355. Alternatively, the single-stranded antisense oligonucleotide molecules inhibit a target mRNA by hydridizing to the target and cleaving the target through an RNaseH cleavage event. The single-stranded antisense oligonucleotide molecule may be about 10 to about 30 nucleotides in length and have a sequence that is complementary to a target sequence. For example, the single-stranded antisense oligonucleotide molecule may comprise a sequence that is at least about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more contiguous nucleotides from any one of the antisense nucleotide sequences described herein, e.g., the sequences provided in any one of Tables, 1, 2, 4, 5, 8, 10, and 12, or bind any of the target sites described herein. The single-stranded antisense oligonucleotide molecules may comprise modified RNA, DNA, or a combination thereof.


In another embodiment, an “iRNA” for use in the compositions, uses, and methods of the invention is a double-stranded RNA and is referred to herein as a “double stranded RNAi agent,” “double-stranded RNA (dsRNA) molecule,” “dsRNA agent,” or “dsRNA”. The term “dsRNA”, refers to a complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary nucleic acid strands, referred to as having “sense” and “antisense” orientations with respect to a target RNA, i.e., a TMPRSS6 gene. In some embodiments of the invention, a double-stranded RNA (dsRNA) triggers the degradation of a target RNA, e.g., an mRNA, through a post-transcriptional gene-silencing mechanism referred to herein as RNA interference or RNAi.


In general, the majority of nucleotides of each strand of a dsRNA molecule are ribonucleotides, but as described in detail herein, each or both strands can also include one or more non-ribonucleotides, e.g., a deoxyribonucleotide and/or a modified nucleotide. In addition, as used in this specification, an “RNAi agent” may include ribonucleotides with chemical modifications; an RNAi agent may include substantial modifications at multiple nucleotides. Such modifications may include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a siRNA type molecule, are encompassed by “RNAi agent” for the purposes of this specification and claims.


The two strands forming the duplex structure may be different portions of one larger RNA molecule, or they may be separate RNA molecules. Where the two strands are part of one larger molecule, and therefore are connected by an uninterrupted chain of nucleotides between the 3′-end of one strand and the 5′-end of the respective other strand forming the duplex structure, the connecting RNA chain is referred to as a “hairpin loop.” Where the two strands are connected covalently by means other than an uninterrupted chain of nucleotides between the 3′-end of one strand and the 5′-end of the respective other strand forming the duplex structure, the connecting structure is referred to as a “linker.” The RNA strands may have the same or a different number of nucleotides. The maximum number of base pairs is the number of nucleotides in the shortest strand of the dsRNA minus any overhangs that are present in the duplex. In addition to the duplex structure, an RNAi agent may comprise one or more nucleotide overhangs.


In one embodiment, an RNAi agent of the invention is a dsRNA of 24-30 nucleotides that interacts with a target RNA sequence, e.g., a TMPRSS6 target mRNA sequence, to direct the cleavage of the target RNA. Without wishing to be bound by theory, long double stranded RNA introduced into cells is broken down into siRNA by a Type III endonuclease known as Dicer (Sharp et al. (2001) Genes Dev. 15:485). Dicer, a ribonuclease-III-like enzyme, processes the dsRNA into 19-23 base pair short interfering RNAs with characteristic two base 3′ overhangs (Bernstein, et al., (2001) Nature 409:363). The siRNAs are then incorporated into an RNA-induced silencing complex (RISC) where one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition (Nykanen, et al., (2001) Cell 107:309). Upon binding to the appropriate target mRNA, one or more endonucleases within the RISC cleave the target to induce silencing (Elbashir, et al., (2001) Genes Dev. 15:188).


As used herein, a “nucleotide overhang” refers to the unpaired nucleotide or nucleotides that protrude from the duplex structure of an RNAi agent when a 3′-end of one strand of the RNAi agent extends beyond the 5′-end of the other strand, or vice versa. “Blunt” or “blunt end” means that there are no unpaired nucleotides at that end of the double stranded RNAi agent, i.e., no nucleotide overhang. A “blunt ended” RNAi agent is a dsRNA that is double-stranded over its entire length, i.e., no nucleotide overhang at either end of the molecule. The RNAi agents of the invention include RNAi agents with nucleotide overhangs at one end (i.e., agents with one overhang and one blunt end) or with nucleotide overhangs at both ends.


The term “antisense strand” refers to the strand of a double stranded RNAi agent which includes a region that is substantially complementary to a target sequence (e.g., a human TMPRSS6 mRNA). As used herein, the term “region complementary to part of an mRNA encoding transthyretin” refers to a region on the antisense strand that is substantially complementary to part of a TMPRSS6 mRNA sequence. Where the region of complementarity is not fully complementary to the target sequence, the mismatches are most tolerated in the terminal regions and, if present, are generally in a terminal region or regions, e.g., within 6, 5, 4, 3, or 2 nucleotides of the 5′ and/or 3′ terminus.


The term “sense strand,” as used herein, refers to the strand of a dsRNA that includes a region that is substantially complementary to a region of the antisense strand.


As used herein, the term “cleavage region” refers to a region that is located immediately adjacent to the cleavage site. The cleavage site is the site on the target at which cleavage occurs. In some embodiments, the cleavage region comprises three bases on either end of, and immediately adjacent to, the cleavage site. In some embodiments, the cleavage region comprises two bases on either end of, and immediately adjacent to, the cleavage site. In some embodiments, the cleavage site specifically occurs at the site bound by nucleotides 10 and 11 of the antisense strand, and the cleavage region comprises nucleotides 11, 12 and 13.


As used herein, and unless otherwise indicated, the term “complementary,” when used to describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person. Such conditions can, for example, be stringent conditions, where stringent conditions may include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50° C. or 70° C. for 12-16 hours followed by washing. Other conditions, such as physiologically relevant conditions as may be encountered inside an organism, can apply. For example, a complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g, RNAi. The skilled person will be able to determine the set of conditions most appropriate for a test of complementarity of two sequences in accordance with the ultimate application of the hybridized nucleotides.


Sequences can be “fully complementary” with respect to each when there is base-pairing of the nucleotides of the first nucleotide sequence with the nucleotides of the second nucleotide sequence over the entire length of the first and second nucleotide sequences. However, where a first sequence is referred to as “substantially complementary” with respect to a second sequence herein, the two sequences can be fully complementary, or they may form one or more, but generally not more than 4, 3 or 2 mismatched base pairs upon hybridization, while retaining the ability to hybridize under the conditions most relevant to their ultimate application. However, where two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity. For example, a dsRNA comprising one oligonucleotide 21 nucleotides in length and another oligonucleotide 23 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 21 nucleotides that is fully complementary to the shorter oligonucleotide, may yet be referred to as “fully complementary” for the purposes described herein.


“Complementary” sequences, as used herein, may also include, or be formed entirely from, non-Watson-Crick base pairs and/or base pairs formed from non-natural and modified nucleotides, in as far as the above requirements with respect to their ability to hybridize are fulfilled. Such non-Watson-Crick base pairs includes, but not limited to, G:U Wobble or Hoogstein base pairing.


The terms “complementary,” “fully complementary” and “substantially complementary” herein may be used with respect to the base matching between the sense strand and the antisense strand of a dsRNA, or between the antisense strand of a dsRNA and a target sequence, as will be understood from the context of their use.


As used herein, a polynucleotide that is “substantially complementary to at least part of” a messenger RNA (mRNA) refers to a polynucleotide that is substantially complementary to a contiguous portion of the mRNA of interest (e.g., an mRNA encoding TMPRSS6) including a 5′ UTR, an open reading frame (ORF), or a 3′ UTR. For example, a polynucleotide is complementary to at least a part of a TMPRSS6 mRNA if the sequence is substantially complementary to a non-interrupted portion of an mRNA encoding TMPRSS6.


The term “inhibiting,” as used herein, is used interchangeably with “reducing,” “silencing,” “downregulating,” “suppressing” and other similar terms, and includes any level of inhibition.


The phrase “inhibiting expression of a TMPRSS6,” as used herein, includes inhibition of expression of any TMPRSS6 gene (such as, e.g., a mouse TMPRSS6 gene, a rat TMPRSS6 gene, a monkey TMPRSS6 gene, or a human TMPRSS6 gene) as well as variants, (e.g., naturally occurring variants), or mutants of a TMPRSS6 gene. Thus, the TMPRSS6 gene may be a wild-type TMPRSS6 gene, a mutant TMPRSS6 gene, or a transgenic TMPRSS6 gene in the context of a genetically manipulated cell, group of cells, or organism.


“Inhibiting expression of a TMPRSS6 gene” includes any level of inhibition of a TMPRSS6 gene, e.g., at least partial suppression of the expression of a TMPRSS6 gene, such as an inhibition of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%. at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%.


The expression of a TMPRSS6 gene may be assessed based on the level of any variable associated with TMPRSS6 gene expression, e.g., TMPRSS6 mRNA level, TMPRSS6 protein level, hepcidin mRNA level, hepcidin protein level, or iron levels in tissues or serum. Inhibition may be assessed by a decrease in an absolute or relative level of one or more of these variables compared with a control level. The control level may be any type of control level that is utilized in the art, e.g., a pre-dose baseline level, or a level determined from a similar subject, cell, or sample that is untreated or treated with a control (such as, e.g., buffer only control or inactive agent control).


The phrase “contacting a cell with a double stranded RNAi agent,” as used herein, includes contacting a cell by any possible means. Contacting a cell with a double stranded RNAi agent includes contacting a cell in vitro with the RNAi agent or contacting a cell in vivo with the RNAi agent. The contacting may be done directly or indirectly. Thus, for example, the RNAi agent may be put into physical contact with the cell by the individual performing the method, or alternatively, the RNAi agent may be put into a situation that will permit or cause it to subsequently come into contact with the cell.


Contacting a cell in vitro may be done, for example, by incubating the cell with the RNAi agent. Contacting a cell in vivo may be done, for example, by injecting the RNAi agent into or near the tissue where the cell is located, or by injecting the RNAi agent into another area, the bloodstream or the subcutaneous space, such that the agent will subsequently reach the tissue where the cell to be contacted is located. For example, the RNAi agent may contain and/or be coupled to a ligand, e.g., a GalNAc3 ligand, that directs the RNAi agent to a site of interest, e.g., the liver. Combinations of in vitro and in vivo methods of contacting are also possible. In connection with the methods of the invention, a cell might also be contacted in vitro with an RNAi agent and subsequently transplanted into a subject.


A “patient” or “subject,” as used herein, is intended to include either a human or non-human animal, preferably a mammal, e.g., human or a monkey. Most preferably, the subject or patient is a human.


A “TMPRSS6 associated disorder”, as used herein, is intended to include any disorder that can be treated or prevented, or the symptoms of which can be alleviated, by inhibiting the expression of TMPRSS6. In some embodiments, the TMPRSS6 associated disorder is also associated with iron overload, a condition characterized by elevated iron levels, or iron dysregulation. Iron overload may be caused, for example, by hereditary conditions, by elevated iron uptake from diet, or by excess iron administered parenterally that includes intravenous injection of excess iron, and transfusional iron overload.


TMPRSS6 associated disorders include, but are not limited to, hereditary hemochromatosis, idiopathic hemochromatosis, primary hemochromatosis, secondary hemochromatosis, severe juvenile hemochromatosis, neonatal hemochromatosis, sideroblastic anemia, hemolytic anemia, dyserythropoietic anemia, sickle-cell anemia, hemoglobinopathy, thalassemia (e.g., β-thalassemia and α-thalassemia), chronic liver diseases, porphyria cutanea tarda, erythropoietic porphyria, atransferrinemia, hereditary tyrosinemia, cerebrohepatorenal syndrome, idiopathic pulmonary hemosiderosis, renal hemosiderosis.


TMPRSS6 associated disorders include disorders associated with oral administration of excess iron, transfusional iron overload and intravenous injection of excess iron.


TMPRSS6 associated disorders also include disorders with symptoms that are associated with or may be caused by iron overload. Such symptoms include increased risk for liver disease (cirrhosis, cancer), heart attack or heart failure, diabetes mellitus, osteoarthritis, osteoporosis, metabolic syndrome, hypothyroidism, hypogonadism, and in some cases premature death. In one embodiment, TMPRSS6 associated disorders include neurodegenerative disorders associated with iron overload and/or iron dysregulation, such as Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Friedreich's Ataxia, epilepsy and multiple sclerosis. Administration of an iRNA that targets TMPRSS6, e.g, an iRNA described in any one of Tables 1, 2, 4, 5, 8, 10, and 12 can treat one or more of these symptoms, or prevent the development or progression of a disease or disorder that is aggravated by increased iron levels.


In one embodiment, a TMPRSS6 associated disorder is a β-thalassemia. A β-thalassemia is any one of a group of hereditary disorders characterized by a genetic deficiency in the synthesis of beta-globin chains. In the homozygous state, beta thalassemia (“thalassemia major”) causes severe, transfusion-dependent anemia. In the heterozygous state, the beta thalassemia trait (“thalassemia minor”) causes mild to moderate microcytic anemia.


“Thalassemia intermedia” is a β-thalassemia that results in subjects in whom the clinical severity of the disease is somewhere between the mild symptoms of β-thalassemia minor and the β-thalassemia major. The diagnosis is a clinical one that is based on the patient maintaining a satisfactory hemoglobin (Hb) level of at least 6-7 g/dL at the time of diagnosis without the need for regular blood transfusions.


In one embodiment, a β-thalassemia is thalassemia major. In another embodiment, a β-thalassemia is thalassemia intermedia.


“Therapeutically effective amount,” as used herein, is intended to include the amount of an RNAi agent that, when administered to a patient for treating a TMPRSS6 associated disease, is sufficient to effect treatment of the disease (e.g., by diminishing, ameliorating or maintaining the existing disease or one or more symptoms of disease). The “therapeutically effective amount” may vary depending on the RNAi agent, how the agent is administered, the disease and its severity and the history, age, weight, family history, genetic makeup, stage of pathological processes mediated by TMPRSS6 expression, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.


“Prophylactically effective amount,” as used herein, is intended to include the amount of an RNAi agent that, when administered to a subject who does not yet experience or display symptoms of a TMPRSS6-associated disease, but who may be predisposed to the disease, is sufficient to prevent or ameliorate the disease or one or more symptoms of the disease. Ameliorating the disease includes slowing the course of the disease or reducing the severity of later-developing disease. The “prophylactically effective amount” may vary depending on the RNAi agent, how the agent is administered, the degree of risk of disease, and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.


A “therapeutically-effective amount” or “prophylactically effective amount” also includes an amount of an RNAi agent that produces some desired local or systemic effect at a reasonable benefit/risk ratio applicable to any treatment. RNAi gents employed in the methods of the present invention may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.


The term “sample,” as used herein, includes a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject. Examples of biological fluids include blood, serum and serosal fluids, plasma, cerebrospinal fluid, ocular fluids, lymph, urine, saliva, and the like. Tissue samples may include samples from tissues, organs or localized regions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organs. In certain embodiments, samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g., hepatocytes). In preferred embodiments, a “sample derived from a subject” refers to blood or plasma drawn from the subject. In further embodiments, a “sample derived from a subject” refers to liver tissue (or subcomponents thereof) derived from the subject.


II. iRNAs of the Invention

Described herein are improved double-stranded RNAi agents which inhibit the expression of a TMPRSS6 gene in a cell, such as a cell within a subject, e.g., a mammal, such as a human having a TMPRSS6 associated disorder, e.g., β-thalassemia (e.g, β-thalassemia major and β-thalassemia intermedia) or hemochromatosis, and uses of such double-stranded RNAi agents.


Accordingly, the invention provides double-stranded RNAi agents with chemical modifications capable of inhibiting the expression of a target gene (i.e., a TMPRSS6 gene) in vivo. In certain aspects of the invention, substantially all of the nucleotides of an iRNA of the invention are modified. In other embodiments of the invention, all of the nucleotides of an iRNA of the invention are modified. iRNAs of the invention in which “substantially all of the nucleotides are modified” are largely but not wholly modified and can include not more than 5, 4, 3, 2, or 1 unmodified nucleotides.


The RNAi agent comprises a sense strand and an antisense strand. Each strand of the RNAi agent may range from 12-30 nucleotides in length. For example, each strand may be between 14-30 nucleotides in length, 17-30 nucleotides in length, 19-30 nucleotides in length, 25-30 nucleotides in length, 27-30 nucleotides in length, 17-23 nucleotides in length, 17-21 nucleotides in length, 17-19 nucleotides in length, 19-25 nucleotides in length, 19-23 nucleotides in length, 19-21 nucleotides in length, 21-25 nucleotides in length, or 21-23 nucleotides in length.


The sense strand and antisense strand typically form a duplex double stranded RNA (“dsRNA”), also referred to herein as an “RNAi agent.” The duplex region of an RNAi agent may be 12-30 nucleotide pairs in length. For example, the duplex region can be between 14-30 nucleotide pairs in length, 17-30 nucleotide pairs in length, 27-30 nucleotide pairs in length, 17-23 nucleotide pairs in length, 17-21 nucleotide pairs in length, 17-19 nucleotide pairs in length, 19-25 nucleotide pairs in length, 19-23 nucleotide pairs in length, 19-21 nucleotide pairs in length, 21-25 nucleotide pairs in length, or 21-23 nucleotide pairs in length. In another example, the duplex region is selected from 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27 nucleotides in length.


In one embodiment, the RNAi agent may contain one or more overhang regions and/or capping groups at the 3′-end, 5′-end, or both ends of one or both strands. The overhang can be 1-6 nucleotides in length, for instance 2-6 nucleotides in length, 1-5 nucleotides in length, 2-5 nucleotides in length, 1-4 nucleotides in length, 2-4 nucleotides in length, 1-3 nucleotides in length, 2-3 nucleotides in length, or 1-2 nucleotides in length. The overhangs can be the result of one strand being longer than the other, or the result of two strands of the same length being staggered. The overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be another sequence. The first and second strands can also be joined, e.g., by additional bases to form a hairpin, or by other non-base linkers.


In one embodiment, the nucleotides in the overhang region of the RNAi agent can each independently be a modified or unmodified nucleotide including, but no limited to 2′-sugar modified, such as, 2-F, 2′-O-methyl, thymidine (T), 2′-O-methoxyethyl-5-methyluridine (Teo), 2′-O-methoxyethyladenosine (Aeo), 2′-O-methoxyethyl-5-methylcytidine (m5Ceo), and any combinations thereof. For example, TT can be an overhang sequence for either end on either strand. The overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be another sequence.


The 5′- or 3′-overhangs at the sense strand, antisense strand or both strands of the RNAi agent may be phosphorylated. In some embodiments, the overhang region(s) contains two nucleotides having a phosphorothioate between the two nucleotides, where the two nucleotides can be the same or different. In one embodiment, the overhang is present at the 3′-end of the sense strand, antisense strand, or both strands. In one embodiment, this 3′-overhang is present in the antisense strand. In one embodiment, this 3′-overhang is present in the sense strand.


The RNAi agent may contain only a single overhang, which can strengthen the interference activity of the RNAi, without affecting its overall stability. For example, the single-stranded overhang may be located at the 3′-terminal end of the sense strand or, alternatively, at the 3′-terminal end of the antisense strand. The RNAi may also have a blunt end, located at the 5′-end of the antisense strand (or the 3′-end of the sense strand) or vice versa. Generally, the antisense strand of the RNAi has a nucleotide overhang at the 3′-end, and the 5′-end is blunt. While not wishing to be bound by theory, the asymmetric blunt end at the 5′-end of the antisense strand and 3′-end overhang of the antisense strand favor the guide strand loading into RISC process.


Any of the nucleic acids featured in the invention can be synthesized and/or modified by methods well established in the art, such as those described in “Current protocols in nucleic acid chemistry,” Beaucage, S. L. et al. (Edrs.), John Wiley & Sons, Inc., New York, N.Y., USA, which is hereby incorporated herein by reference. Modifications include, for example, end modifications, e.g., 5′-end modifications (phosphorylation, conjugation, inverted linkages) or 3′-end modifications (conjugation, DNA nucleotides, inverted linkages, clef base modifications, e.g., replacement with stabilizing bases, destabilizing bases, or bases that base pair with an expanded repertoire of partners, removal of bases (abasic nucleotides), or conjugated bases; sugar modifications (e.g, at the 2′-position or 4′-position) or replacement of the sugar; and/or backbone modifications, including modification or replacement of the phosphodiester linkages. Specific examples of iRNA compounds useful in the embodiments described herein include, but are not limited to RNAs containing modified backbones or no natural internucleoside linkages. RNAs having modified backbones include, among others, those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified RNAs that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides. In some embodiments, a modified iRNA will have a phosphorus atom in its internucleoside backbone.


Modified RNA backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′ linkages, 2′-5′-linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixed salts and free acid forms are also included.


Representative U.S. patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,195; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,316; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,625,050; 6,028,188; 6,124,445; 6,160,109; 6,169,170; 6,172,209; 6,239,265; 6,277,603; 6,326,199; 6,346,614; 6,444,423; 6,531,590; 6,534,639; 6,608,035; 6,683,167; 6,858,715; 6,867,294; 6,878,805; 7,015,315; 7,041,816; 7,273,933; 7,321,029; and U.S. Pat. RE39464, the entire contents of each of which are hereby incorporated herein by reference.


Modified RNA backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts.


Representative U.S. patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and, 5,677,439, the entire contents of each of which are hereby incorporated herein by reference.


In other embodiments, suitable RNA mimetics are contemplated for use in iRNAs, in which both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an RNA mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar backbone of an RNA is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.


Representative U.S. patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, the entire contents of each of which are hereby incorporated herein by reference. Additional PNA compounds suitable for use in the iRNAs of the invention are described in, for example, in Nielsen et al., Science, 1991, 254, 1497-1500.


Some embodiments featured in the invention include RNAs with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular —CH2—NH—CH2—, —CH2—N(CH3)—O—CH2-[known as a methylene (methylimino) or MMI backbone], —CH2—O—N(CH3)—CH2—, —CH2—N(CH3)—N(CH3)—CH2— and —N(CH3)—CH2—CH2-[wherein the native phosphodiester backbone is represented as —O—P—O—CH2-] of the above-referenced U.S. Pat. No. 5,489,677, and the amide backbones of the above-referenced U.S. Pat. No. 5,602,240. In some embodiments, the RNAs featured herein have morpholino backbone structures of the above-referenced U.S. Pat. No. 5,034,506.


Modified RNAs can also contain one or more substituted sugar moieties. The iRNAs, e.g., dsRNAs, featured herein can include one of the following at the 2′-position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl can be substituted or unsubstituted C1 to C10 alkyl or C2 to C10 alkenyl and alkynyl. Exemplary suitable modifications include O[(CH2)nO]mCH3, O(CH2).nOCH3, O(CH2)nNH2, O(CH2)nCH3, O(CH2)nONH2, and O(CH2)nON[(CH2)nCH3)]2, where n and m are from 1 to about 10. In other embodiments, dsRNAs include one of the following at the 2′ position: C1 to C10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an iRNA, or a group for improving the pharmacodynamic properties of an iRNA, and other substituents having similar properties. In some embodiments, the modification includes a 2′-methoxyethoxy (2′-O—CH2CH2OCH3, also known as 2′-O-(2-methoxyethyl) or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78:486-504) i.e., an alkoxy-alkoxy group. Another exemplary modification is 2′-dimethylaminooxyethoxy, i.e., a O(CH2)2ON(CH3)2 group, also known as 2′-DMAOE, as described in examples herein below, and 2′-dimethylaminoethoxyethoxy (also known in the art as 2′-O-dimethylaminoethoxyethyl or 2′-DMAEOE), i.e., 2′-O—CH2—O—CH2—N(CH2)2.


Other modifications include 2′-methoxy (2′-OCH3), 2′-aminopropoxy (2′-OCH2CH2CH2NH2) and 2′-fluoro (2′-F). Similar modifications can also be made at other positions on the RNA of an iRNA, particularly the 3′ position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linked dsRNAs and the 5′ position of 5′ terminal nucleotide. iRNAs can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative U.S. patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, certain of which are commonly owned with the instant application. The entire contents of each of the foregoing are hereby incorporated herein by reference.


An iRNA can also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as deoxy-thymine (dT), 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl anal other 8-substituted adenines and guanines, 5-halo, particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methyl guanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-daazaadenine and 3-deazaguanine and 3-deazaadenine. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in Modified Nucleosides in Biochemistry, Biotechnology and Medicine, Herdewijn, P. ed. Wiley-VCH, 2008; those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. L, ed. John Wiley & Sons, 1990, these disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y S., Chapter 15, dsRNA Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., Ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds featured in the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., Eds., dsRNA Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are exemplary base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.


Representative U.S. patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Pat. Nos. 3,687,808, 4,845,205; 5,130,30; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; 5,681,941; 5,750,692; 6,015,886; 6,147,200; 6,166,197; 6,222,025; 6,235,887; 6,380,368; 6,528,640; 6,639,062; 6,617,438; 7,045,610; 7,427,672; and 7,495,088, the entire contents of each of which are hereby incorporated herein by reference.


The RNA of an iRNA can also be modified to include one or more locked nucleic acids (LNA). A locked nucleic acid is a nucleotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2′ and 4′ carbons. This structure effectively “locks” the ribose in the 3′-endo structural conformation. The addition of locked nucleic acids to siRNAs has been shown to increase siRNA stability in serum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33(1):439-447; Mook, O R. et al., (2007) Mol Cane Ther 6(3):833-843; Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193).


Representative U.S. patents that teach the preparation of locked nucleic acid nucleotides include, but are not limited to, the following: U.S. Pat. Nos. 6,268,490; 6,670,461; 6,794,499; 6,998,484; 7,053,207; 7,084,125; and 7,399,845, the entire contents of each of which are hereby incorporated herein by reference.


Potentially stabilizing modifications to the ends of RNA molecules can include N-(acetylaminocaproyl)-4-hydroxyprolinol (Hyp-C6-NHAc), N-(caproyl-4-hydroxyprolinol (Hyp-C6), N-(acetyl-4-hydroxyprolinol (Hyp-NHAc), thymidine-2′-O-deoxythymidine (ether), N-(aminocaproyl)-4-hydroxyprolinol (Hyp-C6-amino), 2-docosanoyl-uridine-3″-phosphate, inverted base dT(idT) and others. Disclosure of this modification can be found in PCT Publication No. WO 2011/005861.


A. Modified iRNAs Comprising Motifs of the Invention


In certain aspects of the invention, the double-stranded RNAi agents of the invention include agents with chemical modifications as disclosed, for example, in U.S. Provisional Application No. 61/561,710, filed on Nov. 18, 2011, or in PCT/US2012/065691, filed on Nov. 16, 2012, the entire contents of each of which are incorporated herein by reference.


As shown herein and in Provisional Application No. 61/561,710, a superior result may be obtained by introducing one or more motifs of three identical modifications on three consecutive nucleotides into a sense strand and/or antisense strand of a RNAi agent, particularly at or near the cleavage site. In some embodiments, the sense strand and antisense strand of the RNAi agent may otherwise be completely modified. The introduction of these motifs interrupts the modification pattern, if present, of the sense and/or antisense strand. The RNAi agent may be optionally conjugated with a GalNAc derivative ligand, for instance on the sense strand. The resulting RNAi agents present superior gene silencing activity.


More specifically, it has been surprisingly discovered that when the sense strand and antisense strand of the double-stranded RNAi agent are modified to have one or more motifs of three identical modifications on three consecutive nucleotides at or near the cleavage site of at least one strand of an RNAi agent, the gene silencing activity of the RNAi agent was superiorly enhanced.


In one embodiment, the RNAi agent is a double ended bluntmer of 19 nucleotides in length, wherein the sense strand contains at least one motif of three 2′-F modifications on three consecutive nucleotides at positions 7, 8, 9 from the 5′end. The antisense strand contains at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5′end.


In another embodiment, the RNAi agent is a double ended bluntmer of 20 nucleotides in length, wherein the sense strand contains at least one motif of three 2′-F modifications on three consecutive nucleotides at positions 8, 9, 10 from the 5′end. The antisense strand contains at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5′end.


In yet another embodiment, the RNAi agent is a double ended bluntmer of 21 nucleotides in length, wherein the sense strand contains at least one motif of three 2′-F modifications on three consecutive nucleotides at positions 9, 10, 11 from the 5′end. The antisense strand contains at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5′end.


In one embodiment, the RNAi agent comprises a 21 nucleotide sense strand and a 23 nucleotide antisense strand, wherein the sense strand contains at least one motif of three 2′-F modifications on three consecutive nucleotides at positions 9, 10, 11 from the 5′end; the antisense strand contains at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5′end, wherein one end of the RNAi agent is blunt, while the other end comprises a 2 nucleotide overhang. Preferably, the 2 nucleotide overhang is at the 3′-end of the antisense strand. When the 2 nucleotide overhang is at the 3′-end of the antisense strand, there may be two phosphorothioate internucleotide linkages between the terminal three nucleotides, wherein two of the three nucleotides are the overhang nucleotides, and the third nucleotide is a paired nucleotide next to the overhang nucleotide. In one embodiment, the RNAi agent additionally has two phosphorothioate internucleotide linkages between the terminal three nucleotides at both the 5′-end of the sense strand and at the 5′-end of the antisense strand. In one embodiment, every nucleotide in the sense strand and the antisense strand of the RNAi agent, including the nucleotides that are part of the motifs are modified nucleotides. In one embodiment each residue is independently modified with a 2′-O-methyl or 3′-fluoro, e.g., in an alternating motif. Optionally, the RNAi agent further comprises a ligand (preferably GalNAc3).


In one embodiment, the RNAi agent comprises sense and antisense strands, wherein the RNAi agent comprises a first strand having a length which is at least 25 and at most 29 nucleotides and a second strand having a length which is at most 30 nucleotides with at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at position 11, 12, 13 from the 5′ end; wherein the 3′ end of the first strand and the 5′ end of the second strand form a blunt end and the second strand is 1-4 nucleotides longer at its 3′ end than the first strand, wherein the duplex region which is at least 25 nucleotides in length, and the second strand is sufficiently complementary to a target mRNA along at least 19 nucleotide of the second strand length to reduce target gene expression when the RNAi agent is introduced into a mammalian cell, and wherein dicer cleavage of the RNAi agent preferentially results in an siRNA comprising the 3′ end of the second strand, thereby reducing expression of the target gene in the mammal. Optionally, the RNAi agent further comprises a ligand.


In one embodiment, the sense strand of the RNAi agent contains at least one motif of three identical modifications on three consecutive nucleotides, where one of the motifs occurs at the cleavage site in the sense strand.


In one embodiment, the antisense strand of the RNAi agent can also contain at least one motif of three identical modifications on three consecutive nucleotides, where one of the motifs occurs at or near the cleavage site in the antisense strand


For an RNAi agent having a duplex region of 17-23 nucleotide in length, the cleavage site of the antisense strand is typically around the 10, 11 and 12 positions from the 5′-end. Thus the motifs of three identical modifications may occur at the 9, 10, 11 positions; 10, 11, 12 positions; 11, 12, 13 positions; 12, 13, 14 positions; or 13, 14, 15 positions of the antisense strand, the count starting from the 1st nucleotide from the 5′-end of the antisense strand, or, the count starting from the 1st paired nucleotide within the duplex region from the 5′-end of the antisense strand. The cleavage site in the antisense strand may also change according to the length of the duplex region of the RNAi from the 5′-end.


The sense strand of the RNAi agent may contain at least one motif of three identical modifications on three consecutive nucleotides at the cleavage site of the strand; and the antisense strand may have at least one motif of three identical modifications on three consecutive nucleotides at or near the cleavage site of the strand. When the sense strand and the antisense strand form a dsRNA duplex, the sense strand and the antisense strand can be so aligned that one motif of the three nucleotides on the sense strand and one motif of the three nucleotides on the antisense strand have at least one nucleotide overlap, i.e., at least one of the three nucleotides of the motif in the sense strand forms a base pair with at least one of the three nucleotides of the motif in the antisense strand. Alternatively, at least two nucleotides may overlap, or all three nucleotides may overlap.


In one embodiment, the sense strand of the RNAi agent may contain more than one motif of three identical modifications on three consecutive nucleotides. The first motif may occur at or near the cleavage site of the strand and the other motifs may be a wing modification. The term “wing modification” herein refers to a motif occurring at another portion of the strand that is separated from the motif at or near the cleavage site of the same strand. The wing modification is either adjacent to the first motif or is separated by at least one or more nucleotides. When the motifs are immediately adjacent to each other then the chemistry of the motifs are distinct from each other and when the motifs are separated by one or more nucleotide than the chemistries can be the same or different. Two or more wing modifications may be present. For instance, when two wing modifications are present, each wing modification may occur at one end relative to the first motif which is at or near cleavage site or on either side of the lead motif.


Like the sense strand, the antisense strand of the RNAi agent may contain more than one motifs of three identical modifications on three consecutive nucleotides, with at least one of the motifs occurring at or near the cleavage site of the strand. This antisense strand may also contain one or more wing modifications in an alignment similar to the wing modifications that may be present on the sense strand.


In one embodiment, the wing modification on the sense strand or antisense strand of the RNAi agent typically does not include the first one or two terminal nucleotides at the 3′-end, 5′-end or both ends of the strand.


In another embodiment, the wing modification on the sense strand or antisense strand of the RNAi agent typically does not include the first one or two paired nucleotides within the duplex region at the 3′-end, 5′-end or both ends of the strand.


When the sense strand and the antisense strand of the RNAi agent each contain at least one wing modification, the wing modifications may fall on the same end of the duplex region, and have an overlap of one, two or three nucleotides.


When the sense strand and the antisense strand of the RNAi agent each contain at least two wing modifications, the sense strand and the antisense strand can be so aligned that two modifications each from one strand fall on one end of the duplex region, having an overlap of one, two or three nucleotides; two modifications each from one strand fall on the other end of the duplex region, having an overlap of one, two or three nucleotides; two modifications one strand fall on each side of the lead motif, having an overlap of one, two or three nucleotides in the duplex region.


In one embodiment, every nucleotide in the sense strand and antisense strand of the RNAi agent, including the nucleotides that are part of the motifs, may be modified. Each nucleotide may be modified with the same or different modification which can include one or more alteration of one or both of the non-linking phosphate oxygens and/or of one or more of the linking phosphate oxygens; alteration of a constituent of the ribose sugar, e.g., of the 2′ hydroxyl on the ribose sugar; wholesale replacement of the phosphate moiety with “dephospho” linkers; modification or replacement of a naturally occurring base; and replacement or modification of the ribose-phosphate backbone.


As nucleic acids are polymers of subunits, many of the modifications occur at a position which is repeated within a nucleic acid, e.g., a modification of a base, or a phosphate moiety, or a non-linking O of a phosphate moiety. In some cases the modification will occur at all of the subject positions in the nucleic acid but in many cases it will not. By way of example, a modification may only occur at a 3′ or 5′ terminal position, may only occur in a terminal region, e.g, at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand. A modification may occur in a double strand region, a single strand region, or in both. A modification may occur only in the double strand region of a RNA or may only occur in a single strand region of a RNA. For example, a phosphorothioate modification at a non-linking O position may only occur at one or both termini, may only occur in a terminal region, e.g., at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand, or may occur in double strand and single strand regions, particularly at termini. The 5′ end or ends can be phosphorylated.


It may be possible, e.g., to enhance stability, to include particular bases in overhangs, or to include modified nucleotides or nucleotide surrogates, in single strand overhangs, e.g., in a 5′ or 3′ overhang, or in both. For example, it can be desirable to include purine nucleotides in overhangs. In some embodiments all or some of the bases in a 3′ or 5′ overhang may be modified, e.g., with a modification described herein. Modifications can include, e.g., the use of modifications at the 2′ position of the ribose sugar with modifications that are known in the art, e.g., the use of deoxyribonucleotides, 2′-deoxy-2′-fluoro (2′-F) or 2′-O-methyl modified instead of the ribosugar of the nucleobase, and modifications in the phosphate group, e.g., phosphorothioate modifications. Overhangs need not be homologous with the target sequence.


In one embodiment, each residue of the sense strand and antisense strand is independently modified with LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O-methyl, 2′-O-allyl, 2′-C-allyl, 2′-deoxy, 2′-hydroxyl, or 2′-fluoro. The strands can contain more than one modification. In one embodiment, each residue of the sense strand and antisense strand is independently modified with 2′-O-methyl or 2′-fluoro.


At least two different modifications are typically present on the sense strand and antisense strand. Those two modifications may be the 2′-O-methyl or 2′-fluoro modifications, or others.


In one embodiment, the Na and/or Nb comprise modifications of an alternating pattern. The term “alternating motif” as used herein refers to a motif having one or more modifications, each modification occurring on alternating nucleotides of one strand. The alternating nucleotide may refer to one per every other nucleotide or one per every three nucleotides, or a similar pattern. For example, if A, B and C each represent one type of modification to the nucleotide, the alternating motif can be “ABAB ABAB ABAB . . . ,” “AABBAABBAABB . . . ,” “AABAABAABAAB . . . ,” “AAABAAABAAAB . . . ,” “AAABBBAAABBB . . . ,” or “ABCABCABCABC . . . ,” etc.


The type of modifications contained in the alternating motif may be the same or different. For example, if A, B, C, D each represent one type of modification on the nucleotide, the alternating pattern, i.e., modifications on every other nucleotide, may be the same, but each of the sense strand or antisense strand can be selected from several possibilities of modifications within the alternating motif such as “ABABAB . . . ”, “AC AC AC . . . ” “BDBDBD . . . ” or “CDCDCD . . . ,” etc.


In one embodiment, the RNAi agent of the invention comprises the modification pattern for the alternating motif on the sense strand relative to the modification pattern for the alternating motif on the antisense strand is shifted. The shift may be such that the modified group of nucleotides of the sense strand corresponds to a differently modified group of nucleotides of the antisense strand and vice versa. For example, the sense strand when paired with the antisense strand in the dsRNA duplex, the alternating motif in the sense strand may start with “ABABAB” from 5′-3′ of the strand and the alternating motif in the antisense strand may start with “BAB ABA” from 5′-3′ of the strand within the duplex region. As another example, the alternating motif in the sense strand may start with “AABBAABB” from 5′-3′ of the strand and the alternating motif in the antisense strand may start with “BBAABBAA” from 5′-3′ of the strand within the duplex region, so that there is a complete or partial shift of the modification patterns between the sense strand and the antisense strand.


In one embodiment, the RNAi agent comprises the pattern of the alternating motif of 2′-O-methyl modification and 2′-F modification on the sense strand initially has a shift relative to the pattern of the alternating motif of 2′-O-methyl modification and 2′-F modification on the antisense strand initially, i.e., the 2′-O-methyl modified nucleotide on the sense strand base pairs with a 2′-F modified nucleotide on the antisense strand and vice versa. The 1 position of the sense strand may start with the 2′-F modification, and the 1 position of the antisense strand may start with the 2′-O-methyl modification.


The introduction of one or more motifs of three identical modifications on three consecutive nucleotides to the sense strand and/or antisense strand interrupts the initial modification pattern present in the sense strand and/or antisense strand. This interruption of the modification pattern of the sense and/or antisense strand by introducing one or more motifs of three identical modifications on three consecutive nucleotides to the sense and/or antisense strand surprisingly enhances the gene silencing activity to the target gene.


In one embodiment, when the motif of three identical modifications on three consecutive nucleotides is introduced to any of the strands, the modification of the nucleotide next to the motif is a different modification than the modification of the motif. For example, the portion of the sequence containing the motif is “ . . . NaYYYNb . . . ,” where “Y” represents the modification of the motif of three identical modifications on three consecutive nucleotide, and “Na” and “Nb” represent a modification to the nucleotide next to the motif “YYY” that is different than the modification of Y, and where Na and Nb can be the same or different modifications. Alternatively, Na and/or Nb may be present or absent when there is a wing modification present.


The RNAi agent may further comprise at least one phosphorothioate or methylphosphonate internucleotide linkage. The phosphorothioate or methylphosphonate internucleotide linkage modification may occur on any nucleotide of the sense strand or antisense strand or both strands in any position of the strand. For instance, the internucleotide linkage modification may occur on every nucleotide on the sense strand and/or antisense strand; each internucleotide linkage modification may occur in an alternating pattern on the sense strand and/or antisense strand; or the sense strand or antisense strand may contain both internucleotide linkage modifications in an alternating pattern. The alternating pattern of the internucleotide linkage modification on the sense strand may be the same or different from the antisense strand, and the alternating pattern of the internucleotide linkage modification on the sense strand may have a shift relative to the alternating pattern of the internucleotide linkage modification on the antisense strand.


In one embodiment, the RNAi comprises a phosphorothioate or methylphosphonate internucleotide linkage modification in the overhang region. For example, the overhang region may contain two nucleotides having a phosphorothioate or methylphosphonate internucleotide linkage between the two nucleotides. Internucleotide linkage modifications also may be made to link the overhang nucleotides with the terminal paired nucleotides within the duplex region. For example, at least 2, 3, 4, or all the overhang nucleotides may be linked through phosphorothioate or methylphosphonate internucleotide linkage, and optionally, there may be additional phosphorothioate or methylphosphonate internucleotide linkages linking the overhang nucleotide with a paired nucleotide that is next to the overhang nucleotide. For instance, there may be at least two phosphorothioate internucleotide linkages between the terminal three nucleotides, in which two of the three nucleotides are overhang nucleotides, and the third is a paired nucleotide next to the overhang nucleotide. These terminal three nucleotides may be at the 3′-end of the antisense strand, the 3′-end of the sense strand, the 5′-end of the antisense strand, and/or the 5′end of the antisense strand.


In one embodiment, the 2 nucleotide overhang is at the 3′-end of the antisense strand, and there are two phosphorothioate internucleotide linkages between the terminal three nucleotides, wherein two of the three nucleotides are the overhang nucleotides, and the third nucleotide is a paired nucleotide next to the overhang nucleotide. Optionally, the RNAi agent may additionally have two phosphorothioate internucleotide linkages between the terminal three nucleotides at both the 5′-end of the sense strand and at the 5′-end of the antisense strand.


In one embodiment, the RNAi agent comprises mismatch(es) with the target, within the duplex, or combinations thereof. The mismatch may occur in the overhang region or the duplex region. The base pair may be ranked on the basis of their propensity to promote dissociation or melting (e.g., on the free energy of association or dissociation of a particular pairing, the simplest approach is to examine the pairs on an individual pair basis, though next neighbor or similar analysis can also be used). In terms of promoting dissociation: A:U is preferred over G:C; G:U is preferred over G:C; and I:C is preferred over G:C (I=inosine). Mismatches, e.g., non-canonical or other than canonical pairings (as described elsewhere herein) are preferred over canonical (A:T, A:U, G:C) pairings; and pairings which include a universal base are preferred over canonical pairings.


In one embodiment, the RNAi agent comprises at least one of the first 1, 2, 3, 4, or 5 base pairs within the duplex regions from the 5′-end of the antisense strand independently selected from the group of: A:U, G:U, I:C, and mismatched pairs, e.g, non-canonical or other than canonical pairings or pairings which include a universal base, to promote the dissociation of the antisense strand at the 5′-end of the duplex.


In one embodiment, the nucleotide at the 1 position within the duplex region from the 5′-end in the antisense strand is selected from the group consisting of A, dA, dU, U, and dT. Alternatively, at least one of the first 1, 2 or 3 base pair within the duplex region from the 5′-end of the antisense strand is an AU base pair. For example, the first base pair within the duplex region from the 5′-end of the antisense strand is an AU base pair.


In one embodiment, the sense strand sequence may be represented by formula (I):





5′np-Na—(XXX)i—Nb—YYY—Nb—(ZZZ)j—Na-nq3′  (I)


wherein:


i and j are each independently 0 or 1;


p and q are each independently 0-6;


each Na independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;


each Nb independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;


each np and nq independently represent an overhang nucleotide;


wherein Nb and Y do not have the same modification; and


XXX, YYY and ZZZ each independently represent one motif of three identical modifications on three consecutive nucleotides. Preferably YYY is all 2′-F modified nucleotides.


In one embodiment, the Na and/or Nb comprise modifications of alternating pattern.


In one embodiment, the YYY motif occurs at or near the cleavage site of the sense strand. For example, when the RNAi agent has a duplex region of 17-23 nucleotides in length, the YYY motif can occur at or the vicinity of the cleavage site (e.g.: can occur at positions 6, 7, 8, 7, 8, 9, 8, 9, 10, 9, 10, 11, 10, 11, 12 or 11, 12, 13) of—the sense strand, the count starting from the 1st nucleotide, from the 5′-end; or optionally, the count starting at the 1st paired nucleotide within the duplex region, from the 5′-end.


In one embodiment, i is 1 and j is 0, or i is 0 and j is 1, or both i and j are 1. The sense strand can therefore be represented by the following formulas:





5′np-Na—YYY—Nb—ZZZ—Na-nq3′  (Ib);





5′np-Na—XXX—Nb—YYY—Na-nq3′  (Ic); or





5′np-Na—XXX—Nb—YYY—Nb—ZZZ—Na-nq3′  (Id).


When the sense strand is represented by formula (Ib), Nb represents an oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na independently can represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


When the sense strand is represented as formula (Ic), Nb represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na can independently represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


When the sense strand is represented as formula (Id), each Nb independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides.


Preferably, Nb is 0, 1, 2, 3, 4, 5 or 6 Each Na can independently represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


Each of X, Y and Z may be the same or different from each other.


In other embodiments, i is 0 and j is 0, and the sense strand may be represented by the formula:





5′np-Na—YYY—Na-nq3′  (Ia).


When the sense strand is represented by formula (Ia), each Na independently can represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


In one embodiment, the antisense strand sequence of the RNAi may be represented by formula (II):





5′nq′—Na′—(Z′Z′Z′)k—Nb′—Y′Y′Y′—Nb′—(X′X′X′)l—N′a-np′3′  (II)


wherein:


k and l are each independently 0 or 1;


p′ and q′ are each independently 0-6;


each Na′ independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;


each Nb′ independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;


each np′ and nq′ independently represent an overhang nucleotide;


wherein Nb′ and Y′ do not have the same modification;


and


X′X′X′, Y′Y′Y′ and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides.


In one embodiment, the Na′ and/or Nb′ comprise modifications of alternating pattern.


The Y′Y′Y′ motif occurs at or near the cleavage site of the antisense strand. For example, when the RNAi agent has a duplex region of 17-23 nucleotide in length, the Y′Y′Y′ motif can occur at positions 9, 10, 11; 10, 11, 12; 11, 12, 13; 12, 13, 14; or 13, 14, 15 of the antisense strand, with the count starting from the 1st nucleotide, from the 5′-end; or optionally, the count starting at the 1st paired nucleotide within the duplex region, from the 5′-end. Preferably, the Y′Y′Y′ motif occurs at positions 11, 12, 13.


In one embodiment, Y′Y′Y′ motif is all 2′-OMe modified nucleotides.


In one embodiment, k is 1 and l is 0, or k is 0 and l is 1, or both k and l are 1.


The antisense strand can therefore be represented by the following formulas:





5′nq′—Na′—Z′Z′Z′—Nb′—Y′Y′Y′—Na′-np′3′  (IIb);





5′nq′—Na′—Y′Y′Y′—Nb′—X′X′X′-np′3′  (IIc); or





5′nq′—Na′—Z′Z′Z′—Nb′—Y′Y′Y′—Nb′—X′X′X′—Na′-np′3′  (IId).


When the antisense strand is represented by formula (IIb), Nb represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


When the antisense strand is represented as formula (IIc), Nb′ represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


When the antisense strand is represented as formula (IId), each Nb′ independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides. Preferably, Nb is 0, 1, 2, 3, 4, 5 or 6.


In other embodiments, k is 0 and l is 0 and the antisense strand may be represented by the formula:





5′np′—Na′—Y′Y′Y′—Na′-nq′3′  (Ia).


When the antisense strand is represented as formula (IIa), each Na′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


Each of X′, Y′ and Z′ may be the same or different from each other.


Each nucleotide of the sense strand and antisense strand may be independently modified with LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O-methyl, 2′-O-allyl, 2′-C-allyl, 2′-hydroxyl, or 2′-fluoro. For example, each nucleotide of the sense strand and antisense strand is independently modified with 2′-O-methyl or 2′-fluoro. Each X, Y, Z, X′, Y′ and Z′, in particular, may represent a 2′-O-methyl modification or a 2′-fluoro modification.


In one embodiment, the sense strand of the RNAi agent may contain YYY motif occurring at 9, 10 and 11 positions of the strand when the duplex region is 21 nt, the count starting from the 1st nucleotide from the 5′-end, or optionally, the count starting at the 1st paired nucleotide within the duplex region, from the 5′-end; and Y represents 2′-F modification. The sense strand may additionally contain XXX motif or ZZZ motifs as wing modifications at the opposite end of the duplex region; and XXX and ZZZ each independently represents a 2′-OMe modification or 2′-F modification.


In one embodiment the antisense strand may contain Y′YY motif occurring at positions 11, 12, 13 of the strand, the count starting from the 1st nucleotide from the 5′-end, or optionally, the count starting at the 1st paired nucleotide within the duplex region, from the 5′-end; and Y′ represents 2′-O-methyl modification. The antisense strand may additionally contain X′X′X′ motif or Z′Z′Z′ motifs as wing modifications at the opposite end of the duplex region; and X′X′X′ and Z′Z′Z′ each independently represents a 2′-OMe modification or 2′-F modification.


The sense strand represented by any one of the above formulas (Ia), (Ib), (Ic), and (Id) forms a duplex with a antisense strand being represented by any one of formulas (IIa), (IIb), (IIc), and (IId), respectively.


Accordingly, the RNAi agents for use in the methods of the invention may comprise a sense strand and an antisense strand, each strand having 14 to 30 nucleotides, the RNAi duplex represented by formula (III):





sense: 5′np-Na—(XXX)i—Nb—YYY—Nb—(ZZZ)j—Na-nq3′





antisense: 3′np′—Na′—(X′X′X′)k—Nb′—YYY′—Nb′—(Z′Z′Z′)l—Na′-nq′5′   (III)


wherein:


i, j, k, and l are each independently 0 or 1;


p, p′, q, and q′ are each independently 0-6;


each Na and Na independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;


each Nb and Nb independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;


wherein


each np′, np, nq′, and nq, each of which may or may not be present, independently represents an overhang nucleotide; and


XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides.


In one embodiment, i is 0 and j is 0; or i is 1 and j is 0; or i is 0 and j is 1; or both i and j are 0; or both i and j are 1. In another embodiment, k is 0 and l is 0; or k is 1 and l is 0; k is 0 and l is 1; or both k and l are 0; or both k and l are 1.


Exemplary combinations of the sense strand and antisense strand forming a RNAi duplex include the formulas below:





5′np-Na—YYY—Na-nq3′





3′np′—Na′—Y′Y′Y′—Na′nq′5′   (IIIa)





5′np-Na—YYY—Nb—ZZZ—Na-nq3′





3′np′—Na′—YYY′—Nb—Z′Z′Z′—Na′nq′5′   (IIIb)





5′np-Na—XXX—Nb—YYY—Na-nq3′





3′np′—Na′—X′X′X′—Nb′—YYY′—Na′-nq′5′   (IIIc)





5′np-Na—XXX—Nb—YYY—Nb—ZZZ—Na-nq3′





3′np′—Na′—X′X′X′—Nb′—YYY′—Nb′—Z′Z′Z′—Na-nq′5′   (IIId)


When the RNAi agent is represented by formula (IIIa), each Na independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


When the RNAi agent is represented by formula (IIIb), each Nb independently represents an oligonucleotide sequence comprising 1-10, 1-7, 1-5 or 1-4 modified nucleotides. Each Na independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


When the RNAi agent is represented as formula (IIIc), each Nb, Nb′ independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.


When the RNAi agent is represented as formula (IIId), each Nb, Nb′ independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each Na, Na independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides. Each of Na, Na′, Nb and Nb independently comprises modifications of alternating pattern.


Each of X, Y and Z in formulas (III), (IIIa), (IIIb), (IIIc), and (IIId) may be the same or different from each other.


When the RNAi agent is represented by formula (III), (IIIa), (IIIb), (IIIc), and (IIId), at least one of the Y nucleotides may form a base pair with one of the Y′ nucleotides. Alternatively, at least two of the Y nucleotides form base pairs with the corresponding Y′ nucleotides; or all three of the Y nucleotides all form base pairs with the corresponding Y′ nucleotides.


When the RNAi agent is represented by formula (IIIb) or (IIId), at least one of the Z nucleotides may form a base pair with one of the Z′ nucleotides. Alternatively, at least two of the Z nucleotides form base pairs with the corresponding Z′ nucleotides; or all three of the Z nucleotides all form base pairs with the corresponding Z′ nucleotides.


When the RNAi agent is represented as formula (IIIc) or (IIId), at least one of the X nucleotides may form a base pair with one of the X′ nucleotides. Alternatively, at least two of the X nucleotides form base pairs with the corresponding X′ nucleotides; or all three of the X nucleotides all form base pairs with the corresponding X′ nucleotides.


In one embodiment, the modification on the Y nucleotide is different than the modification on the Y′ nucleotide, the modification on the Z nucleotide is different than the modification on the Z′ nucleotide, and/or the modification on the X nucleotide is different than the modification on the X′ nucleotide.


In one embodiment, when the RNAi agent is represented by formula (IIId), the Na modifications are 2′-O-methyl or 2′-fluoro modifications. In another embodiment, when the RNAi agent is represented by formula (IIId), the Na modifications are 2′-O-methyl or 2′-fluoro modifications and np′>0 and at least one np′ is linked to a neighboring nucleotide a via phosphorothioate linkage. In yet another embodiment, when the RNAi agent is represented by formula (IIId), the Na modifications are 2′-O-methyl or 2′-fluoro modifications, np′>0 and at least one np′ is linked to a neighboring nucleotide via phosphorothioate linkage, and the sense strand is conjugated to one or more GalNAc derivatives attached through a bivalent or trivalent branched linker. In another embodiment, when the RNAi agent is represented by formula (IIId), the Na modifications are 2′-O-methyl or 2′-fluoro modifications, np′>0 and at least one np′ is linked to a neighboring nucleotide via phosphorothioate linkage, the sense strand comprises at least one phosphorothioate linkage, and the sense strand is conjugated to one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.


In one embodiment, when the RNAi agent is represented by formula (IIIa), the Na modifications are 2′-O-methyl or 2′-fluoro modifications, np′>0 and at least one np′ is linked to a neighboring nucleotide via phosphorothioate linkage, the sense strand comprises at least one phosphorothioate linkage, and the sense strand is conjugated to one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.


In one embodiment, the RNAi agent is a multimer containing at least two duplexes represented by formula (III), (IIIa), (IIIb), (IIIc), and (IIId), wherein the duplexes are connected by a linker. The linker can be cleavable or non-cleavable. Optionally, the multimer further comprises a ligand. Each of the duplexes can target the same gene or two different genes; or each of the duplexes can target same gene at two different target sites.


In one embodiment, the RNAi agent is a multimer containing three, four, five, six or more duplexes represented by formula (III), (IIIa), (IIIb), (IIIc), and (IIId), wherein the duplexes are connected by a linker. The linker can be cleavable or non-cleavable. Optionally, the multimer further comprises a ligand. Each of the duplexes can target the same gene or two different genes; or each of the duplexes can target same gene at two different target sites.


In one embodiment, two RNAi agents represented by formula (III), (IIIa), (IIIb), (IIIc), and (IIId) are linked to each other at the 5′ end, and one or both of the 3′ ends and are optionally conjugated to a ligand. Each of the agents can target the same gene or two different genes; or each of the agents can target same gene at two different target sites.


Various publications describe multimeric RNAi agents that can be used in the methods of the invention. Such publications include WO2007/091269, U.S. Pat. No. 7,858,769, WO2010/141511, WO2007/117686, WO2009/014887 and WO2011/031520 the entire contents of each of which are hereby incorporated herein by reference.


The RNAi agent that contains conjugations of one or more carbohydrate moieties to a RNAi agent can optimize one or more properties of the RNAi agent. In many cases, the carbohydrate moiety will be attached to a modified subunit of the RNAi agent. For example, the ribose sugar of one or more ribonucleotide subunits of a dsRNA agent can be replaced with another moiety, e.g., a non-carbohydrate (preferably cyclic) carrier to which is attached a carbohydrate ligand. A ribonucleotide subunit in which the ribose sugar of the subunit has been so replaced is referred to herein as a ribose replacement modification subunit (RRMS). A cyclic carrier may be a carbocyclic ring system, i.e., all ring atoms are carbon atoms, or a heterocyclic ring system, i.e., one or more ring atoms may be a heteroatom, e.g, nitrogen, oxygen, sulfur. The cyclic carrier may be a monocyclic ring system, or may contain two or more rings, e.g. fused rings. The cyclic carrier may be a fully saturated ring system, or it may contain one or more double bonds.


The ligand may be attached to the polynucleotide via a carrier. The carriers include (i) at least one “backbone attachment point,” preferably two “backbone attachment points” and (ii) at least one “tethering attachment point.” A “backbone attachment point” as used herein refers to a functional group, e.g. a hydroxyl group, or generally, a bond available for, and that is suitable for incorporation of the carrier into the backbone, e.g, the phosphate, or modified phosphate, e.g, sulfur containing, backbone, of a ribonucleic acid. A “tethering attachment point” (TAP) in some embodiments refers to a constituent ring atom of the cyclic carrier, e.g, a carbon atom or a heteroatom (distinct from an atom which provides a backbone attachment point), that connects a selected moiety. The moiety can be, e.g, a carbohydrate, e.g. monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide and polysaccharide. Optionally, the selected moiety is connected by an intervening tether to the cyclic carrier. Thus, the cyclic carrier will often include a functional group, e.g, an amino group, or generally, provide a bond, that is suitable for incorporation or tethering of another chemical entity, e.g, a ligand to the constituent ring.


The RNAi agents may be conjugated to a ligand via a carrier, wherein the carrier can be cyclic group or acyclic group; preferably, the cyclic group is selected from pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolane, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl and decalin; preferably, the acyclic group is selected from serinol backbone or diethanolamine backbone.


In certain specific embodiments, the RNAi agent for use in the methods of the invention is an agent selected from the group of agents listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12.


In one embodiment, when the agent is an agent listed in Table 12, the agent may lack a terminal dT.


The present invention further includes double-stranded RNAi agents comprising any one of the sequences listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12 which comprise a 5′ phosphate or phosphate mimetic on the antisense strand (see, e.g., PCT Publication No. WO 2011005860). Further, the present invention includes double-stranded RNAi agents comprising any one of the sequences listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12 which include a 2′fluoro group in place of a 2′-OMe group at the 5′end of the sense strand.


These agents may further comprise a ligand.


In one embodiment, the agent is AD-60940 (sense strand: CfsusGfgUfaUfuUfCfCfuAfgGfgUfaCfaAfL96; antisense strand: usUfsgUfaCfcCfuAfggaAfaUfaCfcAfgsasg).


A. Ligands


The double-stranded RNA (dsRNA) agents of the invention may optionally be conjugated to one or more ligands. The ligand can be attached to the sense strand, antisense strand or both strands, at the 3′-end, 5′-end or both ends. For instance, the ligand may be conjugated to the sense strand. In preferred embodiments, the ligand is conjugated to the 3′-end of the sense strand. In one preferred embodiment, the ligand is a GalNAc ligand. In particularly preferred embodiments, the ligand is GalNAc3:




embedded image


In some embodiments, the ligand, e.g., GalNAc ligand, is attached to the 3′ end of the RNAi agent. In one embodiment, the RNAi agent is conjugated to the ligand, e.g., GalNAc ligand, as shown in the following schematic




embedded image


wherein X is O or S. In one embodiment, X is O.


A wide variety of entities can be coupled to the RNAi agents of the present invention. Preferred moieties are ligands, which are coupled, preferably covalently, either directly or indirectly via an intervening tether.


In preferred embodiments, a ligand alters the distribution, targeting or lifetime of the molecule into which it is incorporated. In preferred embodiments a ligand provides an enhanced affinity for a selected target, e.g., molecule, cell or cell type, compartment, receptor e.g, a cellular or organ compartment, tissue, organ or region of the body, as, e.g., compared to a species absent such a ligand. Ligands providing enhanced affinity for a selected target are also termed targeting ligands.


Some ligands can have endosomolytic properties. The endosomolytic ligands promote the lysis of the endosome and/or transport of the composition of the invention, or its components, from the endosome to the cytoplasm of the cell. The endosomolytic ligand may be a polyanionic peptide or peptidomimetic which shows pH-dependent membrane activity and fusogenicity. In one embodiment, the endosomolytic ligand assumes its active conformation at endosomal pH. The “active” conformation is that conformation in which the endosomolytic ligand promotes lysis of the endosome and/or transport of the composition of the invention, or its components, from the endosome to the cytoplasm of the cell. Exemplary endosomolytic ligands include the GALA peptide (Subbarao et al., Biochemistry, 1987, 26: 2964-2972), the EALA peptide (Vogel et al., J. Am. Chem. Soc., 1996, 118: 1581-1586), and their derivatives (Turk et al., Biochem. Biophys. Acta, 2002, 1559: 56-68). In one embodiment, the endosomolytic component may contain a chemical group (e.g, an amino acid) which will undergo a change in charge or protonation in response to a change in pH. The endosomolytic component may be linear or branched.


Ligands can improve transport, hybridization, and specificity properties and may also improve nuclease resistance of the resultant natural or modified oligoribonucleotide, or a polymeric molecule comprising any combination of monomers described herein and/or natural or modified ribonucleotides.


Ligands in general can include therapeutic modifiers, e.g., for enhancing uptake; diagnostic compounds or reporter groups e.g., for monitoring distribution; cross-linking agents; and nuclease-resistance conferring moieties. General examples include lipids, steroids, vitamins, sugars, proteins, peptides, polyamines, and peptide mimics.


Ligands can include a naturally occurring substance, such as a protein (e.g, human serum albumin (HSA), low-density lipoprotein (LDL), high-density lipoprotein (HDL), or globulin); a carbohydrate (e.g, a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin or hyaluronic acid); or a lipid. The ligand may also be a recombinant or synthetic molecule, such as a synthetic polymer, e.g, a synthetic polyamino acid, an oligonucleotide (e.g, an aptamer). Examples of polyamino acids include polyamino acid is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolied) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacryllic acid), N-isopropylacrylamide polymers, or polyphosphazine. Example of polyamines include: polyethylenimine, polylysine (PLL), spermine, spermidine, polyamine, pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, arginine, amidine, protamine, cationic lipid, cationic porphyrin, quaternary salt of a polyamine, or an alpha helical peptide.


Ligands can also include targeting groups, e.g, a cell or tissue targeting agent, e.g, a lectin, glycoprotein, lipid or protein, e.g, an antibody, that binds to a specified cell type such as a kidney cell. A targeting group can be a thyrotropin, melanotropin, lectin, glycoprotein, surfactant protein A, Mucin carbohydrate, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, multivalent fucose, glycosylated polyaminoacids, multivalent galactose, transferrin, bisphosphonate, polyglutamate, polyaspartate, a lipid, cholesterol, a steroid, bile acid, folate, vitamin B12, biotin, an RGD peptide, an RGD peptide mimetic or an aptamer.


Other examples of ligands include dyes, intercalating agents (e.g., acridines), cross-linkers (e.g., psoralene, mitomycin C), porphyrins (TPPC4, texaphyrin, Sapphyrin), polycyclic aromatic hydrocarbons (e.g., phenazine, dihydrophenazine), artificial endonucleases or a chelator (e.g., EDTA), lipophilic molecules, e.g, cholesterol, cholic acid, adamantane acetic acid, 1-pyrene butyric acid, dihydrotestosterone, 1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid, myristic acid, O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine) and peptide conjugates (e.g., antennapedia peptide, Tat peptide), alkylating agents, phosphate, amino, mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG]2, polyamino, alkyl, substituted alkyl, radiolabeled markers, enzymes, haptens (e.g., biotin), transport/absorption facilitators (e.g., aspirin, vitamin E, folic acid), synthetic ribonucleases (e.g., imidazole, bisimidazole, histamine, imidazole clusters, acridine-imidazole conjugates, Eu3+ complexes of tetraazamacrocycles), dinitrophenyl, HRP, or AP.


Ligands can be proteins, e.g, glycoproteins, or peptides, e.g, molecules having a specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell. Ligands may also include hormones and hormone receptors. They can also include non-peptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, multivalent fucose, or aptamers. The ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF-κB.


The ligand can be a substance, e.g, a drug, which can increase the uptake of the iRNA agent into the cell, for example, by disrupting the cell's cytoskeleton, e.g, by disrupting the cell's microtubules, microfilaments, and/or intermediate filaments. The drug can be, for example, taxon, vincristine, vinblastine, cytochalasin, nocodazole, japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.


The ligand can increase the uptake of the oligonucleotide into the cell by, for example, activating an inflammatory response. Exemplary ligands that would have such an effect include tumor necrosis factor alpha (TNFalpha), interleukin-1 beta, or gamma interferon.


In one aspect, the ligand is a lipid or lipid-based molecule. Such a lipid or lipid-based molecule preferably binds a serum protein, e.g, human serum albumin (HSA). An HSA binding ligand allows for distribution of the conjugate to a target tissue, e.g, a non-kidney target tissue of the body. For example, the target tissue can be the liver, including parenchymal cells of the liver. Other molecules that can bind HSA can also be used as ligands. For example, naproxen or aspirin can be used. A lipid or lipid-based ligand can (a) increase resistance to degradation of the conjugate, (b) increase targeting or transport into a target cell or cell membrane, and/or (c) can be used to adjust binding to a serum protein, e.g, HSA.


A lipid based ligand can be used to modulate, e.g, control the binding of the conjugate to a target tissue. For example, a lipid or lipid-based ligand that binds to HSA more strongly will be less likely to be targeted to the kidney and therefore less likely to be cleared from the body. A lipid or lipid-based ligand that binds to HSA less strongly can be used to target the conjugate to the kidney.


In a preferred embodiment, the lipid based ligand binds HSA. Preferably, it binds HSA with a sufficient affinity such that the conjugate will be preferably distributed to a non-kidney tissue. However, it is preferred that the affinity not be so strong that the HSA-ligand binding cannot be reversed.


In another preferred embodiment, the lipid based ligand binds HSA weakly or not at all, such that the conjugate will be preferably distributed to the kidney. Other moieties that target to kidney cells can also be used in place of or in addition to the lipid based ligand.


In another aspect, the ligand is a moiety, e.g., a vitamin, which is taken up by a target cell, e.g., a proliferating cell. These are particularly useful for treating disorders characterized by unwanted cell proliferation, e.g., of the malignant or non-malignant type, e.g., cancer cells. Exemplary vitamins include vitamin A, E, and K. Other exemplary vitamins include B vitamins, e.g, folic acid, B12, riboflavin, biotin, pyridoxal or other vitamins or nutrients taken up by cancer cells. Also included are HAS, low density lipoprotein (LDL) and high-density lipoprotein (HDL).


In another aspect, the ligand is a cell-permeation agent, preferably a helical cell-permeation agent. Preferably, the agent is amphipathic. An exemplary agent is a peptide such as tat or antennopedia. If the agent is a peptide, it can be modified, including a peptidylmimetic, invertomers, non-peptide or pseudo-peptide linkages, and use of D-amino acids. The helical agent is preferably an alpha-helical agent, which preferably has a lipophilic and a lipophobic phase.


The ligand can be a peptide or peptidomimetic. A peptidomimetic (also referred to herein as an oligopeptidomimetic) is a molecule capable of folding into a defined three-dimensional structure similar to a natural peptide. The peptide or peptidomimetic moiety can be about 5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long. A peptide or peptidomimetic can be, for example, a cell permeation peptide, cationic peptide, amphipathic peptide, or hydrophobic peptide (e.g, consisting primarily of Tyr, Trp or Phe). The peptide moiety can be a dendrimer peptide, constrained peptide or crosslinked peptide. In another alternative, the peptide moiety can include a hydrophobic membrane translocation sequence (MTS). An exemplary hydrophobic MTS-containing peptide is RFGF having the amino acid sequence AAVALLPAVLLALLAP (SEQ ID NO: 11). An RFGF analogue (e.g, amino acid sequence AALLPVLLAAP (SEQ ID NO: 12)) containing a hydrophobic MTS can also be a targeting moiety. The peptide moiety can be a “delivery” peptide, which can carry large polar molecules including peptides, oligonucleotides, and protein across cell membranes. For example, sequences from the HIV Tat protein (GRKKRRQRRRPPQ) (SEQ ID NO: 13) and the Drosophila Antennapedia protein (RQIKIWFQNRRMKWKK) (SEQ ID NO: 14) have been found to be capable of functioning as delivery peptides. A peptide or peptidomimetic can be encoded by a random sequence of DNA, such as a peptide identified from a phage-display library, or one-bead-one-compound (OBOC) combinatorial library (Lam et al., Nature, 354:82-84, 1991). Preferably the peptide or peptidomimetic tethered to an iRNA agent via an incorporated monomer unit is a cell targeting peptide such as an arginine-glycine-aspartic acid (RGD)-peptide, or RGD mimic. A peptide moiety can range in length from about 5 amino acids to about 40 amino acids. The peptide moieties can have a structural modification, such as to increase stability or direct conformational properties. Any of the structural modifications described below can be utilized. An RGD peptide moiety can be used to target a tumor cell, such as an endothelial tumor cell or a breast cancer tumor cell (Zitzmann et al., Cancer Res., 62:5139-43, 2002). An RGD peptide can facilitate targeting of an iRNA agent to tumors of a variety of other tissues, including the lung, kidney, spleen, or liver (Aoki et al., Cancer Gene Therapy 8:783-787, 2001). Preferably, the RGD peptide will facilitate targeting of an iRNA agent to the kidney. The RGD peptide can be linear or cyclic, and can be modified, e.g., glycosylated or methylated to facilitate targeting to specific tissues. For example, a glycosylated RGD peptide can deliver an iRNA agent to a tumor cell expressing αVβ3 (Haubner et al., Jour. Nucl. Med., 42:326-336, 2001). Peptides that target markers enriched in proliferating cells can be used. For example, RGD containing peptides and peptidomimetics can target cancer cells, in particular cells that exhibit an integrin. Thus, one could use RGD peptides, cyclic peptides containing RGD, RGD peptides that include D-amino acids, as well as synthetic RGD mimics. In addition to RGD, one can use other moieties that target the integrin ligand. Generally, such ligands can be used to control proliferating cells and angiogeneis. Preferred conjugates of this type of ligand target PECAM-1, VEGF, or other cancer gene, e.g., a cancer gene described herein.


A “cell permeation peptide” is capable of permeating a cell, e.g., a microbial cell, such as a bacterial or fungal cell, or a mammalian cell, such as a human cell. A microbial cell-permeating peptide can be, for example, an α-helical linear peptide (e.g., LL-37 or Ceropin P1), a disulfide bond-containing peptide (e.g, α-defensin, β-defensin or bactenecin), or a peptide containing only one or two dominating amino acids (e.g, PR-39 or indolicidin). A cell permeation peptide can also include a nuclear localization signal (NLS). For example, a cell permeation peptide can be a bipartite amphipathic peptide, such as MPG, which is derived from the fusion peptide domain of HIV-1 gp41 and the NLS of SV40 large T antigen (Simeoni et al., Nucl. Acids Res. 31:2717-2724, 2003).


In one embodiment, a targeting peptide can be an amphipathic α-helical peptide. Exemplary amphipathic α-helical peptides include, but are not limited to, cecropins, lycotoxins, paradaxins, buforin, CPF, bombinin-like peptide (BLP), cathelicidins, ceratotoxins, S. clava peptides, hagfish intestinal antimicrobial peptides (HFIAPs), magainines, brevinins-2, dermaseptins, melittins, pleurocidin, H2A peptides, Xenopus peptides, esculentinis-1, and caerins. A number of factors will preferably be considered to maintain the integrity of helix stability. For example, a maximum number of helix stabilization residues will be utilized (e.g., leu, ala, or lys), and a minimum number helix destabilization residues will be utilized (e.g., proline, or cyclic monomeric units. The capping residue will be considered (for example Gly is an exemplary N-capping residue and/or C-terminal amidation can be used to provide an extra H-bond to stabilize the helix. Formation of salt bridges between residues with opposite charges, separated by i±3, or i±4 positions can provide stability. For example, cationic residues such as lysine, arginine, homo-arginine, ornithine or histidine can form salt bridges with the anionic residues glutamate or aspartate.


Peptide and peptidomimetic ligands include those having naturally occurring or modified peptides, e.g, D or L peptides; α, β, or γ peptides; N-methyl peptides; azapeptides; peptides having one or more amide, i.e., peptide, linkages replaced with one or more urea, thiourea, carbamate, or sulfonyl urea linkages; or cyclic peptides.


The targeting ligand can be any ligand that is capable of targeting a specific receptor. Examples are: folate, GalNAc, galactose, mannose, mannose-6P, clusters of sugars such as GalNAc cluster, mannose cluster, galactose cluster, or an apatamer. A cluster is a combination of two or more sugar units. The targeting ligands also include integrin receptor ligands, Chemokine receptor ligands, transferrin, biotin, serotonin receptor ligands, PSMA, endothelin, GCPII, somatostatin, LDL and HDL ligands. The ligands can also be based on nucleic acid, e.g, an aptamer. The aptamer can be unmodified or have any combination of modifications disclosed herein.


Endosomal release agents include imidazoles, poly or oligoimidazoles, PEIs, peptides, fusogenic peptides, polycaboxylates, polyacations, masked oligo or poly cations or anions, acetals, polyacetals, ketals/polyketyals, orthoesters, polymers with masked or unmasked cationic or anionic charges, dendrimers with masked or unmasked cationic or anionic charges.


PK modulator stands for pharmacokinetic modulator. PK modulators include lipophiles, bile acids, steroids, phospholipid analogues, peptides, protein binding agents, PEG, vitamins etc. Examplary PK modulators include, but are not limited to, cholesterol, fatty acids, cholic acid, lithocholic acid, dialkylglycerides, diacylglyceride, phospholipids, sphingolipids, naproxen, ibuprofen, vitamin E, biotin etc. Oligonucleotides that comprise a number of phosphorothioate linkages are also known to bind to serum protein, thus short oligonucleotides, e.g, oligonucleotides of about 5 bases, 10 bases, 15 bases or 20 bases, comprising multiple phosphorothioate linkages in the backbaone are also amenable to the present invention as ligands (e.g., as PK modulating ligands).


In addition, aptamers that bind serum components (e.g., serum proteins) are also amenable to the present invention as PK modulating ligands.


Other ligand conjugates amenable to the invention are described in U.S. patent application Ser. No. 10/916,185, filed Aug. 10, 2004; U.S. Ser. No. 10/946,873, filed Sep. 21, 2004; U.S. Ser. No. 10/833,934, filed Aug. 3, 2007; U.S. Ser. No. 11/115,989 filed Apr. 27, 2005 and U.S. Ser. No. 11/944,227 filed Nov. 21, 2007, which are incorporated by reference in their entireties for all purposes.


When two or more ligands are present, the ligands can all have same properties, all have different properties or some ligands have the same properties while others have different properties. For example, a ligand can have targeting properties, have endosomolytic activity or have PK modulating properties. In a preferred embodiment, all the ligands have different properties.


Ligands can be coupled to the oligonucleotides at various places, for example, 3′-end, 5′-end, and/or at an internal position. In preferred embodiments, the ligand is attached to the oligonucleotides via an intervening tether, e.g, a carrier described herein. The ligand or tethered ligand may be present on a monomer when the monomer is incorporated into the growing strand. In some embodiments, the ligand may be incorporated via coupling to a “precursor” monomer after the “precursor” monomer has been incorporated into the growing strand. For example, a monomer having, e.g, an amino-terminated tether (i.e., having no associated ligand), e.g, TAP—(CH2)nNH2 may be incorporated into a growing oligonucleotide strand. In a subsequent operation, i.e., after incorporation of the precursor monomer into the strand, a ligand having an electrophilic group, e.g, a pentafluorophenyl ester or aldehyde group, can subsequently be attached to the precursor monomer by coupling the electrophilic group of the ligand with the terminal nucleophilic group of the precursor monomer's tether.


In another example, a monomer having a chemical group suitable for taking part in Click Chemistry reaction may be incorporated, e.g, an azide or alkyne terminated tether/linker. In a subsequent operation, i.e., after incorporation of the precursor monomer into the strand, a ligand having complementary chemical group, e.g. an alkyne or azide can be attached to the precursor monomer by coupling the alkyne and the azide together.


For double-stranded oligonucleotides, ligands can be attached to one or both strands. In some embodiments, a double-stranded iRNA agent contains a ligand conjugated to the sense strand. In other embodiments, a double-stranded iRNA agent contains a ligand conjugated to the antisense strand.


In some embodiments, ligand can be conjugated to nucleobases, sugar moieties, or internucleosidic linkages of nucleic acid molecules. Conjugation to purine nucleobases or derivatives thereof can occur at any position including, endocyclic and exocyclic atoms. In some embodiments, the 2-, 6-, 7-, or 8-positions of a purine nucleobase are attached to a conjugate moiety. Conjugation to pyrimidine nucleobases or derivatives thereof can also occur at any position. In some embodiments, the 2-, 5-, and 6-positions of a pyrimidine nucleobase can be substituted with a conjugate moiety. Conjugation to sugar moieties of nucleosides can occur at any carbon atom. Example carbon atoms of a sugar moiety that can be attached to a conjugate moiety include the 2′, 3′, and 5′ carbon atoms. The 1′ position can also be attached to a conjugate moiety, such as in an abasic residue. Internucleosidic linkages can also bear conjugate moieties. For phosphorus-containing linkages (e.g., phosphodiester, phosphorothioate, phosphorodithiotate, phosphoroamidate, and the like), the conjugate moiety can be attached directly to the phosphorus atom or to an O, N, or S atom bound to the phosphorus atom. For amine- or amide-containing internucleosidic linkages (e.g., PNA), the conjugate moiety can be attached to the nitrogen atom of the amine or amide or to an adjacent carbon atom.


Any suitable ligand in the field of RNA interference may be used, although the ligand is typically a carbohydrate e.g. monosaccharide (such as GalNAc), disaccharide, trisaccharide, tetrasaccharide, polysaccharide.


Linkers that conjugate the ligand to the nucleic acid include those discussed above. For example, the ligand can be one or more GalNAc (V-acetyl glucosamine) derivatives attached through a bivalent or trivalent branched linker.


In one embodiment, the dsRNA of the invention is conjugated to a bivalent and trivalent branched linkers include the structures shown in any of formula (IV)-(VII):




embedded image


wherein:


q2A, q2B, q3A, q3B, q4A, q4B, q5A, q5B and q5C represent independently for each occurrence 0-20 and wherein the repeating unit can be the same or different;


P2A, P2B, P3A, P3B, P4A, P4B, P5A, P5B, P5C, T2A, T2B, T3A, T3B, T4A, T4B, T4A, T5B, T5C are each independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O), CH2, CH2NH or CH2O;


Q2A, Q2B, Q3A, Q3B, Q4A, Q4B, Q5A, Q5B, Q5C are independently for each occurrence absent, alkylene, substituted alkylene wherein one or more methylenes can be interrupted or terminated by one or more of O, S, S(O), SO2, N(Rn), C(R′)═C(R″), C≡C or C(O);


R2A, R2B, R3A, R3B, R4A, R4B, R5A, R5B, R5C are each independently for each occurrence absent, NH, O, S, CH2, C(O)O, C(O)NH, NHCH(Ra)C(O), —C(O)—CH(Ra)—NH—, CO, CH═N—O,




embedded image


or heterocyclyl;


L2A, L2B, L3A, L3B, L4A, L4B, L5A, L5B and L5C represent the ligand; i.e. each independently for each occurrence a monosaccharide (such as GalNAc), disaccharide, trisaccharide, tetrasaccharide, oligosaccharide, or polysaccharide; and


Ra is H or amino acid side chain.


Trivalent conjugating GalNAc derivatives are particularly useful for use with RNAi agents for inhibiting the expression of a target gene, such as those of formula (VII):




embedded image


wherein L5A, L5B and L5C represent a monosaccharide, such as GalNAc derivative. Examples of suitable bivalent and trivalent branched linker groups conjugating GalNAc derivatives include, but are not limited to, the following compounds:




embedded image


embedded image


embedded image


In other embodiments, the RNAi agent for use in the methods of the invention is AD-59743.


III. Delivery of an iRNA of the Invention

The delivery of an iRNA agent of the invention to a cell e.g., a cell within a subject, such as a human subject (e.g, a subject in need thereof, such as a subject having a TMPRSS6 associated disorder, such as a hemochromatosis) can be achieved in a number of different ways. For example, delivery may be performed by contacting a cell with an iRNA of the invention either in vitro or in vivo. In vivo delivery may also be performed directly by administering a composition comprising an iRNA, e.g, a dsRNA, to a subject. Alternatively, in vivo delivery may be performed indirectly by administering one or more vectors that encode and direct the expression of the iRNA. These alternatives are discussed further below.


In general, any method of delivering a nucleic acid molecule (in vitro or in vivo) can be adapted for use with an iRNA of the invention (see e.g., Akhtar S. and Julian R L. (1992) Trends Cell. Biol. 2(5): 139-144 and WO94/02595, which are incorporated herein by reference in their entireties). For in vivo delivery, factors to consider in order to deliver an iRNA molecule include, for example, biological stability of the delivered molecule, prevention of non-specific effects, and accumulation of the delivered molecule in the target tissue. The non-specific effects of an iRNA can be minimized by local administration, for example, by direct injection or implantation into a tissue or topically administering the preparation. Local administration to a treatment site maximizes local concentration of the agent, limits the exposure of the agent to systemic tissues that can otherwise be harmed by the agent or that can degrade the agent, and permits a lower total dose of the iRNA molecule to be administered. Several studies have shown successful knockdown of gene products when an iRNA is administered locally. For example, intraocular delivery of a VEGF dsRNA by intravitreal injection in cynomolgus monkeys (Tolentino, M J., et al (2004) Retina 24:132-138) and subretinal injections in mice (Reich, S J., et al (2003) Mol. Vis. 9:210-216) were both shown to prevent neovascularization in an experimental model of age-related macular degeneration. In addition, direct intratumoral injection of a dsRNA in mice reduces tumor volume (Pille, J., et al (2005) Mol. Ther. 11261-274) and can prolong survival of tumor-bearing mice (Kim, W J., et al (2006) Mol. Ther. 14:343-350; Li, S., et al (2007) Mol. Ther. 15:515-523). RNA interference has also shown success with local delivery to the CNS by direct injection (Dorn, G., et al. (2004) Nucleic Acids 32:e49; Tan, P H., et al (2005) Gene Ther. 12:59-66; Makimura, H., et al (2002) BMCNeurosci. 3:18; Shishkina, G T., et al (2004) Neuroscience 129:521-528; Thakker, E R., et al (2004) Proc. Natl. Acad. Sci. U.S.A. 101:17270-17275; Akaneya, Y., et al (2005) J. Neurophysiol 93:594-602) and to the lungs by intranasal administration (Howard, K A., et al (2006) Mol. Ther. 14:476-484; Zhang, X., et al (2004) J. Biol. Chem. 279:10677-10684; Bitko, V., et al (2005) Nat. Med. 11:50-55). For administering an iRNA systemically for the treatment of a disease, the RNA can be modified or alternatively delivered using a drug delivery system; both methods act to prevent the rapid degradation of the dsRNA by endo- and exo-nucleases in vivo. Modification of the RNA or the pharmaceutical carrier can also permit targeting of the iRNA composition to the target tissue and avoid undesirable off-target effects. iRNA molecules can be modified by chemical conjugation to lipophilic groups such as cholesterol to enhance cellular uptake and prevent degradation. For example, an iRNA directed against ApoB conjugated to a lipophilic cholesterol moiety was injected systemically into mice and resulted in knockdown of apoB mRNA in both the liver and jejunum (Soutschek, J., et al (2004) Nature 432:173-178). Conjugation of an iRNA to an aptamer has been shown to inhibit tumor growth and mediate tumor regression in a mouse model of prostate cancer (McNamara, J O., et al (2006) Nat. Biotechnol 24:1005-1015). In an alternative embodiment, the iRNA can be delivered using drug delivery systems such as a nanoparticle, a dendrimer, a polymer, liposomes, or a cationic delivery system. Positively charged cationic delivery systems facilitate binding of an iRNA molecule (negatively charged) and also enhance interactions at the negatively charged cell membrane to permit efficient uptake of an iRNA by the cell. Cationic lipids, dendrimers, or polymers can either be bound to an iRNA, or induced to form a vesicle or micelle (see e.g., Kim S H., et al (2008) Journal of Controlled Release 129(2): 107-116) that encases an iRNA. The formation of vesicles or micelles further prevents degradation of the iRNA when administered systemically. Methods for making and administering cationic-iRNA complexes are well within the abilities of one skilled in the art (see e.g., Sorensen, D R., et al (2003) J. Mol. Biol 327:761-766; Verma, U N., et al (2003) Clin. Cancer Res. 9:1291-1300; Arnold, A S et al (2007) J. Hypertens. 25:197-205, which are incorporated herein by reference in their entirety). Some non-limiting examples of drug delivery systems useful for systemic delivery of iRNAs include DOTAP (Sorensen, D R., et al (2003), supra; Verma, U N., et al (2003), supra), Oligofectamine, “solid nucleic acid lipid particles” (Zimmermann, T S., et al (2006) Nature 441:111-114), cardiolipin (Chien, P Y., et al (2005) Cancer Gene Ther. 12:321-328; Pal, A., et al (2005) Int J. Oncol. 26:1087-1091), polyethyleneimine (Bonnet M E., et al (2008) Pharm. Res. August 16 Epub ahead of print; Aigner, A. (2006) J. Biomed. Biotechnol. 71659), Arg-Gly-Asp (RGD) peptides (Liu, S. (2006)Mol. Pharm. 3:472-487), and polyamidoamines (Tomalia, D A., et al (2007) Biochem. Soc. Trans. 35:61-67; Yoo, E L, et al (1999) Pharm. Res. 16:1799-1804). In some embodiments, an iRNA forms a complex with cyclodextrin for systemic administration. Methods for administration and pharmaceutical compositions of iRNAs and cyclodextrins can be found in U.S. Pat. No. 7,427,605, which is herein incorporated by reference in its entirety.


A. Vector Encoded iRNAs of the Invention


iRNA targeting the TMPRSS6 gene can be expressed from transcription units inserted into DNA or RNA vectors (see, e.g., Couture, A, et al., TIG. (1996), 12:5-10; Skillern, A., et al., International PCT Publication No. WO 00/22113, Conrad, International PCT Publication No. WO 00/22114, and Conrad, U.S. Pat. No. 6,054,299). Expression can be transient (on the order of hours to weeks) or sustained (weeks to months or longer), depending upon the specific construct used and the target tissue or cell type. These transgenes can be introduced as a linear construct, a circular plasmid, or a viral vector, which can be an integrating or non-integrating vector. The transgene can also be constructed to permit it to be inherited as an extrachromosomal plasmid (Gassmann, et al., Proc. Natl. Acad. Sci. USA (1995) 92:1292).


The individual strand or strands of an iRNA can be transcribed from a promoter on an expression vector. Where two separate strands are to be expressed to generate, for example, a dsRNA, two separate expression vectors can be co-introduced (e.g, by transfection or infection) into a target cell. Alternatively each individual strand of a dsRNA can be transcribed by promoters both of which are located on the same expression plasmid. In one embodiment, a dsRNA is expressed as inverted repeat polynucleotides joined by a linker polynucleotide sequence such that the dsRNA has a stem and loop structure.


iRNA expression vectors are generally DNA plasmids or viral vectors. Expression vectors compatible with eukaryotic cells, preferably those compatible with vertebrate cells, can be used to produce recombinant constructs for the expression of an iRNA as described herein. Eukaryotic cell expression vectors are well known in the art and are available from a number of commercial sources. Typically, such vectors are provided containing convenient restriction sites for insertion of the desired nucleic acid segment. Delivery of iRNA expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that allows for introduction into a desired target cell.


iRNA expression plasmids can be transfected into target cells as a complex with cationic lipid carriers (e.g., Oligofectamine) or non-cationic lipid-based carriers (e.g, Transit-TKO™). Multiple lipid transfections for iRNA-mediated knockdowns targeting different regions of a target RNA over a period of a week or more are also contemplated by the invention. Successful introduction of vectors into host cells can be monitored using various known methods. For example, transient transfection can be signaled with a reporter, such as a fluorescent marker, such as Green Fluorescent Protein (GFP). Stable transfection of cells ex vivo can be ensured using markers that provide the transfected cell with resistance to specific environmental factors (e.g., antibiotics and drugs), such as hygromycin B resistance.


Viral vector systems which can be utilized with the methods and compositions described herein include, but are not limited to, (a) adenovirus vectors; (b) retrovirus vectors, including but not limited to lentiviral vectors, moloney murine leukemia virus, etc.; (c) adeno-associated virus vectors; (d) herpes simplex virus vectors; (e) SV 40 vectors; (f) polyoma virus vectors; (g) papilloma virus vectors; (h) picomavirus vectors; (i) pox virus vectors such as an orthopox, e.g, vaccinia virus vectors or avipox, e.g. canary pox or fowl pox; and (j) a helper-dependent or gutless adenovirus. Replication-defective viruses can also be advantageous. Different vectors will or will not become incorporated into the cells' genome. The constructs can include viral sequences for transfection, if desired. Alternatively, the construct can be incorporated into vectors capable of episomal replication, e.g. EPV and EBV vectors. Constructs for the recombinant expression of an iRNA will generally require regulatory elements, e.g, promoters, enhancers, etc., to ensure the expression of the iRNA in target cells. Other aspects to consider for vectors and constructs are further described below.


Vectors useful for the delivery of an iRNA will include regulatory elements (promoter, enhancer, etc.) sufficient for expression of the iRNA in the desired target cell or tissue. The regulatory elements can be chosen to provide either constitutive or regulated/inducible expression.


Expression of the iRNA can be precisely regulated, for example, by using an inducible regulatory sequence that is sensitive to certain physiological regulators, e.g., circulating glucose levels, or hormones (Docherty et al., 1994, FASEB J. 8:20-24). Such inducible expression systems, suitable for the control of dsRNA expression in cells or in mammals include, for example, regulation by ecdysone, by estrogen, progesterone, tetracycline, chemical inducers of dimerization, and isopropyl-beta-D1-thiogalactopyranoside (IPTG). A person skilled in the art would be able to choose the appropriate regulatory/promoter sequence based on the intended use of the iRNA transgene.


Viral vectors that contain nucleic acid sequences encoding an iRNA can be used. For example, a retroviral vector can be used (see Miller et al., Meth. Enzymol. 217:581-599 (1993)). These retroviral vectors contain the components necessary for the correct packaging of the viral genome and integration into the host cell DNA. The nucleic acid sequences encoding an iRNA are cloned into one or more vectors, which facilitate delivery of the nucleic acid into a patient. More detail about retroviral vectors can be found, for example, in Boesen et al., Biotherapy 6:291-302 (1994), which describes the use of a retroviral vector to deliver the mdr1 gene to hematopoietic stem cells in order to make the stem cells more resistant to chemotherapy. Other references illustrating the use of retroviral vectors in gene therapy are: Clowes et al., J. Clin. Invest. 93:644-651 (1994); Kiem et al, Blood 83:1467-1473 (1994); Salmons and Gunzberg, Human Gene Therapy 4:129-141 (1993); and Grossman and Wilson, Curr. Opin. in Genetics and Devel. 3:110-114 (1993). Lentiviral vectors contemplated for use include, for example, the HIV based vectors described in U.S. Pat. Nos. 6,143,520; 5,665,557; and 5,981,276, which are herein incorporated by reference.


Adenoviruses are also contemplated for use in delivery of iRNAs of the invention. Adenoviruses are especially attractive vehicles, e.g., for delivering genes to respiratory epithelia. Adenoviruses naturally infect respiratory epithelia where they cause a mild disease. Other targets for adenovirus-based delivery systems are liver, the central nervous system, endothelial cells, and muscle. Adenoviruses have the advantage of being capable of infecting non-dividing cells. Kozarsky and Wilson, Current Opinion in Genetics and Development 3:499-503 (1993) present a review of adenovirus-based gene therapy. Bout et al., Human Gene Therapy 5:3-10 (1994) demonstrated the use of adenovirus vectors to transfer genes to the respiratory epithelia of rhesus monkeys. Other instances of the use of adenoviruses in gene therapy can be found in Rosenfeld et al., Science 252:431-434 (1991); Rosenfeld et al, Cell 68:143-155 (1992); Mastrangeli et al., J. Clin. Invest. 91:225-234 (1993); PCT Publication WO94/12649; and Wang, et al., Gene Therapy 2:775-783 (1995). A suitable AV vector for expressing an iRNA featured in the invention, a method for constructing the recombinant AV vector, and a method for delivering the vector into target cells, are described in Xia H et al. (2002), Nat. Biotech. 20: 1006-1010.


Adeno-associated virus (AAV) vectors may also be used to delivery an iRNA of the invention (Walsh et al, Proc. Soc. Exp. Biol. Med. 204:289-300 (1993); U.S. Pat. No. 5,436,146). In one embodiment, the iRNA can be expressed as two separate, complementary single-stranded RNA molecules from a recombinant AAV vector having, for example, either the U6 or H1 RNA promoters, or the cytomegalovirus (CMV) promoter. Suitable AAV vectors for expressing the dsRNA featured in the invention, methods for constructing the recombinant AV vector, and methods for delivering the vectors into target cells are described in Samulski R et al. (1987), J. Virol. 61: 3096-3101; Fisher K J et al. (1996), J Virol, 70: 520-532; Samulski R et al. (1989), J. Virol. 63: 3822-3826; U.S. Pat. Nos. 5,252,479; 5,139,941; International Patent Application No. WO 94/13788; and International Patent Application No. WO 93/24641, the entire disclosures of which are herein incorporated by reference.


Another viral vector suitable for delivery of an iRNA of the inevtion is a pox virus such as a vaccinia virus, for example an attenuated vaccinia such as Modified Virus Ankara (MVA) or NYVAC, an avipox such as fowl pox or canary pox.


The tropism of viral vectors can be modified by pseudotyping the vectors with envelope proteins or other surface antigens from other viruses, or by substituting different viral capsid proteins, as appropriate. For example, lentiviral vectors can be pseudotyped with surface proteins from vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and the like. AAV vectors can be made to target different cells by engineering the vectors to express different capsid protein serotypes; see, e.g., Rabinowitz J E et al. (2002), J Virol 76:791-801, the entire disclosure of which is herein incorporated by reference.


The pharmaceutical preparation of a vector can include the vector in an acceptable diluent, or can include a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system.


IV. Pharmaceutical Compositions of the Invention

The present invention also includes pharmaceutical compositions and formulations which include the iRNAs of the invention. In one embodiment, provided herein are pharmaceutical compositions containing an iRNA, as described herein, and a pharmaceutically acceptable carrier. The pharmaceutical compositions containing the iRNA are useful for treating a TMPRSS6 associated disease or disorder, e.g. hemochromatosis. Such pharmaceutical compositions are formulated based on the mode of delivery. One example is compositions that are formulated for systemic administration via parenteral delivery, e.g., by intravenous (IV) delivery. Another example is compositions that are formulated for direct delivery into the brain parenchyma, e.g., by infusion into the brain, such as by continuous pump infusion.


The pharmaceutical compositions comprising RNAi agents of the invention may be, for example, solutions with or without a buffer, or compositions containing pharmaceutically acceptable carriers. Such compositions include, for example, aqueous or crystalline compositions, liposomal formulations, micellar formulations, emulsions, and gene therapy vectors.


In the methods of the invention, the RNAi agent may be administered in a solution. A free RNAi agent may be administered in an unbuffered solution, e.g., in saline or in water. Alternatively, the free siRNA may also be administered in a suitable buffer solution. The buffer solution may comprise acetate, citrate, prolamine, carbonate, or phosphate, or any combination thereof. In a preferred embodiment, the buffer solution is phosphate buffered saline (PBS). The pH and osmolarity of the buffer solution containing the RNAi agent can be adjusted such that it is suitable for administering to a subject.


In some embodiments, the buffer solution further comprises an agent for controlling the osmolarity of the solution, such that the osmolarity is kept at a desired value, e.g., at the physiologic values of the human plasma. Solutes which can be added to the buffer solution to control the osmolarity include, but are not limited to, proteins, peptides, amino acids, non-metabolized polymers, vitamins, ions, sugars, metabolites, organic acids, lipids, or salts. In some embodiments, the agent for controlling the osmolarity of the solution is a salt. In certain embodiments, the agent for controlling the osmolarity of the solution is sodium chloride or potassium chloride.


The pharmaceutical compositions of the invention may be administered in dosages sufficient to inhibit expression of a TMPRSS6 gene.


In general, a suitable dose of an iRNA of the invention will be in the range of about 0.001 to about 200.0 milligrams per kilogram body weight of the recipient per day, generally in the range of about 1 to 50 mg per kilogram body weight per day. For example, the dsRNA can be administered at about 0.01 mg/kg, about 0.05 mg/kg, about 0.5 mg/kg, about 1 mg/kg, about 1.5 mg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg, about 5 mg/kg, about 6 mg/kg, about 7 mg/kg, about 8 mg/kg, about 9 mg/kg about 10 mg/kg, about 20 mg/kg, about 30 mg/kg, about 40 mg/kg, or about 50 mg/kg per single dose.


For example, the RNAi agent, e.g, dsRNA, may be administered at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or about 10 mg/kg. Values and ranges intermediate to the recited values are also intended to be part of this invention.


In another embodiment, the RNAi agent, e.g, dsRNA, is administered at a dose of about 0.1 to about 50 mg/kg, about 0.25 to about 50 mg/kg, about 0.5 to about 50 mg/kg, about 0.75 to about 50 mg/kg, about 1 to about 50 mg/mg, about 1.5 to about 50 mg/kb, about 2 to about 50 mg/kg, about 2.5 to about 50 mg/kg, about 3 to about 50 mg/kg, about 3.5 to about 50 mg/kg, about 4 to about 50 mg/kg, about 4.5 to about 50 mg/kg, about 5 to about 50 mg/kg, about 7.5 to about 50 mg/kg, about 10 to about 50 mg/kg, about 15 to about 50 mg/kg, about 20 to about 50 mg/kg, about 20 to about 50 mg/kg, about 25 to about 50 mg/kg, about 25 to about 50 mg/kg, about 30 to about 50 mg/kg, about 35 to about 50 mg/kg, about 40 to about 50 mg/kg, about 45 to about 50 mg/kg, about 0.1 to about 45 mg/kg, about 0.25 to about 45 mg/kg, about 0.5 to about 45 mg/kg, about 0.75 to about 45 mg/kg, about 1 to about 45 mg/mg, about 1.5 to about 45 mg/kb, about 2 to about 45 mg/kg, about 2.5 to about 45 mg/kg, about 3 to about 45 mg/kg, about 3.5 to about 45 mg/kg, about 4 to about 45 mg/kg, about 4.5 to about 45 mg/kg, about 5 to about 45 mg/kg, about 7.5 to about 45 mg/kg, about 10 to about 45 mg/kg, about 15 to about 45 mg/kg, about 20 to about 45 mg/kg, about 20 to about 45 mg/kg, about 25 to about 45 mg/kg, about 25 to about 45 mg/kg, about 30 to about 45 mg/kg, about 35 to about 45 mg/kg, about 40 to about 45 mg/kg, about 0.1 to about 40 mg/kg, about 0.25 to about 40 mg/kg, about 0.5 to about 40 mg/kg, about 0.75 to about 40 mg/kg, about 1 to about 40 mg/mg, about 1.5 to about 40 mg/kb, about 2 to about 40 mg/kg, about 2.5 to about 40 mg/kg, about 3 to about 40 mg/kg, about 3.5 to about 40 mg/kg, about 4 to about 40 mg/kg, about 4.5 to about 40 mg/kg, about 5 to about 40 mg/kg, about 7.5 to about 40 mg/kg, about 10 to about 40 mg/kg, about 15 to about 40 mg/kg, about 20 to about 40 mg/kg, about 20 to about 40 mg/kg, about 25 to about 40 mg/kg, about 25 to about 40 mg/kg, about 30 to about 40 mg/kg, about 35 to about 40 mg/kg, about 0.1 to about 30 mg/kg, about 0.25 to about 30 mg/kg, about 0.5 to about 30 mg/kg, about 0.75 to about 30 mg/kg, about 1 to about 30 mg/mg, about 1.5 to about 30 mg/kb, about 2 to about 30 mg/kg, about 2.5 to about 30 mg/kg, about 3 to about 30 mg/kg, about 3.5 to about 30 mg/kg, about 4 to about 30 mg/kg, about 4.5 to about 30 mg/kg, about 5 to about 30 mg/kg, about 7.5 to about 30 mg/kg, about 10 to about 30 mg/kg, about 15 to about 30 mg/kg, about 20 to about 30 mg/kg, about 20 to about 30 mg/kg, about 25 to about 30 mg/kg, about 0.1 to about 20 mg/kg, about 0.25 to about 20 mg/kg, about 0.5 to about 20 mg/kg, about 0.75 to about 20 mg/kg, about 1 to about 20 mg/mg, about 1.5 to about 20 mg/kb, about 2 to about 20 mg/kg, about 2.5 to about 20 mg/kg, about 3 to about 20 mg/kg, about 3.5 to about 20 mg/kg, about 4 to about 20 mg/kg, about 4.5 to about 20 mg/kg, about 5 to about 20 mg/kg, about 7.5 to about 20 mg/kg, about 10 to about 20 mg/kg, or about 15 to about 20 mg/kg. Values and ranges intermediate to the recited values are also intended to be part of this invention.


For example, the RNAi agent, e.g., dsRNA, may be administered at a dose of about 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or about 10 mg/kg.


Values and ranges intermediate to the recited values are also intended to be part of this invention. In another embodiment, the RNAi agent, e.g., dsRNA, is administered at a dose of about 0.5 to about 50 mg/kg, about 0.75 to about 50 mg/kg, about 1 to about 50 mg/mg, about 1.5 to about 50 mg/kg, about 2 to about 50 mg/kg, about 2.5 to about 50 mg/kg, about 3 to about 50 mg/kg, about 3.5 to about 50 mg/kg, about 4 to about 50 mg/kg, about 4.5 to about 50 mg/kg, about 5 to about 50 mg/kg, about 7.5 to about 50 mg/kg, about 10 to about 50 mg/kg, about 15 to about 50 mg/kg, about 20 to about 50 mg/kg, about 20 to about 50 mg/kg, about 25 to about 50 mg/kg, about 25 to about 50 mg/kg, about 30 to about 50 mg/kg, about 35 to about 50 mg/kg, about 40 to about 50 mg/kg, about 45 to about 50 mg/kg, about 0.5 to about 45 mg/kg, about 0.75 to about 45 mg/kg, about 1 to about 45 mg/mg, about 1.5 to about 45 mg/kb, about 2 to about 45 mg/kg, about 2.5 to about 45 mg/kg, about 3 to about 45 mg/kg, about 3.5 to about 45 mg/kg, about 4 to about 45 mg/kg, about 4.5 to about 45 mg/kg, about 5 to about 45 mg/kg, about 7.5 to about 45 mg/kg, about 10 to about 45 mg/kg, about 15 to about 45 mg/kg, about 20 to about 45 mg/kg, about 20 to about 45 mg/kg, about 25 to about 45 mg/kg, about 25 to about 45 mg/kg, about 30 to about 45 mg/kg, about 35 to about 45 mg/kg, about 40 to about 45 mg/kg, about 0.5 to about 40 mg/kg, about 0.75 to about 40 mg/kg, about 1 to about 40 mg/mg, about 1.5 to about 40 mg/kb, about 2 to about 40 mg/kg, about 2.5 to about 40 mg/kg, about 3 to about 40 mg/kg, about 3.5 to about 40 mg/kg, about 4 to about 40 mg/kg, about 4.5 to about 40 mg/kg, about 5 to about 40 mg/kg, about 7.5 to about 40 mg/kg, about 10 to about 40 mg/kg, about 15 to about 40 mg/kg, about 20 to about 40 mg/kg, about 20 to about 40 mg/kg, about 25 to about 40 mg/kg, about 25 to about 40 mg/kg, about 30 to about 40 mg/kg, about 35 to about 40 mg/kg, about 0.5 to about 30 mg/kg, about 0.75 to about 30 mg/kg, about 1 to about 30 mg/mg, about 1.5 to about 30 mg/kb, about 2 to about 30 mg/kg, about 2.5 to about 30 mg/kg, about 3 to about 30 mg/kg, about 3.5 to about 30 mg/kg, about 4 to about 30 mg/kg, about 4.5 to about 30 mg/kg, about 5 to about 30 mg/kg, about 7.5 to about 30 mg/kg, about 10 to about 30 mg/kg, about 15 to about 30 mg/kg, about 20 to about 30 mg/kg, about 20 to about 30 mg/kg, about 25 to about 30 mg/kg, about 0.5 to about 20 mg/kg, about 0.75 to about 20 mg/kg, about 1 to about 20 mg/mg, about 1.5 to about 20 mg/kb, about 2 to about 20 mg/kg, about 2.5 to about 20 mg/kg, about 3 to about 20 mg/kg, about 3.5 to about 20 mg/kg, about 4 to about 20 mg/kg, about 4.5 to about 20 mg/kg, about 5 to about 20 mg/kg, about 7.5 to about 20 mg/kg, about 10 to about 20 mg/kg, or about 15 to about 20 mg/kg. In one embodiment, the dsRNA is administered at a dose of about 10 mg/kg to about 30 mg/kg. Values and ranges intermediate to the recited values are also intended to be part of this invention.


For example, subjects can be administered a therapeutic amount of iRNA, such as about 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10, 10.5, 11, 11.5, 12, 12.5, 13, 13.5, 14, 14.5, 15, 15.5, 16, 16.5, 17, 17.5, 18, 18.5, 19, 19.5, 20, 20.5, 21, 21.5, 22, 22.5, 23, 23.5, 24, 24.5, 25, 25.5, 26, 26.5, 27, 27.5, 28, 28.5, 29, 29.5, 30, 31, 32, 33, 34, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or about 50 mg/kg. Values and ranges intermediate to the recited values are also intended to be part of this invention.


In certain embodiments, for example, when a composition of the invention comprises a dsRNA as described herein and a lipid, subjects can be administered a therapeutic amount of iRNA, such as about 0.01 mg/kg to about 5 mg/kg, about 0.01 mg/kg to about 10 mg/kg, about 0.05 mg/kg to about 5 mg/kg, about 0.05 mg/kg to about 10 mg/kg, about 0.1 mg/kg to about 5 mg/kg, about 0.1 mg/kg to about 10 mg/kg, about 0.2 mg/kg to about 5 mg/kg, about 0.2 mg/kg to about 10 mg/kg, about 0.3 mg/kg to about 5 mg/kg, about 0.3 mg/kg to about 10 mg/kg, about 0.4 mg/kg to about 5 mg/kg, about 0.4 mg/kg to about 10 mg/kg, about 0.5 mg/kg to about 5 mg/kg, about 0.5 mg/kg to about 10 mg/kg, about 1 mg/kg to about 5 mg/kg, about 1 mg/kg to about 10 mg/kg, about 1.5 mg/kg to about 5 mg/kg, about 1.5 mg/kg to about 10 mg/kg, about 2 mg/kg to about 2.5 mg/kg, about 2 mg/kg to about 10 mg/kg, about 3 mg/kg to about 5 mg/kg, about 3 mg/kg to about 10 mg/kg, about 3.5 mg/kg to about 5 mg/kg, about 4 mg/kg to about 5 mg/kg, about 4.5 mg/kg to about 5 mg/kg, about 4 mg/kg to about 10 mg/kg, about 4.5 mg/kg to about 10 mg/kg, about 5 mg/kg to about 10 mg/kg, about 5.5 mg/kg to about 10 mg/kg, about 6 mg/kg to about 10 mg/kg, about 6.5 mg/kg to about 10 mg/kg, about 7 mg/kg to about 10 mg/kg, about 7.5 mg/kg to about 10 mg/kg, about 8 mg/kg to about 10 mg/kg, about 8.5 mg/kg to about 10 mg/kg, about 9 mg/kg to about 10 mg/kg, or about 9.5 mg/kg to about 10 mg/kg. Values and ranges intermediate to the recited values are also intended to be part of this invention. For example, the dsRNA may be administered at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or about 10 mg/kg. Values and ranges intermediate to the recited values are also intended to be part of this invention.


In certain embodiments of the invention, for example, when a double-stranded RNAi agent includes modifications (e.g., one or more motifs of three identical modifications on three consecutive nucleotides, including one such motif at or near the cleavage site of the agent), six phosphorothioate linkages, and a ligand, such an agent is administered at a dose of about 0.01 to about 0.5 mg/kg, about 0.01 to about 0.4 mg/kg, about 0.01 to about 0.3 mg/kg, about 0.01 to about 0.2 mg/kg, about 0.01 to about 0.1 mg/kg, about 0.01 mg/kg to about 0.09 mg/kg, about 0.01 mg/kg to about 0.08 mg/kg, about 0.01 mg/kg to about 0.07 mg/kg, about 0.01 mg/kg to about 0.06 mg/kg, about 0.01 mg/kg to about 0.05 mg/kg, about 0.02 to about 0.5 mg/kg, about 0.02 to about 0.4 mg/kg, about 0.02 to about 0.3 mg/kg, about 0.02 to about 0.2 mg/kg, about 0.02 to about 0.1 mg/kg, about 0.02 mg/kg to about 0.09 mg/kg, about 0.02 mg/kg to about 0.08 mg/kg, about 0.02 mg/kg to about 0.07 mg/kg, about 0.02 mg/kg to about 0.06 mg/kg, about 0.02 mg/kg to about 0.05 mg/kg, about 0.03 to about 0.5 mg/kg, about 0.03 to about 0.4 mg/kg, about 0.03 to about 0.3 mg/kg, about 0.03 to about 0.2 mg/kg, about 0.03 to about 0.1 mg/kg, about 0.03 mg/kg to about 0.09 mg/kg, about 0.03 mg/kg to about 0.08 mg/kg, about 0.03 mg/kg to about 0.07 mg/kg, about 0.03 mg/kg to about 0.06 mg/kg, about 0.03 mg/kg to about 0.05 mg/kg, about 0.04 to about 0.5 mg/kg, about 0.04 to about 0.4 mg/kg, about 0.04 to about 0.3 mg/kg, about 0.04 to about 0.2 mg/kg, about 0.04 to about 0.1 mg/kg, about 0.04 mg/kg to about 0.09 mg/kg, about 0.04 mg/kg to about 0.08 mg/kg, about 0.04 mg/kg to about 0.07 mg/kg, about 0.04 mg/kg to about 0.06 mg/kg, about 0.05 to about 0.5 mg/kg, about 0.05 to about 0.4 mg/kg, about 0.05 to about 0.3 mg/kg, about 0.05 to about 0.2 mg/kg, about 0.05 to about 0.1 mg/kg, about 0.05 mg/kg to about 0.09 mg/kg, about 0.05 mg/kg to about 0.08 mg/kg, or about 0.05 mg/kg to about 0.07 mg/kg. Values and ranges intermediate to the foregoing recited values are also intended to be part of this invention, e.g., the RNAi agent may be administered to the subject at a dose of about 0.015 mg/kg to about 0.45 mg/mg.


For example, the RNAi agent, e.g, RNAi agent in a pharmaceutical composition, may be administered at a dose of about 0.01 mg/kg, 0.0125 mg/kg, 0.015 mg/kg, 0.0175 mg/kg, 0.02 mg/kg, 0.0225 mg/kg, 0.025 mg/kg, 0.0275 mg/kg, 0.03 mg/kg, 0.0325 mg/kg, 0.035 mg/kg, 0.0375 mg/kg, 0.04 mg/kg, 0.0425 mg/kg, 0.045 mg/kg, 0.0475 mg/kg, 0.05 mg/kg, 0.0525 mg/kg, 0.055 mg/kg, 0.0575 mg/kg, 0.06 mg/kg, 0.0625 mg/kg, 0.065 mg/kg, 0.0675 mg/kg, 0.07 mg/kg, 0.0725 mg/kg, 0.075 mg/kg, 0.0775 mg/kg, 0.08 mg/kg, 0.0825 mg/kg, 0.085 mg/kg, 0.0875 mg/kg, 0.09 mg/kg, 0.0925 mg/kg, 0.095 mg/kg, 0.0975 mg/kg, 0.1 mg/kg, 0.125 mg/kg, 0.15 mg/kg, 0.175 mg/kg, 0.2 mg/kg, 0.225 mg/kg, 0.25 mg/kg, 0.275 mg/kg, 0.3 mg/kg, 0.325 mg/kg, 0.35 mg/kg, 0.375 mg/kg, 0.4 mg/kg, 0.425 mg/kg, 0.45 mg/kg, 0.475 mg/kg, or about 0.5 mg/kg. Values intermediate to the foregoing recited values are also intended to be part of this invention.


The pharmaceutical composition can be administered once daily, or the iRNA can be administered as two, three, or more sub-doses at appropriate intervals throughout the day or even using continuous infusion or delivery through a controlled release formulation. In that case, the iRNA contained in each sub-dose must be correspondingly smaller in order to achieve the total daily dosage. The dosage unit can also be compounded for delivery over several days, e.g., using a conventional sustained release formulation which provides sustained release of the iRNA over a several day period. Sustained release formulations are well known in the art and are particularly useful for delivery of agents at a particular site, such as could be used with the agents of the present invention. In this embodiment, the dosage unit contains a corresponding multiple of the daily dose.


In other embodiments, a single dose of the pharmaceutical compositions can be long lasting, such that subsequent doses are administered at not more than 3, 4, or 5 day intervals, or at not more than 1, 2, 3, or 4 week intervals. In some embodiments of the invention, a single dose of the pharmaceutical compositions of the invention is administered once per week. In other embodiments of the invention, a single dose of the pharmaceutical compositions of the invention is administered bi-monthly.


The skilled artisan will appreciate that certain factors can influence the dosage and timing required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present. Moreover, treatment of a subject with a therapeutically effective amount of a composition can include a single treatment or a series of treatments. Estimates of effective dosages and in vivo half-lives for the individual iRNAs encompassed by the invention can be made using conventional methodologies or on the basis of in vivo testing using an appropriate animal model, as described elsewhere herein.


Advances in mouse genetics have generated a number of mouse models for the study of various human diseases, such as a disorder associated with iron overload that would benefit from reduction in the expression of TMPRSS6. Such models can be used for in vivo testing of iRNA, as well as for determining a therapeutically effective dose. Suitable mouse models are known in the art and include, for example, the thalassemic Th3/+ mouse as a model of β-thalassemia (Douet et al., Am. J. Pathol. (2011), 178(2):774-83), the HFE knockout mouse as a model of hereditary hemochromatosis (Zhou et al. (1998) Proc. Natl. Acad. Sci USA, 85:2492-2497); a Uros(mut248) mouse as a model of congenital erythropoietic porphyria (Ged et al. (2006) Genomics, 87(1):84-92).


The pharmaceutical compositions of the present invention can be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration can be topical (e.g., by a transdermal patch), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal, oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; subdermal, e.g., via an implanted device; or intracranial, e.g., by intraparenchymal, intrathecal or intraventricular, administration


The iRNA can be delivered in a manner to target a particular tissue, such as the liver (e.g., the hepatocytes of the liver).


Pharmaceutical compositions and formulations for topical administration can include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like can be necessary or desirable. Coated condoms, gloves and the like can also be useful. Suitable topical formulations include those in which the iRNAs featured in the invention are in admixture with a topical delivery agent such as lipids, liposomes, fatty acids, fatty acid esters, steroids, chelating agents and surfactants. Suitable lipids and liposomes include neutral (e.g, dioleoylphosphatidyl DOPE ethanolamine, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline) negative (e.g, dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g, dioleoyltetramethylaminopropyl DOTAP and dioleoylphosphatidyl ethanolamine DOTMA). iRNAs featured in the invention can be encapsulated within liposomes or can form complexes thereto, in particular to cationic liposomes. Alternatively, iRNAs can be complexed to lipids, in particular to cationic lipids. Suitable fatty acids and esters include but are not limited to arachidonic acid, oleic acid, eicosanoic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acyl choline, or a C1-20 alkyl ester (e.g, isopropylmyristate IPM), monoglyceride, diglyceride or pharmaceutically acceptable salt thereof). Topical formulations are described in detail in U.S. Pat. No. 6,747,014, which is incorporated herein by reference.


A. iRNA Formulations Comprising Membranous Molecular Assemblies


An iRNA for use in the compositions and methods of the invention can be formulated for delivery in a membranous molecular assembly, e.g., a liposome or a micelle. As used herein, the term “liposome” refers to a vesicle composed of amphiphilic lipids arranged in at least one bilayer, e.g., one bilayer or a plurality of bilayers. Liposomes include unilamellar and multilamellar vesicles that have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the iRNA composition. The lipophilic material isolates the aqueous interior from an aqueous exterior, which typically does not include the iRNA composition, although in some examples, it may. Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomal bilayer fuses with bilayer of the cellular membranes. As the merging of the liposome and cell progresses, the internal aqueous contents that include the iRNA are delivered into the cell where the iRNA can specifically bind to a target RNA and can mediate RNAi. In some cases the liposomes are also specifically targeted, e.g., to direct the iRNA to particular cell types.


A liposome containing a RNAi agent can be prepared by a variety of methods. In one example, the lipid component of a liposome is dissolved in a detergent so that micelles are formed with the lipid component. For example, the lipid component can be an amphipathic cationic lipid or lipid conjugate. The detergent can have a high critical micelle concentration and may be nonionic. Exemplary detergents include cholate, CHAPS, octylglucoside, deoxycholate, and lauroyl sarcosine. The RNAi agent preparation is then added to the micelles that include the lipid component. The cationic groups on the lipid interact with the RNAi agent and condense around the RNAi agent to form a liposome. After condensation, the detergent is removed, e.g., by dialysis, to yield a liposomal preparation of RNAi agent.


If necessary a carrier compound that assists in condensation can be added during the condensation reaction, e.g., by controlled addition. For example, the carrier compound can be a polymer other than a nucleic acid (e.g., spermine or spermidine). pH can also adjusted to favor condensation.


Methods for producing stable polynucleotide delivery vehicles, which incorporate a polynucleotide/cationic lipid complex as structural components of the delivery vehicle, are further described in, e.g., WO 96/37194, the entire contents of which are incorporated herein by reference. Liposome formation can also include one or more aspects of exemplary methods described in Feigner, P. L. et al, Proc. Natl. Acad Sci., USA 8:7413-7417, 1987; U.S. Pat. Nos. 4,897,355; 5,171,678; Bangham, et al. M. Mol. Biol. 23:238, 1965; Olson, et al. Biochim. Biophys. Acta 557:9, 1979; Szoka, et al. Proc. Natl Acad Sci. 75: 4194, 1978; Mayhew, et al. Biochim. Biophys. Acta 775:169, 1984; Kim, et al. Biochim. Biophys. Acta 728:339, 1983; and Fukunaga, et al. Endocrinol. 115:757, 1984. Commonly used techniques for preparing lipid aggregates of appropriate size for use as delivery vehicles include sonication and freeze-thaw plus extrusion (see, e.g., Mayer, et al. Biochim. Biophys. Acta 858:161, 1986). Microfluidization can be used when consistently small (50 to 200 nm) and relatively uniform aggregates are desired (Mayhew, et al. Biochim. Biophys. Acta 775:169, 1984). These methods are readily adapted to packaging RNAi agent preparations into liposomes.


Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes which interact with the negatively charged nucleic acid molecules to form a stable complex. The positively charged nucleic acid/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al., Biochem. Biophys. Res. Commun., 1987, 147, 980-985).


Liposomes which are pH-sensitive or negatively-charged, entrap nucleic acids rather than complex with it. Since both the nucleic acid and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some nucleic acid is entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes have been used to deliver nucleic acids encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 1992, 19, 269-274).


One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine. Neutral liposome compositions, for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC). Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC. Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.


Examples of other methods to introduce liposomes into cells in vitro and in vivo include U.S. Pat. Nos. 5,283,185; 5,171,678; WO 94/00569; WO 93/24640; WO 91/16024; Feigner, J. Biol. Chem. 269:2550, 1994; Nabel, Proc. Natol. Acad. Set. 90:11307, 1993; Nabel, Human Gene Ther. 3:649, 1992; Gershon, Biochem. 32:7143, 1993; and Strauss EMBO J. 11:417, 1992.


Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome™ I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome™ II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the dermis of mouse skin. Results indicated that such non-ionic liposomal systems were effective in facilitating the deposition of cyclosporine A into different layers of the skin (Hu et al. S.T.P. Pharma. Sci., 1994, 4(6) 466).


Liposomes also include “sterically stabilized” liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids that, when incorporated into liposomes, result in enhanced circulation lifetimes relative to liposomes lacking such specialized lipids. Examples of sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside Gm, or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety. While not wishing to be bound by any particular theory, it is thought in the art that, at least for sterically stabilized liposomes containing gangliosides, sphingomyelin, or PEG-derivatized lipids, the enhanced circulation half-life of these sterically stabilized liposomes derives from a reduced uptake into cells of the reticuloendothelial system (RES) (Allen et al., FEBS Letters, 1987, 223, 42; Wu et al., Cancer Research, 1993, 53, 3765).


Various liposomes comprising one or more glycolipids are known in the art. Papahadjopoulos et al. (Ann. N.Y. Acad Sci., 1987, 507, 64) reported the ability of monosialoganglioside Gm, galactocerebroside sulfate and phosphatidylinositol to improve blood half-lives of liposomes. These findings were expounded upon by Gabizon et al. (Proc. Natl. Acad Sci. U.S.A., 1988, 85, 6949). U.S. Pat. No. 4,837,028 and WO 88/04924, both to Allen et al., disclose liposomes comprising (1) sphingomyelin and (2) the ganglioside Gm or a galactocerebroside sulfate ester. U.S. Pat. No. 5,543,152 (Webb et al.) discloses liposomes comprising sphingomyelin. Liposomes comprising 1,2-sn-dimyristoylphosphatidylcholine are disclosed in WO 97/13499 (Lim et al).


In one embodiment, cationic liposomes are used. Cationic liposomes possess the advantage of being able to fuse to the cell membrane. Non-cationic liposomes, although not able to fuse as efficiently with the plasma membrane, are taken up by macrophages in vivo and can be used to deliver RNAi agents to macrophages.


Further advantages of liposomes include: liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated RNAi agents in their internal compartments from metabolism and degradation (Rosoff, in “Pharmaceutical Dosage Forms,” Lieberman, Rieger and Banker (Eds.), 1988, volume 1, p. 245). Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.


A positively charged synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA) can be used to form small liposomes that interact spontaneously with nucleic acid to form lipid-nucleic acid complexes which are capable of fusing with the negatively charged lipids of the cell membranes of tissue culture cells, resulting in delivery of RNAi agent (see, e.g., Feigner, P. L. et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987 and U.S. Pat. No. 4,897,355 for a description of DOTMA and its use with DNA).


A DOTMA analogue, 1,2-bis(oleoyloxy)-3-(trimethylammonia)propane (DOTAP) can be used in combination with a phospholipid to form DNA-complexing vesicles. Lipofectin™ Bethesda Research Laboratories, Gaithersburg, Md.) is an effective agent for the delivery of highly anionic nucleic acids into living tissue culture cells that comprise positively charged DOTMA liposomes which interact spontaneously with negatively charged polynucleotides to form complexes. When enough positively charged liposomes are used, the net charge on the resulting complexes is also positive. Positively charged complexes prepared in this way spontaneously attach to negatively charged cell surfaces, fuse with the plasma membrane, and efficiently deliver functional nucleic acids into, for example, tissue culture cells. Another commercially available cationic lipid, 1,2-bis(oleoyloxy)-3,3-(trimethylammonia)propane (“DOTAP”) (Boehringer Mannheim, Indianapolis, Ind.) differs from DOTMA in that the oleoyl moieties are linked by ester, rather than ether linkages.


Other reported cationic lipid compounds include those that have been conjugated to a variety of moieties including, for example, carboxyspermine which has been conjugated to one of two types of lipids and includes compounds such as 5-carboxyspermylglycine dioctaoleoylamide (“DOGS”) (Transfectam™, Promega, Madison, Wis.) and dipalmitoylphosphatidylethanolamine 5-carboxyspermyl-amide (“DPPES”) (see, e.g., U.S. Pat. No. 5,171,678).


Another cationic lipid conjugate includes derivatization of the lipid with cholesterol (“DC-Chol”) which has been formulated into liposomes in combination with DOPE (See, Gao, X. and Huang, L., Biochim. Biophys. Res. Commun. 179:280, 1991). Lipopolylysine, made by conjugating polylysine to DOPE, has been reported to be effective for transfection in the presence of serum (Zhou, X. et al., Biochim. Biophys. Acta 1065:8, 1991). For certain cell lines, these liposomes containing conjugated cationic lipids, are said to exhibit lower toxicity and provide more efficient transfection than the DOTMA-containing compositions. Other commercially available cationic lipid products include DMRIE and DMRIE-HP (Vical, La Jolla, Calif.) and Lipofectamine (DOSPA) (Life Technology, Inc., Gaithersburg, Md.). Other cationic lipids suitable for the delivery of oligonucleotides are described in WO 98/39359 and WO 96/37194.


Liposomal formulations are particularly suited for topical administration, liposomes present several advantages over other formulations. Such advantages include reduced side effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer RNAi agent into the skin. In some implementations, liposomes are used for delivering RNAi agent to epidermal cells and also to enhance the penetration of RNAi agent into dermal tissues, e.g., into skin. For example, the liposomes can be applied topically. Topical delivery of drugs formulated as liposomes to the skin has been documented (see, e.g., Weiner el al, Journal of Drug Targeting, 1992, vol. 2, 405-410 and du Plessis et al., Antiviral Research, 18, 1992, 259-265; Mannino, R. J. and Fould-Fogerite, S., Biotechniques 6:682-690, 1988; Itani, T. et al. Gene 56:267-276. 1987; Nicolau, C. et al. Meth. Enz. 149:157-176, 1987; Straubinger, R. M. and Papahadjopoulos, D. Meth. Enz. 101:512-527, 1983; Wang, C. Y. and Huang, L., Proc. Natl. Acad Sci. USA 84:7851-7855, 1987).


Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver a drug into the dermis of mouse skin. Such formulations with RNAi agent are useful for treating a dermatological disorder.


Liposomes that include iRNA can be made highly deformable. Such deformability can enable the liposomes to penetrate through pore that are smaller than the average radius of the liposome. For example, transfersomes are a type of deformable liposomes. Transferosomes can be made by adding surface edge activators, usually surfactants, to a standard liposomal composition. Transfersomes that include RNAi agent can be delivered, for example, subcutaneously by infection in order to deliver RNAi agent to keratinocytes in the skin. In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. In addition, due to the lipid properties, these transferosomes can be self-optimizing (adaptive to the shape of pores, e.g, in the skin), self-repairing, and can frequently reach their targets without fragmenting, and often self-loading.


Other formulations amenable to the present invention are described in U.S. provisional application Ser. No. 61/018,616, filed Jan. 2, 2008; 61/018,611, filed Jan. 2, 2008; 61/039,748, filed Mar. 26, 2008; 61/047,087, filed Apr. 22, 2008 and 61/051,528, filed May 8, 2008. PCT application no PCT/US2007/080331, filed Oct. 3, 2007 also describes formulations that are amenable to the present invention.


Transfersomes are yet another type of liposomes, and are highly deformable lipid aggregates which are attractive candidates for drug delivery vehicles. Transfersomes can be described as lipid droplets which are so highly deformable that they are easily able to penetrate through pores which are smaller than the droplet. Transfersomes are adaptable to the environment in which they are used, e.g., they are self-optimizing (adaptive to the shape of pores in the skin), self-repairing, frequently reach their targets without fragmenting, and often self-loading. To make transfersomes it is possible to add surface edge-activators, usually surfactants, to a standard liposomal composition. Transfersomes have been used to deliver serum albumin to the skin. The transfersome-mediated delivery of serum albumin has been shown to be as effective as subcutaneous injection of a solution containing serum albumin.


Surfactants find wide application in formulations such as emulsions (including microemulsions) and liposomes. The most common way of classifying and ranking the properties of the many different types of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile balance (HLB). The nature of the hydrophilic group (also known as the “head”) provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).


If the surfactant molecule is not ionized, it is classified as a nonionic surfactant. Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure. Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class. The polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.


If the surfactant molecule carries a negative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic. Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates. The most important members of the anionic surfactant class are the alkyl sulfates and the soaps.


If the surfactant molecule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic. Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.


If the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.


The use of surfactants in drug products, formulations and in emulsions has been reviewed (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).


The iRNA for use in the methods of the invention can also be provided as micellar formulations. “Micelles” are defined herein as a particular type of molecular assembly in which amphipathic molecules are arranged in a spherical structure such that all the hydrophobic portions of the molecules are directed inward, leaving the hydrophilic portions in contact with the surrounding aqueous phase. The converse arrangement exists if the environment is hydrophobic.


A mixed micellar formulation suitable for delivery through transdermal membranes may be prepared by mixing an aqueous solution of the siRNA composition, an alkali metal Cx to C22 alkyl sulphate, and a micelle forming compounds. Exemplary micelle forming compounds include lecithin, hyaluronic acid, pharmaceutically acceptable salts of hyaluronic acid, glycolic acid, lactic acid, chamomile extract, cucumber extract, oleic acid, linoleic acid, linolenic acid, monoolein, monooleates, monolaurates, borage oil, evening of primrose oil, menthol, trihydroxy oxo cholanyl glycine and pharmaceutically acceptable salts thereof, glycerin, polyglycerin, lysine, polylysine, triolein, polyoxyethylene ethers and analogues thereof, polidocanol alkyl ethers and analogues thereof, chenodeoxycholate, deoxycholate, and mixtures thereof. The micelle forming compounds may be added at the same time or after addition of the alkali metal alkyl sulphate. Mixed micelles will form with substantially any kind of mixing of the ingredients but vigorous mixing in order to provide smaller size micelles.


In one method a first micellar composition is prepared which contains the siRNA composition and at least the alkali metal alkyl sulphate. The first micellar composition is then mixed with at least three micelle forming compounds to form a mixed micellar composition. In another method, the micellar composition is prepared by mixing the siRNA composition, the alkali metal alkyl sulphate and at least one of the micelle forming compounds, followed by addition of the remaining micelle forming compounds, with vigorous mixing.


Phenol and/or m-cresol may be added to the mixed micellar composition to stabilize the formulation and protect against bacterial growth. Alternatively, phenol and/or m-cresol may be added with the micelle forming ingredients. An isotonic agent such as glycerin may also be added after formation of the mixed micellar composition.


For delivery of the micellar formulation as a spray, the formulation can be put into an aerosol dispenser and the dispenser is charged with a propellant. The propellant, which is under pressure, is in liquid form in the dispenser. The ratios of the ingredients are adjusted so that the aqueous and propellant phases become one, i.e., there is one phase. If there are two phases, it is necessary to shake the dispenser prior to dispensing a portion of the contents, e.g., through a metered valve. The dispensed dose of pharmaceutical agent is propelled from the metered valve in a fine spray.


Propellants may include hydrogen-containing chlorofluorocarbons, hydrogen-containing fluorocarbons, dimethyl ether and diethyl ether. In certain embodiments, HFA 134a (1,1,1,2 tetrafluoroethane) may be used.


The specific concentrations of the essential ingredients can be determined by relatively straightforward experimentation. For absorption through the oral cavities, it is often desirable to increase, e.g, at least double or triple, the dosage for through injection or administration through the gastrointestinal tract.


B. Lipid Particles


iRNAs, e.g, dsRNAs of in the invention may be fully encapsulated in a lipid formulation, e.g, a LNP, or other nucleic acid-lipid particle.


As used herein, the term “LNP” refers to a stable nucleic acid-lipid particle. LNPs contain a cationic lipid, a non-cationic lipid, and a lipid that prevents aggregation of the particle (c-g; a PEG-lipid conjugate). LNPs are extremely useful for systemic applications, as they exhibit extended circulation lifetimes following intravenous (i.v.) injection and accumulate at distal sites (e.g., sites physically separated from the administration site). LNPs include “pSPLP,” which include an encapsulated condensing agent-nucleic acid complex as set forth in PCT Publication No. WO 00/03683. The particles of the present invention typically have a mean diameter of about 50 nm to about 150 nm, more typically about 60 nm to about 130 nm, more typically about 70 nm to about 110 nm, most typically about 70 nm to about 90 nm, and are substantially nontoxic. In addition, the nucleic acids when present in the nucleic acid-lipid particles of the present invention are resistant in aqueous solution to degradation with a nuclease. Nucleic acid-lipid particles and their method of preparation are disclosed in, e.g., U.S. Pat. Nos. 5,976,567; 5,981,501; 6,534,484; 6,586,410; 6,815,432; U.S. Publication No. 2010/0324120 and PCT Publication No. WO 96/40964.


In one embodiment, the lipid to drug ratio (mass/mass ratio) (e.g., lipid to dsRNA ratio) will be in the range of from about 1:1 to about 50:1, from about 1:1 to about 25:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, or about 6:1 to about 9:1. Ranges intermediate to the above recited ranges are also contemplated to be part of the invention.


The cationic lipid can be, for example, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N—(I-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), N—(I-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-dimethyl-2,3-dioleyloxy)propylamine (DODMA), 1,2-DiLinoleyloxy-N,N-dimethylaminopropane (DLinDMA), 1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA), 1,2-Dilinoleylcarbamoyloxy-3-dimethylaminopropane (DLin-C-DAP), 1,2-Dilinoleyoxy-3-(dimethylamino)acetoxypropane (DLin-DAC), 1,2-Dilinoleyoxy-3-morpholinopropane (DLin-MA), 1,2-Dilinoleoyl-3-dimethylaminopropane (DLinDAP), 1,2-Dilinoleylthio-3-dimethylaminopropane (DLin-S-DMA), 1-Linoleoyl-2-linoleyloxy-3-dimethylaminopropane (DLin-2-DMAP), 1,2-Dilinoleyloxy-3-trimethylaminopropane chloride salt (DLin-TMA.Cl), 1,2-Dilinoleoyl-3-trimethylaminopropane chloride salt (DLin-TAP.Cl), 1,2-Dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPZ), or 3-(N,N-Dilinoleylamino)-1,2-propanediol (DLinAP), 3-(N,N-Dioleylamino)-1,2-propanedio (DOAP), 1,2-Dilinoleyloxo-3-(2-N,N-dimethylamino)ethoxypropane (DLin-EG-DMA), 1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLinDMA), 2,2-Dilinoleyl-4-dimethylaminomethyl-[1,3]-dioxolane (DLin-K-DMA) or analogs thereof, (3aR,5s,6aS)—N,N-dimethyl-2,2-di((9Z,12Z)-octadeca-9,12-dienyl)tetrahydro-3aH-cyclopenta[d][1,3]dioxol-5-amine (ALN100), (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate (MC3), 1,1′-(2-(4-(2-((2-(bis(2-hydroxydodecyl)amino)ethyl)(2-hydroxydodecyl)amino)ethyl)piperazin-1-yl)ethylazanediyl)didodecan-2-ol (Tech G1), or a mixture thereof. The cationic lipid can comprise from about 20 mol % to about 50 mol % or about 40 mol % of the total lipid present in the particle.


In another embodiment, the compound 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane can be used to prepare lipid-siRNA nanoparticles. Synthesis of 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane is described in U.S. provisional patent application No. 61/107,998 filed on Oct. 23, 2008, which is herein incorporated by reference. In one embodiment, the lipid-siRNA particle includes 40% 2, 2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane: 10% DSPC: 40% Cholesterol: 10% PEG-C-DOMG (mole percent) with a particle size of 63.0±20 nm and a 0.027 siRNA/Lipid Ratio.


The ionizable/non-cationic lipid can be an anionic lipid or a neutral lipid including, but not limited to, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl-phosphatidylethanolamine 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (DOPE-mal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DMPE), distearoyl-phosphatidyl-ethanolamine (DSPE), 16-O-monomethyl PE, 16-O-dimethyl PE, 18-1-trans PE, 1-stearoyl-2-oleoyl-phosphatidyethanolamine (SOPE), cholesterol, or a mixture thereof. The non-cationic lipid can be from about 5 mol % to about 90 mol %, about 10 mol %, or about 58 mol % if cholesterol is included, of the total lipid present in the particle.


The conjugated lipid that inhibits aggregation of particles can be, for example, a polyethyleneglycol (PEG)-lipid including, without limitation, a PEG-diacylglycerol (DAG), a PEG-dialkyloxypropyl (DAA), a PEG-phospholipid, a PEG-ceramide (Cer), or a mixture thereof. The PEG-DAA conjugate can be, for example, a PEG-dilauryloxypropyl (Ci2), a PEG-dimyristyloxypropyl (Ci4), a PEG-dipalmityloxypropyl (Ci6), or a PEG-distearyloxypropyl (C]8). The conjugated lipid that prevents aggregation of particles can be from 0 mol % to about mol % or about 2 mol % of the total lipid present in the particle.


In some embodiments, the nucleic acid-lipid particle further includes cholesterol at, e.g., about 10 mol % to about 60 mol % or about 48 mol % of the total lipid present in the particle.


In one embodiment, the lipidoid ND98-4HCl (MW 1487) (see U.S. patent application Ser. No. 12/056,230, filed Mar. 26, 2008, which is incorporated herein by reference), Cholesterol (Sigma-Aldrich), and PEG-Ceramide C16 (Avanti Polar Lipids) can be used to prepare lipid-dsRNA nanoparticles (i.e., LNP01 particles). Stock solutions of each in ethanol can be prepared as follows: ND98, 133 mg/ml; Cholesterol, 25 mg/ml, PEG-Ceramide C16, 100 mg/ml. TheND98, Cholesterol, and PEG-Ceramide C16 stock solutions can then be combined in a, e.g., 42:48:10 molar ratio. The combined lipid solution can be mixed with aqueous dsRNA (e.g., in sodium acetate pH 5) such that the final ethanol concentration is about 35-45% and the final sodium acetate concentration is about 100-300 mM. Lipid-dsRNA nanoparticles typically form spontaneously upon mixing. Depending on the desired particle size distribution, the resultant nanoparticle mixture can be extruded through a polycarbonate membrane (e.g., 100 nm cut-off) using, for example, a thermobarrel extruder, such as Lipex Extruder (Northern Lipids, Inc). In some cases, the extrusion step can be omitted. Ethanol removal and simultaneous buffer exchange can be accomplished by, for example, dialysis or tangential flow filtration. Buffer can be exchanged with, for example, phosphate buffered saline (PBS) at about pH 7, e.g., about pH 6.9, about pH 7.0, about pH 7.1, about pH 7.2, about pH 7.3, or about pH 7.4.




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LNP01 formulations are described, e.g., in International Application Publication No. WO 2008/042973, which is hereby incorporated by reference.


Additional exemplary lipid-dsRNA formulations are described in Table A.











TABLE A







cationic lipid/non-cationic




lipid/cholesterol/PEG-lipid conjugate



Ionizable/Cationic Lipid
Lipid:siRNA ratio







LNP-1
1,2-Dilinolenyloxy-N,N-dimethylaminopropane
DLinDMA/DPPC/Cholesterol/PEG-cDMA



(DLinDMA)
(57.1/7.1/34.4/1.4)




lipid:siRNA ~7:1


2-XTC
2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-
XTC/DPPC/Cholesterol/PEG-cDMA



dioxolane (XTC)
57.1/7.1/34.4/1.4




lipid:siRNA ~7:1


LNP05
2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-
XTC/DSPC/Cholesterol/PEG-DMG



dioxolane (XTC)
57.5/7.5/31.5/3.5




lipid:siRNA ~6:1


LNP06
2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-
XTC/DSPC/Cholesterol/PEG-DMG



dioxolane (XTC)
57.5/7.5/31.5/3.5




lipid:siRNA ~11:1


LNP07
2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-
XTC/DSPC/Cholesterol/PEG-DMG



dioxolane (XTC)
60/7.5/31/1.5,




lipid:siRNA ~6:1


LNP08
2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-
XTC/DSPC/Cholesterol/PEG-DMG



dioxolane (XTC)
60/7.5/31/1.5,




lipid:siRNA ~11:1


LNP09
2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-
XTC/DSPC/Cholesterol/PEG-DMG



dioxolane (XTC)
50/10/38.5/1.5




Lipid:siRNA 10:1


LNP10
(3aR,5s,6aS)-N,N-dimethyl-2,2-di((9Z,12Z)-
ALN100/DSPC/Cholesterol/PEG-DMG



octadeca-9,12-dienyl)tetrahydro-3aH-
50/10/38.5/1.5



cyclopenta[d][1,3]dioxol-5-amine (ALN100)
Lipid:siRNA 10:1


LNP11
(6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-
MC-3/DSPC/Cholesterol/PEG-DMG



tetraen-19-yl 4-(dimethylamino)butanoate
50/10/38.5/1.5



(MC3)
Lipid:siRNA 10:1


LNP12
1,1′-(2-(4-(2-((2-(bis(2-
Tech G1/DSPC/Cholesterol/PEG-DMG



hydroxydodecyl)amino)ethyl)(2-
50/10/38.5/1.5



hydroxydodecyl)amino)ethyl)piperazin-1-
Lipid:siRNA 10:1



yl)ethylazanediyl)didodecan-2-ol (Tech G1)



LNP13
XTC
XTC/DSPC/Chol/PEG-DMG




50/10/38.5/1.5




Lipid:siRNA: 33:1


LNP14
MC3
MC3/DSPC/Chol/PEG-DMG




40/15/40/5




Lipid:siRNA: 11:1


LNP15
MC3
MC3/DSPC/Chol/PEG-DSG/GalNAc-PEG-DSG




50/10/35/4.5/0.5




Lipid:siRNA: 11:1


LNP16
MC3
MC3/DSPC/Chol/PEG-DMG




50/10/38.5/1.5




Lipid:siRNA: 7:1


LNP17
MC3
MC3/DSPC/Chol/PEG-DSG




50/10/38.5/1.5




Lipid:siRNA: 10:1


LNP18
MC3
MC3/DSPC/Chol/PEG-DMG




50/10/38.5/1.5




Lipid:siRNA: 12:1


LNP19
MC3
MC3/DSPC/Chol/PEG-DMG




50/10/35/5




Lipid:siRNA: 8:1


LNP20
MC3
MC3/DSPC/Chol/PEG-DPG




50/10/38.5/1.5




Lipid:siRNA: 10:1


LNP21
C12-200
C12-200/DSPC/Chol/PEG-DSG




50/10/38.5/1.5




Lipid:siRNA: 7:1


LNP22
XTC
XTC/DSPC/Chol/PEG-DSG




50/10/38.5/1.5




Lipid:siRNA: 10:1





DSPC: distearoylphosphatidylcholine


DPPC: dipalmitoylphosphatidylcholine


PEG-DMG: PEG-didimyristoyl glycerol (C14-PEG, or PEG-C14) (PEG with avg mol wt of 2000)


PEG-DSG: PEG-distyryl glycerol (C18-PEG, or PEG-C18) (PEG with avg mol wt of 2000)


PEG-cDMA: PEG-carbamoyl-1,2-dimyristyloxypropylamine (PEG with avg mol wt of 2000)


LNP (1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLinDMA)) comprising formulations are described in International Publication No. WO2009/127060, filed Apr. 15, 2009, which is hereby incorporated by reference.


XTC comprising formulations are described, e.g., in U.S. Provisional Ser. No. 61/148,366, filed Jan. 29, 2009; U.S. Provisional Ser. No. 61/156,851, filed Mar. 2, 2009; U.S. Provisional Ser. No. filed Jun. 10, 2009; U.S. Provisional Ser. No. 61/228,373, filed Jul. 24, 2009; U.S. Provisional Ser. No. 61/239,686, filed Sep. 3, 2009, and International Application No. PCT/US2010/022614, filed Jan. 29, 2010, which are hereby incorporated by reference.


MC3 comprising formulations are described, e.g., in U.S. Publication No. 2010/0324120, filed Jun. 10, 2010, the entire contents of which are hereby incorporated by reference.


ALNY-100 comprising formulations as described, e.g., International patent application number PCT/US09/63933, filed on Nov. 10, 2009, which is hereby incorporated by reference.


C12-200 comprising formulations are described in U.S. Provisional Ser. No. 61/175,770, filed May 5, 2009 and International Application No. PCT/US10/33777, filed May 5, 2010, which are hereby incorporated by reference.






Synthesis of Ionizable/Cationic Lipids


Any of the compounds, e.g., cationic lipids and the like, used in the nucleic acid-lipid particles of the invention can be prepared by known organic synthesis techniques, including the methods described in more detail in the Examples. All substituents are as defined below unless indicated otherwise.


“Alkyl” means a straight chain or branched, noncyclic or cyclic, saturated aliphatic hydrocarbon containing from 1 to 24 carbon atoms. Representative saturated straight chain alkyls include methyl, ethyl, n-propyl, n-butyl, n-pentyl, n-hexyl, and the like; while saturated branched alkyls include isopropyl, sec-butyl, isobutyl, tert-butyl, isopentyl, and the like. Representative saturated cyclic alkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like; while unsaturated cyclic alkyls include cyclopentenyl and cyclohexenyl, and the like.


“Alkenyl” means an alkyl, as defined above, containing at least one double bond between adjacent carbon atoms. Alkenyls include both cis and trans isomers. Representative straight chain and branched alkenyls include ethylenyl, propylenyl, 1-butenyl, 2-butenyl, isobutylenyl, 1-pentenyl, 2-pentenyl, 3-methyl-1-butenyl, 2-methyl-2-butenyl, 2,3-dimethyl-2-butenyl, and the like.


“Alkynyl” means any alkyl or alkenyl, as defined above, which additionally contains at least one triple bond between adjacent carbons. Representative straight chain and branched alkynyls include acetylenyl, propynyl, 1-butynyl, 2-butynyl, 1-pentynyl, 2-pentynyl, 3-methyl-1 butynyl, and the like.


“Acyl” means any alkyl, alkenyl, or alkynyl wherein the carbon at the point of attachment is substituted with an oxo group, as defined below. For example, —C(═O)alkyl, —C(═O)alkenyl, and —C(═O)alkynyl are acyl groups.


“Heterocycle” means a 5- to 7-membered monocyclic, or 7- to 10-membered bicyclic, heterocyclic ring which is either saturated, unsaturated, or aromatic, and which contains from 1 or 2 heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the nitrogen and sulfur heteroatoms can be optionally oxidized, and the nitrogen heteroatom can be optionally quaternized, including bicyclic rings in which any of the above heterocycles are fused to a benzene ring. The heterocycle can be attached via any heteroatom or carbon atom. Heterocycles include heteroaryls as defined below. Heterocycles include morpholinyl, pyrrolidinonyl, pyrrolidinyl, piperidinyl, piperizynyl, hydantoinyl, valerolactamyl, oxiranyl, oxetanyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydropyridinyl, tetrahydroprimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydropyrimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, and the like.


The terms “optionally substituted alkyl”, “optionally substituted alkenyl”, “optionally substituted alkynyl”, “optionally substituted acyl”, and “optionally substituted heterocycle” means that, when substituted, at least one hydrogen atom is replaced with a substituent. In the case of an oxo substituent (═O) two hydrogen atoms are replaced. In this regard, substituents include oxo, halogen, heterocycle, —CN, —ORx, —NRxRy, —NRxC(═O)Ry, —NRxSO2Ry, —C(═O)Rx, —C(═O)ORx, —C(═O)NRxRy, —SOnRx and —SOnNRxRy, wherein n is 0, 1 or 2, Rx and Ry are the same or different and independently hydrogen, alkyl or heterocycle, and each of said alkyl and heterocycle substituents can be further substituted with one or more of oxo, halogen, —OH, —CN, alkyl, —ORx, heterocycle, —NRxRy, —NRxC(═O)Ry, —NRxSO2Ry, —C(═O)Rx, —C(═O)ORx, —C(═O)NRxRy, —SOnRx and —SOnNRxRy.


“Halogen” means fluoro, chloro, bromo and iodo.


In some embodiments, the methods of the invention can require the use of protecting groups. Protecting group methodology is well known to those skilled in the art (see, for example, Protective Groups in Organic Synthesis, Green, T. W. et al., Wiley-Interscience, New York City, 1999). Briefly, protecting groups within the context of this invention are any group that reduces or eliminates unwanted reactivity of a functional group. A protecting group can be added to a functional group to mask its reactivity during certain reactions and then removed to reveal the original functional group. In some embodiments an “alcohol protecting group” is used. An “alcohol protecting group” is any group which decreases or eliminates unwanted reactivity of an alcohol functional group. Protecting groups can be added and removed using techniques well known in the art.


Synthesis of Formula A


In some embodiments, nucleic acid-lipid particles of the invention are formulated using a cationic lipid of formula A:




embedded image


where R1 and R2 are independently alkyl, alkenyl or alkynyl, each can be optionally substituted, and R3 and R4 are independently lower alkyl or R3 and R4 can be taken together to form an optionally substituted heterocyclic ring. In some embodiments, the cationic lipid is XTC (2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane). In general, the lipid of formula A above can be made by the following Reaction Schemes 1 or 2, wherein all substituents are as defined above unless indicated otherwise.




embedded image


Lipid A, where R1 and R2 are independently alkyl, alkenyl or alkynyl, each can be optionally substituted, and R3 and R4 are independently lower alkyl or R3 and R4 can be taken together to form an optionally substituted heterocyclic ring, can be prepared according to Scheme 1. Ketone 1 and bromide 2 can be purchased or prepared according to methods known to those of ordinary skill in the art. Reaction of 1 and 2 yields ketal 3. Treatment of ketal 3 with amine 4 yields lipids of formula A. The lipids of formula A can be converted to the corresponding ammonium salt with an organic salt of formula 5, where X is anion counter ion selected from halogen, hydroxide, phosphate, sulfate, or the like.




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Alternatively, the ketone 1 starting material can be prepared according to Scheme 2. Grignard reagent 6 and cyanide 7 can be purchased or prepared according to methods known to those of ordinary skill in the art. Reaction of 6 and 7 yields ketone 1. Conversion of ketone 1 to the corresponding lipids of formula A is as described in Scheme 1.


Synthesis of MC3


Preparation of DLin-M-C3-DMA (i.e., (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate) was as follows. A solution of (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-ol (0.53 g), 4-N,N-dimethylaminobutyric acid hydrochloride (0.51 g), 4-N,N-dimethylaminopyridine (0.61 g) and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (0.53 g) in dichloromethane (5 mL) was stirred at room temperature overnight. The solution was washed with dilute hydrochloric acid followed by dilute aqueous sodium bicarbonate. The organic fractions were dried over anhydrous magnesium sulphate, filtered and the solvent removed on a rotovap. The residue was passed down a silica gel column (20 g) using a 1-5% methanol/dichloromethane elution gradient. Fractions containing the purified product were combined and the solvent removed, yielding a colorless oil (0.54 g).


Synthesis of ALNY-100


Synthesis of ketal 519 [ALNY-100] was performed using the following scheme 3:




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Synthesis of 515


To a stirred suspension of LiAlH4 (3.74 g, 0.09852 mol) in 200 ml anhydrous THF in a two neck RBF (1 L), was added a solution of 514 (10 g, 0.04926 mol) in 70 mL of THF slowly at 0 0 C under nitrogen atmosphere. After complete addition, reaction mixture was warmed to room temperature and then heated to reflux for 4 h. Progress of the reaction was monitored by TLC. After completion of reaction (by TLC) the mixture was cooled to 0 0 C and quenched with careful addition of saturated Na2SO4 solution. Reaction mixture was stirred for 4 h at room temperature and filtered off. Residue was washed well with THF. The filtrate and washings were mixed and diluted with 400 mL dioxane and 26 mL cone. HCl and stirred for 20 minutes at room temperature. The volatilities were stripped off under vacuum to furnish the hydrochloride salt of 515 as a white solid. Yield: 7.12 g 1H-NMR (DMSO, 400 MHz): δ=9.34 (broad, 2H), 5.68 (s, 2H), 3.74 (m, 1H), 2.66-2.60 (m, 2H), 2.50-2.45 (m, 5H).


Synthesis of 516


To a stirred solution of compound 515 in 100 mL dry DCM in a 250 mL two neck RBF, was added NEt3 (37.2 mL, 0.2669 mol) and cooled to 0 0 C under nitrogen atmosphere. After a slow addition of N-(benzyloxy-carbonyloxy)-succinimide (20 g, 0.08007 mol) in 50 mL dry DCM, reaction mixture was allowed to warm to room temperature. After completion of the reaction (2-3 h by TLC) mixture was washed successively with 1N HCl solution (1×100 mL) and saturated NaHCO3 solution (1×50 mL). The organic layer was then dried over anhyd. Na2SO4 and the solvent was evaporated to give crude material which was purified by silica gel column chromatography to get 516 as sticky mass. Yield: 11 g (89%). 1H-NMR (CDCl3, 400 MHz): δ=7.36-7.27 (m, 5H), 5.69 (s, 2H), 5.12 (s, 2H), 4.96 (br., 1H) 2.74 (s, 3H), 2.60 (m, 2H), 2.30-2.25 (m, 2H). LC-MS [M+H]−232.3 (96.94%).


Synthesis of 517A and 517B


The cyclopentene 516 (5 g, 0.02164 mol) was dissolved in a solution of 220 mL acetone and water (10:1) in a single neck 500 mL RBF and to it was added N-methyl morpholine-N-oxide (7.6 g, 0.06492 mol) followed by 4.2 mL of 7.6% solution of Os04 (0.275 g, 0.00108 mol) in tert-butanol at room temperature. After completion of the reaction (3 h), the mixture was quenched with addition of solid Na2SO3 and resulting mixture was stirred for 1.5 h at room temperature. Reaction mixture was diluted with DCM (300 mL) and washed with water (2×100 mL) followed by saturated NaHCO3 (1×50 mL) solution, water (1×30 mL) and finally with brine (lx 50 mL). Organic phase was dried over an.Na2SO4 and solvent was removed in vacuum. Silica gel column chromatographic purification of the crude material was afforded a mixture of diastereomers, which were separated by prep HPLC. Yield: −6 g crude 517A—Peak-1 (white solid), 5.13 g (96%). 1H-NMR (DMSO, 400 MHz): δ=7.39-7.31 (m, 5H), 5.04 (s, 2H), 4.78-4.73 (m, 1H), 4.48-4.47 (d, 2H), 3.94-3.93 (m, 2H), 2.71 (s, 3H), 1.72-1.67 (m, 4H). LC-MS—[M+H]-266.3, [M+NH4+]-283.5 present, HPLC-97.86%. Stereochemistry confirmed by X-ray.


Synthesis of 518


Using a procedure analogous to that described for the synthesis of compound 505, compound 518 (1.2 g, 41%) was obtained as a colorless oil. 1H-NMR (CDCl3, 400 MHz): δ=7.35-7.33 (m, 4H), 7.30-7.27 (m, 1H), 5.37-5.27 (m, 8H), 5.12 (s, 2H), 4.75 (m, 1H), 4.58-4.57 (m, 2H), 2.78-2.74 (m, 7H), 2.06-2.00 (m, 8H), 1.96-1.91 (m, 2H), 1.62 (m, 4H), 1.48 (m, 2H), 1.37-1.25 (br m, 36H), 0.87 (m, 6H). HPLC-98.65%.


General Procedure for the Synthesis of Compound 519


A solution of compound 518 (1 eq) in hexane (15 mL) was added in a drop-wise fashion to an ice-cold solution of LAH in THF (1 M, 2 eq). After complete addition, the mixture was heated at 40° C. over 0.5 h then cooled again on an ice bath. The mixture was carefully hydrolyzed with saturated aqueous Na2SO4 then filtered through celite and reduced to an oil. Column chromatography provided the pure 519 (1.3 g, 68%) which was obtained as a colorless oil. 13C NMR δ=130.2, 130.1 (x2), 127.9 (x3), 112.3, 79.3, 64.4, 44.7, 38.3, 35.4, 31.5, 29.9 (x2), 29.7, 29.6 (x2), 29.5 (x3), 29.3 (x2), 27.2 (x3), 25.6, 24.5, 23.3, 226, 14.1; Electrospray MS (+ve): Molecular weight for C44H80NO2 (M+H)+ Calc. 654.6, Found 654.6.


Formulations prepared by either the standard or extrusion-free method can be characterized in similar manners. For example, formulations are typically characterized by visual inspection. They should be whitish translucent solutions free from aggregates or sediment. Particle size and particle size distribution of lipid-nanoparticles can be measured by light scattering using, for example, a Malvern Zetasizer Nano ZS (Malvern, USA). Particles should be about 20-300 nm, such as 40-100 nm in size. The particle size distribution should be unimodal. The total dsRNA concentration in the formulation, as well as the entrapped fraction, is estimated using a dye exclusion assay. A sample of the formulated dsRNA can be incubated with an RNA-binding dye, such as Ribogreen (Molecular Probes) in the presence or absence of a formulation disrupting surfactant, e.g., 0.5% Triton-X100. The total dsRNA in the formulation can be determined by the signal from the sample containing the surfactant, relative to a standard curve. The entrapped fraction is determined by subtracting the “free” dsRNA content (as measured by the signal in the absence of surfactant) from the total dsRNA content. Percent entrapped dsRNA is typically >85%. For LNP formulation, the particle size is at least 30 nm, at least 40 nm, at least 50 nm, at least 60 nm, at least 70 nm, at least 80 nm, at least 90 nm, at least 100 nm, at least 110 nm, and at least 120 nm. The suitable range is typically about at least 50 nm to about at least 110 nm, about at least 60 nm to about at least 100 nm, or about at least 80 nm to about at least 90 nm.


Compositions and formulations for oral administration include powders or granules, microparticulates, nanoparticulates, suspensions or solutions in water or non-aqueous media, capsules, gel capsules, sachets, tablets or minitablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders can be desirable. In some embodiments, oral formulations are those in which dsRNAs featured in the invention are administered in conjunction with one or more penetration enhancer surfactants and chelators. Suitable surfactants include fatty acids and/or esters or salts thereof, bile acids and/or salts thereof. Suitable bile acids/salts include chenodeoxycholic acid (CDCA) and ursodeoxychenodeoxycholic acid (UDCA), cholic acid, dehydrocholic acid, deoxycholic acid, glucholic acid, glycholic acid, glycodeoxycholic acid, taurocholic acid, taurodeoxycholic acid, sodium tauro-24,25-dihydro-fusidate and sodium glycodihydrofusidate. Suitable fatty acids include arachidonic acid, undecanoic acid, oleic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcamitine, an acylcholine, or a monoglyceride, a diglyceride or a pharmaceutically acceptable salt thereof (e.g., sodium). In some embodiments, combinations of penetration enhancers are used, for example, fatty acids/salts in combination with bile acids/salts. One exemplary combination is the sodium salt of lauric acid, capric acid and UDCA. Further penetration enhancers include polyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether. DsRNAs featured in the invention can be delivered orally, in granular form including sprayed dried particles, or complexed to form micro or nanoparticles. DsRNA complexing agents include poly-amino acids; polyimines; polyacrylates; polyalkylacrylates, polyoxethanes, polyalkylcyanoacrylates; cationized gelatins, albumins, starches, acrylates, polyethyleneglycols (PEG) and starches; polyalkylcyanoacrylates; DEAE-derivatized polyimines, pollulans, celluloses and starches. Suitable complexing agents include chitosan, N-trimethylchitosan, poly-L-lysine, polyhistidine, polyornithine, polyspermines, protamine, polyvinylpyridine, polythiodiethylaminomethylethylene P(TDAE), polyaminostyrene (e.g., p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate), poly(butylcyanoacrylate), poly(isobutylcyanoacrylate), poly(isohexylcynaoacrylate), DEAE-methacrylate, DEAE-hexylacrylate, DEAE-acrylamide, DEAE-albumin and DEAE-dextran, polymethylacrylate, polyhexylacrylate, poly(D,L-lactic acid), poly(DL-lactic-co-glycolic acid (PLGA), alginate, and polyethyleneglycol (PEG). Oral formulations for dsRNAs and their preparation are described in detail in U.S. Pat. No. 6,887,906, US Publn. No. 20030027780, and U.S. Pat. No. 6,747,014, each of which is incorporated herein by reference.


Compositions and formulations for parenteral, intraparenchymal (into the brain), intrathecal, intraventricular or intrahepatic administration can include sterile aqueous solutions which can also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.


Pharmaceutical compositions of the present invention include, but are not limited to, solutions, emulsions, and liposome-containing formulations. These compositions can be generated from a variety of components that include, but are not limited to, preformed liquids, self-emulsifying solids and self-emulsifying semisolids. Particularly preferred are formulations that target the liver when treating hepatic disorders such as hepatic carcinoma.


The pharmaceutical formulations of the present invention, which can conveniently be presented in unit dosage form, can be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general, the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.


The compositions of the present invention can be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present invention can also be formulated as suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions can further contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension can also contain stabilizers.


C. Additional Formulations

i. Emulsions


The compositions of the present invention can be prepared and formulated as emulsions. Emulsions are typically heterogeneous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 μm in diameter (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., Volume 1, p. 245; Block in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 2, p. 335; Higuchi et al., in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 301). Emulsions are often biphasic systems comprising two immiscible liquid phases intimately mixed and dispersed with each other. In general, emulsions can be of either the water-in-oil (w/o) or the oil-in-water (o/w) variety. When an aqueous phase is finely divided into and dispersed as minute droplets into a bulk oily phase, the resulting composition is called a water-in-oil (w/o) emulsion. Alternatively, when an oily phase is finely divided into and dispersed as minute droplets into a bulk aqueous phase, the resulting composition is called an oil-in-water (o/w) emulsion. Emulsions can contain additional components in addition to the dispersed phases, and the active drug which can be present as a solution in either the aqueous phase, oily phase or itself as a separate phase. Pharmaceutical excipients such as emulsifiers, stabilizers, dyes, and anti-oxidants can also be present in emulsions as needed. Pharmaceutical emulsions can also be multiple emulsions that are comprised of more than two phases such as, for example, in the case of oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions. Such complex formulations often provide certain advantages that simple binary emulsions do not. Multiple emulsions in which individual oil droplets of an o/w emulsion enclose small water droplets constitute a w/o/w emulsion. Likewise a system of oil droplets enclosed in globules of water stabilized in an oily continuous phase provides an o/w/o emulsion.


Emulsions are characterized by little or no thermodynamic stability. Often, the dispersed or discontinuous phase of the emulsion is well dispersed into the external or continuous phase and maintained in this form through the means of emulsifiers or the viscosity of the formulation. Either of the phases of the emulsion can be a semi solid or a solid, as is the case of emulsion-style ointment bases and creams. Other means of stabilizing emulsions entail the use of emulsifiers that can be incorporated into either phase of the emulsion. Emulsifiers can broadly be classified into four categories: synthetic surfactants, naturally occurring emulsifiers, absorption bases, and finely dispersed solids (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).


Synthetic surfactants, also known as surface active agents, have found wide applicability in the formulation of emulsions and have been reviewed in the literature (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199). Surfactants are typically amphiphilic and comprise a hydrophilic and a hydrophobic portion. The ratio of the hydrophilic to the hydrophobic nature of the surfactant has been termed the hydrophile/lipophile balance (HLB) and is a valuable tool in categorizing and selecting surfactants in the preparation of formulations. Surfactants can be classified into different classes based on the nature of the hydrophilic group: nonionic, anionic, cationic and amphoteric (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y. Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285).


Naturally occurring emulsifiers used in emulsion formulations include lanolin, beeswax, phosphatides, lecithin and acacia. Absorption bases possess hydrophilic properties such that they can soak up water to form w/o emulsions yet retain their semisolid consistencies, such as anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations. These include polar inorganic solids, such as heavy metal hydroxides, nonswelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and nonpolar solids such as carbon or glyceryl tri stearate.


A large variety of non-emulsifying materials are also included in emulsion formulations and contribute to the properties of emulsions. These include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives and antioxidants (Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).


Hydrophilic colloids or hydrocolloids include naturally occurring gums and synthetic polymers such as polysaccharides (for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth), cellulose derivatives (for example, carboxymethylcellulose and carboxypropylcellulose), and synthetic polymers (for example, carbomers, cellulose ethers, and carboxyvinyl polymers). These disperse or swell in water to form colloidal solutions that stabilize emulsions by forming strong interfacial films around the dispersed-phase droplets and by increasing the viscosity of the external phase.


Since emulsions often contain a number of ingredients such as carbohydrates, proteins, sterols and phosphatides that can readily support the growth of microbes, these formulations often incorporate preservatives. Commonly used preservatives included in emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid. Antioxidants are also commonly added to emulsion formulations to prevent deterioration of the formulation. Antioxidants used can be free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.


The application of emulsion formulations via dermatological, oral and parenteral routes and methods for their manufacture have been reviewed in the literature (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Emulsion formulations for oral delivery have been very widely used because of ease of formulation, as well as efficacy from an absorption and bioavailability standpoint (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Mineral-oil base laxatives, oil-soluble vitamins and high fat nutritive preparations are among the materials that have commonly been administered orally as o/w emulsions.


ii. Microemulsions


In one embodiment of the present invention, the compositions of iRNAs and nucleic acids are formulated as microemulsions. A microemulsion can be defined as a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Typically microemulsions are systems that are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a fourth component, generally an intermediate chain-length alcohol to form a transparent system. Therefore, microemulsions have also been described as thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules (Leung and Shah, in: Controlled Release of Drugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH Publishers, New York, pages 185-215). Microemulsions commonly are prepared via a combination of three to five components that include oil, water, surfactant, cosurfactant and electrolyte. Whether the microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the properties of the oil and surfactant used and on the structure and geometric packing of the polar heads and hydrocarbon tails of the surfactant molecules (Schott, in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 271).


The phenomenological approach utilizing phase diagrams has been extensively studied and has yielded a comprehensive knowledge, to one skilled in the art, of how to formulate microemulsions (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335). Compared to conventional emulsions, microemulsions offer the advantage of solubilizing water-insoluble drugs in a formulation of thermodynamically stable droplets that are formed spontaneously.


Surfactants used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750), decaglycerol decaoleate (DAO750), alone or in combination with cosurfactants. The cosurfactant, usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules. Microemulsions can, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art. The aqueous phase can typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol. The oil phase can include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.


Microemulsions are particularly of interest from the standpoint of drug solubilization and the enhanced absorption of drugs. Lipid based microemulsions (both o/w and w/o) have been proposed to enhance the oral bioavailability of drugs, including peptides (see e.g., U.S. Pat. Nos. 6,191,105; 7,063,860; 7,070,802; 7,157,099; Constantinides et al., Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find Exp. Clin. Pharmacol., 1993, 13, 205). Microemulsions afford advantages of improved drug solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (see e.g., U.S. Pat. Nos. 6,191,105; 7,063,860; 7,070,802; 7,157,099; Constantinides et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm. Sci., 1996, 85, 138-143). Often microemulsions can form spontaneously when their components are brought together at ambient temperature. This can be particularly advantageous when formulating thermolabile drugs, peptides or iRNAs. Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications. It is expected that the microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of iRNAs and nucleic acids from the gastrointestinal tract, as well as improve the local cellular uptake of iRNAs and nucleic acids.


Microemulsions of the present invention can also contain additional components and additives such as sorbitan monostearate (Grill 3), Labrasol, and penetration enhancers to improve the properties of the formulation and to enhance the absorption of the iRNAs and nucleic acids of the present invention. Penetration enhancers used in the microemulsions of the present invention can be classified as belonging to one of five broad categories-surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of these classes has been discussed above.


iii. Microparticles


An RNAi agent of the invention may be incorporated into a particle, e.g., a microparticle. Microparticles can be produced by spray-drying, but may also be produced by other methods including lyophilization, evaporation, fluid bed drying, vacuum drying, or a combination of these techniques.


iv. Penetration Enhancers


In one embodiment, the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly iRNAs, to the skin of animals. Most drugs are present in solution in both ionized and nonionized forms. However, usually only lipid soluble or lipophilic drugs readily cross cell membranes. It has been discovered that even non-lipophilic drugs can cross cell membranes if the membrane to be crossed is treated with a penetration enhancer. In addition to aiding the diffusion of non-lipophilic drugs across cell membranes, penetration enhancers also enhance the permeability of lipophilic drugs.


Penetration enhancers can be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (see e.g, Malmsten, M. Surfactants and polymers in drug delivery, Informa Health Care, New York, N.Y., 2002; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of the above mentioned classes of penetration enhancers are described below in greater detail.


Surfactants (or “surface-active agents”) are chemical entities which, when dissolved in an aqueous solution, reduce the surface tension of the solution or the interfacial tension between the aqueous solution and another liquid, with the result that absorption of iRNAs through the mucosa is enhanced. In addition to bile salts and fatty acids, these penetration enhancers include, for example, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether) (see e.g., Malmsten, M. Surfactants and polymers in drug delivery, Informa Health Care, New York, N.Y., 2002; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92); and perfluorochemical emulsions, such as FC-43. Takahashi et al., J. Pharm. Pharmacol., 1988, 40, 252).


Various fatty acids and their derivatives which act as penetration enhancers include, for example, oleic acid, lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein (1-monooleoyl-rac-glycerol), dilaurin, caprylic acid, arachidonic acid, glycerol 1-monocaprate, 1-dodecylazacycloheptan-2-one, acyl carnitines, acylcholines, C1-20 alkyl esters thereof (e.g., methyl, isopropyl and t-butyl), and mono- and di-glycerides thereof (i.e., oleate, laurate, caprate, myristate, palmitate, stearate, linoleate, etc.) (see e.g, Touitou, E., et al. Enhancement in Drug Delivery, CRC Press, Danvers, Mass., 2006; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm. Pharmacol., 1992, 44, 651-654).


The physiological role of bile includes the facilitation of dispersion and absorption of lipids and fat-soluble vitamins (see e.g, Malmsten, M. Surfactants and polymers in drug delivery, Informa Health Care, New York, N.Y., 2002; Brunton, Chapter 38 in: Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al. Eds., McGraw-Hill, New York, 1996, pp. 934-935). Various natural bile salts, and their synthetic derivatives, act as penetration enhancers. Thus the term “bile salts” includes any of the naturally occurring components of bile as well as any of their synthetic derivatives. Suitable bile salts include, for example, cholic acid (or its pharmaceutically acceptable sodium salt, sodium cholate), dehydrocholic acid (sodium dehydrocholate), deoxycholic acid (sodium deoxycholate), glucholic acid (sodium glucholate), glycholic acid (sodium glycocholate), glycodeoxycholic acid (sodium glycodeoxycholate), taurocholic acid (sodium taurocholate), taurodeoxycholic acid (sodium taurodeoxycholate), chenodeoxycholic acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA), sodium tauro-24,25-dihydro-fusidate (STDHF), sodium glycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (see e.g, Malmsten, M. Surfactants and polymers in drug delivery, Informa Health Care, New York, N.Y., 2002; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Swinyard, Chapter 39 In: Remington's Pharmaceutical Sciences, 18th Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990, pages 782-783; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharm. Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm. Sci., 1990, 79, 579-583).


Chelating agents, as used in connection with the present invention, can be defined as compounds that remove metallic ions from solution by forming complexes therewith, with the result that absorption of iRNAs through the mucosa is enhanced. With regards to their use as penetration enhancers in the present invention, chelating agents have the added advantage of also serving as DNase inhibitors, as most characterized DNA nucleases require a divalent metal ion for catalysis and are thus inhibited by chelating agents (Jarrett, J. Chromatogr., 1993, 618, 315-339). Suitable chelating agents include but are not limited to disodium ethylenediaminetetraacetate (EDTA), citric acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate and homovanilate), N-acyl derivatives of collagen, laureth-9 and N-amino acyl derivatives of beta-diketones (enamines)(see e.g., Katdare, A. et al., Excipient development for pharmaceutical, biotechnology, and drug delivery, CRC Press, Danvers, Mass., 2006; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Buur et al., J. Control Rel., 1990, 14, 43-51).


As used herein, non-chelating non-surfactant penetration enhancing compounds can be defined as compounds that demonstrate insignificant activity as chelating agents or as surfactants but that nonetheless enhance absorption of iRNAs through the alimentary mucosa (see e.g., Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33). This class of penetration enhancers includes, for example, unsaturated cyclic ureas, 1-alkyl- and 1-alkenylazacyclo-alkanone derivatives (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92); and non-steroidal anti-inflammatory agents such as diclofenac sodium, indomethacin and phenylbutazone (Yamashita et al., J. Pharm. Pharmacol., 1987, 39, 621-626).


Agents that enhance uptake of iRNAs at the cellular level can also be added to the pharmaceutical and other compositions of the present invention. For example, cationic lipids, such as lipofectin (Junichi et al. U.S. Pat. No. 5,705,188), cationic glycerol derivatives, and polycationic molecules, such as polylysine (Lollo et al., PCT Application WO 97/30731), are also known to enhance the cellular uptake of dsRNAs. Examples of commercially available transfection reagents include, for example Lipofectamine™ (Invitrogen; Carlsbad, Calif.), Lipofectamine 2000™ (Invitrogen; Carlsbad, Calif.), 293Fectin™ (Invitrogen; Carlsbad, Calif.), Cellfectin™ (Invitrogen; Carlsbad, Calif.), DMRIE-C™ (Invitrogen; Carlsbad, Calif.), FreeStyle™MAX (Invitrogen; Carlsbad, Calif.), Lipofectamine™ 2000 CD (Invitrogen; Carlsbad, Calif.), Lipofectamine™ (Invitrogen; Carlsbad, Calif.), RNAiMAX (Invitrogen; Carlsbad, Calif.), Oligofectamine™ (Invitrogen; Carlsbad, Calif.), Optifect™ (Invitrogen; Carlsbad, Calif.), X-tremeGENE Q2 Transfection Reagent (Roche; Grenzacherstrasse, Switzerland), DOTAP Liposomal Transfection Reagent (Grenzacherstrasse, Switzerland), DOSPER Liposomal Transfection Reagent (Grenzacherstrasse, Switzerland), or Fugene (Grenzacherstrasse, Switzerland), Transfectam® Reagent (Promega; Madison, Wis.), TransFast™ Transfection Reagent (Promega; Madison, Wis.), Tfx™-20 Reagent (Promega; Madison, Wis.), Tfx™-50 Reagent (Promega; Madison, Wis.), DreamFect™ (OZ Biosciences; Marseille, France), EcoTransfect (OZ Biosciences; Marseille, France), TransPassa D1 Transfection Reagent (New England Biolabs; Ipswich, Mass., USA), LyoVec™/LipoGen™ (Invitrogen; San Diego, Calif., USA), PerFectin Transfection Reagent (Genlantis; San Diego, Calif., USA), NeuroPORTER Transfection Reagent (Genlantis; San Diego, Calif., USA), GenePORTER Transfection reagent (Genlantis; San Diego, Calif., USA), GenePORTER 2 Transfection reagent (Genlantis; San Diego, Calif., USA), Cytofectin Transfection Reagent (Genlantis; San Diego, Calif., USA), BaculoPORTER Transfection Reagent (Genlantis; San Diego, Calif., USA), TroganPORTER™ transfection Reagent (Genlantis; San Diego, Calif., USA), RiboFect (Bioline; Taunton, Mass., USA), PlasFect (Bioline; Taunton, Mass., USA), UniFECTOR (B-Bridge International; Mountain View, Calif., USA), SureFECTOR (B-Bridge International; Mountain View, Calif., USA), or HiFect™ (B-Bridge International, Mountain View, Calif., USA), among others.


Other agents can be utilized to enhance the penetration of the administered nucleic acids, including glycols such as ethylene glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and terpenes such as limonene and menthone.


v. Carriers


Certain compositions of the present invention also incorporate carrier compounds in the formulation. As used herein, “carrier compound” or “carrier” can refer to a nucleic acid, or analog thereof, which is inert (i.e., does not possess biological activity per se) but is recognized as a nucleic acid by in vivo processes that reduce the bioavailability of a nucleic acid having biological activity by, for example, degrading the biologically active nucleic acid or promoting its removal from circulation. The coadministration of a nucleic acid and a carrier compound, typically with an excess of the latter substance, can result in a substantial reduction of the amount of nucleic acid recovered in the liver, kidney or other extracirculatory reservoirs, presumably due to competition between the carrier compound and the nucleic acid for a common receptor. For example, the recovery of a partially phosphorothioate dsRNA in hepatic tissue can be reduced when it is coadministered with polyinosinic acid, dextran sulfate, polycytidic acid or 4-acetamido-4′isothiocyano-stilbene-2,2′-disulfonic acid (Miyao et al., DsRNA Res. Dev., 1995, 5, 115-121; Takakura et al., DsRNA & Nucl. Acid Drug Dev., 1996, 6, 177-183.


vi. Excipients


In contrast to a carrier compound, a “pharmaceutical carrier” or “excipient” is a pharmaceutically acceptable solvent, suspending agent or any other pharmacologically inert vehicle for delivering one or more nucleic acids to an animal. The excipient can be liquid or solid and is selected, with the planned manner of administration in mind, so as to provide for the desired bulk, consistency, etc., when combined with a nucleic acid and the other components of a given pharmaceutical composition. Typical pharmaceutical carriers include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calcium hydrogen phosphate, etc); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, corn starch, polyethylene glycols, sodium benzoate, sodium acetate, etc); disintegrants (e.g., starch, sodium starch glycolate, etc); and wetting agents (e.g., sodium lauryl sulphate, etc).


Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can also be used to formulate the compositions of the present invention. Suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.


Formulations for topical administration of nucleic acids can include sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the nucleic acids in liquid or solid oil bases. The solutions can also contain buffers, diluents and other suitable additives. Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can be used.


Suitable pharmaceutically acceptable excipients include, but are not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.


vii. Other Components


The compositions of the present invention can additionally contain other adjunct components conventionally found in pharmaceutical compositions, at their art-established usage levels. Thus, for example, the compositions can contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or can contain additional materials useful in physically formulating various dosage forms of the compositions of the present invention, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. However, such materials, when added, should not unduly interfere with the biological activities of the components of the compositions of the present invention. The formulations can be sterilized and, if desired, mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously interact with the nucleic acid(s) of the formulation.


Aqueous suspensions can contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension can also contain stabilizers.


In some embodiments, pharmaceutical compositions featured in the invention include (a) one or more iRNA compounds and (b) one or more agents which function by a non-RNAi mechanism and which are useful in treating a bleeding disorder. Examples of such agents include, but are not limited to an anti-inflammatory agent, anti-steatosis agent, anti-viral, and/or anti-fibrosis agent. In addition, other substances commonly used to protect the liver, such as silymarin, can also be used in conjunction with the iRNAs described herein. Other agents useful for treating liver diseases include telbivudine, entecavir, and protease inhibitors such as telaprevir and other disclosed, for example, in Tung et al., U.S. Application Publication Nos. 2005/0148548, 2004/0167116, and 2003/0144217; and in Hale et al., U.S. Application Publication No. 2004/0127488.


Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds that exhibit high therapeutic indices are preferred.


The data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of compositions featured herein in the invention lies generally within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage can vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the methods featured in the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range of the compound or, when appropriate, of the polypeptide product of a target sequence (e.g., achieving a decreased concentration of the polypeptide) that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma can be measured, for example, by high performance liquid chromatography.


In addition to their administration, as discussed above, the iRNAs featured in the invention can be administered in combination with other known agents effective in treatment of pathological processes that are mediated by iron overload and that can be treated by inhibiting TMPRSS6 expression. In any event, the administering physician can adjust the amount and timing of iRNA administration on the basis of results observed using standard measures of efficacy known in the art or described herein.


V. Methods For Inhibiting TMPRSS6 Expression

The present invention provides methods of inhibiting expression of TMPRSS6 (matriptase-2) in a cell. The methods include contacting a cell with an RNAi agent, e.g., a double stranded RNAi agent, in an amount effective to inhibit expression of the TMPRSS6 in the cell, thereby inhibiting expression of the TMPRSS6 in the cell. Contacting of a cell with a double stranded RNAi agent may be done in vitro or in vivo.


Contacting a cell in vivo with the RNAi agent includes contacting a cell or group of cells within a subject, e.g., a human subject, with the RNAi agent. Combinations of in vitro and in vivo methods of contacting are also possible. Contacting may be direct or indirect, as discussed above. Furthermore, contacting a cell may be accomplished via a targeting ligand, including any ligand described herein or known in the art. In preferred embodiments, the targeting ligand is a carbohydrate moiety, e.g, a GalNAc3 ligand, or any other ligand that directs the RNAi agent to a site of interest, e.g, the liver of a subject.


The term “inhibiting,” as used herein, is used interchangeably with “reducing,” “silencing,” “downregulating” and other similar terms, and includes any level of inhibition.


The phrase “inhibiting expression of a TMPRSS6” is intended to refer to inhibition of expression of any TMPRSS6 gene (such as, e.g., a mouse TMPRSS6 gene, a rat TMPRSS6 gene, a monkey TMPRSS6 gene, or a human TMPRSS6 gene) as well as variants or mutants of a TMPRSS6 gene. Thus, the TMPRSS6 gene may be a wild-type TMPRSS6 gene, a mutant TMPRSS6 gene, or a transgenic TMPRSS6 gene in the context of a genetically manipulated cell, group of cells, or organism.


“Inhibiting expression of a TMPRSS6 gene” includes any level of inhibition of a TMPRSS6 gene, e.g., at least partial suppression of the expression of a TMPRSS6 gene. The expression of the TMPRSS6 gene may be assessed based on the level, or the change in the level, of any variable associated with TMPRSS6 gene expression, e.g., TMPRSS6 mRNA level, TMPRSS6 protein level, or lipid levels. This level may be assessed in an individual cell or in a group of cells, including, for example, a sample derived from a subject.


Inhibition may be assessed by a decrease in an absolute or relative level of one or more variables that are associated with TMPRSS6 expression compared with a control level. The control level may be any type of control level that is utilized in the art, e.g, a pre-dose baseline level, or a level determined from a similar subject, cell, or sample that is untreated or treated with a control (such as, e.g, buffer only control or inactive agent control).


In some embodiments of the methods of the invention, expression of a TMPRSS6 gene is inhibited by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%. at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%.


Inhibition of the expression of a TMPRSS6 gene may be manifested by a reduction of the amount of mRNA expressed by a first cell or group of cells (such cells may be present, for example, in a sample derived from a subject) in which a TMPRSS6 gene is transcribed and which has or have been treated (e.g, by contacting the cell or cells with an RNAi agent of the invention, or by administering an RNAi agent of the invention to a subject in which the cells are or were present) such that the expression of a TMPRSS6 gene is inhibited, as compared to a second cell or group of cells substantially identical to the first cell or group of cells but which has not or have not been so treated (control cell(s)). In preferred embodiments, the inhibition is assessed by expressing the level of mRNA in treated cells as a percentage of the level of mRNA in control cells, using the following formula:










(

mRNA





in





control





cells

)

-

(

mRNA





in





treated





cells

)



(

mRNA





in





control





cells

)


·
100


%




Alternatively, inhibition of the expression of a TMPRSS6 gene may be assessed in terms of a reduction of a parameter that is functionally linked to TMPRSS6 gene expression, e.g, TMPRSS6 protein expression, hepcidin gene or protein expression, or iron levels in tissues or serum. TMPRSS6 gene silencing may be determined in any cell expressing TMPRSS6, either constitutively or by genomic engineering, and by any assay known in the art. The liver is the major site of TMPRSS6 expression. Other significant sites of expression include the kidneys and the uterus.


Inhibition of the expression of a TMPRSS6 protein may be manifested by a reduction in the level of the TMPRSS6 protein that is expressed by a cell or group of cells (e.g, the level of protein expressed in a sample derived from a subject). As explained above for the assessment of mRNA suppression, the inhibition of protein expression levels in a treated cell or group of cells may similarly be expressed as a percentage of the level of protein in a control cell or group of cells.


A control cell or group of cells that may be used to assess the inhibition of the expression of a TMPRSS6 gene includes a cell or group of cells that has not yet been contacted with an RNAi agent of the invention. For example, the control cell or group of cells may be derived from an individual subject (e.g., a human or animal subject) prior to treatment of the subject with an RNAi agent.


The level of TMPRSS6 mRNA that is expressed by a cell or group of cells may be determined using any method known in the art for assessing mRNA expression. In one embodiment, the level of expression of TMPRSS6 in a sample is determined by detecting a transcribed polynucleotide, or portion thereof, e.g, mRNA of the TMPRSS6 gene. RNA may be extracted from cells using RNA extraction techniques including, for example, using acid phenol/guanidine isothiocyanate extraction (RNAzol B; Biogenesis), RNeasy RNA preparation kits (Qiagen) or PAXgene (PreAnalytix, Switzerland). Typical assay formats utilizing ribonucleic acid hybridization include nuclear run-on assays, RT-PCR, RNase protection assays (Melton et al., Nuc. Acids Res. 12:7035), Northern blotting, in situ hybridization, and microarray analysis.


In one embodiment, the level of expression of TMPRSS6 is determined using a nucleic acid probe. The term “probe”, as used herein, refers to any molecule that is capable of selectively binding to a specific TMPRSS6. Probes can be synthesized by one of skill in the art, or derived from appropriate biological preparations. Probes may be specifically designed to be labeled. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molecules.


Isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, polymerase chain reaction (PCR) analyses and probe arrays. One method for the determination of mRNA levels involves contacting the isolated mRNA with a nucleic acid molecule (probe) that can hybridize to TMPRSS6 mRNA. In one embodiment, the mRNA is immobilized on a solid surface and contacted with a probe, for example by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane, such as nitrocellulose. In an alternative embodiment, the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an Affymetrix gene chip array. A skilled artisan can readily adapt known mRNA detection methods for use in determining the level of TMPRSS6 mRNA.


An alternative method for determining the level of expression of TMPRSS6 in a sample involves the process of nucleic acid amplification and/or reverse transcriptase (to prepare cDNA) of for example mRNA in the sample, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88:189-193), self sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio Technology 6:1197), rolling circle replication (Lizardi et al., U.S. Pat. No. 5,854,033) or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers. In particular aspects of the invention, the level of expression of TMPRSS6 is determined by quantitative fluorogenic RT-PCR (i.e., the TaqMan™ System).


The expression levels of TMPRSS6 mRNA may be monitored using a membrane blot (such as used in hybridization analysis such as Northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are incorporated herein by reference. The determination of TMPRSS6 expression level may also comprise using nucleic acid probes in solution.


In preferred embodiments, the level of mRNA expression is assessed using branched DNA (bDNA) assays or real time PCR (qPCR). The use of these methods is described and exemplified in the Examples presented herein.


The level of TMPRSS6 protein expression may be determined using any method known in the art for the measurement of protein levels. Such methods include, for example, electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, fluid or gel precipitin reactions, absorption spectroscopy, a colorimetric assays, spectrophotometric assays, flow cytometry, immunodiffusion (single or double), immunoelectrophoresis, Western blotting, radioimmunoassay (RIA), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, electrochemiluminescence assays, and the like.


The term “sample” as used herein refers to a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject. Examples of biological fluids include blood, serum and serosal fluids, plasma, lymph, urine, cerebrospinal fluid, saliva, ocular fluids, and the like. Tissue samples may include samples from tissues, organs or localized regions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organs. In certain embodiments, samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g., hepatocytes). In preferred embodiments, a “sample derived from a subject” refers to blood or plasma drawn from the subject. In further embodiments, a “sample derived from a subject” refers to liver tissue derived from the subject.


In some embodiments of the methods of the invention, the RNAi agent is administered to a subject such that the RNAi agent is delivered to a specific site within the subject. The inhibition of expression of TMPRSS6 may be assessed using measurements of the level or change in the level of TMPRSS6 mRNA or TMPRSS6 protein in a sample derived from fluid or tissue from the specific site within the subject. In preferred embodiments, the site is the liver. The site may also be a subsection or subgroup of cells from any one of the aforementioned sites. The site may also include cells that express a particular type of receptor.


VI. Methods for Treating or Preventing a TMPRSS6 Associated Disorder

The present invention also provides methods for treating or preventing diseases and conditions that can be modulated by TMPRSS6 gene expression. For example, the compositions described herein can be used to treat any disorder associated with iron overload, e.g, a thalassemia (e.g, β-thalassemia or α-thalassemia), primary hemochromatosis, secondary hemochromatosis, severe juvenile hemochromatosis, erythropoietic porphyria, sideroblastic anemia, hemolytic anemia, dyserythropoietic anemia, or sickle-cell anemia. In one embodiment, a TMPRSS6 iRNA is used to treat a hemoglobinopathy. The TMPRSS6 iRNAs of the invention can also be used to treat elevated levels of iron due to other conditions, such as chronic alcoholism.


In thalassemias, the bone marrow synthesizes insufficient amounts of a hemoglobin chain; this in turn reduces the production of red blood cells and causes anemia. Either the α or the β chain may be affected, but β thalassemias are more common. Newborn babies are healthy because their bodies still produce HbF, which does not have P chains; during the first few months of life, the bone marrow switches to producing HbA, and symptoms start to appear.


β-thalassemias result from mutation with either non-expressing (β°) or low expressing (β+) alleles of the HBB gene, β-thalassemias vary in severity depending on the genotype, and include minor/trait β-thalassemia (β/β° or β/β+), intermedia β-thalassemia (β°/β+), and major β-thalassemia (β°/β° or β″7 β+).


Thalassemia intermedia (TI) typically presents with little hemolysis, while major β-thalassemia (TM) is typically accompanied by abundant hemolysis which causes, e.g., anemia and splenomegaly; and highly ineffective erythropoiesis, which causes bone marrow drive (skeletal changes, oteopenia), increased erythropoietin synthesis, hepato-splenomegaly, consumption of haematinics (megablastic anemia), and high uric acid in blood. The iRNAs of the invention, e.g., TMPRSS6 iRNAs, are better suited for treating the iron overload that typically accompanies thalassemia's that are more TI like (e.g., for treating individuals having a β°/β+, β/β° or β/β+ genotype).


Symptoms of β-thalassemias also include, e.g, complication due to therapy, e.g, iron overload, which causes endocrinopathy, liver fibrosis and cardiac fibrosis. Administration of an iRNA agent that targets TMPRSS6 can be effective to treat one or more of these symptoms.


α-thalassemias result from mutation with either non-expressing (a°) or low expressing (a+) alleles of the HBA1 or HBA2 genes, orthalassemias vary in severity depending on the genotype, and include trait thalassemia (−α/αα), Hb Bart and Hydrops fetalis (a°/a°), a-Thalaseemia minor (−/αα), (−α/−α), and HbH disease (−/−a). Lower a-globin chains are produced, resulting in an excess of β chains in adults and excess γ chains in newborns. The excess β chains form unstable tetramers (called Hemoglobin H or HbH of 4 beta chains), which have abnormal oxygen dissociation curves. Administration of an iRNA agent that targets TMPRSS6 can be effective to treat iron overload in a subject who has an a-thalassemias.


Symptoms of hemochromatosis include, e.g, abdominal pain, joint pain, fatigue, lack of energy, weakness, darkening of the skin (often referred to as “bronzing”), and loss of body hair. Administration of an iRNA agent that targets TMPRSS6 can be effective to treat one or more of these symptoms.


Other symptoms associated with iron overload include increased risk for liver disease (cirrhosis, cancer), heart attack or heart failure, diabetes mellitus, osteoarthritis, osteoporosis, metabolic syndrome, hypothyroidism, hypogonadism, and in some cases premature death. Iron mismanagement resulting in overload can also accelerate such neurodegenerative diseases as Alzheimer's, early-onset Parkinson's, Huntington's, epilepsy and multiple sclerosis. Administration of an iRNA agent that targets TMPRSS6, e.g, an iRNA described in Tables 1 or 2 can treat one or more of these symptoms, or prevent the development or progression of a disease or disorder that is aggrevated by increased iron levels.


The methods of the invention further relate to the use of an iRNA agent or a pharmaceutical composition thereof, e.g, for treating a disorder associated with iron overload, in combination with other pharmaceuticals and/or other therapeutic methods, e.g., with known pharmaceuticals and/or known therapeutic methods, such as, for example, those which are currently employed for treating these disorders. For example, in certain embodiments, an iRNA agent targeting TMPRSS6 is administered in combination with, e.g., iron chelators (e.g., desferoxamine), folic acid, a blood transfusion, a phlebotomy, agents to manage ulcers, agents to increase fetal hemoglobin levels (e.g, hydroxyurea), agents to control infection (e.g, antibiotics and antivirals), agents to treat thrombotic state, or a stem cell or bone marrow transplant. A stem cell transplant can utilize stem cells from an umbilical cord, such as from a relative, e.g, a sibling. Exemplary iron chelators include desferoxamine, Deferasirox (Exjade), deferiprone, vitamin E, wheat germ oil, tocophersolan, and indicaxanthin.


The iRNA agent and an additional therapeutic agent can be administered in the same composition, e.g, parenterally, or the additional therapeutic agent can be administered as part of a separate composition or by another method described herein. Administration of the iRNA agent and the additional therapeutic agent can be at the same time, or at different times and, in any order.


Administration of the iRNA agent of the invention can lower iron levels, lower ferritin levels, and/or lower transferrin saturation levels. For example, administration of the dsRNA can lower serum iron levels and/or lower serum ferritin levels. Transferrin saturation levels can be lowered by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or more. In another embodiment, the transferrin saturation levels remain lower for 7 days, 10 days, 20 days, 30 days, or more following administration.


Transferrin saturation levels can be lowered to below 50%, below 45%, below 40%, below 35%, below 35%, below 30%, below 25%, below 20%, below 15%, or lower. In another embodiment, the lower transferrin saturation levels are maintained for 7 days, 10 days, 20 days, 30 days, or more following administration. Transferrin saturation is a measure of the amount of iron bound to serum transferrin, and corresponds to the ratio of serum iron and total iron-binding capacity.


Serum iron levels can be lowered by 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more. In another embodiment, the serum iron levels remain lower for 7 days, 10 days, 20 days, 30 days, or more following administration.


Administration of the iRNA agent of the invention preferably results in lowered iron levels in the blood, and more particularly in the serum, or in one or more tissues of the mammal. In some embodiments, iron levels are decreased by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more, as compared to pretreatment levels.


By “lower” in this context is meant a statistically significant decrease in such level. The decrease can be, for example, at least 10%, at least 20%, at least 30%, at least 40% or more, and is preferably down to a level accepted as within the range of normal for an individual without such disorder.


Administration of the iRNA agent of the invention can increase serum hepcidin levels, and/or increase hepcidin gene expression. For example, administration of the dsRNA can increase serum hepcidin by at least about 10%, 25%, 50%, 100%, 150%, 200%, 250%, 300%, or more. In a further example, administration of the dsRNA can increase hepcidin mRNA levels by at least about 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, or greater.


Efficacy of treatment or prevention of disease can be assessed, for example by measuring disease progression, disease remission, symptom severity, reduction in pain, quality of life, dose of a medication required to sustain a treatment effect, level of a disease marker or any other measurable parameter appropriate for a given disease being treated or targeted for prevention. It is well within the ability of one skilled in the art to monitor efficacy of treatment or prevention by measuring any one of such parameters, or any combination of parameters. For example, the levels of transferrin saturation or serum ferritin can be monitored for efficacy of a given treatment regime.


Iron level tests are typically performed on a sample of a pateint's blood. An iron level test measure the amount of iron in the blood serum that is being carried by the proteins transferrin. A TIBC (Total iron-binding capacity) test measures the amount of iron that the blood would carry if the transferrin were fully saturated. Since transferrin is produced by the liver, the TIBC can be used to monitor liver function and nutrition. The transferrin test is a direct measure of transferrin (also called siderophilin) levels in the blood. The saturation level of transferrin can be calculated by dividing the serum iron level by the TIBC. The ferritin test measures the level of a protein in the blood that stores iron for later use by the body.


The iRNA treatments described herein can be used to treat individuals afflicted with a TMPRSS6 associated disorder, e.g., elevated iron levels, as may be indicated by iron levels in serum e.g., iron levels measuring greater than 350 μg/dL, greater than 500 μg/dL, greater than 1000 μg/dL, or more. In an embodiment, elevated levels of iron in serum, e.g., greater than 15, 20, 25, or 30 mg/g dry weight.


The iRNA treatments described herein can also be used to treat individuals having elevated iron levels, as may be indicated by elevated ferritin levels in serum, e.g, ferritin levels measuring greater than 300 μg/L, greater than 500 μg/L, greater than 1000 μg/L, greater than 1500 μg/L, greater than 2000 μg/L, greater than 2500 μg/L, or 3000 μg/L, or more.


The iRNA treatments described herein can further be used to treat individuals having elevated iron levels, as may be indicated by elevated transferrin levels in serum, e.g., transferrin levels measuring greater than 400 mg/dL, greater than 500 mg/L, greater than 1000 mg/dL, or more.


The iRNA treatments described herein can also be used to treat individuals having moderately elevated iron levels, as may be indicated by moderately elevated transferrin saturation levels, e.g., saturation levels of 40%, 45%, or 50% or more. In addition, the treatment described herein may also be used to prevent elevated iron levels in individuals with only minor elevations in transferrin saturation. One of skill in the art can easily monitor the transferrin saturation levels in subjects receiving treatment with iRNA as described herein and assay for a reduction in transferrin saturation levels of at least 5% or 10%.


The iRNA treatments described herein can be used to treat individuals having elevated iron levels, as may be indicated by a TIBC value greater than 400 μg/dL, greater than 500 μg/dL, or greater than 1000 μg/dL, or more.


In some embodiments, individuals in need of treatment with an iRNA agent of the invention have decreased hematocrit levels, decreased hemoglobin levels, increased red blood cell distribution width, increased number of reticulocytes, decreased number of mature red blood cells, increased unsaturated iron binding capacity, decreased ineffective erythropoiesis, decreased extradedullary hematopoiesis, and/or decreased HAMP1 expression levels.


A patient can be further monitored by assay of blood sugar (glucose) level or a fetoprotein level, by echocardiogram (e.g, to examine the heart's function), electrocardiogram (ECG) (e.g., to look at the electrical activity of the heart), imaging tests (such as CT scans, MRI and ultrasound), and liver function tests. Excess iron staining or iron concentrations can be measured on liver biopsy samples, or to confirm the extent of liver damage, e.g, the stage of liver disease.


A treatment or preventive effect is evident when there is a statistically significant improvement in one or more parameters of disease status, or by a failure to worsen or to develop symptoms where they would otherwise be anticipated. As an example, a favorable change of at least 10% in a measurable parameter of disease, and preferably at least 20%, 30%, 40%, 50% or more can be indicative of effective treatment. Efficacy for a given iRNA drug or formulation of that drug can also be judged using an experimental animal model for the given disease as known in the art. When using an experimental animal model, efficacy of treatment is evidenced when a statistically significant reduction in a marker or symptom is observed.


Alternatively, the efficacy can be measured by a reduction in the severity of disease as determined by one skilled in the art of diagnosis based on a clinically accepted disease severity grading scale.


As used herein, a “subject” includes a human or non-human animal, preferably a vertebrate, and more preferably a mammal. A subject may include a transgenic organism. Most preferably, the subject is a human, such as a human suffering from or predisposed to developing a TMPRSS6 associated disorder.


In some embodiments of the methods of the invention, TMPRSS6 expression is decreased for an extended duration, e.g., at least one week, two weeks, three weeks, or four weeks or longer. For example, in certain instances, expression of the TMPRSS6 gene is suppressed by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% by administration of an iRNA agent described herein. In some embodiments, the TMPRSS6 gene is suppressed by at least about 60%, 70%, or 80% by administration of the iRNA agent. In some embodiments, the TMPRSS6 gene is suppressed by at least about 85%, 90%, or 95% by administration of the double-stranded oligonucleotide. In another embodiment, the TMPRSS6 gene remains suppressed for 7 days, 10 days, 20 days, 30 days, or more following administration.


The RNAi agents of the invention may be administered to a subject using any mode of administration known in the art, including, but not limited to subcutaneous, intravenous, intramuscular, intraocular, intrabronchial, intrapleural, intraperitoneal, intraarterial, lymphatic, cerebrospinal, and any combinations thereof. In preferred embodiments, the agents are administered subcutaneously.


In some embodiments, the administration is via a depot injection. A depot injection may release the RNAi agent in a consistent way over a prolonged time period. Thus, a depot injection may reduce the frequency of dosing needed to obtain a desired effect, e.g., a desired inhibition of TMPRSS6, or a therapeutic or prophylactic effect. A depot injection may also provide more consistent serum concentrations. Depot injections may include subcutaneous injections or intramuscular injections. In preferred embodiments, the depot injection is a subcutaneous injection.


In some embodiments, the administration is via a pump. The pump may be an external pump or a surgically implanted pump. In certain embodiments, the pump is a subcutaneously implanted osmotic pump. In other embodiments, the pump is an infusion pump. An infusion pump may be used for intravenous, subcutaneous, arterial, or epidural infusions. In preferred embodiments, the infusion pump is a subcutaneous infusion pump. In other embodiments, the pump is a surgically implanted pump that delivers the RNAi agent to the liver.


Other modes of administration include epidural, intracerebral, intracerebroventricular, nasal administration, intraarterial, intracardiac, intraosseous infusion, intrathecal, and intravitreal, and pulmonary. The mode of administration may be chosen based upon whether local or systemic treatment is desired and based upon the area to be treated. The route and site of administration may be chosen to enhance targeting.


The method includes administering an iRNA agent, e.g., a dose sufficient to depress levels of TMPRSS6 mRNA for at least 5, more preferably 7, 10, 14, 21, 25, 30 or 40 days; and optionally, administering a second single dose of dsRNA, wherein the second single dose is administered at least 5, more preferably 7, 10, 14, 21, 25, 30 or 40 days after the first single dose is administered, thereby inhibiting the expression of the TMPRSS6 gene in a subject.


In one embodiment, doses of iRNA agent of the invention are administered not more than once every four weeks, not more than once every three weeks, not more than once every two weeks, or not more than once every week. In another embodiment, the administrations can be maintained for one, two, three, or six months, or one year or longer. In another embodiment, doses of iRNA agent of the invention are administered once a week for three weeks.


In general, the iRNA agent does not activate the immune system, e.g., it does not increase cytokine levels, such as TNF-alpha or IFN-alpha levels. For example, when measured by an assay, such as an in vitro PBMC assay, such as described herein, the increase in levels of TNF-alpha or IFN-alpha, is less than 30%, 20%, or 10% of control cells treated with a control dsRNA, such as a dsRNA that does not target TMPRSS6.


For example, a subject can be administered a therapeutic amount of an iRNA agent, such as 0.3 mg/kg, 0.5 mg/kg, 1.0 mg/kg, 1.5 mg/kg, 2.0 mg/kg, 2.5 mg/kg, or 3 mg/kg of dsRNA.


The iRNA agent can be administered by intravenous infusion over a period of time, such as over a 5 minute, 10 minute, 15 minute, 20 minute, or 25 minute period. The administration is repeated, for example, on a regular basis, such as biweekly (i.e., every two weeks) for one month, two months, three months, four months or longer. After an initial treatment regimen, the treatments can be administered on a less frequent basis. For example, after administration biweekly for three months, administration can be repeated once per month, for six months or a year or longer. Administration of the iRNA agent can reduce TMPRSS6 levels, e.g, in a cell, tissue, blood, urine or other compartment of the patient by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80% or at least 90% or more.


Before administration of a full dose of the iRNA agent, patients can be administered a smaller dose, such as a dose resulting in less than 5% infusion reaction, and monitored for adverse effects, such as an allergic reaction, or for elevated lipid levels or blood pressure. In another example, the patient can be monitored for unwanted immunostimulatory effects, such as increased cytokine (e.g., TNF-alpha or INF-alpha) levels.


Many disorders associated with elevated iron levels are hereditary. Therefore, a patient in need of a TMPRSS6 iRNA may be identified by taking a family history. A healthcare provider, such as a doctor, nurse, or family member, can take a family history before prescribing or administering a TMPRSS6 dsRNA. A DNA test may also be performed on the patient to identify a mutation in the TMPRSS6 gene, before a TMPRSS6 dsRNA is administered to the patient. For example, diagnosis of hereditary hemochromatosis can be confirmed by identifying the two HFE (Hemochromatosis) gene mutations C282Y and H63D, according to GenBank Accession No. CAB07442.1 (GF 1890180, record dated Oct. 23, 2008).


A treatment or preventive effect is evident when there is a statistically significant improvement in one or more parameters of disease status, or by a failure to worsen or to develop symptoms where they would otherwise be anticipated. As an example, a favorable change of at least 10% in a measurable parameter of disease, and preferably at least 20%, 30%, 40%, 50% or more can be indicative of effective treatment. Efficacy for a given iRNA agent of the invention or formulation of that iRNA agent can also be judged using an experimental animal model for the given disease as known in the art. When using an experimental animal model, efficacy of treatment is evidenced when a statistically significant reduction in a marker or symptom is observed.


In one embodiment, the RNAi agent is administered at a dose of between about 0.25 mg/kg to about 50 mg/kg, e.g., between about 0.25 mg/kg to about 0.5 mg/kg, between about 0.25 mg/kg to about 1 mg/kg, between about 0.25 mg/kg to about 5 mg/kg, between about 0.25 mg/kg to about 10 mg/kg, between about 1 mg/kg to about 10 mg/kg, between about 5 mg/kg to about 15 mg/kg, between about 10 mg/kg to about 20 mg/kg, between about 15 mg/kg to about 25 mg/kg, between about 20 mg/kg to about 30 mg/kg, between about 25 mg/kg to about 35 mg/kg, or between about 40 mg/kg to about 50 mg/kg.


In some embodiments, the RNAi agent is administered at a dose of about 0.25 mg/kg, about 0.5 mg/kg, about 1 mg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg, about 5 mg/kg, about 6 mg/kg, about 7 mg/kg, about 8 mg/kg, about 9 mg/kg, about 10 mg/kg, about 11 mg/kg, about 12 mg/kg, about 13 mg/kg, about 14 mg/kg, about 15 mg/kg, about 16 mg/kg, about 17 mg/kg, about 18 mg/kg, about 19 mg/kg, about 20 mg/kg, about 21 mg/kg, about 22 mg/kg, about 23 mg/kg, about 24 mg/kg, about 25 mg/kg, about 26 mg/kg, about 27 mg/kg, about 28 mg/kg, about 29 mg/kg, 30 mg/kg, about 31 mg/kg, about 32 mg/kg, about 33 mg/kg, about 34 mg/kg, about 35 mg/kg, about 36 mg/kg, about 37 mg/kg, about 38 mg/kg, about 39 mg/kg, about 40 mg/kg, about 41 mg/kg, about 42 mg/kg, about 43 mg/kg, about 44 mg/kg, about 45 mg/kg, about 46 mg/kg, about 47 mg/kg, about 48 mg/kg, about 49 mg/kg or about 50 mg/kg.


In certain embodiments, for example, when a composition of the invention comprises a dsRNA as described herein and a lipid, subjects can be administered a therapeutic amount of iRNA, such as about 0.01 mg/kg to about 5 mg/kg, about 0.01 mg/kg to about 10 mg/kg, about 0.05 mg/kg to about 5 mg/kg, about 0.05 mg/kg to about 10 mg/kg, about 0.1 mg/kg to about 5 mg/kg, about 0.1 mg/kg to about 10 mg/kg, about 0.2 mg/kg to about 5 mg/kg, about 0.2 mg/kg to about 10 mg/kg, about 0.3 mg/kg to about 5 mg/kg, about 0.3 mg/kg to about 10 mg/kg, about 0.4 mg/kg to about 5 mg/kg, about 0.4 mg/kg to about 10 mg/kg, about 0.5 mg/kg to about 5 mg/kg, about 0.5 mg/kg to about 10 mg/kg, about 1 mg/kg to about 5 mg/kg, about 1 mg/kg to about 10 mg/kg, about 1.5 mg/kg to about 5 mg/kg, about 1.5 mg/kg to about 10 mg/kg, about 2 mg/kg to about 2.5 mg/kg, about 2 mg/kg to about 10 mg/kg, about 3 mg/kg to about 5 mg/kg, about 3 mg/kg to about 10 mg/kg, about 3.5 mg/kg to about 5 mg/kg, about 4 mg/kg to about 5 mg/kg, about 4.5 mg/kg to about 5 mg/kg, about 4 mg/kg to about 10 mg/kg, about 4.5 mg/kg to about 10 mg/kg, about 5 mg/kg to about 10 mg/kg, about 5.5 mg/kg to about 10 mg/kg, about 6 mg/kg to about 10 mg/kg, about 6.5 mg/kg to about 10 mg/kg, about 7 mg/kg to about 10 mg/kg, about 7.5 mg/kg to about 10 mg/kg, about 8 mg/kg to about 10 mg/kg, about 8.5 mg/kg to about 10 mg/kg, about 9 mg/kg to about 10 mg/kg, or about 9.5 mg/kg to about 10 mg/kg.


Values and ranges intermediate to the recited values are also intended to be part of this invention. For example, the dsRNA may be administered at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or about 10 mg/kg. Values and ranges intermediate to the recited values are also intended to be part of this invention.


In certain embodiments of the invention, for example, when a double-stranded RNAi agent includes one or more modifications (e.g., motifs of three identical modifications on three consecutive nucleotides, including one such motif at or near the cleavage site of the agent), six phosphorothioate linkages, and a ligand, such an agent is administered at a dose of about 0.01 to about 0.5 mg/kg, about 0.01 to about 0.4 mg/kg, about 0.01 to about 0.3 mg/kg, about 0.01 to about 0.2 mg/kg, about 0.01 to about 0.1 mg/kg, about 0.01 mg/kg to about 0.09 mg/kg, about 0.01 mg/kg to about 0.08 mg/kg, about 0.01 mg/kg to about 0.07 mg/kg, about 0.01 mg/kg to about 0.06 mg/kg, about 0.01 mg/kg to about 0.05 mg/kg, about 0.02 to about 0.5 mg/kg, about 0.02 to about 0.4 mg/kg, about 0.02 to about 0.3 mg/kg, about 0.02 to about 0.2 mg/kg, about 0.02 to about 0.1 mg/kg, about 0.02 mg/kg to about 0.09 mg/kg, about 0.02 mg/kg to about 0.08 mg/kg, about 0.02 mg/kg to about 0.07 mg/kg, about 0.02 mg/kg to about 0.06 mg/kg, about 0.02 mg/kg to about 0.05 mg/kg, about 0.03 to about 0.5 mg/kg, about 0.03 to about 0.4 mg/kg, about 0.03 to about 0.3 mg/kg, about 0.03 to about 0.2 mg/kg, about 0.03 to about 0.1 mg/kg, about 0.03 mg/kg to about 0.09 mg/kg, about 0.03 mg/kg to about 0.08 mg/kg, about 0.03 mg/kg to about 0.07 mg/kg, about 0.03 mg/kg to about 0.06 mg/kg, about 0.03 mg/kg to about 0.05 mg/kg, about 0.04 to about 0.5 mg/kg, about 0.04 to about 0.4 mg/kg, about 0.04 to about 0.3 mg/kg, about 0.04 to about 0.2 mg/kg, about 0.04 to about 0.1 mg/kg, about 0.04 mg/kg to about 0.09 mg/kg, about 0.04 mg/kg to about 0.08 mg/kg, about 0.04 mg/kg to about 0.07 mg/kg, about 0.04 mg/kg to about 0.06 mg/kg, about 0.05 to about 0.5 mg/kg, about 0.05 to about 0.4 mg/kg, about 0.05 to about 0.3 mg/kg, about 0.05 to about 0.2 mg/kg, about 0.05 to about 0.1 mg/kg, about 0.05 mg/kg to about 0.09 mg/kg, about 0.05 mg/kg to about 0.08 mg/kg, or about 0.05 mg/kg to about 0.07 mg/kg. Values and ranges intermediate to the foregoing recited values are also intended to be part of this invention, e.g., the RNAi agent may be administered to the subject at a dose of about 0.015 mg/kg to about 0.45 mg/mg.


For example, the RNAi agent, e.g, RNAi agent in a pharmaceutical composition, may be administered at a dose of about 0.01 mg/kg, 0.0125 mg/kg, 0.015 mg/kg, 0.0175 mg/kg, 0.02 mg/kg, 0.0225 mg/kg, 0.025 mg/kg, 0.0275 mg/kg, 0.03 mg/kg, 0.0325 mg/kg, 0.035 mg/kg, 0.0375 mg/kg, 0.04 mg/kg, 0.0425 mg/kg, 0.045 mg/kg, 0.0475 mg/kg, 0.05 mg/kg, 0.0525 mg/kg, 0.055 mg/kg, 0.0575 mg/kg, 0.06 mg/kg, 0.0625 mg/kg, 0.065 mg/kg, 0.0675 mg/kg, 0.07 mg/kg, 0.0725 mg/kg, 0.075 mg/kg, 0.0775 mg/kg, 0.08 mg/kg, 0.0825 mg/kg, 0.085 mg/kg, 0.0875 mg/kg, 0.09 mg/kg, 0.0925 mg/kg, 0.095 mg/kg, 0.0975 mg/kg, 0.1 mg/kg, 0.125 mg/kg, 0.15 mg/kg, 0.175 mg/kg, 0.2 mg/kg, 0.225 mg/kg, 0.25 mg/kg, 0.275 mg/kg, 0.3 mg/kg, 0.325 mg/kg, 0.35 mg/kg, 0.375 mg/kg, 0.4 mg/kg, 0.425 mg/kg, 0.45 mg/kg, 0.475 mg/kg, or about 0.5 mg/kg. Values intermediate to the foregoing recited values are also intended to be part of this invention.


The dose of an RNAi agent that is administered to a subject may be tailored to balance the risks and benefits of a particular dose, for example, to achieve a desired level of TMPRSS6 gene suppression (as assessed, e.g., based on TMPRSS6 mRNA suppression, TMPRSS6 protein expression, or a reduction in lipid levels) or a desired therapeutic or prophylactic effect, while at the same time avoiding undesirable side effects.


In some embodiments, the RNAi agent is administered in two or more doses. If desired to facilitate repeated or frequent infusions, implantation of a delivery device, e.g, a pump, semi-permanent stent (e.g, intravenous, intraperitoneal, intracisternal or intracapsular), or reservoir may be advisable. In some embodiments, the number or amount of subsequent doses is dependent on the achievement of a desired effect, e.g., the suppression of a TMPRSS6 gene, or the achievement of a therapeutic or prophylactic effect, e.g., reducing iron overload. In some embodiments, the RNAi agent is administered according to a schedule. For example, the RNAi agent may be administered once per week, twice per week, three times per week, four times per week, or five times per week. In some embodiments, the schedule involves regularly spaced administrations, e.g, hourly, every four hours, every six hours, every eight hours, every twelve hours, daily, every 2 days, every 3 days, every 4 days, every 5 days, weekly, biweekly, or monthly. In other embodiments, the schedule involves closely spaced administrations followed by a longer period of time during which the agent is not administered. For example, the schedule may involve an initial set of doses that are administered in a relatively short period of time (e.g, about every 6 hours, about every 12 hours, about every 24 hours, about every 48 hours, or about every 72 hours) followed by a longer time period (e.g, about 1 week, about 2 weeks, about 3 weeks, about 4 weeks, about 5 weeks, about 6 weeks, about 7 weeks, or about 8 weeks) during which the RNAi agent is not administered. In one embodiment, the RNAi agent is initially administered hourly and is later administered at a longer interval (e.g, daily, weekly, biweekly, or monthly). In another embodiment, the RNAi agent is initially administered daily and is later administered at a longer interval (e.g, weekly, biweekly, or monthly). In certain embodiments, the longer interval increases over time or is determined based on the achievement of a desired effect. In a specific embodiment, the RNAi agent is administered once daily during a first week, followed by weekly dosing starting on the eighth day of administration. In another specific embodiment, the RNAi agent is administered every other day during a first week followed by weekly dosing starting on the eighth day of administration.


In some embodiments, the RNAi agent is administered in a dosing regimen that includes a “loading phase” of closely spaced administrations that may be followed by a “maintenance phase”, in which the RNAi agent is administered at longer spaced intervals. In one embodiment, the loading phase comprises five daily administrations of the RNAi agent during the first week.


In another embodiment, the maintenance phase comprises one or two weekly administrations of the RNAi agent. In a further embodiment, the maintenance phase lasts for 5 weeks.


Any of these schedules may optionally be repeated for one or more iterations. The number of iterations may depend on the achievement of a desired effect, e.g, the suppression of a TMPRSS6 gene, and/or the achievement of a therapeutic or prophylactic effect, e.g, reducing iron levels or reducing a symptom of thalassemia, e.g, β-thalassemia, or hemotochromatosis.


In another aspect, the invention features, a method of instructing an end user, e.g., a caregiver or a subject, on how to administer an iRNA agent described herein. The method includes, optionally, providing the end user with one or more doses of the iRNA agent, and instructing the end user to administer the iRNA agent on a regimen described herein, thereby instructing the end user.


VII. Kits

The present invention also provides kits for using any of the iRNA agents and/or performing any of the methods of the invention. Such kits include one or more RNAi agent(s) and instructions for use, e.g., instructions for inhibiting expression of a TMPRSS6 in a cell by contacting the cell with the RNAi agent(s) in an amount effective to inhibit expression of the TMPRSS6. The kits may optionally further comprise means for contacting the cell with the RNAi agent (e.g., an injection device), or means for measuring the inhibition of TMPRSS6 (e.g, means for measuring the inhibition of TMPRSS6 mRNA or TTR protein). Such means for measuring the inhibition of TMPRSS6 may comprise a means for obtaining a sample from a subject, such as, e.g, a plasma sample. The kits of the invention may optionally further comprise means for administering the RNAi agent(s) to a subject or means for determining the therapeutically effective or prophylactically effective amount.


Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the iRNAs and methods featured in the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.


EXAMPLES
Materials and Methods

The following materials and methods were used in the Examples.


cDNA Synthesis Using ABI High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, Calif., Cat #4368813)


A master mix of 2 μl 10× Buffer, 0.8 μl 25× dNTPs, 2 μl Random primers, 1 μl Reverse Transcriptase, 1 μl RNase inhibitor and 3.2 μl of H2O per reaction was added into 10 μl total RNA. cDNA was generated using a Bio-Rad C-1000 or S-1000 thermal cycler (Hercules, Calif.) through the following steps: 25° C. 10 min, 37° C. 120 min, 85° C. 5 sec, 4° C. hold.


Cell Culture and Transfections

Hep3B cells (ATCC, Manassas, Va.) were grown to near confluence at 37° C. in an atmosphere of 5% CO2 in EMEM (ATCC) supplemented with 10% FBS, streptomycin, and glutamine (ATCC) before being released from the plate by trypsinization. Transfection was carried out by adding 14.8 μl of Opti-MEM plus 0.2 μl of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad Calif. cat #13778-150) to 5 μl of siRNA duplexes per well into a 96-well plate and incubated at room temperature for 15 minutes. Subsequently, 80 μl of complete growth media without antibiotic containing ˜2×104 Hep3B cells were then added to the siRNA mixture. Cells were incubated for 24 hours prior to RNA purification. Single dose experiments were performed at 10 nM and 0.1 nM final duplex concentration.


Total RNA Isolation Using DYNABEADS mRNA Isolation Kit (Invitrogen, Part #; 610-12)


Cells were harvested and lysed in 150 μl of Lysis/Binding Buffer then mixed for 5 minute at 850 rpm using a platform shaker (the mixing speed was the same throughout the process). Ten microliters of magnetic beads and 80 μl Lysis/Binding Buffer mixture were added to a round bottom plate and mixed for 1 minute. Magnetic beads were captured using magnetic stand and the supernatant was removed without disturbing the beads. After the supernatant was removed, the lysed cells were added to the remaining beads and mixed for 5 minutes. After the supernatant was removed, magnetic beads were washed 2 times with 150 μl Wash Buffer A and mixed for 1 minute. Beads were capture again and supernatant removed. Beads were then washed with 150 μl Wash Buffer B, captured and supernatant was removed. Beads were next washed with 150 μl Elution Buffer, captured and supernatant removed. Beads were allowed to dry for 2 minutes. After drying, 50 μl of Elution Buffer was added and mixed for 5 minutes at 75° C. Beads were captured on magnet for 5 minutes, and 50 μl of supernatant containing the purified RNA was removed and added to a new 96 well plate.


Real Time PCR

Two μl of cDNA was added to a master mix containing 0.5 μl human GAPDH TaqMan Probe (Applied Biosystems Cat #4326317E), 0.5 μl human TMPRSS6 TaqMan probe (Applied Biosystems cat #Hs00542184_m1) and 5 μl Lightcycler 480 probe master mix (Roche Cat #04887301001) per well in a 384 well plate (Roche cat #04887301001). Real time PCR was performed in a Roche LC480 Real Time PCR system (Roche) using the ΔΔCt(RQ) assay. Each duplex was tested in two independent transfections and each transfection was assayed in duplicate, unless otherwise noted.


To calculate relative fold change, real time data were analyzed using the ΔΔCt method and normalized to assays performed with cells transfected with 10 nM AD-1955, or mock transfected cells.


The sense and antisense sequences of AD-1955 are:











(SEQ ID NO: 15)



SENSE 5′-cuuAcGcuGAGuAcuucGAdTsdT-3';







and







(SEQ ID NO: 16)



ANTISENSE: 5'-UCGAAGuACUcAGCGuAAGdTsdT-3′.













TABLE B







Abbreviations of nucleotide monomers used in nucleic


acid sequence representation.








Abbreviation
Nucleotide(s)





A
Adenosine-3′-phosphate


Ab
beta-L-adenosine-3′-phosphate


Af
2′-fluoroadenosine-3′-phosphate


Afs
2′-fluoroadenosine-3′-phosphorothioate


As
adenosine-3′-phosphorothioate


C
cytidine-3′-phosphate


Cb
beta-L-cytidine-3′-phosphate


Cf
2′-fluorocytidine-3′-phosphate


Cfs
2′-fluorocytidine-3′-phosphorothioate


Cs
cytidine-3′-phosphorothioate


G
guanosine-3′-phosphate


Gb
beta-L-guanosine-3′-phosphate


Gbs
beta-L-guanosine-3′-phosphorothioate


Gf
2′-fluoroguanosine-3′-phosphate


Gfs
2′-fluoroguanosine-3′-phosphorothioate


Gs
guanosine-3′-phosphorothioate


T
5′-methyluridine-3′-phosphate


Tf
2′-fluoro-5-methyluridine-3′-phosphate


Tfs
2′-fluoro-5-methyluridine-3′-phosphorothioate


Ts
5-methyluridine-3′-phosphorothioate


U
Uridine-3′-phosphate


Uf
2′-fluorouridine-3′-phosphate


Ufs
2′-fluorouridine-3′-phosphorothioate


Us
uridine-3′-phosphorothioate


N
any nucleotide (G, A, C, T or U)


a
2′-O-methyladenosine-3′-phosphate


as
2′-O-methyladenosine-3′-phosphorothioate


c
2′-O-methylcytidine-3′-phosphate


cs
2′-O-methylcytidine-3′-phosphorothioate


g
2′-O-methylguanosine-3′-phosphate


gs
2′-O-methylguanosine-3′-phosphorothioate


t
2′-O-methyl-5-methyluridine-3′-phosphate


ts
2′-O-methyl-5-methyluridine-3′-phosphorothioate


u
2′-O-methyluridine-3′-phosphate


us
2′-O-methyluridine-3′-phosphorothioate


dT
2′-deoxythymidine


dTs
2′-deoxythymidine-3′-phosphorothioate


dU
2′-deoxyuridine


s
phosphorothioate linkage


L96
N-[tris(GalNAc-alkyl)-amidodecanoyl)]-4-hydroxyprolinol



Hyp-(GalNAc-alkyl)3


(Aeo)
2′-O-methoxyethyladenosine-3′-phosphate


(Aeos)
2′-O-methoxyethyladenosine-3′-phosphorothioate


(Geo)
2′-O-methoxyethylguanosine-3′-phosphate


(Geos)
2′-O-methoxyethylguanosine-3′-phosphorothioate


(Teo)
2′-O-methoxyethyl-5-methyluridine-3′-phosphate


(Teos)
2′-O-methoxyethyl-5-methyluridine-3′-phosphorothioate


(m5Ceo)
2′-O-methoxyethyl-5-methylcytidine-3′-phosphate


(m5Ceos)
2′-O-methoxyethyl-5-methylcytidine-3′-phosphorothioate


(A3m)
3′-O-methyladenosine-2′-phosphate


(A3mx)
3′-O-methyl-xylofuranosyladenosine-2′-phosphate


(G3m)
3′-O-methylguanosine-2′-phosphate


(G3mx)
3′-O-methyl-xylofuranosylguanosine-2′-phosphate


(C3m)
3′-O-methylcytidine-2′-phosphate


(C3mx)
3′-O-methyl-xylofuranosylcytidine-2′-phosphate


(U3m)
3′-O-methyluridine-2′-phosphate


(U3mx)
3′-O-methylxylouridine-2′-phosphate


(Chd)
2′-O-hexadecyl-cytidine-3′-phosphate


(pshe)
Hydroxyethylphosphorothioate


(Uhd)
2′-O-hexadecyl-uridine-3′-phosphate


(Tgn)
Thymidine-glycol nucleic acid (GNA) S-Isomer


(Cgn)
Cytidine-glycol nucleic acid (GNA)


(Chd)
2′-O-hexadecyl-cytidine-3′-phosphate


(Ggn)
2′-O-hexadecyl-cytidine-3′-phosphate


(Agn)
Adenosine-glycol nucleic acid (GNA)


P
5′-phosphate


(m5Cam)
2′-O-(N-methylacetamide)-5-methylcytidine-3′-phosphate


(m5Cams)
2′-O-(N-methylacetamide)-5-methylcytidine-3′-



phosphorothioate


(Tam)
2′-O-(N-methylacetamide)thymidine-3′-phosphate


(Tams)
2′-O-(N-methylacetamide)thymidine-3′-phosphorothioate


(Aam)
2′-O-(N-methylacetamide)adenosine-3′-phosphate


(Aams)
2′-O-(N-methylacetamide)adenosine-3′-phosphorothioate


(Gam)
2′-O-(N-methylacetamide)guanosine-3′-phosphate


(Gams)
2′-O-(N-methylacetamide)guanosine-3′-phosphorothioate


Y44
2-hydroxymethyl-tetrahydrofurane-5-phosphate









Example 1. Design, Specificity and Efficacy Prediction of Oligonucleotides
Transcripts

siRNA design was carried out to identify siRNAs targeting human, rhesus (Macaca mulatta), mouse, and rat TMPRSS6 transcripts annotated in the NCBI Gene database (http://www.ncbi.nlm.nih.gov/gene/). Design used the following transcripts from the NCBI RefSeq collection: Human—NM_153609.2; Rhesus—XM_001085203.2 and XM_001085319.1; Mouse—NM_027902.2; Rat—NM_001130556.1. Due to high primate/rodent sequence divergence, siRNA duplexes were designed in several separate batches, including but not limited to batches containing duplexes matching human and rhesus transcripts only; human, rhesus, and mouse transcripts only; human, rhesus, mouse, and rat transcripts only; and mouse and rat transcripts only. All siRNA duplexes were designed that shared 100% identity with the listed human transcript and other species transcripts considered in each design batch (above).


The specificity of all possible 19mers was predicted from each sequence. Candidate 19mers that lacked repeats longer than 7 nucleotides were then selected. These 1259 candidate human/rhesus, 91 human/rhesus/mouse, 37 human/rhesus/mouse/rat, and 810 mouse/rat siRNAs were used in comprehensive searches against the appropriate transcriptomes (defined as the set of NM_ and XM_records within the human, rhesus, mouse, or rat NCBI Refseq sets) using an exhaustive “brute-force” algorithm implemented in the python script ‘BruteForce.py’. The script next parsed the transcript-oligo alignments to generate a score based on the position and number of mismatches between the siRNA and any potential ‘off-target’ transcript. The off-target score is weighted to emphasize differences in the ‘seed’ region of siRNAs, in positions 2-9 from the 5′ end of the molecule. Each oligo-transcript pair from the brute-force search was given a mismatch score by summing the individual mismatch scores; mismatches in the position 2-9 were counted as 2.8, mismatches in the cleavage site positions 10-11 were counted as 1.2, and mismatches in region 12-19 counted as 1.0. An additional off-target prediction was carried out by comparing the frequency of heptamers and octomers derived from 3 distinct, seed-derived hexamers of each oligo. The hexamers from positions 2-7 relative to the 5′ start were used to create 2 heptamers and one octomer. Heptamerl was created by adding a 3′ A to the hexamer; heptamer2 was created by adding a 5′ A to the hexamer; the octomer was created by adding an A to both 5′ and 3′ ends of the hexamer. The frequency of octomers and heptamers in the human, rhesus, mouse, or rat 3′UTRome (defined as the subsequence of the transcriptome from NCBI's Refseq database where the end of the coding region, the ‘CDS’, is clearly defined) was pre-calculated. The octomer frequency was normalized to the heptamer frequency using the median value from the range of octomer frequencies. A ‘mirSeedScore’ was then calculated by calculating the sum of ((3× normalized octomer count)+(2×heptamer2 count)+(1×heptamer1 count)).


Both siRNA strands were assigned to a category of specificity according to the calculated scores: a score above 3 qualified as highly specific, equal to 3 as specific and between 2.2 and 2.8 qualified as moderately specific. The siRNAs were sorted by the specificity of the antisense strand. Duplexes from the human/rhesus and mouse/rat sets whose antisense oligos lacked GC at the first position, lacked G at both positions 13 and 14, and had 3 or more Us or As in the seed region (characteristics of duplexes with high predicted efficacy) were then selected. Similarly, duplexes from the human/rhesus/mouse and human/rhesus/mouse/rat sets that had had 3 or more Us or As in the seed region were selected.


Candidate GalNAc-conjugated duplexes, 21 and 23 nucleotides long on the sense and antisense strands respectively, were designed by extending antisense 19mers 4 additional nucleotides in the 3′ direction (preserving perfect complementarity with the target transcript). The sense strand was specified as the reverse complement of the first 21 nucleotides of the antisense 23mer. Duplexes were selected that maintained perfect matches to all selected species transcripts across all 23 nucleotides.


siRNA Sequence Selection


A total of 39 sense and 39 antisense derived human/rhesus, 6 sense and 6 antisense derived human/rhesus/mouse, 3 sense and 3 antisense derived human/rhesus/mouse/rat, and 16 sense and 16 antisense derived mouse/rat siRNA 21/23mer oligos were synthesized and formed into GalNAc-conjugated duplexes.


The sequences of the sense and antisense strands of the modified duplexes are shown in Table 1, and the sequences of the sense and antisense strands of the unmodified duplexes are shown in Table 2.









TABLE 1







TMPRSS6 modified sequences














Sense

SEQ


SEQ


Duplex
sequence

ID
Antisense

ID


ID
ID
Sense sequence
NO:
sequence
Antisense sequence
NO:





AD-
A-119159.1
UfsgsGfcCfuGfgAfGfA
17
A-119160.1
usUfsgAfaGfgAfcAfcc
 65


58686.1

fgGfuGfuCfcUfuCfL96


uCfuCfcAfgGfcsCfsa






AD-
A-119175.1
GfsgsGfgUfgCfuAfCfU
18
A-119176.1
asGfsgAfaAfuAfcCfag
 66


58687.1

fcUfgGfuAfuUfuCfL96


aGfuAfgCfaCfcsCfsc






AD-
A-119191.1
CfsasAfcGfgCfcUfGfG
19
A-119192.1
asGfsuUfuCfuCfuCfau
 67


58688.1

faUfgAfgAfgAfaAfL96


cCfaGfgCfcGfusUfsg






AD-
A-119207.1
AfsusCfgCfcAfcUfUfC
20
A-119208.1
asAfsgAfuCfcUfgGfga
 68


58689.1

fuCfcCfaGfgAfuCfL96


gAfaGfuGfgCfgsAfsu






AD-
A-119223.1
GfsgsUfgGfcAfgGfAfG
21
A-119224.1
asCfsaAfgAfuGfcCfac
 69


58690.1

fgUfgGfcAfuCfuUfL96


cUfcCfuGfcCfasCfsc






AD-
A-119161.1
GfsasCfcGfaCfuGfGfC
22
A-119162.1
asCfsgUfcAfuAfcAfug
 70


58692.1

fcAfuGfuAfuGfaCfL96


gCfcAfgUfcGfgsUfsc






AD-
A-119177.1
GfsgsUfgUfgCfgGfGfU
23
A-119178.1
asAfsgCfcAfuAfgUfgc
 71


58693.1

fgCfaCfuAfuGfgCfL96


aCfcCfgCfaCfasCfsc






AD-
A-119193.1
GfsgsCfcUfgGfaUfGfA
24
A-119194.1
asCfsgCfaGfuUfuCfuc
 72


58694.1

fgAfgAfaAfcUfgCfL96


uCfaUfcCfaGfgsCfsc






AD-
A-119209.1
CfsusCfuGfgUfaUfUfU
25
A-119210.1
usUfsgUfaCfcCfuAfgg
 73


58695.1

fcCfuAfgGfgUfaCfL96


aAfaUfaCfcAfgsAfsg






AD-
A-119225.1
GfscsCfcCfuGfgUfCfU
26
A-119226.1
asGfsaUfcCfcAfaGfuu
 74


58696.1

faAfcUfuGfgGfaUfL96


aGfaCfcAfgGfgsGfsc






AD-
A-119163.1
GfsasGfgCfaGfaAfGfU
27
A-119164.1
asCfsgGfcAfaAfuCfau
 75


58698.1

faUfgAfuUfuGfcCfL96


aCfuUfcUfgCfcsUfsc






AD-
A-119179.1
AfsasGfcCfaGfuGfUfG
28
A-119180.1
asGfscUfaUfgUfcUfuu
 76


58699.1

faAfaGfaCfaUfaGfL96


cAfcAfcUfgGfcsUfsu






AD-
A-119195.1
GfscsCfgGfgAfcCfGfA
29
A-119196.1
asUfsaCfaUfgGfcCfag
 77


58700.1

fcUfgGfcCfaUfgUfL96


uCfgGfuCfcCfgsGfsc






AD-
A-119211.1
CfsusCfcAfgGfuUfCfG
30
A-119212.1
asUfsgUfgUfcGfaCfcc
 78


58701.1

fgGfgUfcGfaCfaCfL96


cGfaAfcCfuGfgsAfsg






AD-
A-119227.1
AfsgsCfcCfcUfgGfUfC
31
A-119228.1
gsAfsuCfcCfaAfgUfua
 79


58702.1

fuAfaCfuUfgGfgAfL96


gAfcCfaGfgGfgsCfsu






AD-
A-119165.1
UfscsGfcCfaCfuUfCfU
32
A-119166.1
usAfsaGfaUfcCfuGfgg
 80


58704.1

fcCfcAfgGfaUfcUfL96


aGfaAfgUfgGfcsGfsa






AD-
A-119181.1
AfscsUfcUfgGfuAfUfU
33
A-119182.1
usGfsuAfcCfcUfaGfga
 81


58705.1

fuCfcUfaGfgGfuAfL96


aAfuAfcCfaGfasGfsu






AD-
A-119197.1
UfscsGfcUfgAfcCfGfC
34
A-119198.1
usGfsuUfaUfcAfcCfca
 82


58706.1

fuGfgGfuGfaUfaAfL96


gCfgGfuCfaGfcsGfsa






AD-
A-119213.1
GfscsCfcCfaAfcGfGfC
35
A-119214.1
usCfsuCfuCfaUfcCfag
 83


58707.1

fcUfgGfaUfgAfgAfL96


gCfcGfuUfgGfgsGfsc






AD-
A-119229.1
GfscsCfaAfgCfaGfGfG
36
A-119230.1
gsAfsaUfaCfuUfgUfcc
 84


58708.1

fgGfaCfaAfgUfaUfL96


cCfcUfgCfuUfgsGfsc






AD-
A-119167.1
UfscsCfcCfuAfcAfGfG
37
A-119168.1
usUfscGfuAfcUfcGfgc
 85


58710.1

fgCfcGfaGfuAfcGfL96


cCfuGfuAfgGfgsGfsa






AD-
A-119183.1
CfsusGfgGfuUfgUfUfA
38
A-119184.1
usAfsgCfuGfuAfgCfgg
 86


58711.1

fcCfgCfuAfcAfgCfL96


uAfaCfaAfcCfcsAfsg






AD-
A-119199.1
CfsusGfgCfcUfgGfAfG
39
A-119200.1
usGfsaAfgGfaCfaCfcu
 87


58712.1

faGfgUfgUfcCfuUfL96


cUfcCfaGfgCfcsAfsg






AD-
A-119215.1
GfsusGfcGfgGfuGfCfA
40
A-119216.1
usAfscAfaGfcCfaUfag
 88


58713.1

fcUfaUfgGfcUfuGfL96


uGfcAfcCfcGfcsAfsc






AD-
A-119231.1
UfsgsGfcAfgGfaGfGfU
41
A-119232.1
asGfsaCfaAfgAfuGfcc
 89


58714.1

fgGfcAfuCfuUfgUfL96


aCfcUfcCfuGfcsCfsa






AD-
A-119169.1
CfscsCfuAfcAfgGfGfC
42
A-119170.1
asCfsuUfcGfuAfcUfcg
 90


58716.1

fcGfaGfuAfcGfaAfL96


gCfcCfuGfuAfgsGfsg






AD-
A-119185.1
AfscsCfuGfcUfuCfUfU
43
A-119186.1
asGfsaAfuGfaAfcCfag
 91


58717.1

fcUfgGfuUfcAfuUfL96


aAfgAfaGfcAfgsGfsu






AD-
A-119201.1
UfsgsCfcUfgUfgAfUfG
44
A-119202.1
asGfsuCfcUfuGfaCfcc
 92


58718.1

fgGfgUfcAfaGfgAfL96


cAfuCfaCfaGfgsCfsa






AD-
A-119217.1
CfsasGfcUfuCfgGfAfA
45
A-119218.1
usAfsgAfcCfaGfgGfgc
 93


58719.1

fgCfcCfcUfgGfuCfL96


uUfcCfgAfaGfcsUfsg






AD-
A-119233.1
CfscsCfcUfgGfuCfUfA
46
A-119234.1
csAfsgAfuCfcCfaAfgu
 94


58720.1

faCfuUfgGfgAfuCfL96


uAfgAfcCfaGfgsGfsg






AD-
A-119171.1
UfsgsCfuUfcUfuCfUfG
47
A-119172.1
usGfsgAfgAfaUfgAfac
 95


58721.1

fgUfuCfaUfuCfuCfL96


cAfgAfaGfaAfgsCfsa






AD-
A-119187.1
CfscsCfaAfcGfgCfCfU
48
A-119188.1
usUfsuCfuCfuCfaUfcc
 96


58722.1

fgGfaUfgAfgAfgAfL96


aGfgCfcGfuUfgsGfsg






AD-
A-119203.1
AfsasGfgGfcCfuGfCfA
49
A-119204.1
usCfsgUfaGfuAfgCfug
 97


58723.1

fcAfgCfuAfcUfaCfL96


uGfcAfgGfcCfcsUfsu






AD-
A-119219.1
GfsusCfuAfaCfuUfGfG
50
A-119220.1
csAfsuUfcCfcAfgAfuc
 98


58724.1

fgAfuCfuGfgGfaAfL96


cCfaAfgUfuAfgsAfsc






AD-
A-119235.1
AfsgsCfuUfcGfgAfAfG
51
A-119236.1
usUfsaGfaCfcAfgGfgg
 99


58725.1

fcCfcCfuGfgUfcUfL96


cUfuCfcGfaAfgsCfsu






AD-
A-119173.1
CfscsAfgUfgUfgAfAfA
52
A-119174.1
usGfscAfgCfuAfuGfuc
100


58726.1

fgAfcAfuAfgCfuGfL96


uUfuCfaCfaCfusGfsg






AD-
A-119189.1
CfscsAfgGfuUfcGfGfG
53
A-119190.1
asGfsaUfgUfgUfcGfac
101


58727.1

fgUfcGfaCfaCfaUfL96


cCfcGfaAfcCfusGfsg






AD-
A-119205.1
UfscsCfaCfgCfuGfGfG
54
A-119206.1
usAfsgCfgGfuAfaCfaa
102


58728.1

fuUfgUfuAfcCfgCfL96


cCfcAfgCfgUfgsGfsa






AD-
A-119221.1
UfsgsCfcAfaGfcAfGfG
55
A-119222.1
asAfsuAfcUfuGfuCfcc
103


58729.1

fgGfgAfcAfaGfuAfL96


cCfuGfcUfuGfgsCfsa






AD-
A-119241.1
AfsusCfcAfgAfaCfAfG
56
A-119242.1
csCfsaCfaCfaGfcCfuc
104


58697.1

fgAfgGfcUfgUfgUfL96


cUfgUfuCfuGfgsAfsu






AD-
A-119243.1
UfsusCfaCfcUfcCfCfA
57
A-119244.1
gsUfsgAfgGfgAfgAfuc
105


58703.1

fgAfuCfuCfcCfuCfL96


uGfgGfaGfgUfgsAfsa






AD-
A-119245.1
CfscsUfcCfgAfgGfGfU
58
A-119246.1
csCfsaUfgGfcCfaCfuc
106


58709.1

fgAfgUfgGfcCfaUfL96


aCfcCfuCfgGfasGfsg






AD-
A-119247.1
UfscsCfaGfaAfcAfGfG
59
A-119248.1
gsCfscAfcAfcAfgCfcu
107


58715.1

faGfgCfuGfuGfuGfL96


cCfuGfuUfcUfgsGfsa






AD-
A-119237.1
GfsusGfuCfcUfcCfGfA
60
A-119238.1
gsGfscCfaCfuCfaCfcc
108


58730.1

fgGfgUfgAfgUfgGfL96


uCfgGfaGfgAfcsAfsc






AD-
A-119249.1
UfsusCfgGfgGfuCfGfA
61
A-119250.1
csCfscAfcAfgAfuGfug
109


58731.1

fcAfcAfuCfuGfuGfL96


uCfgAfcCfcCfgsAfsa






AD-
A-119251.1
UfscsGfgGfgUfcGfAfC
62
A-119252.1
csCfscCfaCfaGfaUfgu
110


58734.1

faCfaUfcUfgUfgGfL96


gUfcGfaCfcCfcsGfsa






AD-
A-119253.1
UfsgsCfuUfcCfaGfGfA
63
A-119254.1
gsCfscAfuGfcUfgUfcc
111


58737.1

fgGfaCfaGfcAfuGfL96


uCfcUfgGfaAfgsCfsa






AD-
A-120243.1
UfscsUfgGfuAfuUfUfC
64
A-120244.1
usGfsuAfcCfcUfaGfga
112


59743.1

fcUfaGfgGfuAfcAfL96


aAfuAfcCfaGfasgsu
















TABLE 2







TMPRSS6 unmodified sequences
















Sense

SEQ
Position
Anti-

SEQ
Position


Duplex
sequence
Sense 
ID
in NM_
sense

ID
in NM_


ID
ID
sequence
NO:
153609.2
sequence
Antisense sequence
NO:
153609.2





AD-
A-
UGGCCUGGAGA
113
2041-2063
A-
UUGAAGGACACCUCUCCAGGCCA
161
2041-2063


58686.1
119159.1
GGUGUCCUUC


119160.1








AD-
A-
GGGGUGCUACU
114
319-341
A-
AGGAAAUACCAGAGUAGCACCCC
162
319-341


58687.1
119175.1
CUGGUAUUUC


119176.1








AD-
A-
CAACGGCCUGG
115
1557-1579
A-
AGUUUCUCUCAUCCAGGCCGUUG
163
1557-1579


58688.1
119191.1
AUGAGAGAAA


119192.1








AD-
A-
AUCGCCACUUC
116
401-423
A-
AAGAUCCUGGGAGAAGUGGCGAU
164
401-423


58689.1
119207.1
UCCCAGGAUC


119208.1








AD-
A-
GGUGGCAGGAG
117
2665-2688
A-
ACAAGAUGCCACCUCCUGCCACC
165
2665-2688


58690.1
119223.1
GUGGCAUCUU


119224.1








AD-
A-
GACCGACUGGC
118
922-944
A-
ACGUCAUACAUGGCCAGUCGGUC
166
922-944


58692.1
119161.1
CAUGUAUGAC


119162.1








AD-
A-
GGUGUGCGGGU
119
1444-1466
A-
AAGCCAUAGUGCACCCGCACACC
167
1444-1466


58693.1
119177.1
GCACUAUGGC


119178.1








AD-
A-
GGCCUGGAUGA
120
1561-1583
A-
ACGCAGUUUCUCUCAUCCAGGCC
168
1561-1583


58694.1
119193.1
GAGAAACUGC


119194.1








AD-
A-
CUCUGGUAUUU
121
328-350
A-
UUGUACCCUAGGAAAUACCAGAG
169
328-350


58695.1
119209.1
CCUAGGGUAC


119210.1








AD-
A-
GCCCCUGGUCU
122
2966-2989
A-
AGAUCCCAAGUUAGACCAGGGGC
170
2966-2989


58696.1
119225.1
AACUUGGGAU


119226.1








AD-
A-
GAGGCAGAAGU
123
1281-1303
A-
ACGGCAAAUCAUACUUCUGCCUC
171
1281-1303


58698.1
119163.1
AUGAUUUGCC


119164.1








AD-
A-
AAGCCAGUGUG
124
731-753
A-
AGCUAUGUCUUUCACACUGGCUU
172
731-753


58699.1
119179.1
AAAGACAUAG


119180.1








AD-
A-
GCCGGGACCGA
125
917-939
A-
AUACAUGGCCAGUCGGUCCCGGC
173
917-939


58700.1
119195.1
CUGGCCAUGU


119196.1








AD-
A-
CUCCAGGUUCG
126
1894-1916
A-
AUGUGUCGACCCCGAACCUGGAG
174
1894-1916


58701.1
119211.1
GGGUCGACAC


119212.1








AD-
A-
AGCCCCUGGUC
127
2965-2988
A-
GAUCCCAAGUUAGACCAGGGGCU
175
2965-2988


58702.1
119227.1
UAACUUGGGA


119228.1








AD-
A-
UCGCCACUUCU
128
402-424
A-
UAAGAUCCUGGGAGAAGUGGCGA
176
402-424


58704.1
119165.1
CCCAGGAUCU


119166.1








AD-
A-
ACUCUGGUAUU
129
327-349
A-
UGUACCCUAGGAAAUACCAGAGU
177
327-349


58705.1
119181.1
UCCUAGGGUA


119182.1








AD-
A-
UCGCUGACCGC
130
1934-1956
A-
UGUUAUCACCCAGCGGUCAGCGA
178
1934-1956


58706.1
119197.1
UGGGUGAUAA


119198.1








AD-
A-
GCCCCAACGGC
131
1553-1575
A-
UCUCUCAUCCAGGCCGUUGGGGC
179
1553-1575


58707.1
119213.1
CUGGAUGAGA


119214.1








AD-
A-
GCCAAGCAGGG
132
2610-2633
A-
GAAUACUUGUCCCCCUGCUUGGC
180
2610-2633


58708.1
119229.1
GGACAAGUAU


119230.1








AD-
A-
UCCCCUACAGG
133
680-702
A-
UUCGUACUCGGCCCUGUAGGGGA
181
680-702


58710.1
119167.1
GCCGAGUACG


119168.1








AD-
A-
CUGGGUUGUUA
134
769-791
A-
UAGCUGUAGCGGUAACAACCCAG
182
769-791


58711.1
119183.1
CCGCUACAGC


119184.1








AD-
A-
CUGGCCUGGAG
135
2040-2062
A-
UGAAGGACACCUCUCCAGGCCAG
183
2040-2062


58712.1
119199.1
AGGUGUCCUU


119200.1








AD-
A-
GUGCGGGUGCA
136
1447-1469
A-
UACAAGCCAUAGUGCACCCGCAC
184
1447-1469


58713.1
119215.1
CUAUGGCUUG


119216.1








AD-
A-
UGGCAGGAGGU
137
2667-2690
A-
AGACAAGAUGCCACCUCCUGCCA
185
2667-2690


58714.1
119231.1
GGCAUCUUGU


119232.1








AD-
A-
CCCUACAGGGC
138
682-704
A-
ACUUCGUACUCGGCCCUGUAGGG
186
682-704


58716.1
119169.1
CGAGUACGAA


119170.1








AD-
A-
ACCUGCUUCUU
139
559-581
A-
AGAAUGAACCAGAAGAAGCAGGU
187
559-581


58717.1
119185.1
CUGGUUCAUU


119186.1








AD-
A-
UGCCUGUGAUG
140
1530-1552
A-
AGUCCUUGACCCCAUCACAGGCA
188
1530-1552


58718.1
119201.1
GGGUCAAGGA


119202.1








AD-
A-
CAGCUUCGGAA
141
2955-2978
A-
UAGACCAGGGGCUUCCGAAGCUG
189
2955-2978


58719.1
119217.1
GCCCCUGGUC


119218.1








AD-
A-
CCCCUGGUCUA
142
2967-2990
A-
CAGAUCCCAAGUUAGACCAGGGG
190
2967-2990


58720.1
119233.1
ACUUGGGAUC


119234.1








AD-
A-
UGCUUCUUCUG
143
562-584
A-
UGGAGAAUGAACCAGAAGAAGCA
191
562-584


58721.1
119171.1
GUUCAUUCUC


119172.1








AD-
A-
CCCAACGGCCU
144
1555-1577
A-
UUUCUCUCAUCCAGGCCGUUGGG
192
1555-1577


58722.1
119187.1
GGAUGAGAGA


119188.1








AD-
A-
AAGGGCCUGCA
145
1054-1076
A-
UCGUAGUAGCUGUGCAGGCCCUU
193
1054-1076


58723.1
119203.1
CAGCUACUAC


119204.1








AD-
A-
GUCUAACUUGG
146
2973-2996
A-
CAUUCCCAGAUCCCAAGUUAGAC
194
2973-2996


58724.1
119219.1
GAUCUGGGAA


119220.1








AD-
A-
AGCUUCGGAAG
147
2956-2979
A-
UUAGACCAGGGGCUUCCGAAGCU
195
2956-2979


58725.1
119235.1
CCCCUGGUCU


119236.1








AD-
A-
CCAGUGUGAAA
148
734-756
A-
UGCAGCUAUGUCUUUCACACUGG
196
734-756


58726.1
119173.1
GACAUAGCUG


119174.1








AD-
A-
CCAGGUUCGGG
149
1896-1918
A-
AGAUGUGUCGACCCCGAACCUGG
197
1896-1918


58727.1
119189.1
GUCGACACAU


119190.1








AD-
A-
UCCACGCUGGG
150
763-785
A-
UAGCGGUAACAACCCAGCGUGGA
198
763-785


58728.1
119205.1
UUGUUACCGC


119206.1








AD-
A-
UGCCAAGCAGG
151
2609-2632
A-
AAUACUUGUCCCCCUGCUUGGCA
199
2609-2632


58729.1
119221.1
GGGACAAGUA


119222.1








AD-
A-
AUCCAGAACAG
152
1324-1346
A-
CCACACAGCCUCCUGUUCUGGAU
200
1324-1346


58697.1
119241.1
GAGGCUGUGU


119242.1








AD-
A-
UUCACCUCCCA
153
1414-1436
A-
GUGAGGGAGAUCUGGGAGGUGAA
201
1414-1436


58703.1
119243.1
GAUCUCCCUC


119244.1








AD-
A-
CCUCCGAGGGU
154
1862-1884
A-
CCAUGGCCACUCACCCUCGGAGG
202
1862-1884


58709.1
119245.1
GAGUGGCCAU


119246.1








AD-
A-
UCCAGAACAGG
155
1325-1347
A-
GCCACACAGCCUCCUGUUCUGGA
203
1325-1347


58715.1
119247.1
AGGCUGUGUG


119248.1








AD-
A-
GUGUCCUCCGA
156
1858-1880
A-
GGCCACUCACCCUCGGAGGACAC
204
1858-1880


58730.1
119237.1
GGGUGAGUGG


119238.1








AD-
A-
UUCGGGGUCGA
157
1901-1923
A-
CCCACAGAUGUGUCGACCCCGAA
205
1901-1923


58731.1
119249.1
CACAUCUGUG


119250.1








AD-
A-
UCGGGGUCGAC
158
1902-1924
A-
CCCCACAGAUGUGUCGACCCCGA
206
1902-1924


58734.1
119251.1
ACAUCUGUGG


119252.1








AD-
A-
UGCUUCCAGGA
159
1966-1988
A-
GCCAUGCUGUCCUCCUGGAAGCA
207
1966-1988


58737.1
119253.1
GGACAGCAUG


119254.1








AD-
A-
UCUGGUAUUUC
160

A-
UGUACCCUAGGAAAUACCAGAGU
208



59743.1
120243.1
CUAGGGUACA


120244.1









Example 2. In Vitro Single Dose Screen

The modified and conjugated TMPRSS6 siRNA duplexes were also evaluated for efficacy by transfection assays in human cell line Hep3B. TMPRSS6 siRNAs were transfected at two doses, 10 nM and 0.1 nM. The results of these assays are shown in Table 3 and the data are expressed as a fraction of the message remaining in cells transfected with siRNAs targeting TMPRSS6, relative to cells transfected with a negative control siRNA, AD-1955±the standard deviation (SD).









TABLE 3







TMPRSS6 single dose screen.











Duplex ID
Avg 10 nM
SD 10 nM
Avg 0.1 nM
SD 0.1 nM














AD-58686.1
71.58
18.94
103.29
32.00


AD-58687.1
89.33
13.14
104.94
20.06


AD-58688.1
34.16
11.36
87.18
8.43


AD-58689.1
79.82
7.28
110.37
6.08


AD-58690.1
69.10
9.83
99.92
24.84


AD-58692.1
79.21
5.67
136.49
0.84


AD-58693.1
77.29
12.12
106.01
17.97


AD-58694.1
50.51
10.36
89.47
3.84


AD-58695.1
54.37
5.75
87.66
13.59


AD-58696.1
93.26
0.06
84.79
3.84


AD-58697.1
72.95
23.41
98.98
10.29


AD-58698.1
42.61
7.81
109.98
16.78


AD-58699.1
24.93
8.58
79.71
12.55


AD-58700.1
74.10
15.37
89.75
7.80


AD-58701.1
79.18
8.18
89.70
9.98


AD-58702.1
96.43
18.38
113.05
10.65


AD-58703.1
79.15
28.50
97.30
6.79


AD-58704.1
67.92
0.87
92.26
1.24


AD-58705.1
59.50
20.47
99.25
3.28


AD-58706.1
71.67
0.75
102.38
14.88


AD-58707.1
77.89
22.26
97.52
1.31


AD-58708.1
73.87
9.61
98.38
1.81


AD-58709.1
94.62
4.69
100.73
16.10


AD-58710.1
59.19
10.57
95.23
11.99


AD-58711.1
63.62
16.83
103.11
3.66


AD-58712.1
65.79
6.96
81.58
1.50


AD-58713.1
84.14
26.41
101.56
5.60


AD-58714.1
64.73
6.06
102.37
1.63


AD-58715.1
91.05
18.67
101.08
11.00


AD-58716.1
70.07
13.02
97.20
2.98


AD-58717.1
11.27
6.91
66.56
4.32


AD-58718.1
62.10
18.62
89.01
15.30


AD-58719.1
72.94
18.26
91.58
9.97


AD-58720.1
60.51
14.43
90.92
5.68


AD-58721.1
17.72
7.70
56.72
2.57


AD-58722.1
51.65
11.33
81.44
0.50


AD-58723.1
53.27
21.60
94.25
16.20


AD-58724.1
58.03
49.89
77.11
4.63


AD-58725.1
54.58
40.10
76.12
1.59


AD-58726.1
10.33
9.88
42.75
7.97


AD-58727.1
62.80
26.45
83.23
13.10


AD-58728.1
49.36
36.27
83.30
1.74


AD-58729.1
43.83
61.99
73.54
19.33


AD-58730.1
59.60
41.85
76.12
1.03


AD-58731.1
85.29
24.78
128.06
32.14


AD-58734.1
85.71
10.74
101.75
6.11


AD-58737.1
79.87
10.59
114.89
7.46









Example 3. In Vivo Single Dose Screen Using AD-59743

The ability of AD-59743 to suppress expression of TMPRSS6 protein was assessed by measuring levels of TMPRSS6 and hepcidin mRNA in the liver of wild-type C57BL/6 mice following administration of AD-59743. A single dose of 1, 3 or 10 mg/kg of AD-59743 was administered subcutaneously, and the mice were sacrificed on day 3 or day 7. Levels of TMPRSS6 and hepcidin mRNA in the liver were measured by qPCR using the methods described above. A control group received injections with PBS.


The levels of TMPRSS6 mRNA following administration of AD-59743 are shown in FIG. 1, and the levels of hepcidin mRNA following administration of AD-59743 are shown in FIG. 2. The results demonstrate a dose-dependent decrease in the levels of TMPRSS6 transcripts that is sustained through day 7.


Example 4. In Vivo Effect of TMPRSS6 iRNA Agents in Combination with an Iron Chelator

The purpose of this study was to test the effect of co-administered TMPRSS6 specific siRNA and iron chelators on iron levels. In the study, 6-week old wild-type C57BL/6 and thalassemic Th3/+ mice (Douet et al., Am. J. Pathol. (2011), 178(2):774-83) were fed low-iron diets containing 3-5 ppm iron. The mice were administered intravevously the formulation AF-011-46273 containing deferiprone, an iron chelator at a dose of 250 mg/kg/day and an iRNA agent with the following structure: oligoSeq-sense—uGGuAuuuccuAGGGuAcAdTsdT (SEQ ID NO: 209); oligoSeq-antisense—UGuACCCuAGGAAAuACcAdTsdT (SEQ ID NO: 210). The formulation also contained MC-3/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5. Liver and spleen tissues were collected and tissue nonheme iron concentrations were determined as described previously (see, e.g., Schmidt et al. (2013) Blood 121(7):1200-8; Cook, J D, et al. Tissue iron stores. In: Cook J D, editor. Methods in Hematology. Vol 1. New York, N.Y.: Churchill Livingstone Press; 1980. p. 104-109).


The results of these experiments demonstrate an additive effect of AD-46273 and deferiprone in Th3/+ mice, with the decreased iron levels relative to the negative controls.


Example 5. Design, Specificity and Efficacy Prediction of Oligonucleotides
Transcripts

siRNA design was carried out to identify siRNAs targeting human, cynomolgus monkey (Macacafascicularis; henceforth “cyno”), mouse, and rat TMPRSS6 transcripts annotated in the NCBI Gene database (http://www.ncbi.nlm.nih.gov/gene/). Design used the following transcripts from the NCBI RefSeq collection: Human—NM_153609.2; Mouse—NM_027902.2; Rat—NM_001130556.1. For cyno, a transcript sequence was obtained via alignment with human TMPRSS6 of sequence assembled from two accessions: “ENSP00000384964 [mRNA] locus=chr10:82446450:82485403:-” and FR874253.1, available from the M. fascicularis genome project and NCBI Nucleotide databases, respectively (http://macaque.genomics.org.cn/page/species/download.jsp and http://www.ncbi.nlm.nih.gov/nucleotide/). Due to high primate/rodent sequence divergence, siRNA duplexes were designed in several separate batches, including but not limited to batches containing duplexes matching human and cyno transcripts only; human, cyno, and mouse transcripts only; and human, cyno, mouse, and rat transcripts only. Most siRNA duplexes were designed that shared 100% identity in the designated region with the listed human transcript and other species transcripts considered in each design batch (above). In some instances, mismatches between duplex and mRNA target were allowed at the first antisense (last sense) position when the antisense strand:target mRNA complementary basepair was a GC or CG pair. In these cases, duplexes were designed with UA or AU pairs at the first anti sense:last sense pair. Thus the duplexes maintained complementarity but were mismatched with respect to target (U:C, U:G, A:C, or A:G).


The specificity of all possible 19mers was predicted from each sequence. Candidate 19mers that lacked repeats longer than 7 nucleotides were then selected. These 1128 candidate human/cyno, 69 human/cyno/mouse, and 23 human/cyno/mouse/rat siRNAs were used in comprehensive searches against the appropriate transcriptomes (defined as the set of NM_and XM_records within the human, mouse, or rat NCBI Refseq sets, and the cyno transcriptome set in NCBI nucleotide) using an exhaustive “brute-force” algorithm implemented in the python script ‘BruteForce.py’. The script next parsed the transcript-oligo alignments to generate a score based on the position and number of mismatches between the siRNA and any potential ‘off-target’ transcript. The off-target score is weighted to emphasize differences in the ‘seed’ region of siRNAs, in positions 2-9 from the 5′ end of the molecule. Each oligo-transcript pair from the brute-force search was given a mismatch score by summing the individual mismatch scores; mismatches in the position 2-9 were counted as 2.8, mismatches in the cleavage site positions 10-11 were counted as 1.2, and mismatches in region 12-19 counted as 1.0. An additional off-target prediction was carried out by comparing the frequency of heptamers and octomers derived from 3 distinct, seed-derived hexamers of each oligo. The hexamers from positions 2-7 relative to the 5′ start were used to create 2 heptamers and one octomer. Heptamerl was created by adding a 3′ A to the hexamer; heptamer2 was created by adding a 5′ A to the hexamer; the octomer was created by adding an A to both 5′ and 3′ ends of the hexamer. The frequency of octomers and heptamers in the human, cyno, mouse, or rat 3′UTRome (defined as the subsequence of the transcriptome from NCBI's Refseq database where the end of the coding region, the ‘CDS’, is clearly defined) was pre-calculated. The octomer frequency was normalized to the heptamer frequency using the median value from the range of octomer frequencies. A ‘mirSeedScore’ was then calculated by calculating the sum of ((3×normalized octomer count)+(2×heptamer2 count)+(1×heptamer1 count)).


Both siRNAs strands were assigned to a category of specificity according to the calculated scores: a score above 3 qualifies as highly specific, equal to 3 as specific and between 2 and 2.8 as moderately specific. We sorted by the specificity of the antisense strand. We then selected moderately (or higher) specific duplexes whose antisense oligos possessed characteristics of duplexes with high predicted efficacy, including maximal UA content in the seed region and low overall GC content.


For GalNaC-conjugated duplexes, sense 21mer and antisense 23mer oligos were designed by extending antisense 19mers (described above) to 23 nucleotides of target-complementary sequence. All species transcripts included in the design batch were checked for complementarity. For each duplex, the sense 21mer was specified as the reverse complement of the first 21 nucleotides of the antisense strand.


siRNA Sequence Selection


A total of 5 sense and 5 antisense human, 32 sense and 32 antisense derived human/cyno, 4 sense and 4 antisense derived human/cyno/mouse, 8 sense and 8 antisense derived human/cyno/mouse/rat, 19 sense and 19 antisense derived human/cyno/rat, 2 sense and 2 antisense derived human/mouse, and 1 sense and 1 antisense derived human/mouse/rat siRNA 21/23mer oligos were synthesized and formed into GalNAc-conjugated duplexes.


The sequences of the sense and antisense strands of the unmodified duplexes are shown in Table 4, and the sequences of the sense and antisense strands of the modified duplexes are shown in Table 5.









TABLE 4







TMPRSS6-unmodified seqeunces





















Position



Sense

SEQ
Antisense

SEQ
in



sequence
Sense
ID
sequence

ID
NM_


Duplex ID
ID
sequence
NO:
ID
Antisense sequence
NO:
153609.2





AD-60944.1
A-122732.1
GGUGCUACUCU
211
A-122733.1
AGGAAAUACCAGAGUAGCACCCC
280
 318




GGUAUUUCCU










AD-59743.1
A-120243.1
UCUGGUAUUUC
212
A-120244.1
UGUACCCUAGGAAAUACCAGAGU
281
 326




CUAGGGUACA










AD-60940.1
A-122745.1
CUGGUAUUUCC
213
A-122746.1
UUGUACCCUAGGAAAUACCAGAG
282
 327




UAGGGUACAA










AD-61002.2
A-122838.1
UGGUAUUUCCU
214
A-122839.1
UUUGUACCCUAGGAAAUACCAGA
283
 328




AGGGUACAAA










AD-61000.1
A-122852.1
GGUAUUUCCUA
215
A-122853.1
UCUUGUACCCUAGGAAAUACCAG
284
 329




GGGUACAAGA










AD-46273.1
A-96908.1
UGGUAUUUCCU
216
A-96909.1
UGUACCCUAGGAAAUACCA
285
 330




AGGGUACA










AD-61003.1
A-122854.1
GUAUUUCCUAG
217
A-122855.1
UCCUUGUACCCUAGGAAAUACCA
286
 330




GGUACAAGGA










AD-60994.1
A-122848.1
AUUUCCUAGGG
218
A-122849.1
UCGCCUUGUACCCUAGGAAAUAC
287
 332




UACAAGGCGA










AD-60990.1
A-122830.1
UUUCCUAGGGU
219
A-122831.1
UCCGCCUUGUACCCUAGGAAAUA
288
 333




ACAAGGCGGA










AD-60956.1
A-122736.1
CGCCACUUCUC
220
A-122737.1
AAGAUCCUGGGAGAAGUGGCGAU
289
 400




CCAGGAUCUU










AD-60981.1
A-122757.1
GCCACUUCUCC
221
A-122758.1
UAAGAUCCUGGGAGAAGUGGCGA
290
 401




CAGGAUCUUA










AD-60953.1
A-122775.1
CUGCUUCUUCU
222
A-122776.1
AGAAUGAACCAGAAGAAGCAGGU
291
 558




GGUUCAUUCU










AD-60977.1
A-122783.1
CUUCUUCUGGU
223
A-122784.1
UGGAGAAUGAACCAGAAGAAGCA
292
 561




UCAUUCUCCA










AD-60964.1
A-119169.2
CCCUACAGGGC
224
A-122764.1
UUCGUACUCGGCCCUGUAGGGGA
293
 679




CGAGUACGAA










AD-60947.1
A-122773.1
CUACAGGGCCG
225
A-122774.1
ACUUCGUACUCGGCCCUGUAGGG
294
 681




AGUACGAAGU










AD-60957.1
A-122751.1
GCCAGUGUGAA
226
A-122752.1
AGCUAUGUCUUUCACACUGGCUU
295
 730




AGACAUAGCU










AD-60960.1
A-122792.1
AGUGUGAAAGA
227
A-122793.1
UGCAGCUAUGUCUUUCACACUGG
296
 733




CAUAGCUGCA










AD-60972.1
A-122796.1
CACGCUGGGUU
228
A-122797.1
UAGCGGUAACAACCCAGCGUGGA
297
 762




GUUACCGCUA










AD-60970.1
A-122765.1
GGGUUGUUACC
229
A-122766.1
UAGCUGUAGCGGUAACAACCCAG
298
 768




GCUACAGCUA










AD-60963.1
A-122753.1
CGGGACCGACU
230
A-122754.1
AUACAUGGCCAGUCGGUCCCGGC
299
 916




GGCCAUGUAU










AD-60968.1
A-122739.1
CCGACUGGCCA
231
A-122740.1
ACGUCAUACAUGGCCAGUCGGUC
300
 921




UGUAUGACGU










AD-60942.1
A-122786.1
GGGCCUGCACA
232
A-122787.1
UCGUAGUAGCUGUGCAGGCCCUU
301
1053




GCUACUACGA










AD-60951.1
A-122749.1
GGCAGAAGUAU
233
A-122750.1
ACGGCAAAUCAUACUUCUGCCUC
302
1280




GAUUUGCCGU










AD-60984.1
A-122800.1
CCAGAACAGGA
234
A-122801.1
CCACACAGCCUCCUGUUCUGGAU
303
1323




GGCUGUGUGG










AD-60955.1
A-122806.1
CAGAACAGGAG
235
A-122807.1
GCCACACAGCCUCCUGUUCUGGA
304
1324




GCUGUGUGGC










AD-60943.1
A-122802.1
CACCUCCCAGA
236
A-122803.1
GUGAGGGAGAUCUGGGAGGUGAA
305
1413




UCUCCCUCAC










AD-61001.1
A-122823.1
CACCUCCCAGA
237
A-122824.1
UUGAGGGAGAUCUGGGAGGUGAA
306
1413




UCUCCCUCAA










AD-60974.1
A-122741.1
UGUGCGGGUGC
238
A-122742.1
AAGCCAUAGUGCACCCGCACACC
307
1443




ACUAUGGCUU










AD-60982.1
A-122769.1
GCGGGUGCACU
239
A-122770.1
UACAAGCCAUAGUGCACCCGCAC
308
1446




AUGGCUUGUA










AD-60996.1
A-122834.1
CCCCUGCCCUG
240
A-122835.1
AGGAACUCUCCAGGGCAGGGGUC
309
1479




GAGAGUUCCU










AD-60997.1
A-122850.1
CCCUGCCCUGG
241
A-122851.1
UAGGAACUCUCCAGGGCAGGGGU
310
1480




AGAGUUCCUA










AD-61006.1
A-122856.1
CCUGCCCUGGA
242
A-122857.1
AGAGGAACUCUCCAGGGCAGGGG
311
1481




GAGUUCCUCU










AD-60988.1
A-122844.1
CUGCCCUGGAG
243
A-122845.1
UAGAGGAACUCUCCAGGGCAGGG
312
1482




AGUUCCUCUA










AD-60959.1
A-122777.1
CCUGUGAUGGG
244
A-122778.1
AGUCCUUGACCCCAUCACAGGCA
313
1529




GUCAAGGACU










AD-60999.1
A-122836.1
GGACUGCCCCA
245
A-122837.1
UCCAGGCCGUUGGGGCAGUCCUU
314
1545




ACGGCCUGGA










AD-60991.1
A-122846.1
ACUGCCCCAAC
246
A-122847.1
UAUCCAGGCCGUUGGGGCAGUCC
315
1547




GGCCUGGAUA










AD-60993.1
A-122832.1
CUGCCCCAACG
247
A-122833.1
UCAUCCAGGCCGUUGGGGCAGUC
316
1548




GCCUGGAUGA










AD-61005.1
A-122840.1
UGCCCCAACGG
248
A-122841.1
UUCAUCCAGGCCGUUGGGGCAGU
317
1549




CCUGGAUGAA










AD-60987.1
A-119213.2
GCCCCAACGGC
249
A-122829.1
UCUCAUCCAGGCCGUUGGGGCAG
318
1550




CUGGAUGAGA










AD-60986.1
A-122842.1
CCCCAACGGCC
250
A-122843.1
UUCUCAUCCAGGCCGUUGGGGCA
319
1551




UGGAUGAGAA










AD-60952.1
A-119187.2
CCCAACGGCCU
251
A-122761.1
UCUCUCAUCCAGGCCGUUGGGGC
320
1552




GGAUGAGAGA










AD-60983.1
A-119191.2
CAACGGCCUGG
252
A-122785.1
UUUCUCUCAUCCAGGCCGUUGGG
321
1554




AUGAGAGAAA










AD-60950.1
A-122734.1
ACGGCCUGGAU
253
A-122735.1
AGUUUCUCUCAUCCAGGCCGUUG
322
1556




GAGAGAAACU










AD-60980.1
A-122743.1
CCUGGAUGAGA
254
A-122744.1
ACGCAGUUUCUCUCAUCCAGGCC
323
1560




GAAACUGCGU










AD-60998.1
A-122821.1
CACUGUGACUG
255
A-122822.1
UUGGAGGCCACAGUCACAGUGCU
324
1804




UGGCCUCCAA










AD-60961.1
A-122808.1
GUCCUCCGAGG
256
A-122809.1
GGCCACUCACCCUCGGAGGACAC
325
1857




GUGAGUGGCC










AD-61004.1
A-122825.1
CUCCGAGGGUG
257
A-122826.1
UAUGGCCACUCACCCUCGGAGGA
326
1860




AGUGGCCAUA










AD-60949.1
A-122804.1
UCCGAGGGUGA
258
A-122805.1
CCAUGGCCACUCACCCUCGGAGG
327
1861




GUGGCCAUGG










AD-60969.1
A-119189.2
CCAGGUUCGGG
259
A-122755.1
AUGUGUCGACCCCGAACCUGGAG
328
1893




GUCGACACAU










AD-60966.1
A-122794.1
AGGUUCGGGGU
260
A-122795.1
AGAUGUGUCGACCCCGAACCUGG
329
1895




CGACACAUCU










AD-60967.1
A-122810.1
CGGGGUCGACA
261
A-122811.1
CCCACAGAUGUGUCGACCCCGAA
330
1900




CAUCUGUGGG










AD-60989.1
A-122816.1
CGGGGUCGACA
262
A-122817.1
UCCACAGAUGUGUCGACCCCGAA
331
1900




CAUCUGUGGA










AD-60973.1
A-122812.1
GGGGUCGACAC
263
A-122813.1
CCCCACAGAUGUGUCGACCCCGA
332
1901




AUCUGUGGGG










AD-60992.1
A-122818.1
GGGGUCGACAC
264
A-122819.1
UCCCACAGAUGUGUCGACCCCGA
333
1901




AUCUGUGGGA










AD-60985.1
A-122827.1
GGGUCGACACA
265
A-122828.1
UCCCCACAGAUGUGUCGACCCCG
334
1902




UCUGUGGGGA










AD-60946.1
A-122759.1
GCUGACCGCUG
266
A-122760.1
UGUUAUCACCCAGCGGUCAGCGA
335
1933




GGUGAUAACA










AD-60979.1
A-122814.1
CUUCCAGGAGG
267
A-122815.1
GCCAUGCUGUCCUCCUGGAAGCA
336
1965




ACAGCAUGGC










AD-60976.1
A-122767.1
GGCCUGGAGAG
268
A-122768.1
UGAAGGACACCUCUCCAGGCCAG
337
2039




GUGUCCUUCA










AD-60939.1
A-122730.1
GCCUGGAGAGG
269
A-122731.1
UUGAAGGACACCUCUCCAGGCCA
338
2040




UGUCCUUCAA










AD-60978.1
A-122798.1
CCAAGCAGGGG
270
A-122799.1
AAUACUUGUCCCCCUGCUUGGCA
339
2608




GACAAGUAUU










AD-60958.1
A-122762.1
CAAGCAGGGGG
271
A-122763.1
GAAUACUUGUCCCCCUGCUUGGC
340
2609




ACAAGUAUUC










AD-60962.1
A-119231.2
UGGCAGGAGGU
272
A-122738.1
ACAAGAUGCCACCUCCUGCCACC
341
2664




GGCAUCUUGU










AD-60941.1
A-122771.1
GCAGGAGGUGG
273
A-122772.1
AGACAAGAUGCCACCUCCUGCCA
342
2666




CAUCUUGUCU










AD-60965.1
A-122779.1
GCUUCGGAAGC
274
A-122780.1
UAGACCAGGGGCUUCCGAAGCUG
343
2954




CCCUGGUCUA










AD-60954.1
A-122790.1
CUUCGGAAGCC
275
A-122791.1
UUAGACCAGGGGCUUCCGAAGCU
344
2955




CCUGGUCUAA










AD-60975.1
A-119233.2
CCCCUGGUCUA
276
A-122756.1
GAUCCCAAGUUAGACCAGGGGCU
345
2964




ACUUGGGAUC










AD-60945.1
A-122747.1
CCCUGGUCUAA
277
A-122748.1
AGAUCCCAAGUUAGACCAGGGGC
346
2965




CUUGGGAUCU










AD-60971.1
A-122781.1
CCUGGUCUAAC
278
A-122782.1
CAGAUCCCAAGUUAGACCAGGGG
347
2966




UUGGGAUCUG










AD-60948.1
A-122788.1
CUAACUUGGGA
279
A-122789.1
CAUUCCCAGAUCCCAAGUUAGAC
348
2972




UCUGGGAAUG
















TABLE 5







TMPRSS6 modified sequences














Sense

SEQ
Antisense

SEQ



sequence

ID
sequence

ID


Duplex ID
ID
Sense sequence
NO:
ID
Antisense sequence
NO:





AD-46273.1
A-96908.1
uGGuAuuuccuAGGGuAcA
349
A-96909.1
UGuACCCuAGGAAAuACcA
418




dTsdT


dTsdT






AD-59743.1
A-120243.1
UfscsUfgGfuAfuUfUfC
350
A-120244.1
usGfsuAfcCfcUfaGfga
419




fcUfaGfgGfuAfcAfL96


aAfuAfcCfaGfasgsu






AD-60939.1
A-122730.1
GfscsCfuGfgAfgAfGfG
351
A-122731.1
usUfsgAfaGfgAfcAfcc
420




fuGfuCfcUfuCfaAfL96


uCfuCfcAfgGfcscsa






AD-60940.1
A-122745.1
CfsusGfgUfaUfuUfCfC
352
A-122746.1
usUfsgUfaCfcCfuAfgg
421




fuAfgGfgUfaCfaAfL96


aAfaUfaCfcAfgsasg






AD-60941.1
A-122771.1
GfscsAfgGfaGfgUfGfG
353
A-122772.1
asGfsaCfaAfgAfuGfcc
422




fcAfuCfuUfgUfcUfL96


aCfcUfcCfuGfcscsa






AD-60942.1
A-122786.1
GfsgsGfcCfuGfcAfCfA
354
A-122787.1
usCfsgUfaGfuAfgCfug
423




fgCfuAfcUfaCfgAfL96


uGfcAfgGfcCfcsusu






AD-60943.1
A-122802.1
CfsasCfcUfcCfcAfGfA
355
A-122803.1
gsUfsgAfgGfgAfgAfuc
424




fuCfuCfcCfuCfaCfL96


uGfgGfaGfgUfgsasa






AD-60944.1
A-122732.1
GfsgsUfgCfuAfcUfCfU
356
A-122733.1
asGfsgAfaAfuAfcCfag
425




fgGfuAfuUfuCfcUfL96


aGfuAfgCfaCfcscsc






AD-60945.1
A-122747.1
CfscsCfuGfgUfcUfAfA
357
A-122748.1
asGfsaUfcCfcAfaGfuu
426




fcUfuGfgGfaUfcUfL96


aGfaCfcAfgGfgsgsc






AD-60946.1
A-122759.1
GfscsUfgAfcCfgCfUfG
358
A-122760.1
usGfsuUfaUfcAfcCfca
427




fgGfuGfaUfaAfcAfL96


gCfgGfuCfaGfcsgsa






AD-60947.1
A-122773.1
CfsusAfcAfgGfgCfCfG
359
A-122774.1
asCfsuUfcGfuAfcUfcg
428




faGfuAfcGfaAfgUfL96


gCfcCfuGfuAfgsgsg






AD-60948.1
A-122788.1
CfsusAfaCfuUfgGfGfA
360
A-122789.1
csAfsuUfcCfcAfgAfuc
429




fuCfuGfgGfaAfuGfL96


cCfaAfgUfuAfgsasc






AD-60949.1
A-122804.1
UfscsCfgAfgGfgUfGfA
361
A-122805.1
csCfsaUfgGfcCfaCfuc
430




fgUfgGfcCfaUfgGfL96


aCfcCfuCfgGfasgsg






AD-60950.1
A-122734.1
AfscsGfgCfcUfgGfAfU
362
A-122735.1
asGfsuUfuCfuCfuCfau
431




fgAfgAfgAfaAfcUfL96


cCfaGfgCfcGfususg






AD-60951.1
A-122749.1
GfsgsCfaGfaAfgUfAfU
363
A-122750.1
asCfsgGfcAfaAfuCfau
432




fgAfuUfuGfcCfgUfL96


aCfuUfcUfgCfcsusc






AD-60952.1
A-119187.2
CfscsCfaAfcGfgCfCfU
364
A-122761.1
usCfsuCfuCfaUfcCfag
433




fgGfaUfgAfgAfgAfL96


gCfcGfuUfgGfgsgsc






AD-60953.1
A-122775.1
CfsusGfcUfuCfuUfCfU
365
A-122776.1
asGfsaAfuGfaAfcCfag
434




fgGfuUfcAfuUfcUfL96


aAfgAfaGfcAfgsgsu






AD-60954.1
A-122790.1
CfsusUfcGfgAfaGfCfC
366
A-122791.1
usUfsaGfaCfcAfgGfgg
435




fcCfuGfgUfcUfaAfL96


cUfuCfcGfaAfgscsu






AD-60955.1
A-122806.1
CfsasGfaAfcAfgGfAfG
367
A-122807.1
gsCfscAfcAfcAfgCfcu
436




fgCfuGfuGfuGfgCfL96


cCfuGfuUfcUfgsgsa






AD-60956.1
A-122736.1
CfsgsCfcAfcUfuCfUfC
368
A-122737.1
asAfsgAfuCfcUfgGfga
437




fcCfaGfgAfuCfuUfL96


gAfaGfuGfgCfgsasu






AD-60957.1
A-122751.1
GfscsCfaGfuGfuGfAfA
369
A-122752.1
asGfscUfaUfgUfcUfuu
438




faGfaCfaUfaGfcUfL96


cAfcAfcUfgGfcsusu






AD-60958.1
A-122762.1
CfsasAfgCfaGfgGfGfG
370
A-122763.1
gsAfsaUfaCfuUfgUfcc
439




faCfaAfgUfaUfuCfL96


cCfcUfgCfuUfgsgsc






AD-60959.1
A-122777.1
CfscsUfgUfgAfuGfGfG
371
A-122778.1
asGfsuCfcUfuGfaCfcc
440




fgUfcAfaGfgAfcUfL96


cAfuCfaCfaGfgscsa






AD-60960.1
A-122792.1
AfsgsUfgUfgAfaAfGfA
372
A-122793.1
usGfscAfgCfuAfuGfuc
441




fcAfuAfgCfuGfcAfL96


uUfuCfaCfaCfusgsg






AD-60961.1
A-122808.1
GfsusCfcUfcCfgAfGfG
373
A-122809.1
gsGfscCfaCfuCfaCfcc
442




fgUfgAfgUfgGfcCfL96


uCfgGfaGfgAfcsasc






AD-60962.1
A-119231.2
UfsgsGfcAfgGfaGfGfU
374
A-122738.1
asCfsaAfgAfuGfcCfac
443




fgGfcAfuCfuUfgUfL96


cUfcCfuGfcCfascsc






AD-60963.1
A-122753.1
CfsgsGfgAfcCfgAfCfU
375
A-122754.1
asUfsaCfaUfgGfcCfag
444




fgGfcCfaUfgUfaUfL96


uCfgGfuCfcCfgsgsc






AD-60964.1
A-119169.2
CfscsCfuAfcAfgGfGfC
376
A-122764.1
usUfscGfuAfcUfcGfgc
445




fcGfaGfuAfcGfaAfL96


cCfuGfuAfgGfgsgsa






AD-60965.1
A-122779.1
GfscsUfuCfgGfaAfGfC
377
A-122780.1
usAfsgAfcCfaGfgGfgc
446




fcCfcUfgGfuCfuAfL96


uUfcCfgAfaGfcsusg






AD-60966.1
A-122794.1
AfsgsGfuUfcGfgGfGfU
378
A-122795.1
asGfsaUfgUfgUfcGfac
447




fcGfaCfaCfaUfcUfL96


cCfcGfaAfcCfusgsg






AD-60967.1
A-122810.1
CfsgsGfgGfuCfgAfCfA
379
A-122811.1
csCfscAfcAfgAfuGfug
448




fcAfuCfuGfuGfgGfL96


uCfgAfcCfcCfgsasa






AD-60968.1
A-122739.1
CfscsGfaCfuGfgCfCfA
380
A-122740.1
asCfsgUfcAfuAfcAfug
449




fuGfuAfuGfaCfgUfL96


gCfcAfgUfcGfgsusc






AD-60969.1
A-119189.2
CfscsAfgGfuUfcGfGfG
381
A-122755.1
asUfsgUfgUfcGfaCfcc
450




fgUfcGfaCfaCfaUfL96


cGfaAfcCfuGfgsasg






AD-60970.1
A-122765.1
GfsgsGfuUfgUfuAfCfC
382
A-122766.1
usAfsgCfuGfuAfgCfgg
451




fgCfuAfcAfgCfuAfL96


uAfaCfaAfcCfcsasg






AD-60971.1
A-122781.1
CfscsUfgGfuCfuAfAfC
383
A-122782.1
csAfsgAfuCfcCfaAfgu
452




fuUfgGfgAfuCfuGfL96


uAfgAfcCfaGfgsgsg






AD-60972.1
A-122796.1
CfsasCfgCfuGfgGfUfU
384
A-122797.1
usAfsgCfgGfuAfaCfaa
453




fgUfuAfcCfgCfuAfL96


cCfcAfgCfgUfgsgsa






AD-60973.1
A-122812.1
GfsgsGfgUfcGfaCfAfC
385
A-122813.1
csCfscCfaCfaGfaUfgu
454




faUfcUfgUfgGfgGfL96


gUfcGfaCfcCfcsgsa






AD-60974.1
A-122741.1
UfsgsUfgCfgGfgUfGfC
386
A-122742.1
asAfsgCfcAfuAfgUfgc
455




faCfuAfuGfgCfuUfL96


aCfcCfgCfaCfascsc






AD-60975.1
A-119233.2
CfscsCfcUfgGfuCfUfA
387
A-122756.1
gsAfsuCfcCfaAfgUfua
456




faCfuUfgGfgAfuCfL96


gAfcCfaGfgGfgscsu






AD-60976.1
A-122767.1
GfsgsCfcUfgGfaGfAfG
388
A-122768.1
usGfsaAfgGfaCfaCfcu
457




fgUfgUfcCfuUfcAfL96


cUfcCfaGfgCfcsasg






AD-60977.1
A-122783.1
CfsusUfcUfuCfuGfGfU
389
A-122784.1
usGfsgAfgAfaUfgAfac
458




fuCfaUfuCfuCfcAfL96


cAfgAfaGfaAfgscsa






AD-60978.1
A-122798.1
CfscsAfaGfcAfgGfGfG
390
A-122799.1
asAfsuAfcUfuGfuCfcc
459




fgAfcAfaGfuAfuUfL96


cCfuGfcUfuGfgscsa






AD-60979.1
A-122814.1
CfsusUfcCfaGfgAfGfG
391
A-122815.1
gsCfscAfuGfcUfgUfcc
460




faCfaGfcAfuGfgCfL96


uCfcUfgGfaAfgscsa






AD-60980.1
A-122743.1
CfscsUfgGfaUfgAfGfA
392
A-122744.1
asCfsgCfaGfuUfuCfuc
461




fgAfaAfcUfgCfgUfL96


uCfaUfcCfaGfgscsc






AD-60981.1
A-122757.1
GfscsCfaCfuUfcUfCfC
393
A-122758.1
usAfsaGfaUfcCfuGfgg
462




fcAfgGfaUfcUfuAfL96


aGfaAfgUfgGfcsgsa






AD-60982.1
A-122769.1
GfscsGfgGfuGfcAfCfU
394
A-122770.1
usAfscAfaGfcCfaUfag
463




faUfgGfcUfuGfuAfL96


uGfcAfcCfcGfcsasc






AD-60983.1
A-119191.2
CfsasAfcGfgCfcUfGfG
395
A-122785.1
usUfsuCfuCfuCfaUfcc
464




faUfgAfgAfgAfaAfL96


aGfgCfcGfuUfgsgsg






AD-60984.1
A-122800.1
CfscsAfgAfaCfaGfGfA
396
A-122801.1
csCfsaCfaCfaGfcCfuc
465




fgGfcUfgUfgUfgGfL96


cUfgUfuCfuGfgsasu






AD-60985.1
A-122827.1
GfsgsGfuCfgAfcAfCfA
397
A-122828.1
usCfscCfcAfcAfgAfug
466




fuCfuGfuGfgGfgAfL96


uGfuCfgAfcCfcscsg






AD-60986.1
A-122842.1
CfscsCfcAfaCfgGfCfC
398
A-122843.1
usUfscUfcAfuCfcAfgg
467




fuGfgAfuGfaGfaAfL96


cCfgUfuGfgGfgscsa






AD-60987.1
A-119213.2
GfscsCfcCfaAfcGfGfC
399
A-122829.1
usCfsuCfaUfcCfaGfgc
468




fcUfgGfaUfgAfgAfL96


cGfuUfgGfgGfcsasg






AD-60988.1
A-122844.1
CfsusGfcCfcUfgGfAfG
400
A-122845.1
usAfsgAfgGfaAfcUfcu
469




faGfuUfcCfuCfuAfL96


cCfaGfgGfcAfgsgsg






AD-60989.1
A-122816.1
CfsgsGfgGfuCfgAfCfA
401
A-122817.1
usCfscAfcAfgAfuGfug
470




fcAfuCfuGfuGfgAfL96


uCfgAfcCfcCfgsasa






AD-60990.1
A-122830.1
UfsusUfcCfuAfgGfGfU
402
A-122831.1
usCfscGfcCfuUfgUfac
471




faCfaAfgGfcGfgAfL96


cCfuAfgGfaAfasusa






AD-60991.1
A-122846.1
AfscsUfgCfcCfcAfAfC
403
A-122847.1
usAfsuCfcAfgGfcCfgu
472




fgGfcCfuGfgAfuAfL96


uGfgGfgCfaGfuscsc






AD-60992.1
A-122818.1
GfsgsGfgUfcGfaCfAfC
404
A-122819.1
usCfscCfaCfaGfaUfgu
473




faUfcUfgUfgGfgAfL96


gUfcGfaCfcCfcsgsa






AD-60993.1
A-122832.1
CfsusGfcCfcCfaAfCfG
405
A-122833.1
usCfsaUfcCfaGfgCfcg
474




fgCfcUfgGfaUfgAfL96


uUfgGfgGfcAfgsusc






AD-60994.1
A-122848.1
AfsusUfuCfcUfaGfGfG
406
A-122849.1
usCfsgCfcUfuGfuAfcc
475




fuAfcAfaGfgCfgAfL96


cUfaGfgAfaAfusasc






AD-60996.1
A-122834.1
CfscsCfcUfgCfcCfUfG
407
A-122835.1
asGfsgAfaCfuCfuCfca
476




fgAfgAfgUfuCfcUfL96


gGfgCfaGfgGfgsusc






AD-60997.1
A-122850.1
CfscsCfuGfcCfcUfGfG
408
A-122851.1
usAfsgGfaAfcUfcUfcc
477




faGfaGfuUfcCfuAfL96


aGfgGfcAfgGfgsgsu






AD-60998.1
A-122821.1
CfsasCfuGfuGfaCfUfG
409
A-122822.1
usUfsgGfaGfgCfcAfca
478




fuGfgCfcUfcCfaAfL96


gUfcAfcAfgUfgscsu






AD-60999.1
A-122836.1
GfsgsAfcUfgCfcCfCfA
410
A-122837.1
usCfscAfgGfcCfgUfug
479




faCfgGfcCfuGfgAfL96


gGfgCfaGfuCfcsusu






AD-61000.1
A-122852.1
GfsgsUfaUfuUfcCfUfA
411
A-122853.1
usCfsuUfgUfaCfcCfua
480




fgGfgUfaCfaAfgAfL96


gGfaAfaUfaCfcsasg






AD-61001.1
A-122823.1
CfsasCfcUfcCfcAfGfA
412
A-122824.1
usUfsgAfgGfgAfgAfuc
481




fuCfuCfcCfuCfaAfL96


uGfgGfaGfgUfgsasa






AD-61002.1
A-122838.1
UfsgsGfuAfuUfuCfCfU
413
A-122839.1
usUfsuGfuAfcCfcUfag
482




faGfgGfuAfcAfaAfL96


gAfaAfuAfcCfasgsa






AD-61003.1
A-122854.1
GfsusAfuUfuCfcUfAfG
414
A-122855.1
usCfscUfuGfuAfcCfcu
483




fgGfuAfcAfaGfgAfL96


aGfgAfaAfuAfcscsa






AD-61004.1
A-122825.1
CfsusCfcGfaGfgGfUfG
415
A-122826.1
usAfsuGfgCfcAfcUfca
484




faGfuGfgCfcAfuAfL96


cCfcUfcGfgAfgsgsa






AD-61005.1
A-122840.1
UfsgsCfcCfcAfaCfGfG
416
A-122841.1
usUfscAfuCfcAfgGfcc
485




fcCfuGfgAfuGfaAfL96


gUfuGfgGfgCfasgsu






AD-61006.1
A-122856.1
CfscsUfgCfcCfuGfGfA
417
A-122857.1
asGfsaGfgAfaCfuCfuc
486




fgAfgUfuCfcUfcUfL96


cAfgGfgCfaGfgsgsg









Example 6. In Vitro Single Dose Screen
Cell Culture and Transfections for Single Dose and Dose Response Studies

Hep3B cells (ATCC, Manassas, Va.) were grown to near confluence at 37° C. in an atmosphere of 5% CO2 in DMEM (ATCC) supplemented with 10% FBS, streptomycin, and glutamine (ATCC) before being released from the plate by trypsinization. Transfection was carried out by adding 14.8 μl of Opti-MEM plus 0.2 μl of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad Calif. cat #13778-150) to 5 μl of siRNA duplexes per well into a 96-well plate and incubated at room temperature for 15 minutes. 80 μl of complete growth media without antibiotic containing ˜2×104 Hep3B cells were then added to the siRNA mixture. Cells were incubated for 24 hours prior to RNA purification. Experiments were performed at 10 nM and 0.1 nM final duplex concentration.


Total RNA Isolation Using DYNABEADS mRNA Isolation Kit (Invitrogen, Part #; 610-12)


Cells were harvested and lysed in 150 μl of Lysis/Binding Buffer then mixed for 5 minutes at 850 rpm using an Eppendorf Thermomixer (the mixing speed was the same throughout the process). Ten microliters of magnetic beads and 80 μl Lysis/Binding Buffer mixture were added to a round bottom plate and mixed for 1 minute. Magnetic beads were captured using magnetic stand and the supernatant was removed without disturbing the beads. After removing supernatant, the lysed cells were added to the remaining beads and mixed for 5 minutes. After removing supernatant, magnetic beads were washed 2 times with 150 μl Wash Buffer A and mixed for 1 minute. Beads were capture again and supernatant removed. Beads were then washed with 150 μl Wash Buffer B, captured and supernatant was removed. Beads were next washed with 150 μl Elution Buffer, captured and supernatant removed. Beads were allowed to dry for 2 minutes. After drying, 50 μl of Elution Buffer was added and mixed for 5 minutes at 70° C. Beads were captured on magnet for 5 minutes. 40 μl of supernatant was removed and added to another 96 well plate.


cDNA Synthesis Using ABI High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, Calif., Cat #4368813)


A master mix of 2 μl 10× Buffer, 0.8 μl 25× dNTPs, 2 μl Random primers, 1 μl Reverse Transcriptase, 1 μl RNase inhibitor and 3.2 μl of H2O per reaction were added into 10 μl total RNA. cDNA was generated using a Bio-Rad C-1000 or S-1000 thermal cycler (Hercules, Calif.) through the following steps: 25° C. 10 min, 37° C. 120 min, 85° C. 5 sec, 4° C. hold.


Real Time PCR

2 μl of cDNA were added to a master mix containing 0.5 μl 1 GAPDH TaqMan Probe (Applied Biosystems Cat #4326317E), 0.5 μl TMPRSS6 TaqMan probe (Applied Biosystems cat #Hs00542184_m1) and 5 μl Lightcycler 480 probe master mix (Roche Cat #04887301001) per well in a 384 well 50 plates (Roche cat #04887301001). Real time PCR was done in an Roche Lightcycler Real Time PCR system (Roche) using the ΔΔCt(RQ) assay. Each duplex was tested in two independent transfections and each transfection was assayed in duplicate, unless otherwise noted in the summary tables.


To calculate relative fold change, real time data were analyzed using the ΔΔCt method and normalized to assays performed with cells transfected with 10 nM AD-1955, or mock transfected cells.


Data are expressed as a fraction of TMPRSS6 message remaining in cells transfected with siRNAs targeting TMPRSS6, relative to naïve cells. All siRNAs were transfected at least two times and qPCR reactions were performed in duplicate. Data are show in Table 6.









TABLE 6







TMPRSS6 single dose screen.











Duplex ID
Avg 10 nM
Avg 0.1 nM
SD 10 nM
SD 0.1 nM














AD-46273
76.5
112.1
14.3
18.6


AD-59743
61.4
108.2
8.7
4.4


AD-60939
38.0
85.7
19.3
25.2


AD-60940
24.2
22.6
10.1
9.7


AD-60941
48.5
84.7
11.7
29.7


AD-60942
102.9
111.2
4.3
44.8


AD-60943
86.2
96.5
2.3
28.8


AD-60944
24.6
78.5
1.1
36.5


AD-60945
65.8
140.9
0.5
59.2


AD-60946
50.3
105.9
4.1
31.2


AD-60947
79.1
147.2
12.3
51.2


AD-60948
81.0
113.9
0.6
32.7


AD-60949
111.3
96.2
8.2
28.1


AD-60950
53.8
93.2
7.6
42.3


AD-60951
74.1
121.6
6.4
56.2


AD-60952
47.6
118.3
8.1
52.4


AD-60953
22.0
56.7
8.3
18.0


AD-60954
23.3
55.8
5.3
31.7


AD-60955
110.8
117.5
1.6
38.7


AD-60956
15.8
29.6
1.7
10.2


AD-60957
22.3
58.3
1.5
6.1


AD-60958
106.4
136.0
24.1
61.7


AD-60959
79.6
123.3
0.6
49.9


AD-60960
17.4
49.4
8.6
10.2


AD-60961
107.7
129.0
6.6
50.5


AD-60962
90.2
113.3
8.0
67.2


AD-60963
117.4
138.1
2.6
16.8


AD-60964
80.7
123.2
24.2
18.9


AD-60965
30.1
80.2
9.0
20.8


AD-60966
54.1
133.6
4.6
44.0


AD-60967
122.2
147.4
11.7
42.0


AD-60968
86.9
142.0
39.9
49.7


AD-60969
106.2
116.3
16.6
39.1


AD-60970
54.6
112.6
7.3
11.8


AD-60971
50.5
118.8
6.9
47.0


AD-60972
55.6
94.2
6.5
3.4


AD-60973
126.1
133.6
8.0
36.8


AD-60974
82.6
115.0
8.7
43.7


AD-60975
88.2
114.3
13.6
43.9


AD-60976
46.3
71.0
11.6
30.2


AD-60977
13.5
26.4
3.4
9.2


AD-60978
72.7
92.9
6.4
31.7


AD-60979
103.8
97.0
13.7
29.2


AD-60980
28.4
58.0
12.3
21.1


AD-60981
56.0
80.6
18.3
4.5


AD-60982
102.4
137.4
15.2
16.4


AD-60983
60.8
87.1
10.1
20.3


AD-60984
53.6
116.7
1.2
47.8


AD-60985
72.6
99.2
0.7
21.7


AD-60986
90.1
96.4
6.6
29.5


AD-60987
83.1
90.7
1.6
13.7


AD-60988
69.4
102.3
2.4
55.4


AD-60989
112.4
105.7
0.6
14.7


AD-60990
90.4
93.4
6.2
4.1


AD-60991
97.6
95.6
15.5
23.4


AD-60992
104.0
131.4
6.9
33.7


AD-60993
118.6
129.2
10.5
30.1


AD-60994
25.9
57.2
6.8
0.3


AD-60996
77.3
94.2
7.8
12.6


AD-60997
60.1
80.9
18.8
7.5


AD-60998
32.6
61.4
5.7
24.6


AD-60999
133.6
110.9
39.7
15.4


AD-61000
55.8
117.6
14.2
24.9


AD-61001
57.9
85.2
8.1
42.0


AD-61002
15.4
31.4
1.5
10.1


AD-61003
82.3
98.1
4.0
11.8


AD-61004
106.4
97.7
38.5
18.8


AD-61005
138.0
141.2
65.7
20.0


AD-61006
31.7
70.9
7.8
6.6









Example 7. In Vivo Effect of Single Dose Administration of TMPRSS6 iRNA Agent

Female C57BL/6 mice were administered a single subcutaneous injection of AD-60940 at a dose of 0.3 mg/kg, 1.0 mg/kg or 3.0 mg/kg, or PBS alone as a control. Three mice were evaluated per dose for hepatic TMPRSS6 mRNA, hepatic hepcidin mRNA, serum hepcidin, total serum iron, and percent transferrin saturation at various time points. Mice receiving 1.0 mg/kg or 3.0 mg/kg of AD-60940 or PBS were evaluated at day 0 (pre-treatment) and 7, 11, 14 and 21 days after treatment. Mice receiving 0.3 mg/kg AD-60940 were evaluated at day 0 (pre-treatment) and at 7 and 11 days after treatment. Hepatic TMPRSS6 mRNA and hepatic hepcidin mRNA levels were determined by qPCR, normalized to GAPDH mRNA levels and expressed relative to the mRNA levels in mice administered PBS alone. Serum hepcidin was measured by ELISA (Intrinsic Life Sciences). Total serum iron and percent transferrin saturation (% TfSat) were measured using an Olympus AU400 Serum Chemistry Analyzer. Each data point represents the mean value from three mice. The standard deviation of the mean is represented by error bars.


Single dose administration of AD-60940 resulted in robust and durable suppression of hepatic TMPRSS6 mRNA relative to the control. TMPRSS6 mRNA concentration was suppressed by greater than 90% for up to three weeks following administration of the 3.0 mg/kg dose (FIG. 3A). As a result of the suppression of hepatic TMPRSS6 mRNA concentration, hepcidin mRNA levels, increased two-fold relative to the control (FIG. 3B), and serum hepcidin concentration increased greater than 2-fold relative to the control (FIG. 3C). In addition, total serum iron (FIG. 3D) decreased and percent transferrin saturation decreased by greater than 50% relative to the control (FIG. 3E). The decreases in total serum iron and percent transferring saturation were durable for up to three weeks following administration of AD-60940. FIG. 3F demonstrates the relative hepatic TMPRSS6 mRNA concentration as a function of AD-60940 dose at 11 days following administration. Each data point represents the maximum suppression of TMPRSS6 mRNA concentration observed at each dose level. The data were fit to the Hill equation.


The degree to which AD-60940 modulates hepcidin and serum iron mobilization is nearly identical to that observed in the previous Hbbth3/+ mouse studies (Schmidt et al., Blood (2013), 121(7), 1200-1208) and indicates that AD-60940 is a potent RNAi therapeutic for producing disease modifying effects in β-Thalassemia.


Example 8. In Vivo Effect of Multi-Dose Administration of TMPRSS6 iRNA Agent

Female C57BL/6 mice were administered a subcutaneous injection of AD-60940 at a dose of 0.3 mg/kg, 1.0 mg/kg, or PBS alone (as a control) once per week for three weeks then sacrificed 7 days after the final dose (FIG. 4A). Three mice per dose were evaluated for hepatic TMPRSS6 mRNA, hepatic hepcidin mRNA, and percent transferrin saturation. Hepatic TMPRSS6 mRNA and hepatic hepcidin mRNA levels were determined by qPCR, normalized to GAPDH mRNA levels and expressed relative to the mRNA levels in mice administered PBS alone. Percent transferrin saturation (% TfSat) was measured using an Olympus AU400 Serum Chemistry Analyzer. Each data point represents the mean value from three mice. The standard deviation of the mean is represented by error bars.


Multi-dose administration of 1.0 mg/kg AD-60940 resulted in greater than 90% suppression of TMPRSS6 mRNA concentration (FIG. 4B). Hepcidin mRNA concentration increased two-fold and percent transferrin saturation decreased by greater than 50% relative to the control (FIG. 4B). FIG. 4C demonstrates the relative hepatic TMPRSS6 mRNA concentration as a function of AD-60940 dose. The data were fit to the Hill equation. These data indicate that the multi-dose ED80 is less than 1.0 mg/kg.


This study demonstrates that AD-60940 exhibits robust and durable suppression of TMPRSS6, resulting in hepcidin induction and systemic iron restriction and indicates that AD-60940 is a potent RNAi therapeutic for producing disease modifying effects in β-Thalassemia.


Example 9. Relationship Between Liver TMPRSS6 mRNA Levels and Serum Hepcidin Concentration and Percent Transferrin Saturation

Data generated using AD-59743, AD-61002, AD-60940, and other TMPRSS6 iRNA agents were further analyzed to evaluate the relationship between liver TMPRSS6 mRNA levels and serum hepcidin levels and percent transferrin saturation. Serum hepcidin concentration demonstrated a non-linear relationship to TMPRSS6 mRNA levels using the Hill equation (FIG. 5A). The percent transferrin saturation demonstrated a linear relationship to TMPRSS6 mRNA levels when fit to a simple linear regression equation (FIG. 5B). The linear relationship between TMPRSS6 mRNA levels and percent transferrin saturation indicate that iron restriction can be precisely and predictably modulated by AD-60940. Serum hepcidin concentration and relative hepcidin mRNA levels also demonstrated a linear relationship when fit to a simple linear regression equation (FIG. 5C). In contrast, the relationship between percent transferrin saturation and serum hepcidin concentration was non-linear and fit to the Hill equation (FIG. 5D).


Example 10. In Vivo Single Dose Screen

TMPRSS6 siRNA duplexes as indicated in FIG. 6 were evaluated for efficacy by their ability to suppress levels of TMPRSS6 mRNA in the liver of female C57BL/6 mice following administration of the siRNA duplex. A single subcutaneous dose of 3 mg/kg of TMPRSS6 siRNA duplex was administered, and the mice were sacrificed 7 days later. The level of TMPRSS6 mRNA in the liver was measured by qPCR using the methods described above. Mice in a control group received an injection of PBS.


The levels of TMPRSS6 mRNA following administration of a TMPRSS6 siRNA duplex are shown in FIG. 6. The results demonstrate that administration of AD-60940, AD-59743 and AD-61002 resulted in substantial suppression of liver TMPRSS6 mRNA with AD60940 producing the greatest silencing. Specifically, TMPRSS6 siRNA duplex AD-60940 reduced TMPRSS6 mRNA by greater than 80% relative to the control. The data also demonstrate that treatment with AD-59743, AD-60940, AD-61002, AD-60994, AD-60998 and AD-61001 result in a decrease in the level of TMPRSS6 transcript that is maintained through day 7.


Example 11. In Vivo Multi-Dose Screen

TMPRSS6 siRNA duplexes as indicated in FIG. 7 were evaluated for efficacy by their ability to suppress levels of TMPRSS6 mRNA in the liver of wild-type C57BL/6 mice following administration of the siRNA duplex. A subcutaneous dose of either 0.3 mg/kg or 1.0 mg/kg of TMPRSS6 siRNA duplex was administered once a week for three weeks. The mice were sacrificed 7 days after the last dose. The level of TMPRSS6 mRNA in the liver was measured by qPCR using the methods described above. Mice in a control group received an injection of PBS.


The levels of TMPRSS6 mRNA following administration of a TMPRSS6 siRNA duplex are shown in FIG. 7. The results demonstrate that the 1.0 mg/kg dosing regimen of TMPRSS6 siRNA duplex AD-60940 reduces TMPRSS6 mRNA by greater than 80% relative to the control.


Example 12. Optimization of AD-60940

Based on the observation that administration of AD-60940 durably reduced TMPRSS6 mRNA by greater than 80% relative to the control, additional siRNAs based on the parent sequence of AD-60940 with a variety of chemical modifications were evaluated for efficacy in single dose screens at 10 nM and 0.1 nM by transfection in Hep3B cells. The sequences of the sense and antisense strands of these agents are shown in Table 8 and the results of this screen are shown in Table 9. The data in Table 9 are expressed as the average fraction message remaining relative to control.


In addition, a subset of siRNA described in Tables 4 and 5, above, were modified to replace a 2′F with a 2′OMe modification at the 5′-end of the sense strand and to add a 5′-phosphate on the antisense strand. These siRNA agents were also evaluated for in vitro efficacy in single dose screens at 10 nM and 0.1 nM by transfection in Hep3B cells. The sequences of the sense and antisense strands of these agents are shown in Table 10 and the results of this screen are shown in Table 11. The data in Table 11 are expressed as the average fraction message remaining relative to control.









TABLE 8







TMSPRSS6 Modified Sequences
















SEQ


SEQ





ID


ID


DuplexID
SenseID
Sense Sequence
NO:
AntisenseID
Antisense Sequence
NO:





AD-63214
A-126586.2
Y44CfsusGfgUfaUfuUf
487
A-126587.2
PusUfsgUfaCfcCfuAfg
544




CfCfuAfgGfgUfaCfaAf


gaAfaUfaCfcAfgsasg





L96









AD-63240
A-122745.11
CfsusGfgUfaUfuUfCfC
488
A-126607.1
usUfsguaCfcCfuAfgga
545




fuAfgGfgUfaCfaAfL96


AfaUfaccagsasg






AD-63209
A-126594.1
csusgguaUfuUfCfCfua
489
A-122746.13
usUfsgUfaCfcCfuAfgg
546




ggGfdTacaaL96


aAfaUfaCfcAfgsasg






AD-63208
A-122745.6
CfsusGfgUfaUfuUfCfC
490
A-126587.1
PusUfsgUfaCfcCfuAfg
547




fuAfgGfgUfaCfaAfL96


gaAfaUfaCfcAfgsasg






AD-63202
A-126586.1
Y44CfsusGfgUfaUfuUf
491
A-122746.6
usUfsgUfaCfcCfuAfgg
548




CfCfuAfgGfgUfaCfaAf


aAfaUfaCfcAfgsasg





L96









AD-63216
A-122745.7
CfsusGfgUfaUfuUfCfC
492
A-126603.1
usUfsgUfaCfccuAfgga
549




fuAfgGfgUfaCfaAfL96


AfaUfaCfcAfgsasg






AD-63219
A-126617.1
gsgsUfaUfuUfCfCfuAf
493
A-126618.1
PusUfsgUfaCfcCfuAfg
550




gGfgUfaCfaAfL96


gaAfaUfaCfcsasg






AD-63228
A-122745.9
CfsusGfgUfaUfuUfCfC
494
A-126605.1
usUfsgUfaCfcCfuAfgg
551




fuAfgGfgUfaCfaAfL96


aAfaUfaccagsasg






AD-63205
A-122745.13
CfsusGfgUfaUfuUfCfC
495
A-126609.1
usUfsgUfaccCfuaggaA
552




fuAfgGfgUfaCfaAfL96


faUfaccAfgsasg






AD-63241
A-126589.2
csusgguaUfuUfCfCfua
496
A-126611.3
usUfsguaCfccUfaggaA
553




ggGfuacaaL96


faUfaccagsasg






AD-63243
A-126621.3
csusGfguaUfuUfCfCfu
497
A-126624.1
usUfsGfuaCfcCfuAfgg
554




AfgGfguAfcaaL96


aAfAfuaCfcAfgsasg






AD-63203
A-126593.1
csusgguaUfuUfCfCfua
498
A-122746.12
usUfsgUfaCfcCfuAfgg
555




ggGfuadCaaL96


aAfaUfaCfcAfgsasg






AD-63223
A-122745.16
CfsusGfgUfaUfuUfCfC
499
A-126612.1
usUfsguaCfccuaggaAf
556




fuAfgGfgUfaCfaAfL96


aUfaccagsasg






AD-63231
A-126621.1
csusGfguaUfuUfCfCfu
500
A-126622.1
usUfsGfuaCfcCfuAfgg
557




AfgGfguAfcaaL96


aAfaUfaCfcAfgsasg






AD-63199
A-122745.12
CfsusGfgUfaUfuUfCfC
501
A-126608.1
usUfsgUfaccCfuAfgga
558




fuAfgGfgUfaCfaAfL96


AfaUfaccAfgsasg






AD-63217
A-122745.15
CfsusGfgUfaUfuUfCfC
502
A-126611.1
usUfsguaCfccUfaggaA
559




fuAfgGfgUfaCfaAfL96


faUfaccagsasg






AD-63229
A-122745.17
CfsusGfgUfaUfuUfCfC
503
A-126613.1
usUfsguaCfcCfUfagga
560




fuAfgGfgUfaCfaAfL96


AfaUfaccagsasg






AD-63255
A-126621.5
csusGfguaUfuUfCfCfu
504
A-126626.1
usUfsGfuAfCfcCfuAfg
561




AfgGfguAfcaaL96


gaAfAfuaCfcAfgsasg






AD-63226
A-126589.1
csusgguaUfuUfCfCfua
505
A-122746.8
usUfsgUfaCfcCfuAfgg
562




ggGfuacaaL96


aAfaUfaCfcAfgsasg






AD-63211
A-122745.14
CfsusGfgUfaUfuUfCfC
506
A-126610.1
usUfsgUfacccuAfggaA
563




fuAfgGfgUfaCfaAfL96


faUfaccAfgsasg






AD-63273
A-126621.8
csusGfguaUfuUfCfCfu
507
A-126629.1
usUfsGfuaCfcCfuAfgg
564




AfgGfguAfcaaL96


aAfAfuAfccagsasg






AD-60940
A-122745.1
CfsusGfgUfaUfuUfCfC
508
A-122746.1
usUfsgUfaCfcCfuAfgg
565




fuAfgGfgUfaCfaAfL96


aAfaUfaCfcAfgsasg






AD-63249
A-126621.4
csusGfguaUfuUfCfCfu
509
A-126625.1
usUfsGfuAfCfcCfuAfg
566




AfgGfguAfcaaL96


gaAfAfuAfCfcAfgsasg






AD-63256
A-122745.19
CfsusGfgUfaUfuUfCfC
510
A-126634.1
usUfsgUfaccCfuAfgga
567




fuAfgGfgUfaCfaAfL96


AfaUfaCfcAfgsasg






AD-63280
A-126639.1
csusGfgUfaUfuUfCfCf
511
A-126587.3
PusUfsgUfaCfcCfuAfg
568




uAfgGfgUfaCfaAfL96


gaAfaUfaCfcAfgsasg






AD-63237
A-126621.2
csusGfguaUfuUfCfCfu
512
A-126623.1
usUfsGfuAfCfcCfuAfg
569




AfgGfguAfcaaL96


gaAfaUfaCfcAfgsasg






AD-63285
A-126621.10
csusGfguaUfuUfCfCfu
513
A-126631.1
usUfsGfuaCfcCfuAfgg
570




AfgGfguAfcaaL96


aAfAfuAfccAfgsasg






AD-63215
A-126595.1
csusgguaUfuUfCfdCua
514
A-122746.14
usUfsgUfaCfcCfuAfgg
571




ggGfuacaaL96


aAfaUfaCfcAfgsasg






AD-63222
A-122745.8
CfsusGfgUfaUfuUfCfC
515
A-126604.1
usUfsguaCfcCfuAfgga
572




fuAfgGfgUfaCfaAfL96


AfaUfaccAfgsasg






AD-63232
A-126590.1
csusgguAfuuUfcCfUfa
516
A-122746.9
usUfsgUfaCfcCfuAfgg
573




gGfGfuacaaL96


aAfaUfaCfcAfgsasg






AD-63218
A-126594.2
csusgguaUfuUfCfCfua
517
A-126611.7
usUfsguaCfccUfaggaA
574




ggGfdTacaaL96


faUfaccagsasg






AD-63261
A-126621.6
csusGfguaUfuUfCfCfu
518
A-126627.1
usUfsGfuaCfcCfuAfgg
575




AfgGfguAfcaaL96


aAfAfuAfCfcagsasg






AD-63267
A-126621.7
csusGfguaUfuUfCfCfu
519
A-126628.1
usUfsGfuAfCfcCfuAfg
576




AfgGfguAfcaaL96


gaAfAfuAfCfcagsasg






AD-63234
A-122745.10
CfsusGfgUfaUfuUfCfC
520
A-126606.1
usUfsguaCfccuAfggaA
577




fuAfgGfgUfaCfaAfL96


faUfaccAfgsasg






AD-63250
A-122745.18
CfsusGfgUfaUfuUfCfC
521
A-126633.1
ususgUfaCfcCfuAfgga
578




fuAfgGfgUfaCfaAfL96


AfaUfaCfcAfgsasg






AD-63212
A-126593.2
csusgguaUfuUfCfCfua
522
A-126611.6
usUfsguaCfccUfaggaA
579




ggGfuadCaaL96


faUfaccagsasg






AD-63210
A-126602.1
csusgguauuucdCuaggg
523
A-122746.21
usUfsgUfaCfcCfuAfgg
580




(Tgn)acaaL96


aAfaUfaCfcAfgsasg






AD-63244
A-126621.11
csusGfguaUfuUfCfCfu
524
A-126632.1
usUfsGfuAfCfcCfuAfg
581




AfgGfguAfcaaL96


gaAfAfuAfccAfgsasg






AD-63235
A-126588.2
csusgguAfuuuCfCfuAf
525
A-126611.2
usUfsguaCfccUfaggaA
582




ggGfuacaaL96


faUfaccagsasg






AD-63279
A-126621.9
csusGfguaUfuUfCfCfu
526
A-126630.1
usUfsGfuAfCfcCfuAfg
583




AfgGfguAfcaaL96


gaAfAfuAfccagsasg






AD-63227
A-126597.1
csusgguAfuuucCfuagg
527
A-122746.16
usUfsgUfaCfcCfuAfgg
584




gdTacaaL96


aAfaUfaCfcAfgsasg






AD-63220
A-126588.1
csusgguAfuuuCfCfuAf
528
A-122746.7
usUfsgUfaCfcCfuAfgg
585




ggGfuacaaL96


aAfaUfaCfcAfgsasg






AD-63238
A-126591.1
csusgguAfuuucCfuagg
529
A-122746.10
usUfsgUfaCfcCfuAfgg
586




guacaaL96


aAfaUfaCfcAfgsasg






AD-63242
A-126598.2
csusgguAfuuucCfdTag
530
A-126611.11
usUfsguaCfccUfaggaA
587




gguacaaL96


faUfaccagsasg






AD-63239
A-126599.1
csusgguauuucCfdTagg
531
A-122746.18
usUfsgUfaCfcCfuAfgg
588




guacaaL96


aAfaUfaCfcAfgsasg






AD-63233
A-126598.1
csusgguAfuuucCfdTag
532
A-122746.17
usUfsgUfaCfcCfuAfgg
589




gguacaaL96


aAfaUfaCfcAfgsasg






AD-63268
A-126636.1
CfsusGfgUfaUfuUfCfc
533
A-122746.22
usUfsgUfaCfcCfuAfgg
590




uAfgGfgUfaCfaAfL96


aAfaUfaCfcAfgsasg






AD-63221
A-126596.1
csusgguAfuuucCfuagg
534
A-122746.15
usUfsgUfaCfcCfuAfgg
591




guadCaaL96


aAfaUfaCfcAfgsasg






AD-63236
A-126597.2
csusgguAfuuucCfuagg
535
A-126611.10
usUfsguaCfccUfaggaA
592




gdTacaaL96


faUfaccagsasg






AD-63197
A-126592.1
csusgguauuucCfUfagg
536
A-122746.11
usUfsgUfaCfcCfuAfgg
593




guacaaL96


aAfaUfaCfcAfgsasg






AD-63224
A-126595.2
csusgguaUfuUfCfdCua
537
A-126611.8
usUfsguaCfccUfaggaA
594




ggGfuacaaL96


faUfaccagsasg






AD-63200
A-126590.2
csusgguAfuuUfcCfUfa
538
A-126611.4
usUfsguaCfccUfaggaA
595




gGfGfuacaaL96


faUfaccagsasg






AD-63262
A-122745.20
CfsusGfgUfaUfuUfCfC
539
A-126635.1
usUfsgUfaCfcCfuAfgg
596




fuAfgGfgUfaCfaAfL96


aaaUfaCfcAfgsasg






AD-63204
A-126601.1
csusgguauuucdCuaggg
540
A-122746.20
usUfsgUfaCfcCfuAfgg
597




uacaaL96


aAfaUfaCfcAfgsasg






AD-63230
A-126596.2
csusgguAfuuucCfuagg
541
A-126611.9
usUfsguaCfccUfaggaA
598




guadCaaL96


faUfaccagsasg






AD-63198
A-126600.1
csusgguauuucdCdTagg
542
A-122746.19
usUfsgUfaCfcCfuAfgg
599




guacaaL96


aAfaUfaCfcAfgsasg






AD-63206
A-126591.2
csusgguAfuuucCfuagg
543
A-126611.5
usUfsguaCfccUfaggaA
600




guacaaL96


faUfaccagsasg
















TABLE 9







TMPRSS6 Single Dose Screen












10 nM
0.1 nM



DuplexID
Avg
Avg














AD-63214
12.40
19.46



AD-63240
12.29
27.03



AD-63209
17.11
23.38



AD-63208
14.77
23.31



AD-63202
14.87
27.08



AD-63216
15.97
34.05



AD-63219
18.47
27.82



AD-63228
19.44
34.52



AD-63205
15.44
38.23



AD-63241
18.81
41.42



AD-63243
19.15
30.87



AD-63203
17.06
42.12



AD-63223
21.98
27.52



AD-63231
22.42
30.68



AD-63199
17.74
39.50



AD-63217
18.81
38.99



AD-63229
22.33
33.42



AD-63255
21.06
34.31



AD-63226
18.36
41.65



AD-63211
26.00
32.07



AD-63273
23.11
34.96



AD-60940
22.99
34.34



AD-63249
30.83
28.35



AD-63256
23.18
35.19



AD-63280
25.10
32.42



AD-63237
23.95
35.43



AD-63285
21.53
39.60



AD-63215
29.27
42.54



AD-63222
23.88
38.24



AD-63232
30.29
35.04



AD-63218
27.02
37.31



AD-63261
24.22
46.61



AD-63267
28.32
38.90



AD-63234
24.42
55.83



AD-63250
26.77
47.92



AD-63212
28.43
46.01



AD-63210
27.91
44.35



AD-63244
30.66
45.65



AD-63235
32.75
51.82



AD-63279
38.00
48.80



AD-63227
33.15
58.12



AD-63220
38.31
54.08



AD-63238
45.56
51.50



AD-63242
47.96
54.26



AD-63239
51.98
49.22



AD-63233
51.37
65.83



AD-63268
41.22
82.16



AD-63221
57.02
65.11



AD-63236
49.86
71.66



AD-63197
47.67
78.29



AD-63224
67.73
60.88



AD-63200
62.89
67.68



AD-63262
64.25
79.72



AD-63204
68.01
80.99



AD-63230
66.88
81.04



AD-63198
65.67
78.28



AD-63206
65.10
82.71
















TABLE 10







TMPRSS6 Modified Sequences
















SEQ


SEQ





ID


ID


DuplexID
SenseID
Sense Sequence
NO:
AntisenseID
Antisense Sequence
NO:





AD-63214
A-126586.2
Y44CfsusGfgUfaUfuUf
601
A-126587.2
PusUfsgUfaCfcCfuAfg
658




CfCfuAfgGfgUfaCfaAf


gaAfaUfaCfcAfgsasg





L96









AD-63240
A-122745.11
CfsusGfgUfaUfuUfCfC
602
A-126607.1
usUfsguaCfcCfuAfgga
659




fuAfgGfgUfaCfaAfL96


AfaUfaccagsasg






AD-63209
A-126594.1
csusgguaUfuUfCfCfua
603
A-122746.13
usUfsgUfaCfcCfuAfgg
660




ggGfdTacaaL96


aAfaUfaCfcAfgsasg






AD-63208
A-122745.6
CfsusGfgUfaUfuUfCfC
604
A-126587.1
PusUfsgUfaCfcCfuAfg
661




fuAfgGfgUfaCfaAfL96


gaAfaUfaCfcAfgsasg






AD-63202
A-126586.1
Y44CfsusGfgUfaUfuUf
605
A-122746.6
usUfsgUfaCfcCfuAfgg
662




CfCfuAfgGfgUfaCfaAf


aAfaUfaCfcAfgsasg





L96









AD-63216
A-122745.7
CfsusGfgUfaUfuUfCfC
606
A-126603.1
usUfsgUfaCfccuAfgga
663




fuAfgGfgUfaCfaAfL96


AfaUfaCfcAfgsasg






AD-63219
A-126617.1
gsgsUfaUfuUfCfCfuAf
607
A-126618.1
PusUfsgUfaCfcCfuAfg
664




gGfgUfaCfaAfL96


gaAfaUfaCfcsasg






AD-63228
A-122745.9
CfsusGfgUfaUfuUfCfC
608
A-126605.1
usUfsgUfaCfcCfuAfgg
665




fuAfgGfgUfaCfaAfL96


aAfaUfaccagsasg






AD-63205
A-122745.13
CfsusGfgUfaUfuUfCfC
609
A-126609.1
usUfsgUfaccCfuaggaA
666




fuAfgGfgUfaCfaAfL96


faUfaccAfgsasg






AD-63241
A-126589.2
csusgguaUfuUfCfCfua
610
A-126611.3
usUfsguaCfccUfaggaA
667




ggGfuacaaL96


faUfaccagsasg






AD-63243
A-126621.3
csusGfguaUfuUfCfCfu
611
A-126624.1
usUfsGfuaCfcCfuAfgg
668




AfgGfguAfcaaL96


aAfAfuaCfcAfgsasg






AD-63203
A-126593.1
csusgguaUfuUfCfCfua
612
A-122746.12
usUfsgUfaCfcCfuAfgg
669




ggGfuadCaaL96


aAfaUfaCfcAfgsasg






AD-63223
A-122745.16
CfsusGfgUfaUfuUfCfC
613
A-126612.1
usUfsguaCfccuaggaAf
670




fuAfgGfgUfaCfaAfL96


aUfaccagsasg






AD-63231
A-126621.1
csusGfguaUfuUfCfCfu
614
A-126622.1
usUfsGfuaCfcCfuAfgg
671




AfgGfguAfcaaL96


aAfaUfaCfcAfgsasg






AD-63199
A-122745.12
CfsusGfgUfaUfuUfCfC
615
A-126608.1
usUfsgUfaccCfuAfgga
672




fuAfgGfgUfaCfaAfL96


AfaUfaccAfgsasg






AD-63217
A-122745.15
CfsusGfgUfaUfuUfCfC
616
A-126611.1
usUfsguaCfccUfaggaA
673




fuAfgGfgUfaCfaAfL96


faUfaccagsasg






AD-63229
A-122745.17
CfsusGfgUfaUfuUfCfC
617
A-126613.1
usUfsguaCfcCfUfagga
674




fuAfgGfgUfaCfaAfL96


AfaUfaccagsasg






AD-63255
A-126621.5
csusGfguaUfuUfCfCfu
618
A-126626.1
usUfsGfuAfCfcCfuAfg
675




AfgGfguAfcaaL96


gaAfAfuaCfcAfgsasg






AD-63226
A-126589.1
csusgguaUfuUfCfCfua
619
A-122746.8
usUfsgUfaCfcCfuAfgg
676




ggGfuacaaL96


aAfaUfaCfcAfgsasg






AD-63211
A-122745.14
CfsusGfgUfaUfuUfCfC
620
A-126610.1
usUfsgUfacccuAfggaA
677




fuAfgGfgUfaCfaAfL96


faUfaccAfgsasg






AD-63273
A-126621.8
csusGfguaUfuUfCfCfu
621
A-126629.1
usUfsGfuaCfcCfuAfgg
678




AfgGfguAfcaaL96


aAfAfuAfccagsasg






AD-60940
A-122745.1
CfsusGfgUfaUfuUfCfC
622
A-122746.1
usUfsgUfaCfcCfuAfgg
679




fuAfgGfgUfaCfaAfL96


aAfaUfaCfcAfgsasg






AD-63249
A-126621.4
csusGfguaUfuUfCfCfu
623
A-126625.1
usUfsGfuAfCfcCfuAfg
680




AfgGfguAfcaaL96


gaAfAfuAfCfcAfgsasg






AD-63256
A-122745.19
CfsusGfgUfaUfuUfCfC
624
A-126634.1
usUfsgUfaccCfuAfgga
681




fuAfgGfgUfaCfaAfL96


AfaUfaCfcAfgsasg






AD-63280
A-126639.1
csusGfgUfaUfuUfCfCf
625
A-126587.3
PusUfsgUfaCfcCfuAfg
682




uAfgGfgUfaCfaAfL96


gaAfaUfaCfcAfgsasg






AD-63237
A-126621.2
csusGfguaUfuUfCfCfu
626
A-126623.1
usUfsGfuAfCfcCfuAfg
683




AfgGfguAfcaaL96


gaAfaUfaCfcAfgsasg






AD-63285
A-126621.10
csusGfguaUfuUfCfCfu
627
A-126631.1
usUfsGfuaCfcCfuAfgg
684




AfgGfguAfcaaL96


aAfAfuAfccAfgsasg






AD-63215
A-126595.1
csusgguaUfuUfCfdCua
628
A-122746.14
usUfsgUfaCfcCfuAfgg
685




ggGfuacaaL96


aAfaUfaCfcAfgsasg






AD-63222
A-122745.8
CfsusGfgUfaUfuUfCfC
629
A-126604.1
usUfsguaCfcCfuAfgga
686




fuAfgGfgUfaCfaAfL96


AfaUfaccAfgsasg






AD-63232
A-126590.1
csusgguAfuuUfcCfUfa
630
A-122746.9
usUfsgUfaCfcCfuAfgg
687




gGfGfuacaaL96


aAfaUfaCfcAfgsasg






AD-63218
A-126594.2
csusgguaUfuUfCfCfua
631
A-126611.7
usUfsguaCfccUfaggaA
688




ggGfdTacaaL96


faUfaccagsasg






AD-63261
A-126621.6
csusGfguaUfuUfCfCfu
632
A-126627.1
usUfsGfuaCfcCfuAfgg
689




AfgGfguAfcaaL96


aAfAfuAfCfcagsasg






AD-63267
A-126621.7
csusGfguaUfuUfCfCfu
633
A-126628.1
usUfsGfuAfCfcCfuAfg
690




AfgGfguAfcaaL96


gaAfAfuAfCfcagsasg






AD-63234
A-122745.10
CfsusGfgUfaUfuUfCfC
634
A-126606.1
usUfsguaCfccuAfggaA
691




fuAfgGfgUfaCfaAfL96


faUfaccAfgsasg






AD-63250
A-122745.18
CfsusGfgUfaUfuUfCfC
635
A-126633.1
ususgUfaCfcCfuAfgga
692




fuAfgGfgUfaCfaAfL96


AfaUfaCfcAfgsasg






AD-63212
A-126593.2
csusgguaUfuUfCfCfua
636
A-126611.6
usUfsguaCfccUfaggaA
693




ggGfuadCaaL96


faUfaccagsasg






AD-63210
A-126602.1
csusgguauuucdCuaggg
637
A-122746.21
usUfsgUfaCfcCfuAfgg
694




(Tgn)acaaL96


aAfaUfaCfcAfgsasg






AD-63244
A-126621.11
csusGfguaUfuUfCfCfu
638
A-126632.1
usUfsGfuAfCfcCfuAfg
695




AfgGfguAfcaaL96


gaAfAfuAfccAfgsasg






AD-63235
A-126588.2
csusgguAfuuuCfCfuAf
639
A-126611.2
usUfsguaCfccUfaggaA
696




ggGfuacaaL96


faUfaccagsasg






AD-63279
A-126621.9
csusGfguaUfuUfCfCfu
640
A-126630.1
usUfsGfuAfCfcCfuAfg
697




AfgGfguAfcaaL96


gaAfAfuAfccagsasg






AD-63227
A-126597.1
csusgguAfuuucCfuagg
641
A-122746.16
usUfsgUfaCfcCfuAfgg
698




gdTacaaL96


aAfaUfaCfcAfgsasg






AD-63220
A-126588.1
csusgguAfuuuCfCfuAf
642
A-122746.7
usUfsgUfaCfcCfuAfgg
699




ggGfuacaaL96


aAfaUfaCfcAfgsasg






AD-63238
A-126591.1
csusgguAfuuucCfuagg
643
A-122746.10
usUfsgUfaCfcCfuAfgg
700




guacaaL96


aAfaUfaCfcAfgsasg






AD-63242
A-126598.2
csusgguAfuuucCfdTag
644
A-126611.11
usUfsguaCfccUfagga
701




gguacaaL96


AfaUfaccagsasg






AD-63239
A-126599.1
csusgguauuucCfdTagg
645
A-122746.18
usUfsgUfaCfcCfuAfgg
702




guacaaL96


aAfaUfaCfcAfgsasg






AD-63233
A-126598.1
csusgguAfuuucCfdTag
646
A-122746.17
usUfsgUfaCfcCfuAfgg
703




gguacaaL96


aAfaUfaCfcAfgsasg






AD-63268
A-126636.1
CfsusGfgUfaUfuUfCfc
647
A-122746.22
usUfsgUfaCfcCfuAfgg
704




uAfgGfgUfaCfaAfL96


aAfaUfaCfcAfgsasg






AD-63221
A-126596.1
csusgguAfuuucCfuagg
648
A-122746.15
usUfsgUfaCfcCfuAfgg
705




guadCaaL96


aAfaUfaCfcAfgsasg






AD-63236
A-126597.2
csusgguAfuuucCfuagg
649
A-126611.10
usUfsguaCfccUfaggaA
706




gdTacaaL96


faUfaccagsasg






AD-63197
A-126592.1
csusgguauuucCfUfagg
650
A-122746.11
usUfsgUfaCfcCfuAfgg
707




guacaaL96


aAfaUfaCfcAfgsasg






AD-63224
A-126595.2
csusgguaUfuUfCfdCua
651
A-126611.8
usUfsguaCfccUfaggaA
708




ggGfuacaaL96


faUfaccagsasg






AD-63200
A-126590.2
csusgguAfuuUfcCfUfa
652
A-126611.4
usUfsguaCfccUfaggaA
709




gGfGfuacaaL96


faUfaccagsasg






AD-63262
A-122745.20
CfsusGfgUfaUfuUfCfC
653
A-126635.1
usUfsgUfaCfcCfuAfgg
710




fuAfgGfgUfaCfaAfL96


aaaUfaCfcAfgsasg






AD-63204
A-126601.1
csusgguauuucdCuaggg
654
A-122746.20
usUfsgUfaCfcCfuAfgg
711




uacaaL96


aAfaUfaCfcAfgsasg






AD-63230
A-126596.2
csusgguAfuuucCfuagg
655
A-126611.9
usUfsguaCfccUfaggaA
712




guadCaaL96


faUfaccagsasg






AD-63198
A-126600.1
csusgguauuucdCdTagg
656
A-122746.19
usUfsgUfaCfcCfuAfgg
713




guacaaL96


aAfaUfaCfcAfgsasg






AD-63206
A-126591.2
csusgguAfuuucCfuagg
657
A-126611.5
usUfsguaCfccUfaggaA
714




guacaaL96


faUfaccagsasg
















TABLE 11







TMPRSS6 Single Dose Screen












10 nM

0.1 nM














DuplexID
Avg
SD
Avg
SD
















AD-60998
26.1
3.1
42.9
13.3



AD-60970
24.3
9.3
39.0
24.2



AD-61002
27.5
8.5
32.1
9.8



AD-60994
19.9
5.8
28.2
9.3



AD-60992
57.9
15.4
67.5
13.6



AD-61006
25.8
2.5
33.4
8.7



AD-59743
21.1
3.2
31.7
8.1



AD-60966
64.6
15.6
76.0
18.2



AD-60952
44.1
10.7
76.9
16.5



AD-61000
37.2
5.8
43.3
12.7



AD-60949
94.9
22.3
91.3
13.2



AD-60969
100.7
18.5
124.5
43.0



AD-60967
93.7
6.4
112.1
31.5



AD-60984
44.7
21.4
58.2
9.6



AD-60943
65.6
11.0
61.7
9.8



AD-61001
69.2
8.3
100.8
8.4



AD-60986
38.9
13.9
58.9
4.8



AD-60988
61.7
12.0
68.6
15.2



AD-60993
92.1
13.1
86.5
10.0



AD-60987
113.9
15.3
97.9
21.0



AD-60997
54.8
7.2
75.8
16.4



AD-60973
61.5
15.7
80.8
9.3



AD-61005
116.8
23.4
128.1
10.8



AD-60985
71.2
15.1
78.7
14.6



AD-61003
101.0
15.2
97.5
15.8



AD-60989
75.8
9.8
97.2
20.8



AD-60955
108.6
23.4
102.0
16.6



AD-60991
96.6
19.4
95.6
12.4



AD-61004
111.1
6.4
110.9
18.3



AD-60961
96.9
36.0
84.1
28.2



AD-60999
106.7
12.7
92.3
24.6



AD-60990
92.9
38.4
97.6
16.8



AD-60996
71.2
7.5
101.5
8.9









Example 13. Optimization of AD-60940

Additional duplexes targeting TMPRSS6 were produced and screened in vitro for efficacy using the materials and methods below.


Design, Synthesis, and in Vitro Screening of Additional siRNAs


siRNA Design


TMPRSS6 duplexes, 19 nucleotides long for both the sense and antisense strand, were designed using the human TMPRSS6 mRNA sequence set forth in GenBank Accession No. NM_153609.3. Three thousand one hundred and eighty duplexes were initially identified that did not contain repeats longer than 7 nucleotides, spanning substantially the entire 3209 nucleotide transcript. All 3180 duplexes were then scored for predicted efficacy according to a linear model that evaluates the nucleotide pair at each duplex position, and the dose and cell line used for screening. The duplexes were also matched against all transcripts in the human RefSeq collection using a custom brute force algorithm, and scored for lowest numbers of mismatches (per strand) to transcripts other than TMPRSS6. Duplexes to be synthesized and screened were then selected from the 3180, according to the following scheme: Beginning at the 5′ end of the transcript, a duplex was selected within a “window” of every 10±2 nucleotides that had the highest predicted efficacy, had at least one mismatch in both strands to all transcripts other than TMPRSS6, and had not already been synthesized and screened as part of other duplex sets. If no duplex is identified within a given window that satisfied all criteria, that window was skipped. Three hundred and three duplexes were selected according to the above criteria. An additional 31 duplexes were also selected.


A detailed list of the 334 TMPRSS6 sense and antisense strand sequences is shown in Table 12.


Cell Culture and Transfections

Hep3B2.1-7 cells were obtained from American Type Culture Collection (Rockville, Md., cat. No. HB-8064) and cultured in EMEM (ATCC #30-2003), supplemented to contain 10% fetal calf serum (FCS) (Biochrom AG, Berlin, Germany, cat. No. SOI 15) and Penicillin 100 U/ml, Streptomycin 100 mg/ml (Biochrom AG, Berlin, Germany, cat. No. A2213), at 37° C. in an atmosphere with 5% CO2 in a humidified incubator (Heraeus HERAcell, Kendro Laboratory Products, Langenselbold, Germany).


Transfection of dsRNA was performed directly after seeding 15,000 cells/well on a 96-well plate, and was carried out with Lipofectamine 2000 (Invitrogen GmbH, Karlsruhe, Germany, cat.No. 11668-019) as described by the manufacturer. Transfections were performed in quadruplicates and dsRNAs were transfected at a concentration of 10 nM.


Branched DNA Assays—QuantiGene 2.0 (Panomics cat #; OS0011)

For measurement of TMPRSS6 mRNA cells were harvested 24 hours after transfection and lysed at 53° C. following procedures recommended by the manufacturer of the Quantigene II Kit for TMPRSS6 and Quantigene I Explore Kit for bDNA (Panomics, Fremont, Calif., USA, cat. No. 15735 or QG0004, respectively). Subsequently, 50 μl of the lysates were incubated with probesets specific to human TMPRSS6 and 10 μl of the lysates for human GAPDH and processed according to the manufacturer's protocol for QuantiGene. Chemoluminescence was measured in a Victor2-Light (Perkin Elmer, Wiesbaden, Germany) as RLUs (relative light units) and values obtained with the human TMPRSS6 probeset were normalized to the respective human GAPDH values for each well and then related to the mean of three unrelated control dsRNAs.


The in vitro efficacy of the compounds is shown in Table 13.









TABLE 12







Additional modified TMPRSS6 siRNAs
















SEQ

Position

SEQ




Sense
ID

in NM_

ID
Antisense


Duplex ID
Sequence
NO:
Sense ID
153609.3
Antisense Sequence
NO:
ID





AD-63290.1
UGAGCCAGACCC
 715
A-126858.1
3-21
CUGGACUGGGUCUGGCUCAdTdT
1049
A-126859.1



AGUCCAGdTdT











AD-63296.1
GACCCAGUCCAG
 716
A-126860.1
10-28
ACCAGAGCUGGACUGGGUCdTdT
1050
A-126861.1



CUCUGGUdTdT











AD-63302.1
CUCUGGUGCCUG
 717
A-126862.1
22-40
CAGAGGGCAGGCACCAGAGdTdT
1051
A-126863.1



CCCUCUGdTdT











AD-63308.1
GCCCUCUGGUGC
 718
A-126864.1
33-51
UCAGCUCGCACCAGAGGGCdTdT
1052
A-126865.1



GAGCUGAdTdT











AD-63314.1
GGUGCGAGCUGA
 719
A-126866.1
40-58
UCUCAGGUCAGCUCGCACCdTdT
1053
A-126867.1



CCUGAGAdTdT











AD-63320.1
UGACCUGAGAUG
 720
A-126868.1
49-67
GGAAGUGCAUCUCAGGUCAdTdT
1054
A-126869.1



CACUUCCdTdT











AD-63326.1
UGCACUUCCCUC
 721
A-126870.1
59-77
CACAGAGGAGGGAAGUGCAdTdT
1055
A-126871.1



CUCUGUGdTdT











AD-63332.1
CUGUGAGCUGUC
 722
A-126872.1
73-91
GUGCCGAGACAGCUCACAGdTdT
1056
A-126873.1



UCGGCACdTdT











AD-63291.1
GUCUCGGCACCC
 723
A-126874.1
 82-100
UGCAAGUGGGUGCCGAGACdTdT
1057
A-126875.1



ACUUGCAdTdT











AD-63297.1
CCACUUGCAGUC
 724
A-126876.1
 92-110
CGGCAGUGACUGCAAGUGGdTdT
1058
A-126877.1



ACUGCCGdTdT











AD-63303.1
GUCACUGCCGCC
 725
A-126878.1
101-119
AACAUCAGGCGGCAGUGACdTdT
1059
A-126879.1



UGAUGUUdTdT











AD-63309.1
GCCUGAUGUUGU
 726
A-126880.1
110-128
AAGAGUAACAACAUCAGGCdTdT
1060
A-126881.1



UACUCUUdTdT











AD-63315.1
UUACUCUUCCAC
 727
A-126882.1
121-139
UUUUGGAGUGGAAGAGUAAdTdT
1061
A-126883.1



UCCAAAAdTdT











AD-63321.1
ACUCCAAAAGGA
 728
A-126884.1
131-149
ACGGGCAUCCUUUUGGAGUdTdT
1062
A-126885.1



UGCCCGUdTdT











AD-63327.1
UGCCCGUGGCCG
 729
A-126886.1
143-161
GGGGCCUCGGCCACGGGCAdTdT
1063
A-126887.1



AGGCCCCdTdT











AD-63333.1
UGGCCGAGGCCC
 730
A-126888.1
149-167
ACCUGGGGGGCCUCGGCCAdTdT
1064
A-126889.1



CCCAGGUdTdT











AD-63292.1
CCAGGUGGCUGG
 731
A-126890.1
162-180
CUGCCCGCCAGCCACCUGGdTdT
1065
A-126891.1



CGGGCAGdTdT











AD-63298.1
GCGGGCAGGGGG
 732
A-126892.1
173-191
CCUCCGUCCCCCUGCCCGCdTdT
1066
A-126893.1



ACGGAGGdTdT











AD-63304.1
GGACGGAGGUGA
 733
A-126894.1
183-201
CUCGCCAUCACCUCCGUCCdTdT
1067
A-126895.1



UGGCGAGdTdT











AD-63310.1
GUGAUGGCGAGG
 734
A-126896.1
191-209
UCCGCUUCCUCGCCAUCACdTdT
1068
A-126897.1



AAGCGGAdTdT











AD-63316.1
GAAGCGGAGCCG
 735
A-126898.1
202-220
UCCCCUCCGGCUCCGCUUCdTdT
1069
A-126899.1



GAGGGGAdTdT











AD-63322.1
GCCGGAGGGGAU
 736
A-126900.1
210-228
CUUGAACAUCCCCUCCGGCdTdT
1070
A-126901.1



GUUCAAGdTdT











AD-63328.1
UGUUCAAGGCCU
 737
A-126902.1
221-239
UCCUCACAGGCCUUGAACAdTdT
1071
A-126903.1



GUGAGGAdTdT











AD-63334.1
CUGUGAGGACUC
 738
A-126904.1
231-249
UCUCUUGGAGUCCUCACAGdTdT
1072
A-126905.1



CAAGAGAdTdT











AD-63293.1
ACUCCAAGAGAA
 739
A-126906.1
239-257
CGGGCUUUUCUCUUGGAGUdTdT
1073
A-126907.1



AAGCCCGdTdT











AD-63299.1
GCCCGGGGCUAC
 740
A-126908.1
253-271
GGCGGAGGUAGCCCCGGGCdTdT
1074
A-126909.1



CUCCGCCdTdT











AD-63305.1
ACCUCCGCCUGG
 741
A-126910.1
263-281
AGGGGCACCAGGCGGAGGUdTdT
1075
A-126911.1



UGCCCCUdTdT











AD-63311.1
GCCUGGUGCCCC
 742
A-126912.1
269-287
ACAAACAGGGGCACCAGGCdTdT
1076
A-126913.1



UGUUUGUdTdT











AD-63317.1
UGUUUGUGCUGC
 743
A-126914.1
281-299
AGGGCCAGCAGCACAAACAdTdT
1077
A-126915.1



UGGCCCUdTdT











AD-63323.1
UGCUGGCCCUGC
 744
A-126916.1
290-308
AGCACGAGCAGGGCCAGCAdTdT
1078
A-126917.1



UCGUGCUdTdT











AD-63329.1
GCUCGUGCUGGC
 745
A-126918.1
300-318
CGCCGAAGCCAGCACGAGCdTdT
1079
A-126919.1



UUCGGCGdTdT











AD-63335.1
UCGGCGGGGGUG
 746
A-126920.1
313-331
AGAGUAGCACCCCCGCCGAdTdT
1080
A-126921.1



CUACUCUdTdT











AD-63294.1
CGGCGGGGGUGC
 747
A-126922.1
314-332
CAGAGUAGCACCCCCGCCGdTdT
1081
A-126923.1



UACUCUGdTdT











AD-63300.1
GGCGGGGGUGCU
 748
A-126924.1
315-333
CCAGAGUAGCACCCCCGCCdTdT
1082
A-126925.1



ACUCUGGdTdT











AD-63306.1
GCGGGGGUGCUA
 749
A-126926.1
316-334
ACCAGAGUAGCACCCCCGCdTdT
1083
A-126927.1



CUCUGGUdTdT











AD-63312.1
CGGGGGUGCUAC
 750
A-126928.1
317-335
UACCAGAGUAGCACCCCCGdTdT
1084
A-126929.1



UCUGGUAdTdT











AD-63318.1
GGGGGUGCUACU
 751
A-126930.1
318-336
AUACCAGAGUAGCACCCCCdTdT
1085
A-126931.1



CUGGUAUdTdT











AD-63324.1
GGGUGCUACUCU
 752
A-126932.1
320-338
AAAUACCAGAGUAGCACCCdTdT
1086
A-126933.1



GGUAUUUdTdT











AD-63330.1
GGUGCUACUCUG
 753
A-126934.1
321-339
GAAAUACCAGAGUAGCACCdTdT
1087
A-126935.1



GUAUUUCdTdT











AD-63336.1
GUGCUACUCUGG
 754
A-126936.1
322-340
GGAAAUACCAGAGUAGCACdTdT
1088
A-126937.1



UAUUUCCdTdT











AD-63295.1
GCUACUCUGGUA
 755
A-126938.1
324-342
UAGGAAAUACCAGAGUAGCdTdT
1089
A-126939.1



UUUCCUAdTdT











AD-63301.1
CUACUCUGGUAU
 756
A-126940.1
325-343
CUAGGAAAUACCAGAGUAGdTdT
1090
A-126941.1



UUCCUAGdTdT











AD-63307.1
UACUCUGGUAUU
 757
A-126942.1
326-344
CCUAGGAAAUACCAGAGUAdTdT
1091
A-126943.1



UCCUAGGdTdT











AD-63313.1
ACUCUGGUAUUU
 758
A-126944.1
327-345
CCCUAGGAAAUACCAGAGUdTdT
1092
A-126945.1



CCUAGGGdTdT











AD-63319.1
CUCUGGUAUUUC
 759
A-126946.1
328-346
ACCCUAGGAAAUACCAGAGdTdT
1093
A-126947.1



CUAGGGUdTdT











AD-63325.1
CUGGUAUUUCCU
 760
A-126948.1
330-348
GUACCCUAGGAAAUACCAGdTdT
1094
A-126949.1



AGGGUACdTdT











AD-63331.1
GUAUUUCCUAGG
 761
A-126950.1
333-351
CUUGUACCCUAGGAAAUACdTdT
1095
A-126951.1



GUACAAGdTdT











AD-63337.1
UAUUUCCUAGGG
 762
A-126952.1
334-352
CCUUGUACCCUAGGAAAUAdTdT
1096
A-126953.1



UACAAGGdTdT











AD-63343.1
AUUUCCUAGGGU
 763
A-126954.1
335-353
GCCUUGUACCCUAGGAAAUdTdT
1097
A-126955.1



ACAAGGCdTdT











AD-63349.1
UUUCCUAGGGUA
 764
A-126956.1
336-354
CGCCUUGUACCCUAGGAAAdTdT
1098
A-126957.1



CAAGGCGdTdT











AD-63355.1
UUCCUAGGGUAC
 765
A-126958.1
337-355
CCGCCUUGUACCCUAGGAAdTdT
1099
A-126959.1



AAGGCGGdTdT











AD-63361.1
CCUAGGGUACAA
 766
A-126960.1
339-357
CUCCGCCUUGUACCCUAGGdTdT
1100
A-126961.1



GGCGGAGdTdT











AD-63367.1
CUAGGGUACAAG
 767
A-126962.1
340-358
CCUCCGCCUUGUACCCUAGdTdT
1101
A-126963.1



GCGGAGGdTdT











AD-63373.1
UAGGGUACAAGG
 768
A-126964.1
341-359
ACCUCCGCCUUGUACCCUAdTdT
1102
A-126965.1



CGGAGGUdTdT











AD-63379.1
AGGGUACAAGGC
 769
A-126966.1
342-360
CACCUCCGCCUUGUACCCUdTdT
1103
A-126967.1



GGAGGUGdTdT











AD-63338.1
GGGUACAAGGCG
 770
A-126968.1
343-361
UCACCUCCGCCUUGUACCCdTdT
1104
A-126969.1



GAGGUGAdTdT











AD-63344.1
GGUACAAGGCGG
 771
A-126970.1
344-362
AUCACCUCCGCCUUGUACCdTdT
1105
A-126971.1



AGGUGAUdTdT











AD-63350.1
GUACAAGGCGGA
 772
A-126972.1
345-363
CAUCACCUCCGCCUUGUACdTdT
1106
A-126973.1



GGUGAUGdTdT











AD-63356.1
UACAAGGCGGAG
 773
A-126974.1
346-364
CCAUCACCUCCGCCUUGUAdTdT
1107
A-126975.1



GUGAUGGdTdT











AD-63362.1
ACAAGGCGGAGG
 774
A-126976.1
347-365
ACCAUCACCUCCGCCUUGUdTdT
1108
A-126977.1



UGAUGGUdTdT











AD-63368.1
CAAGGCGGAGGU
 775
A-126978.1
348-366
GACCAUCACCUCCGCCUUGdTdT
1109
A-126979.1



GAUGGUCdTdT











AD-63374.1
AAGGCGGAGGUG
 776
A-126980.1
349-367
UGACCAUCACCUCCGCCUUdTdT
1110
A-126981.1



AUGGUCAdTdT











AD-63380.1
AGGCGGAGGUGA
 777
A-126982.1
350-368
CUGACCAUCACCUCCGCCUdTdT
1111
A-126983.1



UGGUCAGdTdT











AD-63339.1
UGAUGGUCAGCC
 778
A-126984.1
359-377
UACACCUGGCUGACCAUCAdTdT
1112
A-126985.1



AGGUGUAdTdT











AD-63345.1
CCAGGUGUACUC
 779
A-126986.1
369-387
ACUGCCUGAGUACACCUGGdTdT
1113
A-126987.1



AGGCAGUdTdT











AD-63351.1
GCAGUCUGCGUG
 780
A-126988.1
383-401
UUGAGUACACGCAGACUGCdTdT
1114
A-126989.1



UACUCAAdTdT











AD-63357.1
GCGUGUACUCAA
 781
A-126990.1
390-408
GUGGCGAUUGAGUACACGCdTdT
1115
A-126991.1



UCGCCACdTdT











AD-63363.1
UCGCCACUUCUC
 782
A-126992.1
402-420
AUCCUGGGAGAAGUGGCGAdTdT
1116
A-126993.1



CCAGGAUdTdT











AD-63369.1
CUCCCAGGAUCU
 783
A-126994.1
411-429
GCGGGUAAGAUCCUGGGAGdTdT
1117
A-126995.1



UACCCGCdTdT











AD-63375.1
UACCCGCCGGGA
 784
A-126996.1
423-441
ACUAGAUUCCCGGCGGGUAdTdT
1118
A-126997.1



AUCUAGUdTdT











AD-63381.1
CCGGGAAUCUAG
 785
A-126998.1
429-447
GAAGGCACUAGAUUCCCGGdTdT
1119
A-126999.1



UGCCUUCdTdT











AD-63340.1
AGUGCCUUCCGC
 786
A-127000.1
439-457
UUUCACUGCGGAAGGCACUdTdT
1120
A-127001.1



AGUGAAAdTdT











AD-63346.1
GUGAAACCGCCA
 787
A-127002.1
452-470
UGGGCUUUGGCGGUUUCACdTdT
1121
A-127003.1



AAGCCCAdTdT











AD-63352.1
CGCCAAAGCCCA
 788
A-127004.1
459-477
CAUCUUCUGGGCUUUGGCGdTdT
1122
A-127005.1



GAAGAUGdTdT











AD-63358.1
CAGAAGAUGCUC
 789
A-127006.1
469-487
GCUCCUUGAGCAUCUUCUGdTdT
1123
A-127007.1



AAGGAGCdTdT











AD-63364.1
UCAAGGAGCUCA
 790
A-127008.1
479-497
CUGGUGAUGAGCUCCUUGAdTdT
1124
A-127009.1



UCACCAGdTdT











AD-63370.1
ACCAGCACCCGC
 791
A-127010.1
493-511
UUCCCAGGCGGGUGCUGGUdTdT
1125
A-127011.1



CUGGGAAdTdT











AD-63376.1
GCCUGGGAACUU
 792
A-127012.1
503-521
UUGUAGUAAGUUCCCAGGCdTdT
1126
A-127013.1



ACUACAAdTdT











AD-63382.1
GAACUUACUACA
 793
A-127014.1
509-527
CUGGAGUUGUAGUAAGUUCdTdT
1127
A-127015.1



ACUCCAGdTdT











AD-63341.1
AACUCCAGCUCC
 794
A-127016.1
520-538
AAUAGACGGAGCUGGAGUUdTdT
1128
A-127017.1



GUCUAUUdTdT











AD-63347.1
CCGUCUAUUCCU
 795
A-127018.1
530-548
UCCCCAAAGGAAUAGACGGdTdT
1129
A-127019.1



UUGGGGAdTdT











AD-63353.1
UUGGGGAGGGAC
 796
A-127020.1
542-560
GUGAGGGGUCCCUCCCCAAdTdT
1130
A-127021.1



CCCUCACdTdT











AD-63359.1
CCCCUCACCUGC
 797
A-127022.1
553-571
AGAAGAAGCAGGUGAGGGGdTdT
1131
A-127023.1



UUCUUCUdTdT











AD-63365.1
CUGCUUCUUCUG
 798
A-127024.1
561-579
AAUGAACCAGAAGAAGCAGdTdT
1132
A-127025.1



GUUCAUUdTdT











AD-63371.1
CUGGUUCAUUCU
 799
A-127026.1
570-588
GAUUUGGAGAAUGAACCAGdTdT
1133
A-127027.1



CCAAAUCdTdT











AD-63377.1
UCUCCAAAUCCC
 800
A-127028.1
579-597
GUGCUCGGGGAUUUGGAGAdTdT
1134
A-127029.1



CGAGCACdTdT











AD-63383.1
CCGAGCACCGCC
 801
A-127030.1
590-608
AUCAGCCGGCGGUGCUCGGdTdT
1135
A-127031.1



GGCUGAUdTdT











AD-63342.1
GGCUGAUGCUGA
 802
A-127032.1
602-620
UCGGGGCUCAGCAUCAGCCdTdT
1136
A-127033.1



GCCCCGAdTdT











AD-63348.1
UGAGCCCCGAGG
 803
A-127034.1
611-629
UGCACCACCUCGGGGCUCAdTdT
1137
A-127035.1



UGGUGCAdTdT











AD-63354.1
UGGUGCAGGCAC
 804
A-127036.1
623-641
ACCAGCAGUGCCUGCACCAdTdT
1138
A-127037.1



UGCUGGUdTdT











AD-63360.1
AGGCACUGCUGG
 805
A-127038.1
629-647
UCCUCCACCAGCAGUGCCUdTdT
1139
A-127039.1



UGGAGGAdTdT











AD-63366.1
GUGGAGGAGCUG
 806
A-127040.1
640-658
UGGACAGCAGCUCCUCCACdTdT
1140
A-127041.1



CUGUCCAdTdT











AD-63372.1
UGUCCACAGUCA
 807
A-127042.1
653-671
GAGCUGUUGACUGUGGACAdTdT
1141
A-127043.1



ACAGCUCdTdT











AD-63378.1
UCAACAGCUCGG
 808
A-127044.1
662-680
ACGGCAGCCGAGCUGUUGAdTdT
1142
A-127045.1



CUGCCGUdTdT











AD-63384.1
UCGGCUGCCGUC
 809
A-127046.1
670-688
UGUAGGGGACGGCAGCCGAdTdT
1143
A-127047.1



CCCUACAdTdT











AD-63390.1
AGUGGACCCCGA
 810
A-127048.1
702-720
UAGGCCCUCGGGGUCCACUdTdT
1144
A-127049.1



GGGCCUAdTdT











AD-63396.1
AGGGCCUAGUGA
 811
A-127050.1
713-731
UCCAGGAUCACUAGGCCCUdTdT
1145
A-127051.1



UCCUGGAdTdT











AD-63402.1
UAGUGAUCCUGG
 812
A-127052.1
719-737
CUGGCUUCCAGGAUCACUAdTdT
1146
A-127053.1



AAGCCAGdTdT











AD-63408.1
AAGCCAGUGUGA
 813
A-127054.1
731-749
AUGUCUUUCACACUGGCUUdTdT
1147
A-127055.1



AAGACAUdTdT











AD-63414.1
UGAAAGACAUAG
 814
A-127056.1
740-758
AAUGCAGCUAUGUCUUUCAdTdT
1148
A-127057.1



CUGCAUUdTdT











AD-63420.1
UGCAUUGAAUUC
 815
A-127058.1
753-771
CAGCGUGGAAUUCAAUGCAdTdT
1149
A-127059.1



CACGCUGdTdT











AD-63426.1
CUACAGCUACGU
 816
A-127060.1
783-801
CUGGCCCACGUAGCUGUAGdTdT
1150
A-127061.1



GGGCCAGdTdT











AD-63385.1
CUACGUGGGCCA
 817
A-127062.1
789-807
CUGGCCCUGGCCCACGUAGdTdT
1151
A-127063.1



GGGCCAGdTdT











AD-63391.1
AGGGCCAGGUCC
 818
A-127064.1
800-818
AGCCGGAGGACCUGGCCCUdTdT
1152
A-127065.1



UCCGGCUdTdT











AD-63397.1
CCGGCUGAAGGG
 819
A-127066.1
813-831
GUCAGGCCCCUUCAGCCGGdTdT
1153
A-127067.1



GCCUGACdTdT











AD-63403.1
GGGCCUGACCAC
 820
A-127068.1
823-841
AGGCCAGGUGGUCAGGCCCdTdT
1154
A-127069.1



CUGGCCUdTdT











AD-63409.1
CCACCUGGCCUC
 821
A-127070.1
831-849
GCAGCUGGAGGCCAGGUGGdTdT
1155
A-127071.1



CAGCUGCdTdT











AD-63415.1
CCAGCUGCCUGU
 822
A-127072.1
842-860
AGGUGCCACAGGCAGCUGGdTdT
1156
A-127073.1



GGCACCUdTdT











AD-63421.1
CUGUGGCACCUG
 823
A-127074.1
850-868
GGCCCUGCAGGUGCCACAGdTdT
1157
A-127075.1



CAGGGCCdTdT











AD-63427.1
CUGCAGGGCCCC
 824
A-127076.1
859-877
GGUCCUUGGGGCCCUGCAGdTdT
1158
A-127077.1



AAGGACCdTdT











AD-63386.1
CCAAGGACCUCA
 825
A-127078.1
869-887
UUGAGCAUGAGGUCCUUGGdTdT
1159
A-127079.1



UGCUCAAdTdT











AD-63392.1
UGCUCAAACUCC
 826
A-127080.1
881-899
UCCAGCCGGAGUUUGAGCAdTdT
1160
A-127081.1



GGCUGGAdTdT











AD-63398.1
CCGGCUGGAGUG
 827
A-127082.1
891-909
CAGCGUCCACUCCAGCCGGdTdT
1161
A-127083.1



GACGCUGdTdT











AD-63404.1
GACGCUGGCAGA
 828
A-127084.1
903-921
CCGGCACUCUGCCAGCGUCdTdT
1162
A-127085.1



GUGCCGGdTdT











AD-63410.1
GGCAGAGUGCCG
 829
A-127086.1
909-927
UCGGUCCCGGCACUCUGCCdTdT
1163
A-127087.1



GGACCGAdTdT











AD-63416.1
ACCGACUGGCCA
 830
A-127088.1
923-941
UCAUACAUGGCCAGUCGGUdTdT
1164
A-127089.1



UGUAUGAdTdT











AD-63422.1
CCAUGUAUGACG
 831
A-127090.1
932-950
CCGGCCACGUCAUACAUGGdTdT
1165
A-127091.1



UGGCCGGdTdT











AD-63428.1
GUGGCCGGGCCC
 832
A-127092.1
943-961
UCUCCAGGGGCCCGGCCACdTdT
1166
A-127093.1



CUGGAGAdTdT











AD-63387.1
CCCUGGAGAAGA
 833
A-127094.1
953-971
AUGAGCCUCUUCUCCAGGGdTdT
1167
A-127095.1



GGCUCAUdTdT











AD-63393.1
AGAAGAGGCUCA
 834
A-127096.1
959-977
GAGGUGAUGAGCCUCUUCUdTdT
1168
A-127097.1



UCACCUCdTdT











AD-63399.1
ACCUCGGUGUAC
 835
A-127098.1
973-991
UGCAGCCGUACACCGAGGUdTdT
1169
A-127099.1



GGCUGCAdTdT











AD-63405.1
ACGGCUGCAGCC
 836
A-127100.1
 983-1001
UCCUGGCGGCUGCAGCCGUdTdT
1170
A-127101.1



GCCAGGAdTdT











AD-63411.1
GCCGCCAGGAGC
 837
A-127102.1
 992-1010
ACCACGGGCUCCUGGCGGCdTdT
1171
A-127103.1



CCGUGGUdTdT











AD-63417.1
AGCCCGUGGUGG
 838
A-127104.1
1001-1019
AGAACCUCCACCACGGGCUdTdT
1172
A-127105.1



AGGUUCUdTdT











AD-63423.1
GUGGAGGUUCUG
 839
A-127106.1
1009-1027
CCGACGCCAGAACCUCCACdTdT
1173
A-127107.1



GCGUCGGdTdT











AD-63429.1
UGGCGUCGGGGG
 840
A-127108.1
1019-1037
AUGAUGGCCCCCGACGCCAdTdT
1174
A-127109.1



CCAUCAUdTdT











AD-63388.1
CCAUCAUGGCGG
 841
A-127110.1
1031-1049
CAGACGACCGCCAUGAUGGdTdT
1175
A-127111.1



UCGUCUGdTdT











AD-63394.1
GCGGUCGUCUGG
 842
A-127112.1
1039-1057
CCUUCUUCCAGACGACCGCdTdT
1176
A-127113.1



AAGAAGGdTdT











AD-63400.1
GGAAGAAGGGCC
 843
A-127114.1
1049-1067
CUGUGCAGGCCCUUCUUCCdTdT
1177
A-127115.1



UGCACAGdTdT











AD-63406.1
CCUGCACAGCUA
 844
A-127116.1
1059-1077
GUCGUAGUAGCUGUGCAGGdTdT
1178
A-127117.1



CUACGACdTdT











AD-63412.1
ACUACGACCCCU
 845
A-127118.1
1070-1088
AGCACGAAGGGGUCGUAGUdTdT
1179
A-127119.1



UCGUGCUdTdT











AD-63418.1
CCUUCGUGCUCU
 846
A-127120.1
1079-1097
UGCACGGAGAGCACGAAGGdTdT
1180
A-127121.1



CCGUGCAdTdT











AD-63424.1
CCGUGCAGCCGG
 847
A-127122.1
1091-1109
AAGACCACCGGCUGCACGGdTdT
1181
A-127123.1



UGGUCUUdTdT











AD-63430.1
CGGUGGUCUUCC
 848
A-127124.1
1100-1118
CAGGCCUGGAAGACCACCGdTdT
1182
A-127125.1



AGGCCUGdTdT











AD-63389.1
AGGCCUGUGAAG
 849
A-127126.1
1112-1130
AGGUUCACUUCACAGGCCUdTdT
1183
A-127127.1



UGAACCUdTdT











AD-63395.1
AAGUGAACCUGA
 850
A-127128.1
1121-1139
UCCAGCGUCAGGUUCACUUdTdT
1184
A-127129.1



CGCUGGAdTdT











AD-63401.1
GACGCUGGACAA
 851
A-127130.1
1131-1149
GAGCCUGUUGUCCAGCGUCdTdT
1185
A-127131.1



CAGGCUCdTdT











AD-63407.1
ACAACAGGCUCG
 852
A-127132.1
1139-1157
UGGGAGUCGAGCCUGUUGUdTdT
1186
A-127133.1



ACUCCCAdTdT











AD-63413.1
ACUCCCAGGGCG
 853
A-127134.1
1151-1169
CUGAGGACGCCCUGGGAGUdTdT
1187
A-127135.1



UCCUCAGdTdT











AD-63419.1
CCCCGUACUUCC
 854
A-127136.1
1172-1190
UAGCUGGGGAAGUACGGGGdTdT
1188
A-127137.1



CCAGCUAdTdT











AD-63425.1
UUCCCCAGCUAC
 855
A-127138.1
1180-1198
GCGAGUAGUAGCUGGGGAAdTdT
1189
A-127139.1



UACUCGCdTdT











AD-63431.1
ACUACUCGCCCC
 856
A-127140.1
1190-1208
UGGGUUUGGGGCGAGUAGUdTdT
1190
A-127141.1



AAACCCAdTdT











AD-63437.1
CCCAAACCCACU
 857
A-127142.1
1199-1217
CAGGAGCAGUGGGUUUGGGdTdT
1191
A-127143.1



GCUCCUGdTdT











AD-63443.1
GCUCCUGGCACC
 858
A-127144.1
1211-1229
ACCGUGAGGUGCCAGGAGCdTdT
1192
A-127145.1



UCACGGUdTdT











AD-63449.1
ACCUCACGGUGC
 859
A-127146.1
1220-1238
AGAGAGGGCACCGUGAGGUdTdT
1193
A-127147.1



CCUCUCUdTdT











AD-63455.1
CUCUCUGGACUA
 860
A-127148.1
1233-1251
CAAGCCGUAGUCCAGAGAGdTdT
1194
A-127149.1



CGGCUUGdTdT











AD-63461.1
GACUACGGCUUG
 861
A-127150.1
1240-1258
AGAGGGCCAAGCCGUAGUCdTdT
1195
A-127151.1



GCCCUCUdTdT











AD-63467.1
CCCUCUGGUUUG
 862
A-127152.1
1253-1271
UAGGCAUCAAACCAGAGGGdTdT
1196
A-127153.1



AUGCCUAdTdT











AD-63473.1
GUUUGAUGCCUA
 863
A-127154.1
1260-1278
CAGUGCAUAGGCAUCAAACdTdT
1197
A-127155.1



UGCACUGdTdT











AD-63432.1
GCACUGAGGAGG
 864
A-127156.1
1273-1291
ACUUCUGCCUCCUCAGUGCdTdT
1198
A-127157.1



CAGAAGUdTdT











AD-63438.1
GGAGGCAGAAGU
 865
A-127158.1
1280-1298
AAAUCAUACUUCUGCCUCCdTdT
1199
A-127159.1



AUGAUUUdTdT











AD-63444.1
AUGAUUUGCCGU
 866
A-127160.1
1292-1310
UGGGUGCACGGCAAAUCAUdTdT
1200
A-127161.1



GCACCCAdTdT











AD-63450.1
UGCACCCAGGGC
 867
A-127162.1
1303-1321
UCCACUGGCCCUGGGUGCAdTdT
1201
A-127163.1



CAGUGGAdTdT











AD-63456.1
GCCAGUGGACGA
 868
A-127164.1
1313-1331
UUCUGGAUCGUCCACUGGCdTdT
1202
A-127165.1



UCCAGAAdTdT











AD-63462.1
GGACGAUCCAGA
 869
A-127166.1
1319-1337
CUCCUGUUCUGGAUCGUCCdTdT
1203
A-127167.1



ACAGGAGdTdT











AD-63468.1
ACAGGAGGCUGU
 870
A-127168.1
1331-1349
AAGCCACACAGCCUCCUGUdTdT
1204
A-127169.1



GUGGCUUdTdT











AD-63474.1
CUGUGUGGCUUG
 871
A-127170.1
1339-1357
GGAUGCGCAAGCCACACAGdTdT
1205
A-127171.1



CGCAUCCdTdT











AD-63433.1
UGCGCAUCCUGC
 872
A-127172.1
1349-1367
UAGGGCUGCAGGAUGCGCAdTdT
1206
A-127173.1



AGCCCUAdTdT











AD-63439.1
AGCCCUACGCCG
 873
A-127174.1
1361-1379
AUCCUCUCGGCGUAGGGCUdTdT
1207
A-127175.1



AGAGGAUdTdT











AD-63445.1
CCGAGAGGAUCC
 874
A-127176.1
1370-1388
ACCACGGGGAUCCUCUCGGdTdT
1208
A-127177.1



CCGUGGUdTdT











AD-63451.1
CCGUGGUGGCCA
 875
A-127178.1
1382-1400
CCGGCCGUGGCCACCACGGdTdT
1209
A-127179.1



CGGCCGGdTdT











AD-63457.1
CCACGGCCGGGA
 876
A-127180.1
1391-1409
AUGGUGAUCCCGGCCGUGGdTdT
1210
A-127181.1



UCACCAUdTdT











AD-63463.1
GGAUCACCAUCA
 877
A-127182.1
1400-1418
GUGAAGUUGAUGGUGAUCCdTdT
1211
A-127183.1



ACUUCACdTdT











AD-63469.1
UCAACUUCACCU
 878
A-127184.1
1409-1427
AUCUGGGAGGUGAAGUUGAdTdT
1212
A-127185.1



CCCAGAUdTdT











AD-63475.1
CCCAGAUCUCCC
 879
A-127186.1
1421-1439
CCGGUGAGGGAGAUCUGGGdTdT
1213
A-127187.1



UCACCGGdTdT











AD-63434.1
CCCUCACCGGGC
 880
A-127188.1
1430-1448
ACACCGGGCCCGGUGAGGGdTdT
1214
A-127189.1



CCGGUGUdTdT











AD-63440.1
CCCGGUGUGCGG
 881
A-127190.1
1441-1459
AGUGCACCCGCACACCGGGdTdT
1215
A-127191.1



GUGCACUdTdT











AD-63446.1
GCUUGUACAACC
 882
A-127192.1
1463-1481
UCCGACUGGUUGUACAAGCdTdT
1216
A-127193.1



AGUCGGAdTdT











AD-63452.1
ACAACCAGUCGG
 883
A-127194.1
1469-1487
CAGGGGUCCGACUGGUUGUdTdT
1217
A-127195.1



ACCCCUGdTdT











AD-63458.1
ACCCCUGCCCUG
 884
A-127196.1
1481-1499
AACUCUCCAGGGCAGGGGUdTdT
1218
A-127197.1



GAGAGUUdTdT











AD-63464.1
CCUGGAGAGUUC
 885
A-127198.1
1489-1507
AACAGAGGAACUCUCCAGGdTdT
1219
A-127199.1



CUCUGUUdTdT











AD-63470.1
UCUGUUCUGUGA
 886
A-127200.1
1502-1520
AGUCCAUUCACAGAACAGAdTdT
1220
A-127201.1



AUGGACUdTdT











AD-63476.1
GAAUGGACUCUG
 887
A-127202.1
1512-1530
AGGGACACAGAGUCCAUUCdTdT
1221
A-127203.1



UGUCCCUdTdT











AD-63435.1
CUGUGUCCCUGC
 888
A-127204.1
1521-1539
AUCACAGGCAGGGACACAGdTdT
1222
A-127205.1



CUGUGAUdTdT











AD-63441.1
CUGCCUGUGAUG
 889
A-127206.1
1529-1547
UUGACCCCAUCACAGGCAGdTdT
1223
A-127207.1



GGGUCAAdTdT











AD-63447.1
GGUCAAGGACUG
 890
A-127208.1
1542-1560
GUUGGGGCAGUCCUUGACCdTdT
1224
A-127209.1



CCCCAACdTdT











AD-63453.1
UGCCCCAACGGC
 891
A-127210.1
1552-1570
CAUCCAGGCCGUUGGGGCAdTdT
1225
A-127211.1



CUGGAUGdTdT











AD-63459.1
CGGCCUGGAUGA
 892
A-127212.1
1560-1578
GUUUCUCUCAUCCAGGCCGdTdT
1226
A-127213.1



GAGAAACdTdT











AD-63465.1
GAGAGAAACUGC
 893
A-127214.1
1570-1588
UGCAAACGCAGUUUCUCUCdTdT
1227
A-127215.1



GUUUGCAdTdT











AD-63471.1
UUUGCAGAGCCA
 894
A-127216.1
1583-1601
UGGAAUGUGGCUCUGCAAAdTdT
1228
A-127217.1



CAUUCCAdTdT











AD-63477.1
GCCACAUUCCAG
 895
A-127218.1
1591-1609
CUUUGCACUGGAAUGUGGCdTdT
1229
A-127219.1



UGCAAAGdTdT











AD-63436.1
GUGCAAAGAGGA
 896
A-127220.1
1602-1620
UGUGCUGUCCUCUUUGCACdTdT
1230
A-127221.1



CAGCACAdTdT











AD-63442.1
GAGGACAGCACA
 897
A-127222.1
1609-1627
AGAUGCAUGUGCUGUCCUCdTdT
1231
A-127223.1



UGCAUCUdTdT











AD-63448.1
GCAUCUCACUGC
 898
A-127224.1
1622-1640
ACCUUGGGCAGUGAGAUGCdTdT
1232
A-127225.1



CCAAGGUdTdT











AD-63454.1
GCCCAAGGUCUG
 899
A-127226.1
1632-1650
CCCAUCACAGACCUUGGGCdTdT
1233
A-127227.1



UGAUGGGdTdT











AD-63460.1
UGUGAUGGGCAG
 900
A-127228.1
1642-1660
AAUCAGGCUGCCCAUCACAdTdT
1234
A-127229.1



CCUGAUUdTdT











AD-63466.1
GCAGCCUGAUUG
 901
A-127230.1
1650-1668
GUUGAGACAAUCAGGCUGCdTdT
1235
A-127231.1



UCUCAACdTdT











AD-63472.1
GUCUCAACGGCA
 902
A-127232.1
1661-1679
UCGUCGCUGCCGUUGAGACdTdT
1236
A-127233.1



GCGACGAdTdT











AD-63478.1
GCGACGAAGAGC
 903
A-127234.1
1673-1691
UGGCACUGCUCUUCGUCGCdTdT
1237
A-127235.1



AGUGCCAdTdT











AD-63484.1
AGCAGUGCCAGG
 904
A-127236.1
1682-1700
ACCCCUUCCUGGCACUGCUdTdT
1238
A-127237.1



AAGGGGUdTdT











AD-63490.1
GAAGGGGUGCCA
 905
A-127238.1
1693-1711
UCCCACAUGGCACCCCUUCdTdT
1239
A-127239.1



UGUGGGAdTdT











AD-63496.1
CCAUGUGGGACA
 906
A-127240.1
1702-1720
AGGUGAAUGUCCCACAUGGdTdT
1240
A-127241.1



UUCACCUdTdT











AD-63502.1
CAUUCACCUUCC
 907
A-127242.1
1712-1730
UCACACUGGAAGGUGAAUGdTdT
1241
A-127243.1



AGUGUGAdTdT











AD-63508.1
CAGUGUGAGGAC
 908
A-127244.1
1723-1741
AGCUCCGGUCCUCACACUGdTdT
1242
A-127245.1



CGGAGCUdTdT











AD-63514.1
GACCGGAGCUGC
 909
A-127246.1
1732-1750
UCUUCACGCAGCUCCGGUCdTdT
1243
A-127247.1



GUGAAGAdTdT











AD-63520.1
CUGCGUGAAGAA
 910
A-127248.1
1740-1758
GUUGGGCUUCUUCACGCAGdTdT
1244
A-127249.1



GCCCAACdTdT











AD-63479.1
AGCCCAACCCGC
 911
A-127250.1
1751-1769
UCACACUGCGGGUUGGGCUdTdT
1245
A-127251.1



AGUGUGAdTdT











AD-63485.1
CAGUGUGAUGGG
 912
A-127252.1
1762-1780
CGGGCCGCCCAUCACACUGdTdT
1246
A-127253.1



CGGCCCGdTdT











AD-63491.1
GCGGCCCGACUG
 913
A-127254.1
1773-1791
GUCCCUGCAGUCGGGCCGCdTdT
1247
A-127255.1



CAGGGACdTdT











AD-63497.1
CUGCAGGGACGG
 914
A-127256.1
1782-1800
AUCCGAGCCGUCCCUGCAGdTdT
1248
A-127257.1



CUCGGAUdTdT











AD-63503.1
ACGGCUCGGAUG
 915
A-127258.1
1790-1808
UGCUCCUCAUCCGAGCCGUdTdT
1249
A-127259.1



AGGAGCAdTdT











AD-63509.1
UGAGGAGCACUG
 916
A-127260.1
1800-1818
ACAGUCACAGUGCUCCUCAdTdT
1250
A-127261.1



UGACUGUdTdT











AD-63515.1
CUGUGACUGUGG
 917
A-127262.1
1809-1827
CUGGAGGCCACAGUCACAGdTdT
1251
A-127263.1



CCUCCAGdTdT











AD-63521.1
GCCUCCAGGGCC
 918
A-127264.1
1820-1838
CUGGAGGGGCCCUGGAGGCdTdT
1252
A-127265.1



CCUCCAGdTdT











AD-63480.1
CCCCUCCAGCCG
 919
A-127266.1
1830-1848
AACAAUGCGGCUGGAGGGGdTdT
1253
A-127267.1



CAUUGUUdTdT











AD-63486.1
CCGCAUUGUUGG
 920
A-127268.1
1839-1857
AGCUCCACCAACAAUGCGGdTdT
1254
A-127269.1



UGGAGCUdTdT











AD-63492.1
GUGGAGCUGUGU
 921
A-127270.1
1850-1868
UCGGAGGACACAGCUCCACdTdT
1255
A-127271.1



CCUCCGAdTdT











AD-63498.1
CUCCGAGGGUGA
 922
A-127272.1
1863-1881
UGGCCACUCACCCUCGGAGdTdT
1256
A-127273.1



GUGGCCAdTdT











AD-63504.1
GGGUGAGUGGCC
 923
A-127274.1
1869-1887
CUGCCAUGGCCACUCACCCdTdT
1257
A-127275.1



AUGGCAGdTdT











AD-63510.1
AUGGCAGGCCAG
 924
A-127276.1
1881-1899
CUGGAGGCUGGCCUGCCAUdTdT
1258
A-127277.1



CCUCCAGdTdT











AD-63516.1
CCUCCAGGUUCG
 925
A-127278.1
1893-1911
UCGACCCCGAACCUGGAGGdTdT
1259
A-127279.1



GGGUCGAdTdT











AD-63522.1
GGUUCGGGGUCG
 926
A-127280.1
1899-1917
GAUGUGUCGACCCCGAACCdTdT
1260
A-127281.1



ACACAUCdTdT











AD-63481.1
ACAUCUGUGGGG
 927
A-127282.1
1913-1931
AGGGCCCCCCCACAGAUGUdTdT
1261
A-127283.1



GGGCCCUdTdT











AD-63487.1
GUGGGGGGGCCC
 928
A-127284.1
1919-1937
GCGAUGAGGGCCCCCCCACdTdT
1262
A-127285.1



UCAUCGCdTdT











AD-63493.1
AUCGCUGACCGC
 929
A-127286.1
1933-1951
UCACCCAGCGGUCAGCGAUdTdT
1263
A-127287.1



UGGGUGAdTdT











AD-63499.1
ACCGCUGGGUGA
 930
A-127288.1
1940-1958
GCUGUUAUCACCCAGCGGUdTdT
1264
A-127289.1



UAACAGCdTdT











AD-63505.1
UGAUAACAGCUG
 931
A-127290.1
1949-1967
CAGUGGGCAGCUGUUAUCAdTdT
1265
A-127291.1



CCCACUGdTdT











AD-63511.1
CCCACUGCUUCC
 932
A-127292.1
1961-1979
UCCUCCUGGAAGCAGUGGGdTdT
1266
A-127293.1



AGGAGGAdTdT











AD-63517.1
CCAGGAGGACAG
 933
A-127294.1
1971-1989
GGCCAUGCUGUCCUCCUGGdTdT
1267
A-127295.1



CAUGGCCdTdT











AD-63523.1
ACAGCAUGGCCU
 934
A-127296.1
1979-1997
ACCGUGGAGGCCAUGCUGUdTdT
1268
A-127297.1



CCACGGUdTdT











AD-63482.1
CCACGGUGCUGU
 935
A-127298.1
1991-2009
ACGGUCCACAGCACCGUGGdTdT
1269
A-127299.1



GGACCGUdTdT











AD-63488.1
GGACCGUGUUCC
 936
A-127300.1
2003-2021
UUGCCCAGGAACACGGUCCdTdT
1270
A-127301.1



UGGGCAAdTdT











AD-63494.1
UCCUGGGCAAGG
 937
A-127302.1
2012-2030
UGCCACACCUUGCCCAGGAdTdT
1271
A-127303.1



UGUGGCAdTdT











AD-63500.1
GUGUGGCAGAAC
 938
A-127304.1
2023-2041
AGCGCGAGUUCUGCCACACdTdT
1272
A-127305.1



UCGCGCUdTdT











AD-63506.1
GAACUCGCGCUG
 939
A-127306.1
2031-2049
UCCAGGCCAGCGCGAGUUCdTdT
1273
A-127307.1



GCCUGGAdTdT











AD-63512.1
GGCCUGGAGAGG
 940
A-127308.1
2042-2060
AAGGACACCUCUCCAGGCCdTdT
1274
A-127309.1



UGUCCUUdTdT











AD-63518.1
AGGUGUCCUUCA
 941
A-127310.1
2051-2069
CUCACCUUGAAGGACACCUdTdT
1275
A-127311.1



AGGUGAGdTdT











AD-63524.1
CAAGGUGAGCCG
 942
A-127312.1
2061-2079
GAGCAGGCGGCUCACCUUGdTdT
1276
A-127313.1



CCUGCUCdTdT











AD-63483.1
GCCUGCUCCUGC
 943
A-127314.1
2072-2090
UACGGGUGCAGGAGCAGGCdTdT
1277
A-127315.1



ACCCGUAdTdT











AD-63489.1
GCACCCGUACCA
 944
A-127316.1
2082-2100
CUCUUCGUGGUACGGGUGCdTdT
1278
A-127317.1



CGAAGAGdTdT











AD-63495.1
CCACGAAGAGGA
 945
A-127318.1
2091-2109
AUGGCUGUCCUCUUCGUGGdTdT
1279
A-127319.1



CAGCCAUdTdT











AD-63501.1
AGGACAGCCAUG
 946
A-127320.1
2099-2117
UCGUAGUCAUGGCUGUCCUdTdT
1280
A-127321.1



ACUACGAdTdT











AD-63507.1
ACUACGACGUGG
 947
A-127322.1
2111-2129
AGCAGCGCCACGUCGUAGUdTdT
1281
A-127323.1



CGCUGCUdTdT











AD-63513.1
UGGCGCUGCUGC
 948
A-127324.1
2120-2138
UCGAGCUGCAGCAGCGCCAdTdT
1282
A-127325.1



AGCUCGAdTdT











AD-63519.1
AGCUCGACCACC
 949
A-127326.1
2132-2150
ACCACCGGGUGGUCGAGCUdTdT
1283
A-127327.1



CGGUGGUdTdT











AD-63525.1
CCGGUGGUGCGC
 950
A-127328.1
2143-2161
CGGCCGAGCGCACCACCGGdTdT
1284
A-127329.1



UCGGCCGdTdT











AD-63531.1
UGCGCUCGGCCG
 951
A-127330.1
2150-2168
CGCACGGCGGCCGAGCGCAdTdT
1285
A-127331.1



CCGUGCGdTdT











AD-63537.1
CCGUGCGCCCCG
 952
A-127332.1
2162-2180
AGGCAGACGGGGCGCACGGdTdT
1286
A-127333.1



UCUGCCUdTdT











AD-63543.1
CCGUCUGCCUGC
 953
A-127334.1
2171-2189
CGCGCGGGCAGGCAGACGGdTdT
1287
A-127335.1



CCGCGCGdTdT











AD-63549.1
CCGCGCGCUCCC
 954
A-127336.1
2183-2201
AAGAAGUGGGAGCGCGCGGdTdT
1288
A-127337.1



ACUUCUUdTdT











AD-63555.1
CCCACUUCUUCG
 955
A-127338.1
2192-2210
CCGGGCUCGAAGAAGUGGGdTdT
1289
A-127339.1



AGCCCGGdTdT











AD-63561.1
GAGCCCGGCCUG
 956
A-127340.1
2203-2221
AGCAGUGCAGGCCGGGCUCdTdT
1290
A-127341.1



CACUGCUdTdT











AD-63567.1
GGCCUGCACUGC
 957
A-127342.1
2209-2227
UAAUCCAGCAGUGCAGGCCdTdT
1291
A-127343.1



UGGAUUAdTdT











AD-63526.1
UGGAUUACGGGC
 958
A-127344.1
2221-2239
CGCCCCAGCCCGUAAUCCAdTdT
1292
A-127345.1



UGGGGCGdTdT











AD-63532.1
GCUGGGGCGCCU
 959
A-127346.1
2231-2249
UCGCGCAAGGCGCCCCAGCdTdT
1293
A-127347.1



UGCGCGAdTdT











AD-63538.1
UGCGCGAGGGCG
 960
A-127348.1
2243-2261
AUGGGGCCGCCCUCGCGCAdTdT
1294
A-127349.1



GCCCCAUdTdT











AD-63544.1
AGGGCGGCCCCA
 961
A-127350.1
2249-2267
UUGCUGAUGGGGCCGCCCUdTdT
1295
A-127351.1



UCAGCAAdTdT











AD-63550.1
UCAGCAACGCUC
 962
A-127352.1
2261-2279
UUCUGCAGAGCGUUGCUGAdTdT
1296
A-127353.1



UGCAGAAdTdT











AD-63556.1
UGCAGAAAGUGG
 963
A-127354.1
2273-2291
UGCACAUCCACUUUCUGCAdTdT
1297
A-127355.1



AUGUGCAdTdT











AD-63562.1
AAGUGGAUGUGC
 964
A-127356.1
2279-2297
AUCAACUGCACAUCCACUUdTdT
1298
A-127357.1



AGUUGAUdTdT











AD-63568.1
GCAGUUGAUCCC
 965
A-127358.1
2289-2307
GUCCUGUGGGAUCAACUGCdTdT
1299
A-127359.1



ACAGGACdTdT











AD-63527.1
CACAGGACCUGU
 966
A-127360.1
2300-2318
UCGCUGCACAGGUCCUGUGdTdT
1300
A-127361.1



GCAGCGAdTdT











AD-63533.1
GCAGCGAGGUCU
 967
A-127362.1
2312-2330
UAGCGAUAGACCUCGCUGCdTdT
1301
A-127363.1



AUCGCUAdTdT











AD-63539.1
GUCUAUCGCUAC
 968
A-127364.1
2320-2338
UCACCUGGUAGCGAUAGACdTdT
1302
A-127365.1



CAGGUGAdTdT











AD-63545.1
CCAGGUGACGCC
 969
A-127366.1
2331-2349
CAUGCGUGGCGUCACCUGGdTdT
1303
A-127367.1



ACGCAUGdTdT











AD-63551.1
CCACGCAUGCUG
 970
A-127368.1
2341-2359
CGGCACACAGCAUGCGUGGdTdT
1304
A-127369.1



UGUGCCGdTdT











AD-63557.1
CUGUGUGCCGGC
 971
A-127370.1
2350-2368
UGCGGUAGCCGGCACACAGdTdT
1305
A-127371.1



UACCGCAdTdT











AD-63563.1
ACCGCAAGGGCA
 972
A-127372.1
2363-2381
UCCUUCUUGCCCUUGCGGUdTdT
1306
A-127373.1



AGAAGGAdTdT











AD-63569.1
GCAAGAAGGAUG
 973
A-127374.1
2372-2390
UGACAGGCAUCCUUCUUGCdTdT
1307
A-127375.1



CCUGUCAdTdT











AD-63528.1
GCCUGUCAGGGU
 974
A-127376.1
2383-2401
CUGAGUCACCCUGACAGGCdTdT
1308
A-127377.1



GACUCAGdTdT











AD-63534.1
GUGACUCAGGUG
 975
A-127378.1
2393-2411
AGCGGACCACCUGAGUCACdTdT
1309
A-127379.1



GUCCGCUdTdT











AD-63540.1
GUGGUCCGCUGG
 976
A-127380.1
2402-2420
UUGCACACCAGCGGACCACdTdT
1310
A-127381.1



UGUGCAAdTdT











AD-63546.1
UGGUGUGCAAGG
 977
A-127382.1
2411-2429
CUGAGUGCCUUGCACACCAdTdT
1311
A-127383.1



CACUCAGdTdT











AD-63552.1
GCACUCAGUGGC
 978
A-127384.1
2422-2440
ACCAGCGGCCACUGAGUGCdTdT
1312
A-127385.1



CGCUGGUdTdT











AD-63558.1
GCCGCUGGUUCC
 979
A-127386.1
2432-2450
CCCGCCAGGAACCAGCGGCdTdT
1313
A-127387.1



UGGCGGGdTdT











AD-63564.1
UCCUGGCGGGGC
 980
A-127388.1
2441-2459
CUGACCAGCCCCGCCAGGAdTdT
1314
A-127389.1



UGGUCAGdTdT











AD-63570.1
GCUGGUCAGCUG
 981
A-127390.1
2451-2469
CAGGCCCCAGCUGACCAGCdTdT
1315
A-127391.1



GGGCCUGdTdT











AD-63529.1
GGGCCUGGGCUG
 982
A-127392.1
2463-2481
CCGGCCACAGCCCAGGCCCdTdT
1316
A-127393.1



UGGCCGGdTdT











AD-63535.1
GGCUGUGGCCGG
 983
A-127394.1
2470-2488
AGUUAGGCCGGCCACAGCCdTdT
1317
A-127395.1



CCUAACUdTdT











AD-63541.1
CUAACUACUUCG
 984
A-127396.1
2483-2501
UAGACGCCGAAGUAGUUAGdTdT
1318
A-127397.1



GCGUCUAdTdT











AD-63547.1
CGGCGUCUACAC
 985
A-127398.1
2493-2511
GAUGCGGGUGUAGACGCCGdTdT
1319
A-127399.1



CCGCAUCdTdT











AD-63553.1
ACACCCGCAUCA
 986
A-127400.1
2501-2519
ACACCUGUGAUGCGGGUGUdTdT
1320
A-127401.1



CAGGUGUdTdT











AD-63559.1
ACAGGUGUGAUC
 987
A-127402.1
2512-2530
UCCAGCUGAUCACACCUGUdTdT
1321
A-127403.1



AGCUGGAdTdT











AD-63565.1
UCAGCUGGAUCC
 988
A-127404.1
2522-2540
ACUUGCUGGAUCCAGCUGAdTdT
1322
A-127405.1



AGCAAGUdTdT











AD-63571.1
CAGCAAGUGGUG
 989
A-127406.1
2533-2551
CUCAGGUCACCACUUGCUGdTdT
1323
A-127407.1



ACCUGAGdTdT











AD-63530.1
UGACCUGAGGAA
 990
A-127408.1
2543-2561
GGGGCAGUUCCUCAGGUCAdTdT
1324
A-127409.1



CUGCCCCdTdT











AD-63536.1
GGAACUGCCCCC
 991
A-127410.1
2551-2569
UUUGCAGGGGGGCAGUUCCdTdT
1325
A-127411.1



CUGCAAAdTdT











AD-63542.1
CUGCAAAGCAGG
 992
A-127412.1
2563-2581
GGUGGGCCCUGCUUUGCAGdTdT
1326
A-127413.1



GCCCACCdTdT











AD-63548.1
GCAGGGCCCACC
 993
A-127414.1
2570-2588
UCCAGGAGGUGGGCCCUGCdTdT
1327
A-127415.1



UCCUGGAdTdT











AD-63554.1
CCUCCUGGACUC
 994
A-127416.1
2580-2598
GCUCUCUGAGUCCAGGAGGdTdT
1328
A-127417.1



AGAGAGCdTdT











AD-63560.1
CUCAGAGAGCCC
 995
A-127418.1
2589-2607
UUGCCCUGGGCUCUCUGAGdTdT
1329
A-127419.1



AGGGCAAdTdT











AD-63566.1
CCAGGGCAACUG
 996
A-127420.1
2599-2617
UGCUUGGCAGUUGCCCUGGdTdT
1330
A-127421.1



CCAAGCAdTdT











AD-63572.1
GGACAAGUAUUC
 997
A-127422.1
2621-2639
CCCGCCAGAAUACUUGUCCdTdT
1331
A-127423.1



UGGCGGGdTdT











AD-63578.1
CUGGCGGGGGGU
 998
A-127424.1
2632-2650
CUCCCCCACCCCCCGCCAGdTdT
1332
A-127425.1



GGGGGAGdTdT











AD-63584.1
GGGUGGGGGAGA
 999
A-127426.1
2640-2658
CCUGCUCUCUCCCCCACCCdTdT
1333
A-127427.1



GAGCAGGdTdT











AD-63590.1
AGAGAGCAGGCC
1000
A-127428.1
2649-2667
ACCACAGGGCCUGCUCUCUdTdT
1334
A-127429.1



CUGUGGUdTdT











AD-63596.1
CCCUGUGGUGGC
1001
A-127430.1
2659-2677
ACCUCCUGCCACCACAGGGdTdT
1335
A-127431.1



AGGAGGUdTdT











AD-63602.1
GGAGGUGGCAUC
1002
A-127432.1
2672-2690
GAGACAAGAUGCCACCUCCdTdT
1336
A-127433.1



UUGUCUCdTdT











AD-63608.1
CAUCUUGUCUCG
1003
A-127434.1
2680-2698
UCAGGGACGAGACAAGAUGdTdT
1337
A-127435.1



UCCCUGAdTdT











AD-63614.1
CCCUGAUGUCUG
1004
A-127436.1
2693-2711
ACUGGAGCAGACAUCAGGGdTdT
1338
A-127437.1



CUCCAGUdTdT











AD-63573.1
CUGCUCCAGUGA
1005
A-127438.1
2702-2720
CCUGCCAUCACUGGAGCAGdTdT
1339
A-127439.1



UGGCAGGdTdT











AD-63579.1
AUGGCAGGAGGA
1006
A-127440.1
2713-2731
UUCUCCAUCCUCCUGCCAUdTdT
1340
A-127441.1



UGGAGAAdTdT











AD-63585.1
GGAUGGAGAAGU
1007
A-127442.1
2722-2740
UGCUGGCACUUCUCCAUCCdTdT
1341
A-127443.1



GCCAGCAdTdT











AD-63591.1
UGCCAGCAGCUG
1008
A-127444.1
2733-2751
UGACCCCCAGCUGCUGGCAdTdT
1342
A-127445.1



GGGGUCAdTdT











AD-63597.1
AGCUGGGGGUCA
1009
A-127446.1
2740-2758
GACGUCUUGACCCCCAGCUdTdT
1343
A-127447.1



AGACGUCdTdT











AD-63603.1
UCAAGACGUCCC
1010
A-127448.1
2749-2767
UCCUCAGGGGACGUCUUGAdTdT
1344
A-127449.1



CUGAGGAdTdT











AD-63609.1
CCCUGAGGACCC
1011
A-127450.1
2759-2777
UGGGCCUGGGUCCUCAGGGdTdT
1345
A-127451.1



AGGCCCAdTdT











AD-63615.1
GCCCACACCCAG
1012
A-127452.1
2773-2791
AGAAGGGCUGGGUGUGGGCdTdT
1346
A-127453.1



CCCUUCUdTdT











AD-63574.1
AGCCCUUCUGCC
1013
A-127454.1
2783-2801
AUUGGGAGGCAGAAGGGCUdTdT
1347
A-127455.1



UCCCAAUdTdT











AD-63580.1
CCUCCCAAUUCU
1014
A-127456.1
2793-2811
AGGAGAGAGAAUUGGGAGGdTdT
1348
A-127457.1



CUCUCCUdTdT











AD-63586.1
CUCUCUCCUCCG
1015
A-127458.1
2803-2821
AAGGGGACGGAGGAGAGAGdTdT
1349
A-127459.1



UCCCCUUdTdT











AD-63592.1
UCCGUCCCCUUC
1016
A-127460.1
2811-2829
AGUGGAGGAAGGGGACGGAdTdT
1350
A-127461.1



CUCCACUdTdT











AD-63598.1
CUUCCUCCACUG
1017
A-127462.1
2819-2837
UAGGCAGCAGUGGAGGAAGdTdT
1351
A-127463.1



CUGCCUAdTdT











AD-63604.1
CUGCCUAAUGCA
1018
A-127464.1
2831-2849
ACUGCCUUGCAUUAGGCAGdTdT
1352
A-127465.1



AGGCAGUdTdT











AD-63610.1
GCAAGGCAGUGG
1019
A-127466.1
2840-2858
UGCUGAGCCACUGCCUUGCdTdT
1353
A-127467.1



CUCAGCAdTdT











AD-63616.1
UGGCUCAGCAGC
1020
A-127468.1
2849-2867
CAUUCUUGCUGCUGAGCCAdTdT
1354
A-127469.1



AAGAAUGdTdT











AD-63575.1
CAAGAAUGCUGG
1021
A-127470.1
2860-2878
UGUAGAACCAGCAUUCUUGdTdT
1355
A-127471.1



UUCUACAdTdT











AD-63581.1
UGGUUCUACAUC
1022
A-127472.1
2869-2887
UCCUCGGGAUGUAGAACCAdTdT
1356
A-127473.1



CCGAGGAdTdT











AD-63587.1
CCCGAGGAGUGU
1023
A-127474.1
2880-2898
ACCUCAGACACUCCUCGGGdTdT
1357
A-127475.1



CUGAGGUdTdT











AD-63593.1
GUCUGAGGUGCG
1024
A-127476.1
2890-2908
AGUGGGGCGCACCUCAGACdTdT
1358
A-127477.1



CCCCACUdTdT











AD-63599.1
GCCCCACUCUGU
1025
A-127478.1
2901-2919
CCUCUGUACAGAGUGGGGCdTdT
1359
A-127479.1



ACAGAGGdTdT











AD-63605.1
CUGUACAGAGGC
1026
A-127480.1
2909-2927
CCAAACAGCCUCUGUACAGdTdT
1360
A-127481.1



UGUUUGGdTdT











AD-63611.1
CUGUUUGGGCAG
1027
A-127482.1
2920-2938
GGCAAGGCUGCCCAAACAGdTdT
1361
A-127483.1



CCUUGCCdTdT











AD-63617.1
CUUGCCUCCAGA
1028
A-127484.1
2933-2951
UCUGCUCUCUGGAGGCAAGdTdT
1362
A-127485.1



GAGCAGAdTdT











AD-63576.1
UCCAGAGAGCAG
1029
A-127486.1
2939-2957
CUGGAAUCUGCUCUCUGGAdTdT
1363
A-127487.1



AUUCCAGdTdT











AD-63582.1
GAUUCCAGCUUC
1030
A-127488.1
2950-2968
GGCUUCCGAAGCUGGAAUCdTdT
1364
A-127489.1



GGAAGCCdTdT











AD-63588.1
GAAUGGAAGGUG
1031
A-127490.1
2991-3009
AUGGGAGCACCUUCCAUUCdTdT
1365
A-127491.1



CUCCCAUdTdT











AD-63594.1
GUGCUCCCAUCG
1032
A-127492.1
3000-3018
UCCCCUCCGAUGGGAGCACdTdT
1366
A-127493.1



GAGGGGAdTdT











AD-63600.1
UCGGAGGGGACC
1033
A-127494.1
3009-3027
CUCUGAGGGUCCCCUCCGAdTdT
1367
A-127495.1



CUCAGAGdTdT











AD-63606.1
CCCUCAGAGCCC
1034
A-127496.1
3019-3037
GUCUCCAGGGCUCUGAGGGdTdT
1368
A-127497.1



UGGAGACdTdT











AD-63612.1
GAGACUGCCAGG
1035
A-127498.1
3033-3051
AGGCCCACCUGGCAGUCUCdTdT
1369
A-127499.1



UGGGCCUdTdT











AD-63618.1
AGGUGGGCCUGC
1036
A-127500.1
3042-3060
AGUGGCAGCAGGCCCACCUdTdT
1370
A-127501.1



UGCCACUdTdT











AD-63577.1
CUGCCACUGUAA
1037
A-127502.1
3053-3071
UUUUGGCUUACAGUGGCAGdTdT
1371
A-127503.1



GCCAAAAdTdT











AD-63583.1
CUGUAAGCCAAA
1038
A-127504.1
3059-3077
CCCACCUUUUGGCUUACAGdTdT
1372
A-127505.1



AGGUGGGdTdT











AD-63589.1
GUGGGGAAGUCC
1039
A-127506.1
3073-3091
GGAGUCAGGACUUCCCCACdTdT
1373
A-127507.1



UGACUCCdTdT











AD-63595.1
CCUGACUCCAGG
1040
A-127508.1
3083-3101
CAAGGACCCUGGAGUCAGGdTdT
1374
A-127509.1



GUCCUUGdTdT











AD-63601.1
GGGUCCUUGCCC
1041
A-127510.1
3093-3111
AGGGGUGGGGCAAGGACCCdTdT
1375
A-127511.1



CACCCCUdTdT











AD-63607.1
GCCCCACCCCUG
1042
A-127512.1
3101-3119
UGGCAGGCAGGGGUGGGGCdTdT
1376
A-127513.1



CCUGCCAdTdT











AD-63613.1
CCUGCCACCUGG
1043
A-127514.1
3113-3131
UGAGGGCCCAGGUGGCAGGdTdT
1377
A-127515.1



GCCCUCAdTdT











AD-63619.1
CUGGGCCCUCAC
1044
A-127516.1
3121-3139
CUGGGCUGUGAGGGCCCAGdTdT
1378
A-127517.1



AGCCCAGdTdT











AD-63620.1
UCACAGCCCAGA
1045
A-127518.1
3129-3147
GUGAGGGUCUGGGCUGUGAdTdT
1379
A-127519.1



CCCUCACdTdT











AD-63621.1
CUCACUGGGAGG
1046
A-127520.1
3143-3161
GAGCUCACCUCCCAGUGAGdTdT
1380
A-127521.1



UGAGCUCdTdT











AD-63622.1
GGUGAGCUCAGC
1047
A-127522.1
3153-3171
AAGGGCAGCUGAGCUCACCdTdT
1381
A-127523.1



UGCCCUUdTdT











AD-63623.1
UGGAAUAAAGCU
1048
A-127524.1
3172-3190
AUCAGGCAGCUUUAUUCCAdTdT
1382
A-127525.1



GCCUGAUdTdT
















TABLE 13







TMPRSS6 single dose screen (10 nM) in Hep3B


cells with dT modified siRNAs












Avg % message




Duplex ID
remaining
SD














AD-63290.1
122.8
18.0



AD-63296.1
87.4
6.0



AD-63302.1
71.4
16.9



AD-63308.1
82.1
10.3



AD-63314.1
59.1
5.3



AD-63320.1
90.7
4.5



AD-63326.1
121.0
18.2



AD-63332.1
114.4
11.6



AD-63291.1
84.7
15.0



AD-63297.1
82.8
3.9



AD-63303.1
67.6
5.5



AD-63309.1
55.8
6.5



AD-63315.1
64.2
7.4



AD-63321.1
85.8
6.4



AD-63327.1
91.9
14.9



AD-63333.1
76.4
5.2



AD-63292.1
54.4
22.9



AD-63298.1
54.6
5.0



AD-63304.1
24.6
7.3



AD-63310.1
23.3
0.6



AD-63316.1
50.9
7.2



AD-63322.1
53.7
10.5



AD-63328.1
29.2
2.3



AD-63334.1
28.5
1.2



AD-63293.1
50.9
6.8



AD-63299.1
85.5
2.3



AD-63305.1
43.0
7.2



AD-63311.1
28.9
2.6



AD-63317.1
40.9
2.7



AD-63323.1
40.2
7.3



AD-63329.1
27.9
12.0



AD-63335.1
82.0
4.2



AD-63294.1
21.8
1.0



AD-63300.1
32.3
8.0



AD-63306.1
32.9
8.3



AD-63312.1
26.5
4.6



AD-63318.1
31.3
2.4



AD-63324.1
25.7
1.9



AD-63330.1
24.5
2.0



AD-63336.1
36.1
8.6



AD-63295.1
29.2
1.8



AD-63301.1
28.9
5.2



AD-63307.1
68.8
10.6



AD-63313.1
90.2
8.2



AD-63319.1
21.9
3.3



AD-63325.1
26.1
4.8



AD-63331.1
36.7
4.5



AD-63337.1
67.7
9.3



AD-63343.1
83.9
15.0



AD-63349.1
71.6
3.5



AD-63355.1
62.8
10.4



AD-63361.1
56.0
3.3



AD-63367.1
49.3
8.7



AD-63373.1
54.1
8.2



AD-63379.1
47.5
6.3



AD-63338.1
28.0
2.8



AD-63344.1
29.7
5.7



AD-63350.1
23.0
2.3



AD-63356.1
81.5
13.7



AD-63362.1
19.7
2.9



AD-63368.1
42.2
4.7



AD-63374.1
24.5
2.0



AD-63380.1
24.9
4.9



AD-63339.1
28.9
10.1



AD-63345.1
29.9
5.6



AD-63351.1
20.4
3.7



AD-63357.1
35.8
6.8



AD-63363.1
30.4
2.5



AD-63369.1
29.0
3.1



AD-63375.1
36.6
2.4



AD-63381.1
29.1
4.3



AD-63340.1
40.4
18.8



AD-63346.1
36.4
3.5



AD-63352.1
25.8
3.9



AD-63358.1
42.6
8.1



AD-63364.1
48.1
6.6



AD-63370.1
24.6
2.8



AD-63376.1
22.1
4.2



AD-63382.1
31.0
7.5



AD-63341.1
37.6
13.7



AD-63347.1
27.6
2.0



AD-63353.1
76.4
14.5



AD-63359.1
25.3
1.1



AD-63365.1
27.3
3.4



AD-63371.1
16.3
1.3



AD-63377.1
65.4
7.1



AD-63383.1
72.2
7.0



AD-63342.1
30.8
7.3



AD-63348.1
72.7
9.2



AD-63354.1
38.7
5.0



AD-63360.1
28.7
3.0



AD-63366.1
30.9
6.8



AD-63372.1
84.0
9.0



AD-63378.1
64.1
8.6



AD-63384.1
38.0
2.6



AD-63390.1
48.3
10.6



AD-63396.1
45.6
7.0



AD-63402.1
42.0
9.9



AD-63408.1
40.4
9.1



AD-63414.1
23.8
6.2



AD-63420.1
55.3
5.2



AD-63426.1
61.6
8.5



AD-63385.1
61.6
10.2



AD-63391.1
38.0
3.1



AD-63397.1
66.7
16.8



AD-63403.1
77.2
15.4



AD-63409.1
60.3
10.7



AD-63415.1
35.0
5.4



AD-63421.1
60.6
2.9



AD-63427.1
40.5
7.2



AD-63386.1
42.0
7.4



AD-63392.1
34.2
3.1



AD-63398.1
62.6
18.5



AD-63404.1
65.9
8.1



AD-63410.1
19.7
4.0



AD-63416.1
51.3
9.0



AD-63422.1
59.3
2.7



AD-63428.1
58.2
9.7



AD-63387.1
42.2
4.8



AD-63393.1
27.9
4.4



AD-63399.1
49.6
8.4



AD-63405.1
72.5
9.3



AD-63411.1
45.4
14.9



AD-63417.1
36.7
9.4



AD-63423.1
76.8
4.9



AD-63429.1
77.8
14.4



AD-63388.1
37.4
4.4



AD-63394.1
31.5
4.6



AD-63400.1
60.9
28.6



AD-63406.1
40.7
14.3



AD-63412.1
22.0
7.0



AD-63418.1
22.8
4.3



AD-63424.1
25.5
2.8



AD-63430.1
21.5
3.2



AD-63389.1
34.4
5.3



AD-63395.1
31.1
0.7



AD-63401.1
44.3
9.5



AD-63407.1
41.5
4.9



AD-63413.1
52.4
6.4



AD-63419.1
26.3
5.6



AD-63425.1
78.8
4.6



AD-63431.1
32.8
6.6



AD-63437.1
42.3
1.4



AD-63443.1
56.4
8.9



AD-63449.1
26.0
5.9



AD-63455.1
28.0
9.7



AD-63461.1
32.1
11.1



AD-63467.1
33.8
19.8



AD-63473.1
28.9
3.4



AD-63432.1
36.5
7.4



AD-63438.1
27.3
4.3



AD-63444.1
54.6
36.0



AD-63450.1
42.0
6.1



AD-63456.1
36.6
10.2



AD-63462.1
23.3
3.0



AD-63468.1
48.8
27.3



AD-63474.1
23.8
3.2



AD-63433.1
51.8
13.8



AD-63439.1
41.7
5.5



AD-63445.1
74.6
6.1



AD-63451.1
49.6
9.0



AD-63457.1
26.7
4.9



AD-63463.1
27.8
3.8



AD-63469.1
48.4
14.0



AD-63475.1
40.3
1.4



AD-63434.1
93.3
9.9



AD-63440.1
37.6
4.7



AD-63446.1
38.1
15.4



AD-63452.1
42.3
4.0



AD-63458.1
29.7
7.9



AD-63464.1
25.7
3.4



AD-63470.1
44.8
7.8



AD-63476.1
33.9
4.7



AD-63435.1
23.4
5.2



AD-63441.1
37.1
4.5



AD-63447.1
46.5
9.0



AD-63453.1
73.1
16.8



AD-63459.1
31.8
4.6



AD-63465.1
27.3
6.6



AD-63471.1
19.5
3.1



AD-63477.1
35.2
4.7



AD-63436.1
21.8
4.7



AD-63442.1
44.1
11.2



AD-63448.1
33.6
6.0



AD-63454.1
58.2
16.8



AD-63460.1
27.7
2.4



AD-63466.1
27.1
4.4



AD-63472.1
20.5
4.1



AD-63478.1
36.3
7.3



AD-63484.1
48.4
31.3



AD-63490.1
44.0
6.1



AD-63496.1
45.5
19.9



AD-63502.1
49.0
18.3



AD-63508.1
41.4
2.7



AD-63514.1
36.0
5.1



AD-63520.1
40.9
4.2



AD-63479.1
35.1
6.5



AD-63485.1
45.5
24.0



AD-63491.1
69.0
14.5



AD-63497.1
57.1
25.1



AD-63503.1
36.0
15.3



AD-63509.1
29.7
6.4



AD-63515.1
33.9
5.7



AD-63521.1
117.2
10.2



AD-63480.1
38.6
0.7



AD-63486.1
48.5
12.1



AD-63492.1
38.7
3.7



AD-63498.1
64.6
20.3



AD-63504.1
41.7
1.9



AD-63510.1
39.6
4.0



AD-63516.1
30.9
4.8



AD-63522.1
56.4
15.6



AD-63481.1
72.0
7.3



AD-63487.1
128.8
48.9



AD-63493.1
31.7
6.7



AD-63499.1
44.2
17.7



AD-63505.1
69.4
7.6



AD-63511.1
43.8
5.3



AD-63517.1
75.3
2.2



AD-63523.1
82.1
10.6



AD-63482.1
40.1
12.2



AD-63488.1
42.3
12.7



AD-63494.1
19.0
1.1



AD-63500.1
30.2
11.2



AD-63506.1
30.5
7.6



AD-63512.1
38.1
15.2



AD-63518.1
35.0
7.3



AD-63524.1
60.5
3.7



AD-63483.1
22.7
3.6



AD-63489.1
47.6
13.7



AD-63495.1
31.0
12.7



AD-63501.1
24.3
2.1



AD-63507.1
37.4
7.0



AD-63513.1
32.3
5.1



AD-63519.1
46.0
6.6



AD-63525.1
66.5
14.5



AD-63531.1
104.0
24.1



AD-63537.1
32.1
3.4



AD-63543.1
31.2
3.8



AD-63549.1
35.2
5.2



AD-63555.1
41.7
9.3



AD-63561.1
44.2
7.0



AD-63567.1
39.2
4.9



AD-63526.1
66.9
15.7



AD-63532.1
90.3
17.8



AD-63538.1
50.8
11.5



AD-63544.1
31.9
2.4



AD-63550.1
35.0
8.8



AD-63556.1
31.0
6.0



AD-63562.1
20.2
2.4



AD-63568.1
30.6
2.7



AD-63527.1
28.8
2.4



AD-63533.1
63.3
6.9



AD-63539.1
28.4
3.5



AD-63545.1
26.9
8.5



AD-63551.1
52.5
4.7



AD-63557.1
26.7
2.2



AD-63563.1
28.1
2.7



AD-63569.1
29.2
2.8



AD-63528.1
52.9
9.0



AD-63534.1
42.5
6.8



AD-63540.1
50.5
10.9



AD-63546.1
53.6
10.5



AD-63552.1
38.8
5.0



AD-63558.1
49.3
3.0



AD-63564.1
69.2
3.1



AD-63570.1
50.6
6.0



AD-63529.1
59.5
6.5



AD-63535.1
21.0
1.7



AD-63541.1
40.1
23.4



AD-63547.1
26.0
9.6



AD-63553.1
31.5
6.0



AD-63559.1
34.9
2.7



AD-63565.1
43.3
5.3



AD-63571.1
41.6
4.4



AD-63530.1
127.6
15.0



AD-63536.1
38.0
16.0



AD-63542.1
48.3
8.4



AD-63548.1
41.9
7.9



AD-63554.1
88.2
15.2



AD-63560.1
48.8
17.7



AD-63566.1
33.6
6.8



AD-63572.1
82.4
67.9



AD-63578.1
78.5
11.5



AD-63584.1
55.7
7.2



AD-63590.1
53.4
2.9



AD-63596.1
63.5
8.6



AD-63602.1
49.3
3.6



AD-63608.1
29.2
4.4



AD-63614.1
30.0
7.4



AD-63573.1
96.1
14.7



AD-63579.1
38.1
4.5



AD-63585.1
40.0
2.1



AD-63591.1
30.5
2.5



AD-63597.1
55.1
5.8



AD-63603.1
43.6
4.0



AD-63609.1
37.7
2.7



AD-63615.1
44.4
9.7



AD-63574.1
44.3
10.3



AD-63580.1
33.1
3.5



AD-63586.1
39.3
2.9



AD-63592.1
73.7
1.6



AD-63598.1
32.4
6.6



AD-63604.1
98.7
7.1



AD-63610.1
42.1
7.1



AD-63616.1
55.2
10.4



AD-63575.1
27.8
3.0



AD-63581.1
36.3
3.2



AD-63587.1
36.1
3.3



AD-63593.1
39.2
4.7



AD-63599.1
37.0
5.6



AD-63605.1
49.3
3.7



AD-63611.1
88.8
7.7



AD-63617.1
45.6
6.6



AD-63576.1
59.9
2.9



AD-63582.1
82.9
8.3



AD-63588.1
33.5
6.7



AD-63594.1
64.7
18.0



AD-63600.1
99.5
11.9



AD-63606.1
40.8
2.7



AD-63612.1
44.5
5.3



AD-63618.1
41.7
4.6



AD-63577.1
31.1
0.3



AD-63583.1
57.3
8.6



AD-63589.1
61.9
5.9



AD-63595.1
51.2
8.5



AD-63601.1
70.7
15.4



AD-63607.1
39.4
1.9



AD-63613.1
36.8
2.7



AD-63619.1
83.8
13.8



AD-63620.1
69.4
7.3



AD-63621.1
30.6
3.1



AD-63622.1
51.8
8.4



AD-63623.1
37.3
8.6








Claims
  • 1. A double stranded RNAi agent capable of inhibiting expression of TMPRSS6 in a cell, wherein said double stranded RNAi agent comprises a sense strand and an antisense strand forming a double-stranded region, wherein said sense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:1, SEQ ID NO:4, or SEQ ID NO:1, and said antisense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:1, SEQ ID NO:1, or SEQ ID NON, SEQ ID NO:9, or SEQ ID NO: 10, wherein substantially all of the nucleotides of said sense strand and substantially all of the nucleotides of said antisense strand are modified nucleotides, andwherein said sense strand is conjugated to a ligand attached at the 3′-terminus.
  • 2. The double stranded RNAi agent of claim 1, wherein all of the nucleotides of said sense strand and all of the nucleotides of said antisense strand are modified nucleotides.
  • 3. The double stranded RNAi agent of claim 1, wherein said sense strand and said antisense strand comprise a region of complementarity which comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the antisense sequences listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12.
  • 4. (canceled)
  • 5. The double stranded RNAi agent of any claim 1, wherein at least one strand comprises a 3′ overhang of at least 1 nucleotide or at least 2 nucleotide.
  • 6. (canceled)
  • 7. A double stranded RNAi agent capable of inhibiting expression of TMPRSS6 (matriptase-2) in a cell, wherein said double stranded RNAi agent comprises a sense strand complementary to an antisense strand, wherein said antisense strand comprises a region complementary to part of an mRNA encoding TMPRSS6, wherein each strand is about 14 to about nucleotides in length, wherein said double stranded RNAi agent is represented by formula (III): sense: 5′np-Na—(XXX)i—Nb—YYY—Nb—(ZZZ)j—Na-nq3′antisense: 3′np′—Na′—(X′X′X′)k—Nb′—Y′Y′Y′—Nb′—(Z′Z′Z′)l—Na′-nq′5′  (III)wherein:i, j, k, and l are each independently 0 or 1;p, p′, q, and q′ are each independently 0-6;each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides;each Nb and Nb′ independently represents an oligonucleotide sequence comprising 0-10 nucleotides which are either modified or unmodified or combinations thereof;each np, np′, nq, and nq′, each of which may or may not be present, independently represents an overhang nucleotide;XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides;modifications on Nb differ from the modification on Y and modifications on Nb′ differ from the modification on Y′; andwherein the sense strand is conjugated to at least one ligand.
  • 8-10. (canceled)
  • 11. The double stranded RNAi agent of claim 7, wherein the YYY motif occurs at or near the cleavage site of the sense strand.
  • 12-17. (canceled)
  • 18. The double stranded RNAi agent of claim 7, wherein the double-stranded region is 15-30 nucleotide pairs in length.
  • 19-23. (canceled)
  • 24. The double stranded RNAi agent of claim 7, wherein each strand has 15-30 nucleotides.
  • 25. (canceled)
  • 26. The double stranded RNAi agent of claim 7, wherein the modifications on the nucleotides are selected from the group consisting of LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O-alkyl, 2′-O-allyl, 2′-C-allyl, 2′-fluoro, 2′-deoxy, 2′-hydroxyl, and combinations thereof.
  • 27. (canceled)
  • 28. The double stranded RNAi agent of claim 1, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.
  • 29. The double stranded RNAi agent of claim 1, wherein the ligand is
  • 30. (canceled)
  • 31. (canceled)
  • 32. The double stranded RNAi agent of claim 1, wherein said agent further comprises at least one phosphorothioate or methylphosphonate internucleotide linkage.
  • 33-40. (canceled)
  • 41. The double stranded RNAi agent of claim 32, wherein said RNAi agent comprises 6-8 phosphorothioate internucleotide linkages.
  • 42-52. (canceled)
  • 53. The double stranded RNAi agent of claim 1, wherein said RNAi agent is selected from the group of RNAi agents listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12.
  • 54. (canceled)
  • 55. (canceled)
  • 56. A double stranded RNAi agent capable of inhibiting expression of TMPRSS6 in a cell, wherein said double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region,wherein said sense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO: 1, SEQ ID NO:2, or SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO:5, and said antisense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from any one of the nucleotide sequences of SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO: 10,wherein substantially all of the nucleotides of said sense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification,wherein said sense strand comprises two phosphorothioate internucleotide linkages at the 5′-terminus,wherein substantially all of the nucleotides of said antisense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification,wherein said antisense strand comprises two phosphorothioate internucleotide linkages at the 5′-terminus and two phosphorothioate internucleotide linkages at the 3′-terminus, andwherein said sense strand is conjugated to one or more GalNAc derivatives attached through a branched bivalent or trivalent linker at the 3′-terminus.
  • 57-67. (canceled)
  • 68. A pharmaceutical composition comprising the double stranded RNAi agent of claim 1.
  • 69-73. (canceled)
  • 74. A method of inhibiting TMPRSS6 expression in a cell, the method comprising: (a) contacting the cell with the double stranded RNAi agent of claim 1; and(b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of a TMPRSS6 gene, thereby inhibiting expression of the TMPRSS6 gene in the cell.
  • 75-81. (canceled)
  • 82. A method of treating a subject having a TMPRSS6 associated disorder, comprising administering to the subject a therapeutically effective amount of the double stranded RNAi agent of claim 1 or a pharmaceutical composition of claim 68, thereby treating said subject.
  • 83-100. (canceled)
  • 101. The double stranded RNAi agent of claim 7, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.
  • 102. The double stranded RNAi agent of claim 7, wherein the ligand is
  • 103. The double stranded RNAi agent of claim 7, wherein said agent further comprises at least one phosphorothioate or methylphosphonate internucleotide linkage.
  • 104. The double stranded RNAi agent of claim 103, wherein said RNAi agent comprises 6-8 phosphorothioate internucleotide linkages.
  • 105. The double stranded RNAi agent of claim 7, wherein said RNAi agent is selected from the group of RNAi agents listed in any one of Tables 1, 2, 4, 5, 8, 10, and 12.
RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 16/191,579, filed on Nov. 15, 2018, which is a divisional of U.S. patent application Ser. No. 15/695,254, filed on Sep. 5, 2017, which is a continuation of U.S. patent application Ser. No. 14/947,025, filed on Nov. 20, 2015, now U.S. Pat. No. 9,783,806, issued on Oct. 10, 2017, which is a 35 § U.S.C. 111(a) continuation application which claims the benefit of priority to PCT/US2014/039149, filed on May 22, 2014, which, in turn, claims priority to U.S. Provisional Patent Application No. 61/826,178, filed on May 22, 2013, and U.S. Provisional Patent Application No. 61/912,988, filed on Dec. 6, 2013. The entire contents of each of the foregoing patent applications are hereby incorporated herein by reference.

Provisional Applications (2)
Number Date Country
61912988 Dec 2013 US
61826178 May 2013 US
Divisions (1)
Number Date Country
Parent 15695254 Sep 2017 US
Child 16191579 US
Continuations (3)
Number Date Country
Parent 16191579 Nov 2018 US
Child 17121885 US
Parent 14947025 Nov 2015 US
Child 15695254 US
Parent PCT/US2014/039149 May 2014 US
Child 14947025 US