Patent Application
20080020990
a and b show the results of semi-quantification of the bcl-2 mRNA (
The present inventors investigated the sequences registered as bcl-2 mRNA to a gene database for comparison and confirmed that the full length mRNA sequence of bcl-2 registered as GenBank Accession No. BC027258 was the consensus. Based on the sequence (SEQ ID NO:197) of GenBank Accession No. BC027258, primary, secondary and tertiary screenings were conducted to obtain an oligo double-stranded RNA having an inhibitory activity on the expression of Bcl-2 protein.
The oligo double-stranded RNA in the description is defined as a pair of RNAs of 15 to 31 nucleotides (which may contain partially deoxylribonucleotide(s) or modified nucleotide(s); hereinafter, the same in this paragraph) which have a double-strand forming portion of 15 to 27 base pairs, the pair of RNAs being introduced in a cell and cleaving a mRNA complementary to the oligo double-stranded RNA to inhibit synthesis of the gene product coded by the mRNA.
The oligo double-stranded RNA in the description is not limited to siRNAs described in the Tuschl's report. For example, the oligo double-stranded RNA of the present invention does not necessarily have the overhang at the 3′-terminal, and the number of base in the respective counterpart strand is not limited to 19 to 25 bases. The oligo double-stranded RNA of the present invention is a pair of 15 to 31 nucleotides, preferably a pair of 17 to 23 nucleotides, as well as a pair of 25 to 27 nucleotides.
The double-strand forming portion in the description means the portion in the oligo double-stranded RNA in which a pair of nucleic acids constituting the oligo double-stranded RNA forms a double strand, and which contains a sense strand and an anti-sense strand corresponding to bcl-2 mRNA. In this connection, when there is a single-strand at the 3′- or 5′-terminal side following the double-strand forming portion in the respective RNA strands, this is designated as an overhang.
Details of screening will be shown in Examples. Briefly, the primary screening was carried out on a pool composed of oligo double-stranded RNAs, each comprising a double-strand forming portion which is formed by pairing a sense RNA strand of 19 bases beginning from every 9 bases, in principle, in the ORF (open reading frame) of bcl-2 mRNA and its complementary RNA strand. The secondary screening was carried out on oligo double-stranded RNAs, each having as a sense sequence a sequence which shifts by every 3 bases (either upstream or downstream) from the sequence of bcl-2 mRNA corresponding to the oligo double-stranded RNA in which a high inhibitory activity on the expression of Bcl-2 protein was observed in the primary screening. The tertiary screening was carried out on oligo double-stranded RNAs, each having as a sense sequence a sequence which shifts by every 1 base from the sequence of bcl-2 MRNA corresponding to the oligo double-stranded RNA in which a high inhibitory activity on the expression of Bcl-2 protein was observed in the secondary screening. In addition, screening was also performed to evaluate an inhibitory activity on the expression of Bcl-2 of the sequences of oligo double-stranded RNAs which have various overhangs different in length and those which have a small number of bases.
As shown in detail in Examples mentioned below, the inhibitory activity of oligo double-stranded RNAs having the selected sequence on the expression of Bcl-2 protein was evaluated by introducing the oligo double-stranded RNA into culture cancer cells using a cationic liposome, etc., culturing it for a given period of time, and determining the amount and the decrease of expressed Bcl-2 protein in the cancer cells by Western blotting. In addition, the amount of bcl-2 MRNA was semi-quantified by RT-PCR and/or the inhibitory effect on cell growth was evaluated by a cell-counting assay.
On the basis of the above screening results, the present inventors found that the use of some oligo double-stranded RNAs could greatly decrease the expression of Bcl-2 protein, wherein the oligo double-stranded RNAs are a pair of a nucleic acid of a sequence selected from SEQ ID NO. 1 to SEQ ID NO:81, SEQ ID NO:240 to SEQ ID NO:256, and SEQ ID NO:274 to SEQ ID NO:280, and a complementary nucleic acid of a sequence selected from SEQ ID NO:82 to SEQ ID NO:162, SEQ ID NO:257 to SEQ ID NO:273, and SEQ ID NO:281 to SEQ ID NO:287. In addition, it was found that the oligo double-stranded RNAs having the above-mentioned sequence, regardless of the presence or absence of the overhang and even if the double-strand forming portion is short, can inhibit the expression of Bcl-2 protein.
It has been elucidated by the present inventors that the sequence of the overhang at the 3′-terminal has no effect on the activity. Therefore, the present invention includes an oligo double-stranded RNA capable of inhibiting the expression of Bcl-2 protein, which comprises a double-strand forming portion of 15 to 19 base pairs which is a pair of a sense RNA strand of one sequence selected from SEQ ID NO:1 to SEQ ID NO:81, SEQ ID NO:240 to SEQ ID NO:256, and SEQ ID NO:274 to SEQ ID NO:280 from which 2 dT bases at the 3′-terminal are excluded, and a complementary anti-sense RNA strand of one sequence selected from SEQ ID NO:82 to SEQ ID NO:162, SEQ ID NO:257 to SEQ ID NO:273, and SEQ ID NO:281 to SEQ ID NO:287 from which 2 dT bases at the 3′-terminal are excluded; of which pair a total of up to 4 base pairs may further be excluded from either one or both terminals.
In one mode of the present invention, the oligo double-stranded RNA of the present invention may contain one or more bases of deletion, substitution, insertion or addition in a part of the bases in either or both sequences of an RNA pair of double-strand forming portion. In another mode of the present invention, the oligo double-stranded RNA of the present invention may be substituted by a deoxyribonucleotide(s) or a modified nucleotide(s) in a part(s) of ribonucleotides from either or both strands of an RNA pair of double-strand forming portion or in the whole sense RNA strand.
In a desirable mode of the present invention, a pair of a sense RNA strand with an anti-sense RNA strand includes an oligo double-stranded RNA comprising a double-strand forming portion which is a pair of the sequences represented by SEQ ID NO:11 and SEQ ID NO:92, SEQ ID NO:30 and SEQ ID NO:111, SEQ ID NO:36 and SEQ ID NO:117, SEQ ID NO:43 and SEQ ID NO:124, SEQ ID NO:55 and SEQ ID NO:136, SEQ ID NO:62 and SEQ ID NO:143, or SEQ ID NO:77 and SEQ ID NO:158 from which 2 dT bases at the respective 3′-terminals are excluded.
The oligo double-stranded RNA of the present invention may or may not contain as an overhang a 1-base to 4-base nucleotide at the 3′-terminal or 5′-terminal of at least one strand of the RNAs. In particular, the 7 oligo double-stranded RNAs represented by the pairs according to the above-mentioned sequence identification numbers have a strong inhibitory activity on the expression of Bcl-2 protein even though no overhang exists.
When an overhang exists, the nucleotide constituting the overhang may be either ribonucleotide or deoxyribonucleotide. A particularly desirable mode is an oligo double-stranded RNA having 2 bases of nucleotide as an overhang. A preferable overhang is dTdT, UU, a sequence identical with a part of bcl-2 MRNA following the double-strand forming portion, or a sequence complementary to a part of bcl-2 mRNA following the double-strand forming portion.
In order to enhance in vivo stability such as nuclease resistance, the oligo double-stranded RNA of the present invention may be modified at least partially in the riboses or a phosphate backbone constituting the nucleotide. Preferred modification, if modified, includes modification in 2′-position of sugar, modification of other parts of sugar, modification of phosphate backbone in the oligo double-stranded RNA, and so on. The modification in 2′-position of sugar includes substitution of 240 -hydroxyl group of ribose with H, OR, R, R′, OR, SH, SR, NH2, NHR, NR2, N3, CN, F, Cl, Br, I, etc. Wherein, “R” represents alkyl or aryl, preferably alkyl group of 1 to 6 carbons, and “R′” represents alkylene, preferably alkylene of 1 to 6 carbons. The modified derivative of other parts of sugar includes 4′ thio derivatives. The modified derivative of phosphate backbone includes phosphorothioate, phosphorodithioate, alkyl phosphonate, phosphoroamidate, and the like.
The particularly desirable oligo double-stranded RNA of the present invention includes B043, B436, B469, B533, B614, B631 and B717; the followings show their sequences.
The oligo double-stranded RNA of the present invention, when introduced into a cell, can inhibit the expression of Bcl-2 protein in comparison with the case in which the oligo double-stranded RNA is not present. In inhibiting the expression of Bcl-2 protein using an anti-sense DNA, several hundred nM to several ten AM of the anti-sense DNA is generally required, while the oligo double-stranded RNA of the present invention can inhibit the expression of Bcl-2 protein even at a concentration of several nM to several hundred nM through transfection to a cell and subsequent incubation for 24 hours or more, for example, 72 hours, in comparison with no oligo double-stranded RNA. Preferably, A431 cell (epithelial cancer cell) is transfected with the oligo double-stranded RNA at a concentration of 3-10 nM, followed by incubation for 72 hours, at which stage the expression of Bcl-2 protein is inhibited in comparison with no oligo double-stranded RNA.
A single-stranded nucleic acid of the sense strand alone or the anti-sense strand alone constituting the oligo double-stranded RNA of the present invention also falls within the scope of the present invention. That is, the nucleic acid comprises an RNA of one sequence selected from SEQ ID NO:l to SEQ ID NO:162 from which 2 dT bases at the 3′-terminal are excluded, as a double-strand forming portion.
In one mode of the present invention, the nucleic acid of the present invention may have one or more bases of deletion, substitution, insertion or addition in a part of the bases in the RNA sequence.
The nucleic acid of the present invention may or may not contain as an overhang 1-base to 4-base nucleotide at the 3′-terminal. The nucleotide of the overhang may be either ribonucleotide or deoxyribonucleotide. A particularly desirable mode is a nucleic acid having 2 nucleotide bases as an overhang. A preferable overhang is dTdT, UU, a sequence identical with a part of bcl-2 mRNA following the double-strand forming portion, or a sequence complementary to a part of bcl-2 mRNA following the double-strand forming portion.
In addition, the nucleic acid of the present invention includes a nucleic acid which has one sequence .selected from SEQ ID NO:163 to SEQ ID NO:196 and SEQ ID NO:198 to SEQ ID NO:239.
In another mode of the present invention, the nucleic acid of the present invention may be substituted by a deoxyribonucleotide(s) or a modified nucleotide(s) in a part of ribonucleotides of the RNA sequence of the double-strand forming portion.
A nucleic acid which has one sequence selected from SEQ ID NO:1 to SEQ ID NO:162 and SEQ ID NO:240 to SEQ ID NO:287 from which 2 dT bases at the 3′-terminal are excluded, and in which uridine (U) is thymine (T), as a deoxyribonucleotide, falls within the scope of the present invention. The nucleic acid may be incorporated into a plasmid to generate an oligo double-stranded RNA of the present invention, or may be used as template DNAs to obtain an oligo double-stranded RNA of the present invention by in vitro transcription reaction.
Alternatively, this may be used as an anti-sense probe. In addition, the above-mentioned nucleic acid may be that characterized in that it contains bases having one or more bases of deletion, substitution, insertion or addition in its sequence, and it has an inhibitory activity on the expression of Bcl-2 protein when it works as a template for transcription to generate RNA which constitutes an oligo double-stranded RNA.
Further, the present invention provides a method for screening an oligo double-stranded RNA, which has an inhibitory activity on the expression of Bcl-2 protein, from oligo double-stranded RNAs having double-strand forming portions of 25 to 27 base pairs including 19 base pairs according to the particularly preferred oligo double-stranded RNAs in the present invention: B043 (SEQ ID.NO:11 and SEQ ID NO:92), B436 (SEQ ID NO:30 and SEQ ID NO:111), B469 (SEQ ID NO:36 and SEQ ID NO:117), B533 (SEQ ID NO:43 and SEQ ID NO:124), B614 (SEQ ID NO:55 and SEQ ID NO:136), B631 (SEQ ID NO:62 and SEQ ID NO:143), and B717 (SEQ ID NO:77 and SEQ ID NO:158).
In addition, the present invention provides oligo double-stranded RNAs, which have an inhibitory activity on the expression of Bcl-2 protein, comprising a double-strand forming portion of 25 to 27 base pairs including 19 base pairs of an oligo double-stranded RNA selected from the group consisting of B043, B436, B469, B533, B614, B631, and B717.
As a result of measurement of the inhibitory activity on the expression of Bcl-2 protein, the present inventors found that the expression of Bcl-2 protein greatly decreased when an oligo double-stranded RNA comprising a double-strand forming portion which is a pair of a nucleic acid corresponding to a part of bcl-2 mRNA which has one sequence selected from SEQ ID NO:288 and SEQ ID NO:295 to SEQ ID NO:300 from which 2 dT bases at the 3′-terminal and 6 bases at the 5′-terminal are excluded and to which a total of 6 bases are added at the 3′-terminal and/or 5′-terminal; and a nucleic acid complementary to the part of bcl-2 mRNA which has one sequence selected from SEQ ID NO:319 and SEQ ID NO:326 to SEQ ID NO:331 from which 2 dT bases and the subsequent 6 bases at the 3′-terminal are excluded and to which a total of 6 bases are added at the 3′-terminal and/or 5′-terminal.
In a desirable mode of the present invention, a pair of a sense RNA strand and an anti-sense RNA strand includes an oligo double-stranded RNA of 25 base pairs comprising a double-strand forming portion which is a pair of sequences represented by SEQ ID NO:288 and SEQ ID NO:319, SEQ ID NO:289 and SEQ ID NO:320, SEQ ID NO:290 and SEQ ID NO:321, SEQ ID NO:291 and SEQ ID NO:322, SEQ ID NO:292 and SEQ ID NO:323, SEQ ID NO:293 and SEQ ID NO:324, SEQ ID NO:294 and SEQ ID NO:325, SEQ ID NO:295 and SEQ ID NO:326, SEQ ID NO:296 and SEQ ID NO:327, SEQ ID NO:297 and SEQ ID NO:328, SEQ ID NO:298 and SEQ ID NO:329, SEQ ID NO:299 and SEQ ID NO:330, or SEQ ID NO:300 and SEQ ID NO:331 from which 2 dT bases at the respective 3′-terminals are excluded.
When an overhang exists, the nucleotide constituting the overhang may be either ribonucleotide or deoxyribonucleotide. A particularly desirable mode is an oligo double-stranded RNA having 2 nucleotide bases as an overhang. A more preferred mode is an oligo double-stranded RNA having dTdT, UU or a sequence identical with a part of bcl-2 mRNA following the double-strand forming portion as an overhang at the 3′-terminal of a sense RNA strand, and having dTdT, UU or a sequence complementary to a part of bcl-2 mRNA following the double-strand forming portion as an overhang at the 3′-terminal of an anti-sense RNA strand.
In addition, as one mode of the present invention, the present inventors found that the expression of Bcl-2 protein greatly decreased when an oligo double-stranded RNA of 27 base pairs which is a pair of a nucleic acid corresponding to a part of bcl-2 mRNA which has one sequence selected from SEQ ID NO:288 to SEQ ID NO:300 from which 2 dT bases at the 3′-terminal are excluded and to which a total of 2 bases are added at the 3′-terminal and/or 5′-terminal; and a nucleic acid complementary to the part of bcl-2 mRNA which has one sequence selected from SEQ ID NO:319 to SEQ ID NO:331 from which 2 dT bases at the 3′-terminal are excluded and to which a total of 2 bases are added at the 3′-terminal and/or 5′-terminal.
In a desirable mode of the present invention, a pair of a sense RNA strand and an anti-sense RNA strand includes an oligo double-stranded RNA of 27 base pairs of sequences represented by SEQ ID NO:303 and SEQ ID NO:332, or SEQ ID NO:304 and SEQ ID NO:334.
In one mode of the present invention, the oligo double-stranded RNA of the present invention may contain one or more bases of deletion, substitution, insertion or addition in a part of bases in either or both sequences in a RNA pair of a double-strand forming portion.
Further, in another embodiment of the present invention, the oligo double-stranded RNA of the present invention may be substituted by a deoxyribonucleotide(s) or a modified nucleotide(s) in a part(s) of one or both of the ribonucleotides from either or both strands of an RNA pair of a double-strand forming portion or in the whole sense RNA strand.
In a desirable mode of the present invention, a pair of a sense RNA strand and an anti-sense RNA strand includes an oligo double-stranded RNA comprising a double-strand forming portion which is a pair of sequences represented by SEQ ID NO:305 and SEQ ID NO:319, SEQ ID NO:306 and SEQ ID NO:319, SEQ ID NO:307 and SEQ ID NO:319, SEQ ID NO:308 and SEQ ID NO:319, SEQ ID NO:309 and SEQ ID NO:319, SEQ ID NO:310 and SEQ ID NO:319, SEQ ID NO:311 and SEQ ID NO:319, SEQ ID NO:312 and SEQ ID NO:320, SEQ ID NO:313 and SEQ ID NO:321, SEQ ID NO:314 and SEQ ID NO:322, SEQ ID NO:315 and SEQ ID NO:323, SEQ ID NO:316 and SEQ ID NO:324, or SEQ ID NO:317 and SEQ ID NO:325 from which 2 dT bases at the respective 3′-terminals are excluded.
In order to enhance in vivo stability such as nuclease resistance, the oligo double-stranded RNA of the present invention may be modified at least partially in the ribose or phosphate backbone constituting the nucleotide. Preferred modification, if modified, includes modification in 2′-position of sugar, modification of other parts of sugar, modification of phosphate backbone in the oligo double-stranded RNA, and so on. The modification in 2′-position of sugar includes substitution of 2′-hydroxyl group of ribose with H, OR, R, R′, OR, SH, SR, NH2, NHR, NR2, N3, CN, F, Cl, Br, I, etc. Wherein, “R” represents alkyl or aryl, preferably alkyl group of 1 to 6 carbons, and “R′” represents alkylene, preferably alkylene of 1 to 6 carbons. The modified derivative of other parts of sugar includes 4′ thio derivatives. The modified derivative of phosphate backbone includes phosphorothioate, phosphorodithioate, alkyl phosphonate, phosphoroamidate, and the like.
The particularly desirable oligo double-stranded RNA of the present invention includes B037-25, B038-25, B039-25, B040-25, B041-25, B042-25, B043-25, B430-25, B463-25, B527-25, B608-25, B625-25 and B711-25; the followings show their sequences.
The oligo double-stranded RNA of the present invention, when introduced into a cell, can inhibit the expression of Bcl-2 protein in comparison with the case in which the oligo double-stranded RNA is not present. In inhibiting the expression of Bcl-2 protein using an anti-sense DNA, several hundred nM to several ten AM of the anti-sense DNA is generally required, while the oligo double-stranded RNA of the present invention can inhibit the expression of Bcl-2 protein even at a concentration of several nM to several hundred nM through transfection of a cell and subsequent incubation for 24 hours or more, for example, 72 hours, in comparison with no oligo double-stranded RNA. Preferably, A431 cell (epithelial cancer cell) is transfected with the oligo double-stranded RNA at a concentration of 3-10 nM, followed by incubation for 72 hours, at which stage the expression of Bcl-2 protein is inhibited in comparison with no oligo double-stranded RNA.
A single-stranded nucleic acid of the sense strand alone or the anti-sense strand alone constituting the nucleic acids of the present invention, falls within the scope of the present invention. That is, the nucleic acid includes a nucleic acid corresponding to a part of bcl-2 mRNA which has one sequence selected from SEQ ID NO:288 and SEQ ID NO:295 to SEQ ID NO:300 from which 2 dT bases at the 3′-terminal and 6 bases at the 5′-terminal are excluded and to which a total of 6 bases are added at the 3′-terminal and/or 5′-terminal; or a nuclei acid complementary to the part of bcl-2 mRNA which has one sequence selected from SEQ ID NO:319 and SEQ ID NO:326 to SEQ ID NO:331 from which 2 dT bases and the subsequent 6 bases at the 3′-terminal are excluded and to which a total of 6 bases are added at the 3′-terminal and/or 5′-terminal.
In one mode of the present invention, the nucleic acid of the present invention may contain one or more bases of deletion, substitution, insertion or addition in a part of the bases in the RNA sequence.
In the nucleic acids of the present invention, the nucleotide constituting the overhang may be either ribonucleotide or deoxyribonucleotide. A particularly desirable mode is a nucleic acid having 2 nucleotide bases as an overhang. A preferable overhang is dTdT, UU, a sequence identical with a part of bcl-2 mRNA following a double-strand forming portion, or a sequence complementary to a part of bcl-2 mRNA following a double-strand forming portion.
Preferably, the nucleic acid of the present invention includes a nucleic acid of a sequence selected from SEQ ID NO:288 to SEQ ID NO:300 and SEQ ID NO:319 to SEQ ID NO:331.
In addition, the nucleic acid of the present invention include a nucleic acid corresponding to a part of bcl-2 mRNA which has one sequence selected from SEQ ID NO:288 to SEQ ID NO:300 from which 2 dT bases at the 3′-terminal are excluded and to which a total of 2 bases are added at the 3′-terminal and/or 5′-terminal; or a nucleic acid complementary to the part of bcl-2 mRNA which has one sequence selected from SEQ ID NO:319 to SEQ ID NO:331 from which 2 dT bases at the 3′-terminal are excluded and to which a total of 2 bases are added to the 3′-terminal and/or 5′-terminal.
Preferably, the nucleic acid of the present invention includes a nucleic acid of one sequence selected from SEQ ID NO:303 to SEQ ID NO:304 and SEQ ID NO:332 to SEQ ID NO:334.
In another mode of the present invention, a nucleic acid which has one sequence selected from SEQ ID NO:288 to SEQ ID NO:300 and SEQ ID NO:319 to SEQ ID NO:331 from which 2 dT bases at the 3′-terminal are excluded and in which a part of the ribonucleotides is replaced with a deoxyribonucleotide(s) or a modified. nucleotide(s), falls within the scope of the present invention.
In addition, a nucleic acid which has one sequence selected from SEQ ID NO:288 to SEQ ID NO:300 and SEQ ID NO:319 to SEQ ID NO:331 from which 2 dT bases at the 3′-terminal are excluded and in which uridine (U) thymine (T), as a deoxyribonucleotide, falls within the scope of the present invention. The nucleic acids may be incorporated into a plasmid to generate an oligo double-stranded RNA of the present invention, or may be used as a template DNA to obtain an oligo double-stranded RNA of the present invention by in vitro transcription reaction. Alternatively, it may be used as an anti-sense probe. In addition, the above-mentioned nucleic acid may be those characterized in that it contains one or more bases of deletion, substitution, insertion or addition in its sequence, and it has an inhibitory activity on the expression of Bcl-2 protein when it is used as a template for transcription to generate RNA which constitutes an oligo double-stranded RNA.
RNAs and DNAs of the present invention can be synthesized in a solid or liquid phase by a phosphoramidite method or triester method as well known by persons skilled in the art. In the most typical mode, a solid phase synthetic method by a phosphoramidite method is employed using an automatic synthesizer for nucleic acid or in manual. After termination of the synthesis on a solid phase, the objective product is released from the solid phase, and after removing a protecting group by deprotection, purified. In purification, it is desirable to obtain the nucleic acid in 90% or more purity, preferably 95% or more. When used as an oligo double-stranded RNA, a synthesized and purified sense strand may be mixed and annealed with an anti-sense strand in a molar ratio of 0 to 10 equivalents for 1 equivalent of the anti-sense strand, preferably in 0.5 to 2 equivalents, more preferably in 0.9 to 1.1 equivalents, and most preferably in an equimolar ratio, or alternatively, mixed strands may be used directly without a step of annealing. Annealing typically may be carried out by mixing an approximately equimolar amount of sense and anti-sense strands, heating the mixture at about 94° C. for about 5 minutes, and the slowly cooling it down to room temperature, though another condition well-known by persons skilled in the art may be employed.
The oligo double-stranded RNAs of the present invention may be transfected into a cell using a carrier for transfection such as cationic liposome and other vectors. In another embodiment of the present invention, the RNAs may be introduced directly into a cell by a calcium phosphate method, electroporation or microinjeciton, or the like.
The invention provides a pharmaceutical composition comprising a complex of an oligo double-stranded RNA of the present invention and a carrier which is effective in introducing the oligo double-stranded RNA into a cell. The pharmaceutical composition of the present invention can be used in treatment and/or prevention of diseases caused by over-expression of Bcl-2 protein, diseases for which acceleration of apoptosis is desired, or hematological malignant diseases. Specifically, these diseases are hematological malignant diseases including both of lymphoma and leukemia, and solid tumors, for example, liver cancer, skin cancer, breast cancer, lung cancer, cancers of digestive organs, prostate cancer, uterus cancer, bladder cancer, or the like.
As for the carrier for forming a complex with an oligo double-stranded RNA, cationic carriers such as a cationic liposome and a cationic polymer, or a carrier utilizing virus envelope, which are effective in introducing an oligo double-stranded RNA into a cell, may be used. The preferred cationic liposome includes a liposome comprising 2-O-(2-diethylaminoethyl)carbamoyl-1,3-O-dioleoylglycerol (hereinafter, referred to as “liposome A”), Oligofectamine (Invitrogen), Lipofectin (Invitrogen), Lipofectamine (Invitrogen), Lipofectamine 2000 (Invitrogen), DMRIE-C (Invitrogen), Gene Silencer (Gene Therapy Systems), Trans Messenger (QIAGEN), Trans IT TKO (Mirus), or the like. The preferred cationic polymer includes Jet SI (Qbiogene), Jet-PEI (polyethylenimine; Qbiogene), or the like. The preferred carrier utilizing virus envelope is Genome One (HVJ-E liposome; Ishihara Sangyo) or the like.
The complex of an oligo double-stranded RNA and a carrier contained in the pharmaceutical composition of the present invention can be prepared according to a method well-known by persons skilled in the art. Briefly, the complex can be prepared by mixing a carrier-dispersed solution with an oligo double-stranded RNA-containing solution in a suitable concentration. When a cationic carrier is used, the complex can be readily formed by mixing an oligo double-stranded RNA, which is charged negatively in an aqueous solution with the carrier in an aqueous solution in a conventional way. The aqueous medium used in formation of the complex includes water for injection, distilled water for injection, electrolyte such as saline, sugar solution such as glucose solution, maltose solution. In addition, such mixing conditions as pH and temperature can be determined by persons skilled in the art. For example, in the case of liposome A, the complex can be prepared by slowly adding an oligo double-stranded RNA in 10% maltose solution into a liposome A-dispersed solution of 16 mg/ml in 10% maltose solution at pH 7.4 and 25° C. with stirring.
The complex, if required, may be treated with a supersonic dispersing apparatus, high pressure-emulsifying apparatus or the like to give a homogeneous composition. Persons skilled in the art will be able to choose an optimal method and condition for preparing a complex of a carrier with an oligo double-stranded RNA according to the carrier used, without being bound by the above-mentioned method.
As for the formulating ratio of an oligo double-stranded RNA to a carrier in the complex contained in the pharmaceutical composition of the present invention, the carrier can be used in an amount of 1 to 200 parts by weight for 1 part by weight of oligo double-stranded RNA. Preferably, the carrier is used in 2.5 to 100 parts by weight, more preferably 10 to 20 parts by weight, for 1 part by weight of oligo double-stranded RNA.
The pharmaceutical composition of the present invention may contain a pharmaceutically acceptable carrier or a diluent in addition to the complex of oligo double-stranded RNA and carrier. The pharmaceutically acceptable carrier or diluent is essentially chemically inactive and innocuous compositions and give totally no effect on a biological activity of the pharmaceutical composition of the present invention. Such carrier or diluent includes, but not limited to, salt solution, sugar solution, glycerol solution, ethanol, and the like.
The pharmaceutical composition of the present invention contains an amount of complex effective in treating and/or preventing and is provided in a formulation properly applicable to a subject. The formulation of the pharmaceutical composition of the present invention includes, for example, liquid preparations such as injections, infusions, etc., external preparations such as ointment, lotion, and lyophilized preparations.
The liquid preparations suitably contain the complex in the range of 0.001 to 25% (w/v) in concentration, preferably in the range of 0.01 to 5% (w/v) in concentration, and more preferably in the range of 0.1 to 2% (w/v) in concentration. The pharmaceutical composition of the present invention may optionally contain a proper amount of pharmaceutically acceptable additives, for example, emulsifying auxiliary agents, stabilizers, tonicity adjusting agents, pH controllers, or the like. Specifically, the additives include fatty acids of 6 to 22 carbons (e.g., caprylic acid, capric acid, lauric acid, myristic acid, palmitic acid, stearic acid, oleic acid, linoleic acid, arachidonic acid, docosahexaenoic acid) and their pharmaceutically acceptable salts (e.g., sodium salts, potassium salts, calcium salts); emulsifying auxiliary agents such as albumin, dextran; stabilizers such as cholesterol, phosphatidic acid; tonicity adjusting agents such as sodium chloride, glucose, maltose, lactose, sucrose, trehalose; pH controllers such as hydrochloric acid, nitric acid, phosphoric acid, acetic acid, sodium hydroxide, potassium hydroxide, triethanolamine; and the like. The pharmaceutically acceptable additives can be added at a proper step before or after preparation of the complex.
The lyophilized preparations can be prepared by freeze-drying a complex of an oligo double-stranded RNA and a carrier after preparation of the complex. The lyophilization can be carried out in a conventional method. For example, a predetermined amount of the above complex-containing solution after treatment of dispersion is dispensed into vials under sterile condition, then preliminarily dried at about −40 to −20° C. for about 2 hours, then primarily dried at about 0 to 10° C. under reduced pressure, and secondarily dried at about 15 to 25° C. for lyophilization. Thereafter, in general, the vials are filled with nitrogen gas and closed with stoppers to give the lyophilized preparations of the pharmaceutical composition of the present invention.
In general, the lyophilized preparation of the present invention can be reconstituted in an optional suitable solution (reconstituting solution) and used. The reconstituting solution includes water for injection, electrolyte solution such as saline, glucose solution, and other conventional infusions. The amount of the reconstituting solution depends on the purpose of use and suitably is, but is not limited, in 0.5 to 2 fold for the liquid amount before lyophilization, or 500 ml or less.
The pharmaceutical composition of the present invention is preferably administered in a form of dosage unit and may be administered to animals including humans intravenously, intra-arterially, orally, interstitially, percutaneously, transmucosally or rectally, suitably according to the condition of a subject. Particularly preferred is intravenous, percutaneous or trasmucosal administration. In addition, local application such as direct application into cancers may be accepted. The formulation suitable to these ways of administration includes, for example, a variety of injections, oral preparations, drip infusions, absorbents, eye lotions, ointments, lotions, and suppositories.
For example, it is desirable to determine the dose of the pharmaceutical composition of the present invention in consideration of the drug, formulation, subject's condition such as age and body weight, route for administration, property and degree of disease, or the like, and usually the dose is in the range of 0.1 mg to 10 g/day/subject as an oligo double-stranded RNA for an adult, preferably in the range of 1 mg to 500 mg/day/subject. In some cases, the dose may be lower than that or must be increased in other cases. The composition may be administered once or several times a day and at intervals of one to several days.
In another mode of the present invention, it is possible to incorporate a DNA into the pharmaceutical composition together with pharmaceutically acceptable additives, wherein the DNA is used in generating an oligo double-stranded RNA of the present invention. In this context, the DNA used in generating an oligo double-stranded RNA of the present invention means a plasmid or the like for generating the oligo double-stranded RNA of the present invention, which contains a DNA having as deoxyribonucleotides a sequence of the double-strand forming portion in the oligo double-stranded RNA of the ptesent invention, wherein uridine in the nucleotide sequence is replaced with thymine. When such a pharmaceutical composition is administered to a subject, the oligo double-stranded RNA of the present invention is generated in the body and exerts the same effect as the above-mentioned pharmaceutical composition containing an oligo double-stranded RNA and a suitable carrier, that is, the pharmaceutical composition is effective in treatment and/or prevention of diseases caused by over-expression of Bcl-2. Dosage form and route can be determined in the same manner as in the pharmaceutical composition of the present invention containing a complex of an oligo double-stranded RNA and a carrier, and the administration is achieved depending on subject's condition, and the dose can be determined similarly in consideration of the drug, formulation, subject's condition such as age and body weight, route for administration, property and degree of disease, or the like.
The present invention will be explained by the following examples which are not intended as a limitation of the scope thereof.
i) Preparation of an Oligo Double-Stranded RNA
Nucleic acids constituting oligo double-stranded RNAs were synthesized by a standard solid phase phosphoramidite method using an automatic nucleic acid synthesizer. The synthesis was relied on Dharmacon Co. (Colorado, USA) or Japan Bioservice (Saitama Pref., Japan), or achieved by the present inventors.
Briefly, the present inventors performed the synthesis according to the following procedure. Using an automatic DNA synthesizer (Applied Biosystems, Expedite 8909), monomers were condensed one by one by a standard phosphoramidite method to form a desired sequence. Using a concentrated ammonium hydroxide-ethanol (3:1) mixture, the nucleotide chain was. cleaved from CPG (controlled pore glass) and deprotected in the same solution kept at 55° C. for 18 hours. The mixture was then treated with 1 M tetrabutylammonium fluoride in tetrahydrofuran solution for 20 hours to remove the 2′-silyl group by deprotection. The resulting oligo-ribonucleotide was purified by reverse-phase chromatography. The product was further treated with 80% acetic acid solution at room temperature for 30 minutes to remove the 5′-DMTr group for deprotection, followed by re-purification by ion-exchange chromatography. After desalination, the resulting oligonucleotide was proved to be the objective full length oligonucleotide in 90% or more purity by means of capillary gel electrophoresis.
Thus, a variety of nucleic acids constituting oligo double-stranded RNAs were synthesized. Oligo double-stranded RNAs were prepared by mixing two nucleic acids of which the double-strand forming portion was complementary, in an equimolar amount as mentioned below.
ii) Method of Evaluaiton in Screening
Evaluation in screening was performed by introducing an oligo double-stranded RNA together with a carrier into a various type of cancer cells and determining the amount of expressed protein by Western blotting and by quasi-determining the mRNA amount by RT-PCR (reverse transcription-polymerase chain reaction).
Using liposome A comprising 2-O-(2-diethylaminoethyl)carbamoyl-1,3-O-dioleoylglycerol and purified egg yolk lecithin as a carrier, a complex with an oligo double-stranded RNA was prepared. One part by weight of oligo double-stranded RNA was mixed with 16 parts by weight of liposome A to give a complex. The followings indicate the preparation of 2 ml of complex solution containing 10 μM final concentration of the oligo double-stranded RNA. The concentration of the oligo double-stranded RNA indicates the molar concentration of oligo double-stranded RNA contained in the complex assuming that the oligo double-stranded RNA forms a double-strand completely.
A sense strand and an anti-sense strand were respectively dissolved in water for injection so as to be 300 μM, each of which 66.6 μl was mixed in a test tube. One ml of solution containing each strand in a concentration of 20 μM was prepared by adding 866.8 μl of 10% maltose solution to this mixture. This was used as an oligo double-stranded RNA solution.
One ml of a liposome A-dispersed solution at 4.3 mg/ml was prepared by adding 732 μl of 10% maltose solution to 268 μl of the liposome A-dispersed solution of 16 mg/ml. One ml of the above oligo double-stranded RNA-containing solution was slowly added to 1 ml of the prepared liposome A-dispersed solution with stirring. By the above procedure, a solution containing a complex of liposome A with oligo double-stranded RNA in which the final concentration of oligo double-stranded RNA was 10 μM was prepared. The particles of the complex were homogenized by dispersing with a 600 W bath-type ultra-sonicator for 2 minutes.
Using the above-mentioned complex of liposome A with oligo double-stranded RNA, it was evaluated whether the expression of Bcl-2 protein was inhibited by transfection of the cells with the oligo double-stranded RNA, by evaluating change of the amount of Bcl-2 protein by Western blotting.
On a Petri dish of 6 cm in diameter, A431 cell (epithelial cancer cell), A375 cell (melanoma cell), MDA-MB-231 cell (breast cancer), or A549 cell (lung cancer) was seeded at 2×105 cells/dish, and incubated in a DMEM medium (Sigma, D6046) containing 10% FBS (fetal bovine serum) overnight at 37° C. under 5% CO2. Next day, the culture medium was removed from the dish under suction, and 2.7 ml of 10% FBS-DMEM medium (Sigma, D6046) was added for substitution of the medium. There was added 0.3 ml of the solution containing the complex of oligo double-stranded RNA-liposome A (oligo double-stranded RNA: liposome A=1:16 by weight) mixed in 10% maltose solution, so that the final volume was 3 ml. At this point, the final concentration of oligo double-stranded RNA is 3 nM or 10 nM. This was incubated at 37° C. in a 5% CO2 incubator for 72 hours. The cells were washed twice with PBS (phosphate buffered saline) and moved with a cell scraper into a 1.5 ml tube. After centrifugation at 1000× for 2 minutes and removal of the supernatant, the cells were dissolved in 20-100 μl of lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% NP-40). The mixture was allowed to stand on ice for 30 minutes, centrifuged at 100,000× for 15 minutes, and the supernatant was moved into a fresh tube and kept as a sample for electrophoresis.
Electrophoresis was carried out on polyacrylamide gel (ATTO NPG-520L or E-T520L), on which a sample was applied at 15 μg of total protein for one lane. After termination of electrophoresis, the protein in the gel was transferred on a polyvinylidene fluoride (PVDF) membrane, and blocked in 5% skim milk-containing PBST (PBST-MLK; herein, the composition of PBST was 0.1% Tween 20-containing PBS) at room temperature for 1 hour. First, Bcl-2 protein was detected. The PVDF membrane after blocking was soaked in a mouse anti-human Bcl-2 monoclonal antibody (DAKO M0887) diluted 500 times with PBST-MLK and shaken overnight at 4° C. for binding with a primary antibody. The PVDF membrane was washed with PBST, and shaken with HRP (horse radish peroxidase) labeled anti-mouse Ig antibody (DAKO P0447) diluted 1500 times with PBST-MLK at room temperature for 2 hours to bind a secondary antibody. After washing with PBST, light was emitted from the membrane with Western Lightening Chemiluminescence Reagent Plus (Perkin Elmer) and exposed on a film.
After detection of Bcl-2 protein, the same PVDF membrane was washed with distilled water, and Actin protein was detected in the same manner as Bcl-2. Goat anti-human actin antibody (Santa Cruz sc-1616) was used as a primary antibody, and HRP-labeled anti-goat Ig antibody (DAKO P0449) was used as a secondary antibody. The antibodies were diluted 2500 times and 3000 times, respectively, with PBST-MLK.
The density of band was determined visually by using as a negative control a band density of Bcl-2 protein where transfection with an oligo double-stranded RNA (GL3) inhibiting the expression of luciferase was made, and as a positive control a band density of Bcl-2 protein where transfection with an oligo double-stranded RNA B717 inhibiting the expression of Bcl-2 protein was made. As a result of visual observation, the detection when the density was the same as that of the positive control was designated as “+”; when the density was lighter than that of the positive control, as “++”; and when the density was lighter than that of the negative control, and deeper than that of the positive control, designated as “+/−”. In this connection, when the double-strand forming portion was an oligo double-stranded RNA of 25 or more base pairs, the case where the density was much lighter than that of the negative control in a treating concentration of 10 nM was designated as “++”; slightly lighter, “+”; and the case where the density in a treating concentration of 100 nM was slightly lighter than that of the negative control was designated as “+/−”.
The term “retention of activity” in the description means that, similarly as above, the band density (activity) of Bcl-2 protein where transfection with an objective oligo double-stranded RNA has been made, is “+/−”, “+” or “++” or more.
In order to elucidate whether the inhibitory activity on the expression of Bcl-2 protein by transfection with an oligo double-stranded RNA is caused by inhibition of mRNA expression, the amount of expressed bcl-2 mRNA was semi-quantified by RT-PCR.
On a Petri dish of 6 cm in diameter, A431 cell (epithelial cell) was seeded at a rate of 2×105 cells/dish, and incubated in a DMEM medium (Sigma, D6046) containing 10% FBS (fetal bovine serum) overnight at 37° C. under 5% CO2. Next day, the culture medium was removed from the dish under suction, and 2.7 ml of 10% FBS-DMEM medium (Sigma, D6046) was added for substitution of the medium. There was added 0.3 ml of the solution containing the complex of oligo double-stranded RNA-liposome A (oligo double-stranded RNA: liposome A=1:16 by weight) mixed in 10% maltose solution, so that the final volume was 3 ml. At this point, the final concentration of oligo double-stranded RNA is 10 nM. This was incubated in a CO2 incubator for 24 hours. The cells were washed twice with PBS, then lysed with 0.5 ml of Isogen (Nippon Gene) and moved into a 1.5 ml tube. Chloroform (200 μl) was added, and the aqueous layer was separated from the organic layer, and the total RNA was isolated from the aqueous layer.
Reverse transcription reaction was conducted using 2 μg of total RNA as a template and Thermoscript RT-PCR System (Gibco BRL 11146-016), and cDNA was prepared. Using this cDNA contained in the reaction mixture of reverse transcription as a template in PCR reaction, PCR amplification specific for bcl-2 and a constitutive expression gene GADPH (D-glyceraldehyde-3-phosphate dehydrogenase) was conducted using a capillary PCR detection/quantification system (Lightcycler, Roche Diagnostics), and the amount of mRNA was determined by semi-puantification. In PCR amplification of bcl-2, 100 ng of cDNA derived from total RNA was used as a template, and in PCR amplification of GADPH, 0.5 ng of cDNA derived from total RNA was used as a template. As a negative control, cells transfected with an oligo double-stranded RNA (GL3) inhibiting the expression of luciferase was used. The amount of sample mRNA was evaluated as a relative ratio when the amount of bcl-2 mRNA or GADPH mRNA in the negative control was regarded as 1.
iii) Screening
The sequences registered as a mRNA sequence coding for Bcl-2 protein were compared and investigated, and as a result, it was confirmed that the full length mRNA of bcl-2 registered as GenBank Accession NO. BC027258 was the consensus. On the basis of the sequence of this GenBank Accession NO. BC027258 (hereinafter, referred to as bcl-2 rRNA; SEQ ID NO:197), an oligo double-stranded RNA having an inhibitory activity on the expression of Bcl-2 protein was searched by primary, secondary and tertiary screenings as shown in Examples below.
The oligo double-stranded RNAs used in screening were prepared to have a double-strand forming portion formed from a sense. RNA strand of 19 bases and an anti-sense RNA strand complementary thereto and have a dTdT as an overhang at the 3′-terminal. The oligo double-stranded RNAs used in screening were represented by “Bxxx”, wherein “xxx” was indicated the position number from the initiation point of translation in bcl-2 mRNA of the 5′-teminal base of sense strand in the oligo double-stranded RNA.
The oligo double-stranded RNA pool in primary screening was composed of oligo double-stranded RNAs, each comprising a double-strand forming portion consisting of a sense RNA strand of 19 bases beginning every 9 bases in the ORF (open reading frame) of bcl-2 mRNA, and its complementary anti-sense RNA strand. However, in case the result of BRAST search showed that an oligo double-stranded RNA used for screening contained a sequence of 17 successive bases or more complementary to a mRNA other than bcl-2 mRNA, the sequence of the oligo double-stranded RNA was properly shifted by one or two bases to use an oligo double-stranded RNA containing a sequence of no more than 16 successive bases complementary to a mRNA other than bcl-2 mRNA.
As a result of primary screening, the following oligo double-stranded RNAs were recognized to have an inhibitory activity on the expression of Bcl-2 protein: B002 (SEQ ID NO:1 and SEQ ID NO:82), B010 (SEQ ID NO:2 and SEQ ID NO:83), B028 (SEQ ID NO:3 and SEQ ID NO:84), B037 (SEQ ID NO:6 and SEQ ID NO:87), B046 (SEQ ID NO:14 and SEQ ID NO:95), B055 (SEQ ID NO: 15 and SEQ ID NO:96), B065 (SEQ ID NO:16 and SEQ ID NO:97), B073 (SEQ ID NO:17 and SEQ ID NO:98), B084 (SEQ ID NO:18 and SEQ ID NO:99), B136 (SEQ ID NO:19 and SEQ ID NO:100), B172 (SEQ ID NO:20 and SEQ ID NO:101), B199 (SEQ ID NO:21 and SEQ ID NO:102), B207 (SEQ ID NO:22 and SEQ ID NO:103), B253 (SEQ ID NO:23 and SEQ ID NO:104), B262 (SEQ ID NO:24 and SEQ ID NO:105), B280 (SEQ ID NO:25 and SEQ ID NO:106), B325 (SEQ ID NO:26 and SEQ ID NO:107), B352 (SEQ ID NO:27 and SEQ ID NO:108), B397 (SEQ ID NO:28 and SEQ ID NO:109), B433 (SEQ ID NO:29 and SEQ ID NO:110), B442 (SEQ ID NO:32 and SEQ ID NO:113), B451 (SEQ ID NO:33 and SEQ ID NO:114), B469 (SEQ ID NO:36 and SEQ ID NO:117), B478 (SEQ ID NO:39 and SEQ ID NO:120), B516 (SEQ ID NO:40 and SEQ ID NO:121), B523 (SEQ ID NO:41 and SEQ ID NO:122), B539 (SEQ ID NO:46 and SEQ ID NO:127), B558 (SEQ ID NO:49 and SEQ ID NO:130), B576 (SEQ ID NO:50 and SEQ ID NO:131), B586 (SEQ ID NO:51 and SEQ ID NO:132), B595 (SEQ ID NO:52 and SEQ ID NO:133), B604 (SEQ ID NO:53 and SEQ ID NO:134), B613 (SEQ ID NO:54 and SEQ ID NO:135), B622 (SEQ ID NO:59 and SEQ ID NO:140), B631 (SEQ ID NO:62and SEQ ID NO:143), B642 (SEQ ID NO:65 and SEQ ID NO:146), B649 (SEQ ID NO:66 and SEQ ID NO:147), B654 (SEQ ID NO:67 and SEQ ID NO:148), B658 (SEQ ID NO:68 and SEQ ID NO:149), B667 (SEQ ID NO:69 and SEQ ID NO:150), B676 (SEQ ID NO:70 and SEQ ID NO:151), B703 (SEQ ID NO:73 and SEQ ID NO:154), B712 (SEQ ID NO:76 and SEQ ID NO:157), B717 (SEQ ID NO:77 and SEQ ID NO:158), and B721 (SEQ ID NO:79 and SEQ ID NO:160). These oligo double-stranded RNAs were evaluated by Western blotting for an inhibitory activity of the expression of Bcl-2 protein; Table 1 provided in the last of this section shows the results.
Among the oligo double-stranded RNAs which had an inhibitory activity on the expression of Bcl-2 protein in the primary screening, the following 9 oligo double-stranded RNAs showed a particularly high activity.
For the 9 oligo double-stranded RNAs (B037, B433, B469, B539, B622, B631, B703, B717 and B721) showing a high inhibitory activity on the expression of Bcl-2 protein, the amount of bcl-2 mRNA was evaluated by RT-PCR.
The oligo double-stranded RNA pool in the secondary screening was composed of 8 oligo double-stranded RNAs (B037, B433, B469, B539, B622, B631, B703 and B721) excluding B717 from the above 9 oligo double-stranded RNAs which showed a high inhibitory activity on the expression of Bcl-2 protein in the primary screening; and of such oligo double-stranded RNAs that comprise a double-strand forming portion consisting of a sense RNA strand of 19 bases beginning from the point distant by 3 bases or 6 bases toward upstream or downstream along the bcl-2 mRNA from the 5′-terminal of the sense RNA strand of the respective 8 oligo double-stranded RNAs, and its complementary RNA strand. However, in case the result of BRAST search showed that an oligo double-stranded RNA used for screening contained a sequence of 17 successive bases or more complementary to a mRNA other than bcl-2 YEA, the sequence of the oligo double-stranded RNA was properly shifted by one or two bases to use an oligo double-stranded RNA containing a sequence of no more than 16 successive bases complementary to a mRNA other than bcl-2 mNA.
As a result of secondary screening, the following oligo double-stranded RNAs were recognized to have an inhibitory activity on the expression of Bcl-2 protein: B031 (SEQ ID NO:4 and SEQ ID NO:85), B034 (SEQ ID NO:5 and SEQ ID NO:86), B037 (SEQ ID NO:6 and SEQ ID NO:87), B040 (SEQ ID NO:8 and SEQ ID NO:89), B043 (SEQ ID NO:11 and SEQ ID NO:92), B433 (SEQ ID NO:29 and SEQ ID NO:110), B436 (SEQ ID NO:30 and SEQ ID NO:111), B439 (SEQ ID NO:31 and SEQ ID NO:112), B463 (SEQ ID NO:34 and SEQ ID NO:115), B466 (SEQ ID NO:35 and SEQ ID NO:116), B469 (SEQ ID NO:36 and SEQ ID NO:117), B472 (SEQ ID NO:37 and SEQ ID NO:118), B475 (SEQ ID NO:38 and SEQ ID NO:119), B533 (SEQ ID NO:43 and SEQ ID NO:124), B536 (SEQ ID NO:45 and SEQ ID NO:126), B539 (SEQ ID NO:46 and SEQ ID NO:127), B543 (SEQ ID NO:47 and SEQ ID NO:128), B545 (SEQ ID NO:48 and SEQ ID NO:129), B616 (SEQ ID NO:57 and SEQ ID NO:138), B619 (SEQ ID NO:58 and SEQ ID NO:139), B622 (SEQ ID NO:59 and SEQ ID NO:140),B625 (SEQ ID NO:60 and SEQ ID NO:141), B628 (SEQ ID NO:61 and SEQ ID NO:142), B631 (SEQ ID NO:62 and SEQ ID NO:143), B634 (SEQ ID NO:63 and SEQ ID NO:144), B636 (SEQ ID NO:64 and SEQ ID NO:145), B697 (SEQ ID NO:71 and SEQ ID NO:152), B700 (SEQ ID NO:72 and SEQ ID NO:153), B703 (SEQ ID NO:73 and SEQ ID NO:154), B706 (SEQ ID NO:74 and SEQ ID NO:155), B709 (SEQ ID NO:75 and SEQ ID NO:156), B719 (SEQ ID NO:78 and SEQ ID NO:159), B721 (SEQ ID NO:79 and SEQ ID NO:160), B724 (SEQ ID NO:80 and SEQ ID NO:161), and B727 (SEQ ID NO:81 and SEQ ID NO:162). These oligo double-stranded RNAs were evaluated by Western blotting for an inhibitory activity of the expression of Bcl-2 protein; Table 1 provided in the last of this section shows the results.
Among the oligo double-stranded RNAs which had an inhibitory activity on the expression of Bcl-2 protein in the secondary screening, the following 7 oligo double-stranded RNAs showed a particularly high activity.
Among them, the cells transfected with the respective oligo double-stranded RNAs of B043 and B533 were evaluated for the amount of bcl-2 mRNA by RT-PCR;
Therefore, it was demonstrated that all of the oligo double-stranded RNAs obtained in the secondary screening specifically cleft bcl-2 mRNA and specifically inhibited the expression of Bcl-2 protein.
The oligo double-stranded RNA pool in the tertiary screening was composed of 4 oligo double-stranded RNAs (B037, B043, B533 and B616) which showed a high inhibitory activity on the expression of Bcl-2 protein in the secondary screening; and of such oligo double-stranded RNAs that comprise a double-strand forming portion consisting of a sense RNA strand of 19 bases beginning from the point shifted one by one in the range of about 3 bases toward upstream or downstream along the bcl-2 MRNA from the 5′-terminal of the sense RNA strand of the respective 4 oligo double-stranded RNAs, and its complementary RNA strand. In this operation, however, the sequences of high GC content, which were expected to decrease the synthetic yield, were excluded from the targets for screening.
The results of evaluation of the inhibitory activity on the expression of Bcl-2 protein by Western blotting are shown by photographs in
As a result of tertiary screening, the following oligo double-stranded RNAs were recognized to have an inhibitory activity on the expression of Bcl-2 protein: B037 (SEQ ID NO:6 and SEQ ID NO:87), B039 (SEQ ID NO:7 and SEQ ID NO:88), B040 (SEQ ID NO:8 and SEQ ID NO:89), B041 (SEQ ID NO:9 and SEQ ID NO:90), B042 (SEQ ID NO:10 and SEQ ID NO:91), B043 (SEQ ID NO:11 and SEQ ID NO:92), B044 (SEQ ID NO:12 and SEQ ID NO:93), B045 (SEQ ID NO:13 and SEQ ID NO:94), B531 (SEQ ID NO:42 and SEQ ID NO:123), B533 (SEQ ID NO:43 and SEQ ID NO:124), B534 (SEQ ID NO:44 and SEQ ID NO:125), B614 (SEQ ID NO:55 and SEQ ID NO:136), B615 (SEQ ID NO:56 and SEQ ID NO:137), and B616 (SEQ ID NO:57 and SEQ ID NO:138). These oligo double-stranded RNAs were evaluated by Western blotting for an inhibitory activity of the expression of Bcl-2 protein; Table 1 provided in the last of this section shows the results.
The following 3 oligo double-stranded RNAs having a particularly high inhibitory activity on the expression of Bcl-2 protein were selected.
It was found that these 3 oligo double-stranded RNAs (B043, B533 and B614), when transfected at 10 nM, almost perfectly inhibited the expression of Bcl-2 protein, and even in transfection at 3 nM, the expression of Bcl-2 protein was significantly inhibited (
Table 1 lists the oligo double-stranded RNAs which have been recognized to have an inhibitory activity on the expression of proteins in the course of the primary to tertiary screening.
The screened oligo double-stranded RNAs were introduced to a cancer cell, for which the ability to inhibit cell growth was evaluated by cell counting assay.
i) Method
On a 96-well plate, A431 cell (epithelial cancer cell) was seeded at 5×102 cells/well, and incubated in 10% FBS containing DMEM medium (Sigma, D6046) for 24 hours. The culture medium was removed from the plate under suction, and 135 μl of 10% FBS-containing DMEM medium was added. There was added 15 μl of the solution containing the complex of oligo double-stranded RNA-liposome A (oligo double-stranded RNA: liposome A=1:16 by weight) mixed in 10% maltose-solution, so that the final volume was 150 μl. This was incubated in a CO2 incubator for 6 days. 15 ll each of Cell Counting Kit-8 solution (DOJINDO) was added and subjected to color reaction in a CO2 incubator for 2 hours. The absorbance was measured at 450 nm (reference wavelength: 595 nm) by means of a microplate reader. The rate of relative cell number was evaluated as cell viability when the number of A431 cell which has not been transfected with the oligo double-stranded RNA was regarded as 100%. As a negative control, the cell which was transfected with an oligo double-stranded RNA for firefly luciferase mRNA was used. As a positive control, the cell which was transfected with one of oligo double-stranded RNAs, i.e., B717, inhibiting the expression of Bcl-2 protein, was used. As for the oligo double-stranded RNA having an inhibitory activity on the expression of Bcl-2 protein, B043 and B533 were evaluated.
ii) Results
i) Effect of One-Point Mutation
In order to elucidate the influence exerted by mutation of oligo double-stranded RNAs, a one-point mutant was prepared and its activity as an oligo double-stranded RNA was evaluated by Western blotting.
As oligo double-stranded RNAs having one-point mutation, the following 3 mutants were prepared. The nucleotide changed by one-point mutation was underlined.
In B043-15A, the 15th base pair from the 5′-terminal of B043 sense strand is converted from C-G into A-U; in B533-18U, the 18th base pair, from the 5′-terminal of B533 sense strand, from C-G into U-A; and in B717-10U, the 10th base pair, from A-U into U-A, respectively.
The results of B043-15A are shown in
ii) Effect of the Position of One-Point Mutation
In order to elucidate the influence of the position of mutation of oligo double-stranded RNAs exerted on the activity, 7 types of one-point mutants of the oligo double-stranded RNA in B533 were prepared, in which the position of mutation was different; the inhibitory activity of the oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by means of Western blotting as shown in Example 1.
As one-point mutant oligo double-stranded RNAs, those derived from the oligo double-stranded RNA sense strand of B533 were used, in which one-point mutation was located at 2nd, 5th, 8th, 10th, 12th, 15th, and 18th base from the 5′-terminal of the sense strand. Specific examples of one-point mutants are; in B533-2A, the 2nd base pair from the 5′-terminal of the B533 sense strand, i.e., U-A, was converted into A-U; in B533-5U, the 5th base pair from the 5′-terminal of the B533 sense strand, i.e., G-C, was converted into U-A; in B533-8U, the 8th base pair from the 5′-terminal of the B533 sense strand, i.e., C-G, was converted into U-A; in B533-10A, the 10th base pair from the 5′-terminal of the B533 sense strand, i.e., U-A, was converted into A-U; in B533-12U, the 12th base pair from the 5′-terminal of the B533 sense strand, i.e., A-U, was converted into U-A; in B533-15U, the 15th base pair from the 5′-terminal of the B533 sense strand, i.e., C-G, was converted into U-A; and in B533-18U, the 18th base pair from the 5′-terminal of the B533 sense strand, i.e., C-G, was converted into U-A, respectively.
The B533 oligo double-stranded RNA used and its one-point mutant oligo double-stranded RNAs are as follows.
The results are shown in Table 2.
The inhibitory activity of the oligo double-stranded RNA for the expression of Bcl-2 protein had a tendency to decrease as one-point mutation was located near the center of a double-strand forming portion. However, the lowest active oligo double-stranded RNAs (B533-8U, B553-10A, B533-12U), which had one-point mutation at 8th, 10th and 12th positions from the sense strand of double-strand forming portion, clearly inhibited the expression of Bcl-2 protein when it was introduced to the cell at a concentration of 10 nM. This suggests that one-point mutants are also effective oligo double-stranded RNAs for inhibiting the expression of Bcl-2 protein.
The influence of the base number of nucleic acids constituting the oligo double-stranded RNAs and of the base number of an overhang at the 3′-terminal and 5′-terminal exerted on the inhibitory activity on the expression of Bcl-2 protein was examined. Sense strands and anti-sense strands of 16 to 21 bases involving a part of the double-strand forming portion of B533 were employed. These nucleic acids were combined as shown in Table 3 below to provide oligo double-stranded RNAs in which the double-strand forming portions were composed of 16 to 19 base pairs and the overhang of 0 to 3 bases at the 3′-terminal, or the overhang of 1 to 2 bases at the 5′-terminal. The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting as described in Example 1.
All of the combined oligo double-stranded RNAs as shown in Table 3 showed an inhibitory activity on the expression of Bcl-2 protein. Thus, it was demonstrated that the length of nucleic acids constituting the oligo double-stranded RNAs had no large influence on the inhibitory activity on the expression of Bcl-2 protein. Specifically, it was demonstrated that the double-strand forming portion of oligo double-stranded RNAs, i.e., the complementary portion of the sense strand and anti-sense strand of oligo double-stranded RNA, had no large influence on the activity as far as the length of 15 to 19 base pairs was kept. It was also suggested that there was no large influence on the activity when the base number of the overhang at the 3′-terminal was 0 to 3 and the overhang at the 5′-terminal had 0 to 2 bases.
Further, the overhang at the 3′-terminal of oligo double-stranded RNAs in B533-20b and B534-20b is not dTdT but has a sequence identical with a part of bcl-2 mRNA following the double-strand forming portion and a sequence complementary to a part of bcl-2 MRNA following the double-strand forming portion; this, however, showed a strong inhibitory activity on the expression of Bcl-2 protein (Table 3). Thus, this indicates that the sequence of the overhang at the 3′-terminal may be a sequence identical with a part of bcl-2 mRNA and/or a sequence complementary to a part of bcl-2 mRNA. This also indicates that the activity of oligo double-stranded RNAs are retained even though the sequence of the overhang at the 3′-terminal is in any form including dTdT.
In ribonucleotides constituting oligo double-stranded RNAs, in order to elucidate an influence on the inhibitory activity of the oligo double-stranded RNA for the expression of Bcl-2 protein by replacement of some ribonucleotides with deoxyribonucleotide, the evaluation was performed using a partially DNA-substituted oligo double-stranded RNA.
The nucleic acids constituting oligo double-stranded RNA as used in evaluation were prepared by replacing some of the respective sense and anti-sense strands of B043 and B533 oligo double-stranded RNAs with deoxyribonucleotides as shown below, in addition to the respective sense strand and anti-sense strand constituting the B043 and B533 oligo double-stranded RNAs. The followings indicate the replaced position and sequence of specific deoxyribonucleotides. B043 sense strand line:
A pair of a sense strand selected from the above B043 sense strand line and an anti-sense strand selected from the B043 anti-sense strand line, or a pair of a sense strand selected from the B533 sense strand line and an anti-sense strand selected from the B533 anti-sense strand line were used as an oligo double-stranded RNA for evaluation. Table 4 indicates a combination of the sense strand and the anti-sense strand constituting the oligo double-stranded RNA used. The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting as described in Example 1.
All of the oligo double-stranded RNAs in combination as mentioned in Table 4 showed an inhibitory activity on the expression of Bcl-2 protein. This result demonstrates that the presence of deoxyribonucleotides in some parts of nucleic acids constituting the oligo double-stranded RNAs has no influence on the inhibitory activity on the expression of Bcl-2 protein. Thus, it was elucidated that these partially DNA-substituted oligo double-stranded RNAs can be utilized in inhibition of the expression of Bcl-2 protein.
In the above-mentioned screening, dTdT was used as an overhang. In this screening, the dTdT was converted into a 2′-methoxyethyl derivative, and the influence thereof on the inhibitory activity of the oligo double-stranded RNA for the expression of Bcl-2 protein was examined.
As an oligo double-stranded RNA, B717-MOE in which the overhang at the 3′-terminal of B717 was 2′-methoxyethylated TT was used.
The results are shown in
The influence of the presence or absence of the overhang at the 3′-terminal constituting oligo double-stranded RNAs on the inhibitory activity of an oligo double-stranded RNA for the expression of Bcl-2 protein was examined. Evaluation was performed by using a blunt end oligo double-stranded RNA comprising 18 base pairs or 19 base pairs with no overhang at the 3′-terminal. Table 5 shows specifically the examined oligo double-stranded RNAs and their results. The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting according to the method as described in Example 1.
All of the oligo double-stranded RNAs in combination as mentioned in Table 5 showed an inhibitory activity on the expression.of Bcl-2 protein. This suggests that the blunt end oligo double-stranded RNAs can also retain approximately the same activity as the overhanging type at the 3′-terminal.
A549 cells (106 cells/mouse) were inoculated to the spleen of nude mice (BALB/c, nu/nu, male, 5 weeks of age), and after 10 minutes the spleen was taken out. During 6th to 45th days after inoculation, the complex of oligo double-stranded RNA-liposome A (oligo double-stranded RNA:liposome A=1:16 by weight) containing bcl-2 oligo double-stranded RNA B717 (SEQ ID NO:77 and 158) prepared in the method as shown in Example 1, was administered intravenously in a frequency of once a week (a total of 6 times) or 3 times a week (a total of 18 times). The complex was administered at a dose of 10 mg/kg (body weight) as the oligo double-stranded RNA. To a control group, 10% maltose solution was administered 3 times a week (a total of 18 times). The survival number up to 100 days after inoculation is shown in
A Kaplan-Meier curve between a respective group to which B717 was administered and a control group was applied to a generalized Wilcoxon's test, indicating that there was a statistically significant difference (P<0.01).
A549 cells (106 cells/mouse) were inoculated to the spleen of nude mice (BALB/c, nu/nu, male, 5 weeks of age), and after 10 minutes the spleen was taken out. During 6th to 44th days after inoculation, the complex of oligo double-stranded RNA-liposome A (oligo double-stranded RNA:liposome A=1:16 by weight) containing bcl-2 oligo double-stranded RNA B043 (SEQ ID NO:11 and 92) prepared in the method as shown in Example 1, was administered intravenously in a frequency of twice a week (a total of 12 times). The complex was administered at a dose of 10 mg/kg (body weight) as the oligo double-stranded RNA. To a control group, 10% maltose solution was administered twice a week (a total of 12 times). The survival number up to 100 days after transplatation is shown in
A Kaplan-Meier curve between a group to which B043 was administered and a control group was applied to a generalized Wilcoxon's test, indicating that there was a statistically significant difference (P<0.01).
A549 cells (106 cells/mouse) were inoculated to the spleen of nude mice (BALB/c, nu/nu, male, 5 weeks of age), and after 10 minutes the spleen was taken out. During 6th to 44th days after inoculation, the complex of oligo double-stranded RNA-liposome A (oligo double-stranded RNA:liposome A=1:16 by weight) containing bcl-2 oligo double-stranded RNA B043 (SEQ ID NO:11 and 92) prepared in the method as shown in Example 1, was administered intravenously in a frequency of twice a week (a total of 12 times). The complex was administered at a dose of 1 mg/kg (body weight), 3 mg/kg (body weight) and 10 mg/kg (body weight), respectively, as the oligo double-stranded RNA. To a control group, 10% maltose solution was administered twice a week (a total of 12 times). The results are shown in
A Kaplan-Meier curve among a respective group to which 1 mg/kg (body weight), 3 mg/kg (body weight) or 10 mg/kg (body weight) of B043 was administered and a control group was applied to a generalized Wilcoxon's test, indicating that there was a statistically significant difference (P<0.05, P<0.01, P<0.01, respectively).
A549 cells (106 cells/mouse) were inoculated to the spleen of nude mice (BALB/c, nu/nu, male, 5 weeks of age), and after 10 minutes the spleen was taken out. During 5th to 10th days or 5th to 20th days after inoculation, the complex of oligo double-stranded RNA-liposome A (oligo double-stranded RNA:liposome A=1:16 by weight) containing bcl-2 oligo double-stranded RNA B043 (SEQ ID NO:11 and 92) prepared in the method as shown in Example 1, was administered intravenously in a frequency of 5 times a week (a total of 5 times or 12 times). The complex was administered at a dose of 10 mg/kg (body weight) as the oligo double-stranded RNA. To a control group, 10% maltose solution was administered 5 times a week (a total of 12 times). The results are shown in
Sixty-nine days after inoculation of cancer, all of 10 mice survived in both groups to which the complex was administered 5 times and 12 times, respective. A Kaplan-Meier curve between a respective group to which B043 was administered and a control group was applied to a generalized Wilcoxon's test, indicating that there was a statistically significant difference (P<0.01).
To nude mice (BALB/c, nu/nu, male, 5 weeks of age). was inoculated 100 μL of PC-3 cells (2.5×106 cells) suspension in PBS subcutaneously at the right side. During 7th to 18th days after inoculation, the complex of an oligo double-stranded RNA-liposome A (oligo double-stranded RNA liposome A=1:16 by weight) containing bcl-2 oligo double-stranded RNA B043 (SEQ ID NOs:11 and 92) or B717 (SEQ ID NOs:77 and 158) prepared in the method as shown in Example 1, was administered subcutaneously around cancer in a frequency of 5 times a week (a total of 10 times). The complex was administered at a dose of 0.1 mg/mouse as the oligo double-stranded RNA. To a control group, 10% maltose solution was administered 5 times a week (a total of 10 times). Tumor volume was calculated from a formula: “Volume=minor axis×minor axis×major axis÷2”, where the tumor was regarded as oval. The results are shown in
Increase of the tumor volume, in both groups to which B043 and B717 were administered respectively and in the control group, was statically significantly reduced over 14th to 36th days after cancer inoculation (P<0.01, Dunnett's test).
Evaluation Of An Inhibitory Activity On The Expression Of Bcl-2 Protein In The Peripheral Sequence Of bcl-2 Oligo Double-Stranded RNA Obtained By Screening
On oligo double-stranded RNAs having sequences around the 4 oligo double-stranded RNAs (B436, B469, B533, B631) which showed a high inhibitory activity on the expression of Bcl-2 protein in the secondary screening and that around B717 (an oligo double-stranded RNA used as a positive control in screening), the inhibitory activities on the expression of Bcl-2 protein were evaluated by Western blotting as shown in Example 1. The oligo double-stranded RNAs having the sequences around B436, B469, B533, B631, or B717, are composed of oligo double-stranded RNAs comprising a double-strand forming portion consisting of a sense RNA strand and its complementary RNA strand, in which the sense strand consisted of 19 bases beginning from the point distant by 1 to 3 bases toward upstream or downstream along the bcl-2 MRNA from the 5′-terminal of the sense strand of the respective original oligo double-stranded RNAs. Specific examples of sequences around B436, B469, B533, B631 and B717 are shown in Table 6 below.
Table 6 shows the results of evaluation of the inhibitory activity on the expression of Bcl-2 protein.
It was elucidated that the oligo double-stranded RNAs having the above-mentioned peripheral sequences showed an inhibitory activity on the expression of Bcl-2 protein.
The inhibitory activity of oligo double-stranded RNAs (B521, B557, B584, B635, B734, B735, B736), of which the sequences are specifically shown in Table 7 below, for the expression of Bcl-2 protein was evaluated by Western blotting as shown in Example 1. Table 7 indicates the results.
i) Preparation of Oligo Double-Stranded RNAs
Nucleic acid constituting an oligo double-stranded RNA was synthesized by a standard solid phase phosphoramidite method using an automatic nucleic acid synthesizer. The synthesis was relied on Dharmacon Co. (Colorado, USA) or Japan Bioservice (Saitama Pref., Japan), or achieved by the present inventors.
Briefly, the present inventors performed the synthesis according to the following procedure. Using an automatic DNA synthesizer (Applied Biosystems, Expedite 8909), monomers were condensed one by one by a standard phosphoramidite method to form a desired sequence. Using a concentrated ammonium hydroxide-ethanol (3:1) mixture, the nucleotide chain was cleaved from CPG (controlled pore glass) and deprotected in the same solution kept at 55° C. for 18 hours.
The mixture was then treated with 1M tetrabutylammonium fluoride in tetrahydrofuran solution for 20 hours to remove the 2′-silyl group by deprotection. The resulting oligo-ribonucleotide was purified by reverse-phase chromatography. The product was further treated with 80% acetic acid solution at room temperature for 30 minutes to remove the 5′-DMTr group for deprotection, followed by re-purification by ion-exchange chromatography. After desalination, the resulting oligonucleotide was proved to be the objective full length oligonucleotide in 90% or more purity by means of capillary gel electrophoresis.
Thus, a variety of nucleic acids constituting oligo double-stranded RNAs were synthesized. Oligo double-stranded RNAs were prepared by mixing two nucleic acids of which the double-strand forming portion were complementary, in an equimolar amount as mentioned below.
ii) Method For Evaluation Of The Inhibitory Activity On The Expression Of Bcl-2 Protein
An inhibitory activity on the expression of Bcl-2 protein was evaluated by introducing together with a carrier an oligo double-stranded RNA into a various type of cancer cells and determining the amount of expressed protein by Western blotting.
Using liposome A comprising 2-O-(2-diethylaminoethyl)carbamoyl 1,3-O-dioleoylglycerol and purified egg yolk lecithin as a carrier, a complex with an oligo double-stranded RNA was prepared. One part by weight of oligo double-stranded PNA was mixed with 16 parts by weight of liposome A to give a complex. The followings indicate the preparation of 2 ml of complex solution having a final concentration of 10 μM oligo double-stranded RNA. The concentration of the oligo double-stranded RNA indicates the molar concentration of oligo double-stranded RNA contained in the complex assuming that the oligo double-stranded RNA forms a double-strand completely.
A sense strand and an anti-sense strand were respectively dissolved in water for injection so as to be 300 μM, each of which 66.6 μl was mixed in a test tube. One ml of solution containing each strand in a concentration of 20 μM was prepared by adding 866.8 μl of 10% maltose solution to this mixture. This was used as an oligo double-stranded RNA solution. One ml of a liposome A-dispersed solution at 4.3 mg/ml was prepared by adding 732 μl of 10% maltose solution to 268 μl of the liposome A-dispersed solution of 16 mg/ml. One ml of the above oligo double-stranded RNA-containing solution was slowly added to 1 ml of the liposome A-dispersed solution with stirring. By the above procedure, a solution containing a complex of liposome A with an oligo double-stranded RNA in which the final concentration of oligo double-stranded RNA was 10 μM was prepared. The particles of this complex were homogenized by dispersing with a 600 W bath-type ultra-sonicator for 2 minutes.
Using the above-mentioned complex of liposome A with oligo double-stranded RNA, it was evaluated whether the expression of Bcl-2 protein was inhibited by transfection of the cells with the oligo double-stranded RNA, by evaluating change of the amount of Bcl-2 protein by Western blotting.
On a Petri dish of 6 cm in diameter, A431 cell (epithelial cancer cell), A375 cell (melanoma cell), MDA-MB-231 cell (breast cancer), or A549 cell (lung cancer) was seeded at 2×105 cells/dish, and incubated in a DMEM medium (Sigma, D6046) containing 10% FBS (fetal bovine serum) overnight at 37° C. under 5% CO2. Next day, the culture medium was removed from the dish under suction, and 2.7 ml of 10% FBS-DMEM medium (Sigma, D6046) was added for substitution of the medium. There was added 0.3 ml of the complex-containing solution of oligo double-stranded RNA-liposome A (oligo double-stranded RNA:liposome A=1:16 by weight) mixed in 10% maltose solution, so that the final volume was 3 ml. At this point, the final concentration of oligo double-stranded RNA is 3 nM, 10 nM or 100 nM. This was incubated at 37° C. in a 5% CO2 incubator for 72 hours. The cells were washed twice with PBS (phosphate buffered saline) and moved with a cell scraper into a 1.5 ml tube. After centrifugation at 1000×g for 2 minutes and removal of the supernatant, the cells were dissolved in 20-100 μl of lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% NP-40). The mixture was allowed to stand on ice for 30 minutes, centrifuged at 100,000×g for 15 minutes, and the supernatant was moved into a fresh tube and kept as a sample for electrophoresis.
Electrophoresis was carried out on polyacrylamide gel (ATTO NPG-520L), on which a sample was applied at 15 μg of total protein for one lane. After termination of electrophoresis, the protein in the gel was transferred on a polyvinylidene fluoride (PVDF) membrane, and blocked in 5% skim milk-containing PBST (PBST-MLK; herein, the composition of PBST was 0.1% Tween 20-containing PBS) at room temperature for 1 hour. First, Bcl-2 protein was detected. The PVDF membrane after blocking was soaked in a mouse anti-human Bcl-2 monoclonal antibody (DAKO M0887) diluted 500 times with PBST-MLK and shaken overnight at 4° C. for binding with a primary antibody. The PVDF membrane was washed with PBST, and shaken with HRP (horse radish peroxidase) labeled anti-mouse Ig antibody (DAKO P0260) diluted 2000 times with PBST-MLK at room temperature for 2 hours to bind a secondary antibody. After washing with PBST, light was emitted from the membrane with Western Lightening Chemiluminescence Reagent Plus (Perkin Elmer) and the amount of Bcl-2 protein was detected by ChemiDoc (BioRad).
After detection of Bcl-2 protein, the same PVDF membrane was washed with distilled water, and Actin protein was detected in the same manner as in Bcl-2. Goat anti-human Actin antibody (Santa Cruz SC-1616) was used as a primary antibody, and HRP-labeled anti-goat Ig antibody (DAKO P0449) was used as a secondary antibody. The antibodies were diluted 500 times and 1500 times, respectively, with PBST-MLK.
Comparison with them was determined visually by using the density of band of Bcl-2 protein as a negative control, where transfection with an oligo double-stranded RNA (GL3) inhibiting the expression of luciferase was made. When the double-strand forming portion was an oligo double-stranded RNA of 25 or more base pairs, the case where the density was much lighter than that of the negative control in a treating concentration of 10 nM was designated as “++”; slightly lighter, “+”; and the case where the density in a treating concentration of 100 nM was slightly lighter than that of the negative control was designated as “+/−”. Evaluation of an inhibitory activity on the expression of Bcl-2 protein of an oligo double-stranded RNA in which the complementary portion is 25 base pairs
The oligo double-stranded RNAs used in evaluation of an inhibitory activity on the expression of Bcl-2 protein were provided as the following oligo double-stranded RNAs based on the sequence (hereinafter, referred to as bcl-2 mRNA; SEQ ID NO.197) of GenBank Accession NO. BC027258.
In order to evaluate whether an oligo double-stranded RNA having a double-strand forming portion of 25 base pairs had a strong inhibitory activity on the expression of Bcl-2 protein, the present inventors prepared the B043-25 anti-sense strand and the B043-25 sense strand which was complementary to the B043-25 anti-sense strand, and prepared the oligo-double-stranded RNA of B043-25. In addition, the anti-sense strands of B042-25, B041-25, B040-25, B039-25, B038-25 and B037-25, which had a sequence of 25 bases shifted by 1 to 6 bases toward the 3′-terminal along the sequence complementary to bcl-2 mRNA from the sequence of 25 bases of the B043-25 anti-sense strand with the exclusion of 2 dT bases from the 3′-terminal and had 2 additional dT bases to the shifted 3′-terminal; and the sense strands of B042-25, B041-25, B040-25, B039-25, B038-25 and B037-25, which had a sequence of 25 bases shifted by 1 to 6 bases toward the 5′-terminal along the sequence of bcl-2 mRNA from the sequence of 25 bases of the B043-25 sense strand with the exclusion of 2 dT bases from the 3′-terminal and had 2 additional dT bases to the shifted 3′-terminal were prepared, and the respective oligo double-stranded RNAs were prepared.
In this situation, the oligo double-stranded RNAs used in evaluation of the inhibitory activity on the expression of Bcl-2 protein were represented by “BXXX-25”, wherein “XXX” was indicated the position number from the initiation point of translation in bcl-2 mRNA of the 5′-terminal base of sense strand in the oligo double-stranded RNA. The inhibitory activity on the expression of Bcl-2 protein of the above 7 oligo double-stranded RNAs (B037-25, B038-25, B039-25, B040-25, B041-25, B042-35 and B043-25) were evaluated by Western blotting.
The results are shown in Table 8
It was elucidated that Bcl-2 protein was almost completely inhibited by the oligo nucleic acid RNAs as shown in Table 8 at 100 μM of transfection, and further the expression of Bcl-2 protein was almost completely inhibited even in transfection at 10 nM (
Thus, in addition to B043-25 oligo double-stranded RNA, it was demonstrated that the oligo double-stranded RNAs consisting of an anti-sense strand, which had a sequence of 25 bases shifted by 1 to 6 bases toward the 3′-terminal along the sequence complementary to bcl-2 mRNA from the sequence of 25 bases of the B043-25 anti-sense strand with the exclusion of 2 dT bases from the 3′-terminal and had 2 additional dT bases to the shifted 3′-terminal; and a sense strand complementary to the sequence of 25 bases of the shifted anti-sense strand with the exclusion of 2 dT bases from the 3′-terminal and had 2 additional dT bases to the shifted 3′-terminal, showed an inhibitory activity on the expression of Bcl-2 protein.
The present inventors investigated that the effect of an oligo double-stranded RNA, in which the other complementary strand was composed of 25 base pairs, exerted on an inhibitory activity on the expression of Bcl-2 proteih. The oligo double-stranded RNAs specifically investigated include those of B430-25, B463-25, B527-25, B608-25, B625-25 and B711-25. The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting in the method as described in Example 15.
The results are shown in Table 9.
It was elucidated that Bcl-2 protein was almost completely inhibited by the oligo double-stranded RNAs as shown in Table 9 when transfected at 100 nM, and even in transfection at 10 nM, further the expression of Bcl-2 protein was almost completely inhibited (
Thus, the oligo double-stranded RNAs of which the complementary portion was composed of 25 base pairs showed a strong inhibitory activity on the expression of Bcl-2 protein.
An oligo double-stranded RNA in which the overhang at the 3′-terminal was deoxyribonucleotides dTdT and capable of forming a complementary strand with bcl-2 mRNA following the double-strand forming portion, was investigated on whether there was an influence on an inhibitory activity on the expression of Bcl-2 protein.
Nucleic acids constituting oligo double-stranded RNAs used in evaluation, in addition to the sense and anti-sense strands constituting B037-25 oligo double-stranded RNA, were obtained by preparing nucleic acids having as an overhang a sequence capable of forming a complementary strand with bcl-2 mRNA following the double-strand forming portion instead of the 3′-terminal dTdT of the sense and anti-sense strands of B037-25 oligo double-stranded RNA. The followings are specific examples of the sequences.
Specifically, the examined oligo double-stranded RNAs and the results are shown in Table 10. The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting as described in Example 15.
It was elucidated that Bcl-2 protein was almost completely inhibited by the oligo nucleic acid RNAs as shown in Table 10 when transfected at 100 nM, and even in transfection at 10 nM, further the expression of Bcl-2 protein was almost completely inhibited (
These results indicate that the 3′-overhang which is a sequence capable of forming a complementary strand with bcl-2 mRNA following the double-strand forming portion of the nucleic acid constituting the oligo double-stranded RNA has no large influence on the inhibitory activity on-the expression of Bcl-2 protein. Thus, it was elucidated that these oligo double-stranded RNAs could be utilized in inhibiting the expression of Bcl-2 protein. This indicates that the activity of the oligo double-stranded RNAs is retained even though the 3′-overhang has any type of sequences other than dTdT.
The influence of the presence or absence of the 3′-terminal overhang of a nucleic acid constituting an oligo double-stranded RNA exerted on the inhibitory activity on the expression of Bcl-2 protein by the oligo double-stranded RNA, was investigated. Blunt end oligo double-stranded RNAs of 25 base pairs with the elimination of the 3′-overhang were used for evaluation. Specifically, the examined oligo double-stranded RNAs and their results were shown in Table 11. The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting as described in Example 15.
It was elucidated that Bcl-2 protein was almost completely inhibited by the oligo nucleic acid RNAs as shown in Table 11 when transfected at 100 nM, and even in transfection at 10 nM, further the expression of Bcl-2 protein was almost completely inhibited (
From these results, it was suggested that all of the blunt end oligo double-stranded RNAs showed an inhibitory activity on the expression of Bcl-2 protein, and approximately the same activity as that of the 3′-terminal overhang type was retained even in the blunt end-type oligo double-stranded RNAs.
It was evaluated whether replacing all of the ribonucleotides of the sense strand constituting an oligo double-stranded RNA with deoxyribonucleotides affected the inhibitory activity of the oligo double-stranded RNA for the expression of Bcl-2 protein by using an oligo double-stranded RNA in which all the sense strands were DNA.
The nucleic acids constituting oligo double-stranded RNAs used in evaluation were prepared by replacing the respective sense strands constituting the oligo double-stranded RNAs B037-25, B038-25, B039-25, B040-25, B041-25, B042-25 and B043-25 with deoxyribonucleotides as shown below.
The followings are specific examples of the sequences.
Nucleic acid in which all bases of the B039 sense strand were converted into deoxyribonucleotides (U changed to T).
Nucleic acid in which all bases of the B041 sense strand were converted into deoxyribonucleotides (U changed to T).
Specifically, the examined oligo double-stranded RNAs and the results are shown in Table 12. The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting as described in Example 15.
It was elucidated that Bcl-2 protein was slightly inhibited by the oligo nucleic acid RNAs as shown in Table 12 when transfected at 100 nM, and even in transfection at 10 nM, further the expression of Bcl-2 protein was slightly inhibited (
On the basis of these results, it was confirmed that the oligo double-stranded RNAs of which their constituting sense strand was entirely replaced with deoxyribonucleotides also showed an inhibitory activity on the expression of Bcl-2 protein. Thus, it was found that the oligo double-stranded RNAs of which their constituting sense strand was entirely replaced with deoxyribonucleotides could also be utilized in inhibiting the expression of Bcl-2 protein.
It was evaluated whether partial substitution of the ribonucleotides in the sense strand of oligo double-stranded RNA with deoxyribonucleotides affected the inhibitory activity of an oligo double-stranded RNA for the expression of Bcl-2 protein by using partially DNA-substituted RNAs.
The nucleic acids constituting oligo double-stranded RNAs used in evaluation were prepared by replacing the respective sense strands constituting B037-25 oligo double-stranded RNAs with deoxyribonucleotides as shown below. The followings are specific examples of the sequences.
Nucleic acid in which all ribonucleotide C bases of the B037 sense strand were converted into deoxyribonucleotides.
The pairs of the sense strands selected from the above B037-25 sense strand line and the B037-25 anti-sense strands were used as oligo double-stranded RNAs for evaluation.
The combinations of the sense strands and the anti-sense strands constituting the oligo double-stranded RNAs used are shown in Table 13.
The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting as described in Example 1.
It was elucidated that Bcl-2 protein was almost completely inhibited by the oligo double-stranded RNAs as shown in Table 13 when transfected at 100 nM, and even in transfection at 10 nM, further the expression of Bcl-2 protein was almost completely inhibited (
These results indicate that-the substitution of a part of the sense strand constituting oligo double-stranded RNAs with deoxyribonucleotides has no large influence on the inhibitory activity on the expression of Bcl-2 protein. Thus, it was found that these oligo double-stranded RNAs in which the sense strand was partially substituted by DNA could also be utilized in inhibiting the expression of Bcl-2 protein.
Using oligo double-stranded RNAs having the sense strand in which all of ribonucleotides were replaced with deoxyribonucleotides and all of the phosphoric diester linkages were converted into phosphorothioate linkages, the influence of the oligo double-stranded RNAs on an inhibitory activity on the expression of Bcl-2 protein was evaluated.
The nucleic acids constituting oligo double-stranded RNAs used in evaluation were prepared by replacing all ribonucleotides constituting the sense strands constituting B037-25 oligo double-stranded RNAs with deoxyribonucleotides and converting all of the phosphoric diester linkages into phosphorothioate linkages.
The followings show specific examples of the sequences.
Specifically, the examined oligo double-stranded RNAs and the results are shown in Table 14. The inhibitory activity of these oligo double-stranded RNAs for the expression of Bcl-2 protein was evaluated by Western blotting as described in Example 15.
It was elucidated that Bcl-2 protein was slightly inhibited by the oligo nucleic acid RNAs as shown in Table 14 when transfected at 100 nM, and even in transfection at 10 nM, further the expression of Bcl-2 protein was slightly inhibited (
On the basis of these results, it was proved that the oligo double-stranded RNAs of which their constituting sense strand was entirely replaced with deoxyribonucleotides and all of the phosphoric diester linkages were converted into phosphorothioate linkages, also showed an inhibitory activity on the expression of Bcl-2 protein. Thus, it was found that the oligo double-stranded RNAs of which the constituent sense strand was entirely replaced by deoxyribonucleotides and all of the phosphoric diester linkages were converted into phosphorothioate linkages could also be utilized in inhibiting the expression of Bcl-2 protein.
The present invention contributes to provide oligo double-stranded RNAs which have a high inhibitory activity on the expression of Bcl-2 protein. The present invention contributes to provide pharmaceutical compositions for treatment and/or prevention of diseases caused by over-expression of Bcl-2 protein, such as cancer, and further contributes to the development of a method for treating and/or preventing these diseases.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2003-154668 | May 2003 | JP | national |
| 2003-382639 | Nov 2003 | JP | national |
| 2004-104036 | Mar 2004 | JP | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/JP04/07378 | 5/28/2004 | WO | 00 | 6/5/2006 |
