Patent Application
20210025008
The Instant application contains a Sequence Listing submitted via EFS-Web and hereby incorporated by reference in its entirety. Said ASCII copy, created on Jun. 5, 2020, is named 2020-06-05_01146-0064-01US_Seq_ListST25.txt and is 56,495 bytes in size.
Provided are therapies related to the treatment of pathological conditions, such as cancer.
Colorectal cancer (CRC) with over 100,000 new cases reported annually is the fourth most prevalent cancer and accounts for over 50,000 deaths per year in the United States (Siegel, R. et al., CA: A Cancer Journal for Clinicians 61:212-236 (2011)). Approximately 15% of CRCs exhibit microsatellite instability (MSI) arising from defects in DNA mismatch repair (MMR) system (Fearon, E. R., Annu. Rev. Pathol. 6:479-507 (2011)). The other ˜85% of microsatellite stable (MSS) CRCs are the result of chromosomal instability (CIN) (Fearon, E. R., Annu. Rev. Pathol. 6:479-507 (2011)). Genomic studies have identified acquisition of mutations in genes like APC, KRAS, and TP53 during CRC progression (Fearon, E. R., Annu. Rev. Pathol. 6:479-507 (2011)). Sequencing colon cancer protein-coding exons and whole genomes in a small number of samples have identified several additional mutations and chromosomal structural variants that likely contribute to oncogenesis (Wood, L. D. et al., Science 318:1108-1113 (2007); Timmermann, B. et al., PloS One 5:e15661 (2010)). However, recent insertional mutagenesis screens in mouse models of colon cancer suggested involvement of additional genes and pathways in CRC development (Starr, T. K. et al., Science 323:1747-1750 (2009); March, H. N. et al., Nat. Genet. 43:1202-1209 (2011)).
There remains a need to better understand the pathogenesis of cancers, in particular, human colon cancers and also to identify new therapeutic targets.
The invention provides wnt pathway antagonists including R-spondin-translocation antagonists and methods of using the same.
Provided herein are methods of inhibiting cell proliferation of a cancer cell comprising contacting the cancer cell with an effective amount of an R-spondin-translocation antagonist. Further provided herein are methods of treating cancer in an individual comprising administering to the individual an effective amount of an R-spondin-translocation antagonist. In some embodiments of any of the methods, the cancer or cancer cell comprises an R-spondin translocation.
Provided herein are methods of treating cancer in an individual comprising administering to the individual an effective amount of a wnt pathway antagonist, wherein treatment is based upon the individual having cancer comprising an R-spondin translocation. Provided herein are methods of treating a cancer cell, wherein the cancer cell comprises an R-spondin translocation, and wherein the method comprises providing an effective amount of a wnt pathway antagonist. Also provided herein are methods of treating cancer in an individual provided that the individual has been found to have cancer comprising an R-spondin translocation, the treatment comprising administering to the individual an effective amount of a wnt pathway antagonist.
Further, provided herein are methods for treating cancer in an individual, the method comprising: determining that a sample obtained from the individual comprises an R-spondin translocation, and administering an effective amount of an anti-cancer therapy comprising a wnt pathway antagonist to the individual, whereby the cancer is treated.
Provided herein are methods of treating cancer, comprising: (a) selecting an individual having cancer, wherein the cancer comprising an R-spondin translocation; and (b) administering to the individual thus selected an effective amount of a wnt pathway antagonist, whereby the cancer is treated.
Provided herein are also methods of identifying an individual with cancer who is more likely or less likely to exhibit benefit from treatment with an anti-cancer therapy comprising a wnt pathway antagonist, the method comprising: determining presence or absence of an R-spondin translocation in a sample obtained from the individual, wherein presence of the R-spondin translocation in the sample indicates that the individual is more likely to exhibit benefit from treatment with the anti-cancer therapy comprising the wnt pathway antagonist or absence of the R-spondin translocation indicates that the individual is less likely to exhibit benefit from treatment with the anti-cancer therapy comprising the wnt pathway antagonist. In some embodiments, the method further comprises administering an effective amount of the anti-cancer therapy comprising a wnt pathway antagonist.
Provided herein are methods for predicting whether an individual with cancer is more or less likely to respond effectively to treatment with an anti-cancer therapy comprising a wnt pathway antagonist, the method comprising determining an R-spondin translocation, whereby presence of the R-spondin translocation indicates that the individual is more likely to respond effectively to treatment with the wnt pathway antagonist and absence of the R-spondin translocation indicates that the individual is less likely to respond effectively to treatment with the wnt pathway antagonist. In some embodiments, the method further comprises administering an effective amount of the anti-cancer therapy comprising a wnt pathway antagonist.
Further provided herein are methods of predicting the response or lack of response of an individual with cancer to an anti-cancer therapy comprising a wnt pathway antagonist comprising detecting in a sample obtained from the individual presence or absence of an R-spondin translocation, wherein presence of the R-spondin translocation is predictive of response of the individual to the anti-cancer therapy comprising the wnt pathway antagonist and absence of the R-spondin translocation is predictive of lack of response of the individual to the anti-cancer therapy comprising the wnt pathway antagonist. In some embodiments, the method further comprises administering an effective amount of the anti-cancer therapy comprising a wnt pathway antagonist.
In some embodiments of any of the methods, the R-spondin translocation is a RSPO1 translocation, RSPO2 translocation, RSPO3 translocation and/or RSPO4 translocation. In some embodiments, the R-spondin translocation is a RSPO2 translocation. In some embodiments, the RSPO2 translocation comprises EIF3E and RSPO2. In some embodiments, the RSPO2 translocation comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2 translocation comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2 translocation comprises SEQ ID NO:71 In some embodiments, the R-spondin translocation is a RSPO3 translocation. In some embodiments, the RSPO3 translocation comprises PTPRK and RSPO3. In some embodiments, the RSPO3 translocation comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3 translocation comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3 translocation comprises SEQ ID NO:72 and/or SEQ ID NO:73. In some embodiments of any of the methods, the R-spondin translocation is detected at the chromosomal level (e.g., FISH), DNA level, RNA level (e.g., RSPO1-translocation fusion transcript), and/or protein level (e.g., RSPO1-translocation fusion polypeptide).
In some embodiments of any of the methods, the cancer is colorectal cancer. In some embodiments, the cancer is a colon cancer or rectal cancer.
Provided herein are isolated R-spondin-translocation antagonists, wherein the R-spondin-translocation antagonist is an antibody, binding polypeptide, small molecule, or polynucleotide. In some embodiments, the R-spondin-translocation antagonist binds a RSPO1-translocation fusion polypeptide and/or polynucleotide, RSPO2-translocation fusion polypeptide and/or polynucleotide, RSPO3-translocation fusion polypeptide and/or polynucleotide and/or RSPO4-translocation fusion polypeptide and/or polynucleotide. In some embodiments, the R-spondin-translocation antagonist binds a RSPO2-translocation fusion polypeptide and/or polynucleotide. In some embodiments, the RSPO2-translocation fusion polypeptide and/or polynucleotide comprises EIF3E and RSPO2. In some embodiments, the RSPO2-translocation fusion polypeptide and/or polynucleotide comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2-translocation fusion polypeptide and/or polynucleotide comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2-translocation fusion polypeptide and/or polynucleotide comprises SEQ ID NO:71. In some embodiments, the R-spondin-translocation fusion polypeptide and/or polynucleotide is a RSPO3-translocation fusion polypeptide and/or polynucleotide. In some embodiments, the RSPO3-translocation fusion polypeptide and/or polynucleotide comprises PTPRK and RSPO3. In some embodiments, the RSPO3-translocation fusion polypeptide and/or polynucleotide comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polypeptide and/or polynucleotide comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polypeptide and/or polynucleotide comprises SEQ ID NO:72 and/or SEQ ID NO:73.
The terms “R-spondin” and “RSPO” refer herein to a native R-spondin from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses “full-length,” unprocessed R-spondin as well as any form of R-spondin that results from processing in the cell. The term also encompasses naturally occurring variants of R-spondin, e.g., splice variants or allelic variants. R-spondin is a family of four proteins, R-spondin 1 (RSPO1), R-spondin 2 (RSPO2), R-spondin 3 (RSPO3), and R-spondin 4 (RSPO4). In some embodiments, the R-spondin is RSPO1. The sequence of an exemplary human RSPO1 nucleic acid sequence is SEQ ID NO:1 or an exemplary human RSPO1 is amino acid sequence of SEQ ID NO:2. In some embodiments, the R-spondin is RSPO2. The sequence of an exemplary human RSPO2 nucleic acid sequence is SEQ ID NO:3 or an exemplary human RSPO2 is amino acid sequence of SEQ ID NO:4. In some embodiments, the R-spondin is RSPO3. The sequence of an exemplary human RSPO3 nucleic acid sequence is SEQ ID NO:5 or an exemplary human RSPO3 is amino acid sequence of SEQ ID NO:6. In some embodiments, the R-spondin is RSPO4. The sequence of an exemplary human RSPO4 nucleic acid sequence is SEQ ID NO:7 or an exemplary human RSPO4 is amino acid sequence of SEQ ID NO:8.
“R-Spondin variant,” “RSPO variant,” or variations thereof, means an R-spondin polypeptide or polynucleotide, generally being or encoding an active R-Spondin polypeptide, as defined herein having at least about 80% amino acid sequence identity with any of the R-Spondin as disclosed herein. Such R-Spondin variants include, for instance, R-Spondin wherein one or more nucleic acid or amino acid residues are added or deleted. Ordinarily, an R-spondin variant will have at least about 80% sequence identity, alternatively at least about 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity, to R-Spondin as disclosed herein. Ordinarily, R-Spondin variant are at least about 10 residues in length, alternatively at least about 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600 in length, or more. Optionally, R-Spondin variant will have or encode a sequence having no more than one conservative amino acid substitution as compared to R-Spondin, alternatively no more than 2, 3, 4, 5, 6, 7, 8, 9, or 10 conservative amino acid substitution as compared to R-Spondin.
The terms “R-spondin translocation” and “RSPO translocation” refer herein to an R-spondin wherein a portion of a broken chromosome including, for example, R-spondin, variant, or fragment thereof or a second gene, variant, or fragment thereof, reattaches in a different chromosome location, for example, a chromosome location different from R-spondin native location or a chromosome location in and/or around the R-spondin native location which is different from the second gene's native location. The R-spondin translocation may be a RSPO1 translocation, RSPO2 translocation, RSPO3 translocation, and/or RSPO4 translocation.
The terms “R-spondin-translocation fusion polynucleotide” and “RSPO-translocation fusion polynucleotide” refer herein to the nucleic acid sequence of an R-spondin translocation gene product or fusion polynucleotide. The R-spondin-translocation fusion polynucleotide may be a RSPO1-translocation fusion polynucleotide, RSPO2-translocation fusion polynucleotide, RSPO3-translocation fusion polynucleotide, and/or RSPO4-translocation fusion polynucleotide. The terms “R-spondin-translocation fusion polypeptide” and “RSPO-translocation fusion polypeptide” refer herein to the amino acid sequence of an R-spondin translocation gene product or fusion polynucleotide. The R-spondin-translocation fusion polypeptide may be a RSPO1-translocation fusion polypeptide, RSPO2-translocation fusion polypeptide, RSPO3-translocation fusion polypeptide, and/or RSPO4-translocation fusion polypeptide.
The term “R-spondin-translocation antagonist” as defined herein is any molecule that partially or fully blocks, inhibits, or neutralizes a biological activity mediated by an R-spondin-translocation fusion polypeptide. In some embodiments such antagonist binds to R-spondin-translocation fusion polypeptide. According to one embodiment, the antagonist is a polypeptide. According to another embodiment, the antagonist is an anti-R-spondin-translocation antibody. According to another embodiment, the antagonist is a small molecule antagonist. According to another embodiment, the antagonist is a polynucleotide antagonist. The R-spondin translocation may be a RSPO1-translocation antagonist, RSPO2-translocation antagonist, RSPO3-translocation antagonist, and/or RSPO4-translocation antagonist.
The term “wnt pathway antagonist” as defined herein is any molecule that partially or fully blocks, inhibits, or neutralizes a biological activity mediated by the wnt pathway (e.g., wnt pathway polypeptide). In some embodiments such antagonist binds to a wnt pathway polypeptide. According to one embodiment, the antagonist is a polypeptide. According to another embodiment, the antagonist is an antibody antagonist. According to another embodiment, the antagonist is a small molecule antagonist. According to another embodiment, the antagonist is a polynucleotide antagonist.
“Polynucleotide” or “nucleic acid” as used interchangeably herein, refers to polymers of nucleotides of any length, and include DNA and RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase or by a synthetic reaction. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. A sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may comprise modification(s) made after synthesis, such as conjugation to a label. Other types of modifications include, for example, “caps,” substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those containing pendant moieties, such as, for example, proteins (e.g., nucleases, toxins, antibodies, signal peptides, ply-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotides(s). Further, any of the hydroxyl groups ordinarily present in the sugars may be replaced, for example, by phosphonate groups, phosphate groups, protected by standard protecting groups, or activated to prepare additional linkages to additional nucleotides, or may be conjugated to solid or semi-solid supports. The 5′ and 3′ terminal OH can be phosphorylated or substituted with amines or organic capping group moieties of from 1 to 20 carbon atoms. Other hydroxyls may also be derivatized to standard protecting groups. Polynucleotides can also contain analogous forms of ribose or deoxyribose sugars that are generally known in the art, including, for example, 2′-O-methyl-, 2′-O-allyl-, 2′-fluoro- or 2′-azido-ribose, carbocyclic sugar analogs, α-anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs, and basic nucleoside analogs such as methyl riboside. One or more phosphodiester linkages may be replaced by alternative linking groups. These alternative linking groups include, but are not limited to, embodiments wherein phosphate is replaced by P(O)S (“thioate”), P(S)S (“dithioate”), (O)NR2 (“amidate”), P(O)R, P(O)OR′, CO, or CH2 (“formacetal”), in which each R or R′ is independently H or substituted or unsubstituted alkyl (1-20 C) optionally containing an ether (—O—) linkage, aryl, alkenyl, cycloalkyl, cycloalkenyl or araldyl. Not all linkages in a polynucleotide need be identical. The preceding description applies to all polynucleotides referred to herein, including RNA and DNA.
“Oligonucleotide,” as used herein, refers to generally single-stranded, synthetic polynucleotides that are generally, but not necessarily, less than about 200 nucleotides in length. The terms “oligonucleotide” and “polynucleotide” are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides.
The term “primer” refers to a single stranded polynucleotide that is capable of hybridizing to a nucleic acid and following polymerization of a complementary nucleic acid, generally by providing a free 3′-OH group.
The term “small molecule” refers to any molecule with a molecular weight of about 2000 Daltons or less, preferably of about 500 Daltons or less.
The terms “host cell,” “host cell line,” and “host cell culture” are used interchangeably and refer to cells into which exogenous nucleic acid has been introduced, including the progeny of such cells. Host cells include “transformants” and “transformed cells,” which include the primary transformed cell and progeny derived therefrom without regard to the number of passages. Progeny may not be completely identical in nucleic acid content to a parent cell, but may contain mutations. Mutant progeny that have the same function or biological activity as screened or selected for in the originally transformed cell are included herein.
The term “vector,” as used herein, refers to a nucleic acid molecule capable of propagating another nucleic acid to which it is linked. The term includes the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced. Certain vectors are capable of directing the expression of nucleic acids to which they are operatively linked. Such vectors are referred to herein as “expression vectors.”
An “isolated” antibody is one which has been separated from a component of its natural environment. In some embodiments, an antibody is purified to greater than 95% or 99% purity as determined by, for example, electrophoretic (e.g., SDS-PAGE, isoelectric focusing (IEF), capillary electrophoresis) or chromatographic (e.g., ion exchange or reverse phase HPLC). For review of methods for assessment of antibody purity, see, e.g., Flatman et al., J. Chromatogr. B 848:79-87 (2007).
An “isolated” nucleic acid refers to a nucleic acid molecule that has been separated from a component of its natural environment. An isolated nucleic acid includes a nucleic acid molecule contained in cells that ordinarily contain the nucleic acid molecule, but the nucleic acid molecule is present extrachromosomally or at a chromosomal location that is different from its natural chromosomal location.
The term “antibody” herein is used in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired antigen-binding activity.
An “antibody fragment” refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds the antigen to which the intact antibody binds. Examples of antibody fragments include but are not limited to Fv, Fab, Fab′, Fab′-SH, F(ab′)2; diabodies; linear antibodies; single-chain antibody molecules (e.g., scFv); and multispecific antibodies formed from antibody fragments.
An “antibody that binds to the same epitope” as a reference antibody refers to an antibody that blocks binding of the reference antibody to its antigen in a competition assay by 50% or more, and conversely, the reference antibody blocks binding of the antibody to its antigen in a competition assay by 50% or more. An exemplary competition assay is provided herein.
The terms “full length antibody,” “intact antibody,” and “whole antibody” are used herein interchangeably to refer to an antibody having a structure substantially similar to a native antibody structure or having heavy chains that contain an Fc region as defined herein.
The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variant antibodies, e.g., containing naturally occurring mutations or arising during production of a monoclonal antibody preparation, such variants generally being present in minor amounts. In contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen. Thus, the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by a variety of techniques, including but not limited to the hybridoma method, recombinant DNA methods, phage-display methods, and methods utilizing transgenic animals containing all or part of the human immunoglobulin loci, such methods and other exemplary methods for making monoclonal antibodies being described herein.
“Native antibodies” refer to naturally occurring immunoglobulin molecules with varying structures. For example, native IgG antibodies are heterotetrameric glycoproteins of about 150,000 Daltons, composed of two identical light chains and two identical heavy chains that are disulfide-bonded. From N- to C-terminus, each heavy chain has a variable region (VH), also called a variable heavy domain or a heavy chain variable domain, followed by three constant domains (CH1, CH2, and CH3). Similarly, from N- to C-terminus, each light chain has a variable region (VL), also called a variable light domain or a light chain variable domain, followed by a constant light (CL) domain. The light chain of an antibody may be assigned to one of two types, called kappa (κ) and lambda (λ), based on the amino acid sequence of its constant domain.
The term “chimeric” antibody refers to an antibody in which a portion of the heavy and/or light chain is derived from a particular source or species, while the remainder of the heavy and/or light chain is derived from a different source or species.
A “human antibody” is one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human or a human cell or derived from a non-human source that utilizes human antibody repertoires or other human antibody-encoding sequences. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues.
A “humanized” antibody refers to a chimeric antibody comprising amino acid residues from non-human HVRs and amino acid residues from human FRs. In certain embodiments, a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the HVRs (e.g., CDRs) correspond to those of a non-human antibody, and all or substantially all of the FRs correspond to those of a human antibody. A humanized antibody optionally may comprise at least a portion of an antibody constant region derived from a human antibody. A “humanized form” of an antibody, e.g., a non-human antibody, refers to an antibody that has undergone humanization.
The “class” of an antibody refers to the type of constant domain or constant region possessed by its heavy chain. There are five major classes of antibodies: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2. The heavy chain constant domains that correspond to the different classes of immunoglobulins are called α, δ, ε, γ, and μ, respectively.
“Effector functions” refer to those biological activities attributable to the Fc region of an antibody, which vary with the antibody isotype. Examples of antibody effector functions include: C1q binding and complement dependent cytotoxicity (CDC); Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation.
The term “Fc region” herein is used to define a C-terminal region of an immunoglobulin heavy chain that contains at least a portion of the constant region. The term includes native sequence Fc regions and variant Fc regions. In one embodiment, a human IgG heavy chain Fc region extends from Cys226, or from Pro230, to the carboxyl-terminus of the heavy chain. However, the C-terminal lysine (Lys447) of the Fc region may or may not be present. Unless otherwise specified herein, numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system, also called the EU index, as described in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md., 1991.
“Framework” or “FR” refers to variable domain residues other than hypervariable region (HVR) residues. The FR of a variable domain generally consists of four FR domains: FR1, FR2, FR3, and FR4. Accordingly, the HVR and FR sequences generally appear in the following sequence in VH (or VL): FR1-H1(L1)-FR2-H2(L2)-FR3-H3(L3)-FR4.
A “human consensus framework” is a framework which represents the most commonly occurring amino acid residues in a selection of human immunoglobulin VL or VH framework sequences. Generally, the selection of human immunoglobulin VL or VH sequences is from a subgroup of variable domain sequences. Generally, the subgroup of sequences is a subgroup as in Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91-3242, Bethesda Md. (1991), vols. 1-3. In one embodiment, for the VL, the subgroup is subgroup kappa I as in Kabat et al., supra. In one embodiment, for the VH, the subgroup is subgroup III as in Kabat et al., supra.
An “acceptor human framework” for the purposes herein is a framework comprising the amino acid sequence of a light chain variable domain (VL) framework or a heavy chain variable domain (VH) framework derived from a human immunoglobulin framework or a human consensus framework, as defined below. An acceptor human framework “derived from” a human immunoglobulin framework or a human consensus framework may comprise the same amino acid sequence thereof, or it may contain amino acid sequence changes. In some embodiments, the number of amino acid changes are 10 or less, 9 or less, 8 or less, 7 or less, 6 or less, 5 or less, 4 or less, 3 or less, or 2 or less. In some embodiments, the VL acceptor human framework is identical in sequence to the VL human immunoglobulin framework sequence or human consensus framework sequence.
The term “variable region” or “variable domain” refers to the domain of an antibody heavy or light chain that is involved in binding the antibody to antigen. The variable domains of the heavy chain and light chain (VH and VL, respectively) of a native antibody generally have similar structures, with each domain comprising four conserved framework regions (FRs) and three hypervariable regions (HVRs). (See, e.g., Kindt et al., Kuby Immunology, 6th ed., W.H. Freeman and Co., page 91 (2007).) A single VH or VL domain may be sufficient to confer antigen-binding specificity. Furthermore, antibodies that bind a particular antigen may be isolated using a VH or VL domain from an antibody that binds the antigen to screen a library of complementary VL or VH domains, respectively. See, e.g., Portolano et al., J. Immunol. 150:880-887 (1993); Clarkson et al., Nature 352:624-628 (1991).
The term “hypervariable region” or “HVR,” as used herein, refers to each of the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops (“hypervariable loops”). Generally, native four-chain antibodies comprise six HVRs; three in the VH (H1, H2, H3), and three in the VL (L1, L2, L3). HVRs generally comprise amino acid residues from the hypervariable loops and/or from the “complementarity determining regions” (CDRs), the latter being of highest sequence variability and/or involved in antigen recognition. Exemplary hypervariable loops occur at amino acid residues 26-32 (L1), 50-52 (L2), 91-96 (L3), 26-32 (H1), 53-55 (H2), and 96-101 (H3). (Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987).) Exemplary CDRs (CDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and CDR-H3) occur at amino acid residues 24-34 of L1, 50-56 of L2, 89-97 of L3, 31-35B of H1, 50-65 of H2, and 95-102 of H3. (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991).) With the exception of CDR1 in VH, CDRs generally comprise the amino acid residues that form the hypervariable loops. CDRs also comprise “specificity determining residues,” or “SDRs,” which are residues that contact antigen. SDRs are contained within regions of the CDRs called abbreviated-CDRs, or a-CDRs. Exemplary a-CDRs (a-CDR-L1, a-CDR-L2, a-CDR-L3, a-CDR-H1, a-CDR-H2, and a-CDR-H3) occur at amino acid residues 31-34 of L1, 50-55 of L2, 89-96 of L3, 31-35B of H1, 50-58 of H2, and 95-102 of H3. (See Almagro and Fransson, Front. Biosci. 13:1619-1633 (2008).) Unless otherwise indicated, HVR residues and other residues in the variable domain (e.g., FR residues) are numbered herein according to Kabat et al., supra.
“Affinity” refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein, “binding affinity” refers to intrinsic binding affinity which reflects a 1:1 interaction between members of a binding pair (e.g., antibody and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd) Affinity can be measured by common methods known in the art, including those described herein. Specific illustrative and exemplary embodiments for measuring binding affinity are described in the following.
An “affinity matured” antibody refers to an antibody with one or more alterations in one or more hypervariable regions (HVRs), compared to a parent antibody which does not possess such alterations, such alterations resulting in an improvement in the affinity of the antibody for antigen.
The terms “anti-R-spondin-translocation antibody” and “an antibody that binds to R-spondin-translocation fusion polypeptide” refer to an antibody that is capable of binding R-spondin-translocation fusion polypeptide with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting R-spondin translocation. In one embodiment, the extent of binding of an anti-R-spondin translocation antibody to an unrelated, non-R-spondin-translocation fusion polypeptide, and/or nontranslocated-R-spondin polypeptide is less than about 10% of the binding of the antibody to R-spondin-translocation fusion polypeptides measured, e.g., by a radioimmunoassay (RIA). In certain embodiments, an antibody that binds to R-spondin-translocation fusion polypeptide has a dissociation constant (Kd) of ≤1 μM, ≤100 nM, ≤10 nM, ≤1 nM, ≤0.1 nM, ≤0.01 nM, or ≤0.001 nM (e.g.,10−8 M or less, e.g., from 10−8 M to 10−13 M, e.g., from 10−9 M to 10−13 M). In certain embodiments, an anti-R-spondin translocation antibody binds to an epitope of R-spondin translocation that is unique among R-spondin translocations.
A “blocking” antibody or an “antagonist” antibody is one which inhibits or reduces biological activity of the antigen it binds. Preferred blocking antibodies or antagonist antibodies substantially or completely inhibit the biological activity of the antigen.
A “naked antibody” refers to an antibody that is not conjugated to a heterologous moiety (e.g., a cytotoxic moiety) or radiolabel. The naked antibody may be present in a pharmaceutical formulation.
An “immunoconjugate” is an antibody conjugated to one or more heterologous molecule(s), including but not limited to a cytotoxic agent.
“Percent (%) amino acid sequence identity” with respect to a reference polypeptide sequence is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For purposes herein, however, % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc., and the source code has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, Calif., or may be compiled from the source code. The ALIGN-2 program should be compiled for use on a UNIX operating system, including digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.
In situations where ALIGN-2 is employed for amino acid sequence comparisons, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows:
100 times the fraction X/Y
where X is the number of amino acid residues scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A. Unless specifically stated otherwise, all % amino acid sequence identity values used herein are obtained as described in the immediately preceding paragraph using the ALIGN-2 computer program.
The term “detection” includes any means of detecting, including direct and indirect detection.
The term “biomarker” as used herein refers to an indicator, e.g., predictive, diagnostic, and/or prognostic, which can be detected in a sample. The biomarker may serve as an indicator of a particular subtype of a disease or disorder (e.g., cancer) characterized by certain, molecular, pathological, histological, and/or clinical features. In some embodiments, the biomarker is a gene. In some embodiments, the biomarker is a variation (e.g., mutation and/or polymorphism) of a gene. In some embodiments, the biomarkers is a translocation. Biomarkers include, but are not limited to, polynucleotides (e.g., DNA, and/or RNA), polypeptides, polypeptide and polynucleotide modifications (e.g., posttranslational modifications), carbohydrates, and/or glycolipid-based molecular markers.
The “presence,” “amount,” or “level” of a biomarker associated with an increased clinical benefit to an individual is a detectable level in a biological sample. These can be measured by methods known to one skilled in the art and also disclosed herein. The expression level or amount of biomarker assessed can be used to determine the response to the treatment.
The terms “level of expression” or “expression level” in general are used interchangeably and generally refer to the amount of a biomarker in a biological sample. “Expression” generally refers to the process by which information (e.g., gene-encoded and/or epigenetic) is converted into the structures present and operating in the cell. Therefore, as used herein, “expression” may refer to transcription into a polynucleotide, translation into a polypeptide, or even polynucleotide and/or polypeptide modifications (e.g., posttranslational modification of a polypeptide). Fragments of the transcribed polynucleotide, the translated polypeptide, or polynucleotide and/or polypeptide modifications (e.g., posttranslational modification of a polypeptide) shall also be regarded as expressed whether they originate from a transcript generated by alternative splicing or a degraded transcript, or from a post-translational processing of the polypeptide, e.g., by proteolysis. “Expressed genes” include those that are transcribed into a polynucleotide as mRNA and then translated into a polypeptide, and also those that are transcribed into RNA but not translated into a polypeptide (for example, transfer and ribosomal RNAs).
“Elevated expression,” “elevated expression levels,” or “elevated levels” refers to an increased expression or increased levels of a biomarker in an individual relative to a control, such as an individual or individuals who are not suffering from the disease or disorder (e.g., cancer) or an internal control (e.g., housekeeping biomarker).
“Reduced expression,” “reduced expression levels,” or “reduced levels” refers to a decrease expression or decreased levels of a biomarker in an individual relative to a control, such as an individual or individuals who are not suffering from the disease or disorder (e.g., cancer) or an internal control (e.g., housekeeping biomarker).
The term “housekeeping biomarker” refers to a biomarker or group of biomarkers (e.g., polynucleotides and/or polypeptides) which are typically similarly present in all cell types. In some embodiments, the housekeeping biomarker is a “housekeeping gene.” A “housekeeping gene” refers herein to a gene or group of genes which encode proteins whose activities are essential for the maintenance of cell function and which are typically similarly present in all cell types.
“Amplification,” as used herein generally refers to the process of producing multiple copies of a desired sequence. “Multiple copies” mean at least two copies. A “copy” does not necessarily mean perfect sequence complementarity or identity to the template sequence. For example, copies can include nucleotide analogs such as deoxyinosine, intentional sequence alterations (such as sequence alterations introduced through a primer comprising a sequence that is hybridizable, but not complementary, to the template), and/or sequence errors that occur during amplification.
The term “multiplex-PCR” refers to a single PCR reaction carried out on nucleic acid obtained from a single source (e.g., an individual) using more than one primer set for the purpose of amplifying two or more DNA sequences in a single reaction.
“Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).
“Stringent conditions” or “high stringency conditions”, as defined herein, can be identified by those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) overnight hybridization in a solution that employs 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with a 10 minute wash at 42° C. in 0.2×SSC (sodium chloride/sodium citrate) followed by a 10 minute high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C.
“Moderately stringent conditions” can be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent that those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.
The term “diagnosis” is used herein to refer to the identification or classification of a molecular or pathological state, disease or condition (e.g., cancer). For example, “diagnosis” may refer to identification of a particular type of cancer. “Diagnosis” may also refer to the classification of a particular subtype of cancer, e.g., by histopathological criteria, or by molecular features (e.g., a subtype characterized by expression of one or a combination of biomarkers (e.g., particular genes or proteins encoded by said genes)).
The term “aiding diagnosis” is used herein to refer to methods that assist in making a clinical determination regarding the presence, or nature, of a particular type of symptom or condition of a disease or disorder (e.g., cancer). For example, a method of aiding diagnosis of a disease or condition (e.g., cancer) can comprise detecting certain biomarkers in a biological sample from an individual.
The term “sample,” as used herein, refers to a composition that is obtained or derived from a subject and/or individual of interest that contains a cellular and/or other molecular entity that is to be characterized and/or identified, for example based on physical, biochemical, chemical and/or physiological characteristics. For example, the phrase “disease sample” and variations thereof refers to any sample obtained from a subject of interest that would be expected or is known to contain the cellular and/or molecular entity that is to be characterized. Samples include, but are not limited to, primary or cultured cells or cell lines, cell supernatants, cell lysates, platelets, serum, plasma, vitreous fluid, lymph fluid, synovial fluid, follicular fluid, seminal fluid, amniotic fluid, milk, whole blood, blood-derived cells, urine, cerebro-spinal fluid, saliva, sputum, tears, perspiration, mucus, tumor lysates, and tissue culture medium, tissue extracts such as homogenized tissue, tumor tissue, cellular extracts, and combinations thereof.
By “tissue sample” or “cell sample” is meant a collection of similar cells obtained from a tissue of a subject or individual. The source of the tissue or cell sample may be solid tissue as from a fresh, frozen and/or preserved organ, tissue sample, biopsy, and/or aspirate; blood or any blood constituents such as plasma; bodily fluids such as cerebral spinal fluid, amniotic fluid, peritoneal fluid, or interstitial fluid; cells from any time in gestation or development of the subject. The tissue sample may also be primary or cultured cells or cell lines. Optionally, the tissue or cell sample is obtained from a disease tissue/organ. The tissue sample may contain compounds which are not naturally intermixed with the tissue in nature such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics, or the like.
A “reference sample”, “reference cell”, “reference tissue”, “control sample”, “control cell”, or “control tissue”, as used herein, refers to a sample, cell, tissue, standard, or level that is used for comparison purposes. In one embodiment, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is obtained from a healthy and/or non-diseased part of the body (e.g., tissue or cells) of the same subject or individual. For example, healthy and/or non-diseased cells or tissue adjacent to the diseased cells or tissue (e.g., cells or tissue adjacent to a tumor). In another embodiment, a reference sample is obtained from an untreated tissue and/or cell of the body of the same subject or individual. In yet another embodiment, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is obtained from a healthy and/or non-diseased part of the body (e.g., tissues or cells) of an individual who is not the subject or individual. In even another embodiment, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is obtained from an untreated tissue and/or cell of the body of an individual who is not the subject or individual.
For the purposes herein a “section” of a tissue sample is meant a single part or piece of a tissue sample, e.g., a thin slice of tissue or cells cut from a tissue sample. It is understood that multiple sections of tissue samples may be taken and subjected to analysis, provided that it is understood that the same section of tissue sample may be analyzed at both morphological and molecular levels, or analyzed with respect to both polypeptides and polynucleotides.
By “correlate” or “correlating” is meant comparing, in any way, the performance and/or results of a first analysis or protocol with the performance and/or results of a second analysis or protocol. For example, one may use the results of a first analysis or protocol in carrying out a second protocols and/or one may use the results of a first analysis or protocol to determine whether a second analysis or protocol should be performed. With respect to the embodiment of polynucleotide analysis or protocol, one may use the results of the polynucleotide expression analysis or protocol to determine whether a specific therapeutic regimen should be performed.
“Individual response” or “response” can be assessed using any endpoint indicating a benefit to the individual, including, without limitation, (1) inhibition, to some extent, of disease progression (e.g., cancer progression), including slowing down and complete arrest; (2) a reduction in tumor size; (3) inhibition (i.e., reduction, slowing down or complete stopping) of cancer cell infiltration into adjacent peripheral organs and/or tissues; (4) inhibition (i.e. reduction, slowing down or complete stopping) of metasisis; (5) relief, to some extent, of one or more symptoms associated with the disease or disorder (e.g., cancer); (6) increase in the length of progression free survival; and/or (9) decreased mortality at a given point of time following treatment.
The phrase “substantially similar,” as used herein, refers to a sufficiently high degree of similarity between two numeric values (generally one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to not be of statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values). The difference between said two values may be, for example, less than about 20%, less than about 10%, and/or less than about 5% as a function of the reference/comparator value. The phrase “substantially normal” refers to substantially similar to a reference (e.g., normal reference).
The phrase “substantially different,” refers to a sufficiently high degree of difference between two numeric values (generally one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values). The difference between said two values may be, for example, greater than about 10%, greater than about 20%, greater than about 30%, greater than about 40%, and/or greater than about 50% as a function of the value for the reference/comparator molecule.
The word “label” when used herein refers to a detectable compound or composition. The label is typically conjugated or fused directly or indirectly to a reagent, such as a polynucleotide probe or an antibody, and facilitates detection of the reagent to which it is conjugated or fused. The label may itself be detectable (e.g., radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition which results in a detectable product.
An “effective amount” of an agent refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result.
A “therapeutically effective amount” of a substance/molecule of the invention, agonist or antagonist may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the substance/molecule, agonist or antagonist to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of the substance/molecule, agonist or antagonist are outweighed by the therapeutically beneficial effects. A “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically but not necessarily, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount will be less than the therapeutically effective amount.
The term “pharmaceutical formulation” refers to a preparation which is in such form as to permit the biological activity of an active ingredient contained therein to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the formulation would be administered.
A “pharmaceutically acceptable carrier” refers to an ingredient in a pharmaceutical formulation, other than an active ingredient, which is nontoxic to a subject., A pharmaceutically acceptable carrier includes, but is not limited to, a buffer, excipient, stabilizer, or preservative.
As used herein, “treatment” (and grammatical variations thereof such as “treat” or “treating”) refers to clinical intervention in an attempt to alter the natural course of the individual being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, antibodies of the invention are used to delay development of a disease or to slow the progression of a disease.
The terms “cancer” and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth/proliferation. Examples of cancer include, but are not limited to, carcinoma, lymphoma (e.g., Hodgkin's and non-Hodgkin's lymphoma), blastoma, sarcoma, and leukemia. More particular examples of such cancers include squamous cell cancer, small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastrointestinal cancer, pancreatic cancer, glioma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, leukemia and other lymphoproliferative disorders, and various types of head and neck cancer.
The term “anti-cancer therapy” refers to a therapy useful in treating cancer. Examples of anti-cancer therapeutic agents include, but are limited to, e.g., chemotherapeutic agents, growth inhibitory agents, cytotoxic agents, agents used in radiation therapy, anti-angiogenesis agents, apoptotic agents, anti-tubulin agents, and other agents to treat cancer, anti-CD20 antibodies, platelet derived growth factor inhibitors (e.g., Gleevec™ (Imatinib Mesylate)), a COX-2 inhibitor (e.g., celecoxib), interferons, cytokines, antagonists (e.g., neutralizing antibodies) that bind to one or more of the following targets PDGFR-beta, BlyS, APRIL, BCMA receptor(s), TRAIL/Apo2, and other bioactive and organic chemical agents, etc. Combinations thereof are also included in the invention.
The term “cytotoxic agent” as used herein refers to a substance that inhibits or prevents a cellular function and/or causes cell death or destruction. Cytotoxic agents include, but are not limited to, radioactive isotopes (e.g., At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212 and radioactive isotopes of Lu); chemotherapeutic agents or drugs (e.g., methotrexate, adriamicin, vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin, melphalan, mitomycin C, chlorambucil, daunorubicin or other intercalating agents); growth inhibitory agents; enzymes and fragments thereof such as nucleolytic enzymes; antibiotics; toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof; and the various antitumor or anticancer agents disclosed below.
A “chemotherapeutic agent” refers to a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include alkylating agents such as thiotepa and cyclosphosphamide (CYTOXAN®); alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphoramide and trimethylomelamine; acetogenins (especially bullatacin and bullatacinone); delta-9-tetrahydrocannabinol (dronabinol, MARINOL®); beta-lapachone; lapachol; colchicines; betulinic acid; a camptothecin (including the synthetic analogue topotecan (HYCAMTIN®), CPT-11 (irinotecan, CAMPTOSAR®), acetylcamptothecin, scopolectin, and 9-aminocamptothecin); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); podophyllotoxin; podophyllinic acid; teniposide; cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, chlorophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosoureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e. g., calicheamicin, especially calicheamicin gammall and calicheamicin omegaI1 (see, e.g., Nicolaou et al., Angew. Chem Intl. Ed. Engl., 33: 183-186 (1994)); CDP323, an oral alpha-4 integrin inhibitor; dynemicin, including dynemicin A; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, carminomycin, carzinophilin, chromomycins, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including ADRIAMYCIN®, morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin, doxorubicin HCl liposome injection (DOXIL®), liposomal doxorubicin TLC D-99 (MYOCET®), pegylated liposomal doxorubicin (CAELYX®), and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, porfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate, gemcitabine (GEMZAR®), tegafur (UFTORAL®), capecitabine (XELODA®), an epothilone, and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfornithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; 2-ethylhydrazide; procarbazine; PSK® polysaccharide complex (JHS Natural Products, Eugene, Oreg.); razoxane; rhizoxin; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2′,2′-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine (ELDISINE®, FILDESIN®); dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); thiotepa; taxoid, e.g., paclitaxel (TAXOL®), albumin-engineered nanoparticle formulation of paclitaxel (ABRAXANE™), and docetaxel (TAXOTERE®); chloranbucil; 6-thioguanine; mercaptopurine; methotrexate; platinum agents such as cisplatin, oxaliplatin (e.g., ELOXATIN®), and carboplatin; vincas, which prevent tubulin polymerization from forming microtubules, including vinblastine (VELBAN®), vincristine (ONCOVIN®), vindesine (ELDISINE®, FILDESIN®), and vinorelbine (NAVELBINE®); etoposide (VP-16); ifosfamide; mitoxantrone; leucovorin; novantrone; edatrexate; daunomycin; aminopterin; ibandronate; topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids such as retinoic acid, including bexarotene (TARGRETIN®); bisphosphonates such as clodronate (for example, BONEFOS® or OSTAC®), etidronate (DIDROCAL®), NE-58095, zoledronic acid/zoledronate (ZOMETA®), alendronate (FOSAMAX®), pamidronate (AREDIA®), tiludronate (SKELID®), or risedronate (ACTONEL®); troxacitabine (a 1,3-dioxolane nucleoside cytosine analog); antisense oligonucleotides, particularly those that inhibit expression of genes in signaling pathways implicated in aberrant cell proliferation, such as, for example, PKC-alpha, Raf, H-Ras, and epidermal growth factor receptor (EGF-R); vaccines such as THERATOPE® vaccine and gene therapy vaccines, for example, ALLOVECTIN® vaccine, LEUVECTIN® vaccine, and VAXID® vaccine; topoisomerase 1 inhibitor (e.g., LURTOTECAN®); rmRH (e.g., ABARELIX®); BAY439006 (sorafenib; Bayer); SU-11248 (sunitinib, SUTENT®, Pfizer); perifosine, COX-2 inhibitor (e.g., celecoxib or etoricoxib), proteosome inhibitor (e.g., PS341); bortezomib (VELCADE®); CCI-779; tipifarnib (R11577); orafenib, ABT510; Bcl-2 inhibitor such as oblimersen sodium (GENASENSE®); pixantrone; EGFR inhibitors (see definition below); tyrosine kinase inhibitors (see definition below); serine-threonine kinase inhibitors such as rapamycin (sirolimus, RAPAMUNE®); farnesyltransferase inhibitors such as lonafarnib (SCH 6636, SARASAR™); and pharmaceutically acceptable salts, acids or derivatives of any of the above; as well as combinations of two or more of the above such as CHOP, an abbreviation for a combined therapy of cyclophosphamide, doxorubicin, vincristine, and prednisolone; and FOLFOX, an abbreviation for a treatment regimen with oxaliplatin (ELOXATIN™) combined with 5-FU and leucovorin.
Chemotherapeutic agents as defined herein include “anti-hormonal agents” or “endocrine therapeutics” which act to regulate, reduce, block, or inhibit the effects of hormones that can promote the growth of cancer. They may be hormones themselves, including, but not limited to: anti-estrogens with mixed agonist/antagonist profile, including, tamoxifen (NOLVADEX®), 4-hydroxytamoxifen, toremifene (FARESTON®), idoxifene, droloxifene, raloxifene (EVISTA®), trioxifene, keoxifene, and selective estrogen receptor modulators (SERMs) such as SERM3; pure anti-estrogens without agonist properties, such as fulvestrant (FASLODEX®), and EM800 (such agents may block estrogen receptor (ER) dimerization, inhibit DNA binding, increase ER turnover, and/or suppress ER levels); aromatase inhibitors, including steroidal aromatase inhibitors such as formestane and exemestane (AROMASIN®), and nonsteroidal aromatase inhibitors such as anastrazole (ARIMIDEX®), letrozole (FEMARA®) and aminoglutethimide, and other aromatase inhibitors include vorozole (RIVISOR®), megestrol acetate (MEGASE®), fadrozole, and 4(5)-imidazoles; lutenizing hormone-releaseing hormone agonists, including leuprolide (LUPRON® and ELIGARD®), goserelin, buserelin, and tripterelin; sex steroids, including progestines such as megestrol acetate and medroxyprogesterone acetate, estrogens such as diethylstilbestrol and premarin, and androgens/retinoids such as fluoxymesterone, all transretionic acid and fenretinide; onapristone; anti-progesterones; estrogen receptor down-regulators (ERDs); anti-androgens such as flutamide, nilutamide and bicalutamide; and pharmaceutically acceptable salts, acids or derivatives of any of the above; as well as combinations of two or more of the above.
The term “prodrug” as used in this application refers to a precursor or derivative form of a pharmaceutically active substance that is less cytotoxic to tumor cells compared to the parent drug and is capable of being enzymatically activated or converted into the more active parent form. See, e.g., Wilman, “Prodrugs in Cancer Chemotherapy” Biochemical Society Transactions, 14, pp. 375-382, 615th Meeting Belfast (1986) and Stella et al., “Prodrugs: A Chemical Approach to Targeted Drug Delivery,” Directed Drug Delivery, Borchardt et al., (ed.), pp. 247-267, Humana Press (1985). The prodrugs of this invention include, but are not limited to, phosphate-containing prodrugs, thiophosphate-containing prodrugs, sulfate-containing prodrugs, peptide-containing prodrugs, D-amino acid-modified prodrugs, glycosylated prodrugs, β-lactam-containing prodrugs, optionally substituted phenoxyacetamide-containing prodrugs or optionally substituted phenylacetamide-containing prodrugs, 5-fluorocytosine and other 5-fluorouridine prodrugs which can be converted into the more active cytotoxic free drug. Examples of cytotoxic drugs that can be derivatized into a prodrug form for use in this invention include, but are not limited to, those chemotherapeutic agents described above.
A “growth inhibitory agent” when used herein refers to a compound or composition which inhibits growth of a cell (e.g., a cell whose growth is dependent upon a wnt pathway gene and/or R-spondin translocation expression either in vitro or in vivo). Examples of growth inhibitory agents include agents that block cell cycle progression (at a place other than S phase), such as agents that induce G1 arrest and M-phase arrest. Classical M-phase blockers include the vincas (vincristine and vinblastine), taxanes, and topoisomerase II inhibitors such as doxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin. Those agents that arrest G1 also spill over into S-phase arrest, for example, DNA alkylating agents such as tamoxifen, prednisone, dacarbazine, mechlorethamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C. Further information can be found in The Molecular Basis of Cancer, Mendelsohn and Israel, eds., Chapter 1, entitled “Cell cycle regulation, oncogenes, and antineoplastic drugs” by Murakami et al., (W B Saunders: Philadelphia, 1995), especially p. 13. The taxanes (paclitaxel and docetaxel) are anticancer drugs both derived from the yew tree. Docetaxel (TAXOTERE®, Rhone-Poulenc Rorer), derived from the European yew, is a semisynthetic analogue of paclitaxel (TAXOL®, Bristol-Myers Squibb). Paclitaxel and docetaxel promote the assembly of microtubules from tubulin dimers and stabilize microtubules by preventing depolymerization, which results in the inhibition of mitosis in cells.
By “radiation therapy” is meant the use of directed gamma rays or beta rays to induce sufficient damage to a cell so as to limit its ability to function normally or to destroy the cell altogether. It will be appreciated that there will be many ways known in the art to determine the dosage and duration of treatment. Typical treatments are given as a one time administration and typical dosages range from 10 to 200 units (Grays) per day.
An “individual” or “subject” is a mammal. Mammals include, but are not limited to, domesticated animals (e.g., cows, sheep, cats, dogs, and horses), primates (e.g., humans and non-human primates such as monkeys), rabbits, and rodents (e.g., mice and rats). In certain embodiments, the individual or subject is a human.
The term “concurrently” is used herein to refer to administration of two or more therapeutic agents, where at least part of the administration overlaps in time. Accordingly, concurrent administration includes a dosing regimen when the administration of one or more agent(s) continues after discontinuing the administration of one or more other agent(s).
By “reduce” or “inhibit” is meant the ability to cause an overall decrease of 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or greater. Reduce or inhibit can refer to the symptoms of the disorder being treated, the presence or size of metastases, or the size of the primary tumor.
The term “package insert” is used to refer to instructions customarily included in commercial packages of therapeutic products, that contain information about the indications, usage, dosage, administration, combination therapy, contraindications and/or warnings concerning the use of such therapeutic products.
An “article of manufacture” is any manufacture (e.g., a package or container) or kit comprising at least one reagent, e.g., a medicament for treatment of a disease or disorder (e.g., cancer), or a probe for specifically detecting a biomarker described herein. In certain embodiments, the manufacture or kit is promoted, distributed, or sold as a unit for performing the methods described herein.
A “target audience” is a group of people or an institution to whom or to which a particular medicament is being promoted or intended to be promoted, as by marketing or advertising, especially for particular uses, treatments, or indications, such as individuals, populations, readers of newspapers, medical literature, and magazines, television or internet viewers, radio or internet listeners, physicians, drug companies, etc.
As is understood by one skilled in the art, reference to “about” a value or parameter herein includes (and describes) embodiments that are directed to that value or parameter per se. For example, description referring to “about X” includes description of “X”.
It is understood that aspect and embodiments of the invention described herein include “consisting” and/or “consisting essentially of” aspects and embodiments. As used herein, the singular form “a”, “an”, and “the” includes plural references unless indicated otherwise.
Provided herein are methods utilizing a wnt pathway antagonist. In particular, provided herein are methods utilizing an R-spondin-translocation antagonist. For example, provided herein are methods of inhibiting cell proliferation of a cancer cell comprising contacting the cancer cell with an effective amount of an R-spondin-translocation antagonist. Also provided herein are methods of treating cancer in an individual comprising administering to the individual an effective amount of an R-spondin-translocation antagonist. In some embodiments, the cancer or cancer comprises an R-spondin translocation.
Also provided herein are methods of treating cancer in an individual comprising administering to the individual an effective amount of an anti-cancer therapy, wherein treatment is based upon the individual having cancer comprising one or more biomarkers. In some embodiments, the anti-cancer therapy comprises a wnt pathway antagonist. For example, provided are methods of treating cancer in an individual comprising administering to the individual an effective amount of a wnt pathway antagonist, wherein treatment is based upon the individual having cancer comprising an R-spondin translocation. In some embodiments, the win pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments, the wnt pathway antagonist is an R-spondin-translocation antagonist. In some embodiments, the R-spondin antagonist and/or R-spondin translocation antagonist is an isolated antibody that binds R-spondin (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4).
Further provided herein are methods of treating cancer in an individual provided that the individual has been found to have cancer comprising one or more biomarkers, the treatment comprising administering to the individual an effective amount of an anti-cancer therapy. In some embodiments, the anti-cancer therapy comprises a wnt pathway antagonist. For example, provided herein are methods of treating cancer in an individual provided that the individual has been found to have cancer comprising an R-spondin translocation, the treatment comprising administering to the individual an effective amount of a wnt pathway antagonist. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments, the wnt pathway antagonist is an R-spondin-translocation antagonist. In some embodiments, the R-spondin antagonist and/or R-spondin translocation antagonist is an isolated antibody that binds R-spondin (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4).
Provided herein are methods of treating a cancer cell, wherein the cancer cell comprises one or more biomarkers, the method comprising providing an effective amount of a wnt pathway antagonist. For example, provided herein are methods of treating a cancer cell, wherein the cancer cell comprises an R-spondin translocation, the method comprising providing an effective amount of a wnt pathway antagonist. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments, the wnt pathway antagonist is an R-spondin-translocation antagonist. In some embodiments, the R-spondin antagonist and/or R-spondin translocation antagonist is an isolated antibody that binds R-spondin (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4).
Provided herein are methods for treating cancer in an individual, the method comprising: determining that a sample obtained from the individual comprises one or more biomarkers, and administering an effective amount of an anti-cancer therapy comprising a wnt pathway antagonist to the individual, whereby the cancer is treated. For example, provided herein are methods for treating cancer in an individual, the method comprising: determining that a sample obtained from the individual comprises an R-spondin translocation, and administering an effective amount of an anti-cancer therapy comprising a wnt pathway antagonist to the individual, whereby the cancer is treated. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments, the wnt pathway antagonist is an R-spondin-translocation antagonist. In some embodiments, the R-spondin antagonist and/or R-spondin translocation antagonist is an isolated antibody that binds R-spondin (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4).
Provided herein are also methods of treating cancer, comprising: (a) selecting an individual having cancer, wherein the cancer comprises one or more biomarkers; and (b) administering to the individual thus selected an effective amount of a wnt pathway antagonist, whereby the cancer is treated. For example, provided herein are also methods of treating cancer, comprising: (a) selecting an individual having cancer, wherein the cancer comprises an R-spondin translocation; and (b) administering to the individual thus selected an effective amount of a wnt pathway antagonist, whereby the cancer is treated. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments, the wnt pathway antagonist is an R-spondin-translocation antagonist. In some embodiments, the R-spondin antagonist and/or R-spondin translocation antagonist is an isolated antibody that binds R-spondin (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4).
Further provided herein are methods of identifying an individual with cancer who is more or less likely to exhibit benefit from treatment with an anti-cancer therapy, the method comprising: determining presence or absence of one or more biomarkers in a sample obtained from the individual, wherein presence of the one or more biomarkers in the sample indicates that the individual is more likely to exhibit benefit from treatment with the anti-cancer therapy or absence of the one or more biomarkers indicates that the individual is less likely to exhibit benefit from treatment with the anti-cancer therapy. In some embodiments, the anti-cancer therapy comprises a wnt pathway antagonist. For example, provided herein are methods of identifying an individual with cancer who is more or less likely to exhibit benefit from treatment with an anti-cancer therapy comprising a wnt pathway antagonist, the method comprising: determining presence or absence of an R-spondin translocation in a sample obtained from the individual, wherein presence of the R-spondin translocation in the sample indicates that the individual is more likely to exhibit benefit from treatment with the anti-cancer therapy comprising the wnt pathway antagonist or absence of the R-spondin translocation indicates that the individual is less likely to exhibit benefit from treatment with the anti-cancer therapy comprising the wnt pathway antagonist. In some embodiments, the method further comprises administering an effective amount of a wnt pathway antagonist. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments, the wnt pathway antagonist is an R-spondin-translocation antagonist. In some embodiments, the R-spondin antagonist and/or R-spondin translocation antagonist is an isolated antibody that binds R-spondin (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4).
Provided herein are methods for predicting whether an individual with cancer is more or less likely to respond effectively to treatment with an anti-cancer therapy comprising a wnt pathway antagonist, the method comprising determining one or more biomarkers, whereby presence of the one or more biomarkers indicates that the individual is more likely to respond effectively to treatment with the wnt pathway antagonist and absence of the one or more biomarkers indicates that the individual is less likely to respond effectively to treatment with the wnt pathway antagonist. For example, provided herein are methods for predicting whether an individual with cancer is more or less likely to respond effectively to treatment with an anti-cancer therapy comprising a win pathway antagonist, the method comprising determining an R-spondin translocation, whereby presence of the R-spondin translocation indicates that the individual is more likely to respond effectively to treatment with the wnt pathway antagonist and absence of the R-spondin translocation indicates that the individual is less likely to respond effectively to treatment with the wnt pathway antagonist. In some embodiments, the method further comprises administering an effective amount of a wnt pathway antagonist. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments, the wnt pathway antagonist is an R-spondin-translocation antagonist. In some embodiments, the R-spondin antagonist and/or R-spondin translocation antagonist is an isolated antibody that binds R-spondin (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4).
Provided herein are methods of predicting the response or lack of response of an individual with cancer to an anti-cancer therapy comprising a wnt pathway antagonist comprising detecting in a sample obtained from the individual presence or absence of one or more biomarkers, wherein presence of the one or more biomarkers is predictive of response of the individual to the anti-cancer therapy comprising the wnt pathway antagonist and absence of the one or more biomarkers is predictive of lack of response of the individual to the anti-cancer therapy comprising the wnt pathway antagonist. For example, provided herein are methods of predicting the response or lack of response of an individual with cancer to an anti-cancer therapy comprising a wnt pathway antagonist comprising detecting in a sample obtained from the individual presence or absence of an R-spondin translocation, wherein presence of the R-spondin translocation is predictive of response of the individual to the anti-cancer therapy comprising the wnt pathway antagonist and absence of the R-spondin translocation is predictive of lack of response of the individual to the anti-cancer therapy comprising the wnt pathway antagonist. In some embodiments, the method further comprises administering an effective amount of a wnt pathway antagonist. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments, the wnt pathway antagonist is an R-spondin-translocation antagonist. In some embodiments, the R-spondin antagonist and/or R-spondin translocation antagonist is an isolated antibody that binds R-spondin (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4).
In some embodiments of any of the methods, the one or more biomarkers comprise one or more genes listed in Table 2. In some embodiments, the presence of one or more biomarkers comprises the presence of a variation (e.g., polymorphism or mutation) of one or more genes listed in Table 2 (e.g., a variation (e.g., polymorphism or mutation) in Table 2). In some embodiments of any of the methods, the one or more biomarkers comprise one or more genes listed in Table 3. In some embodiments, the presence of one or more biomarkers comprises the presence of a variation (e.g., polymorphism or mutation) of one or more genes listed in Table 3 (e.g., a variation (e.g., polymorphism or mutation) in Table 3). In some embodiments of any of the methods, the one or more biomarkers comprise one or more genes listed in Table 4. In some embodiments, the presence of one or more biomarkers comprises the presence of a variation (e.g., polymorphism or mutation) of one or more genes listed in Table 4 (e.g., a variation (e.g., polymorphism or mutation) in Table 4). In some embodiments of any of the methods, the one or more biomarkers comprise one or more genes listed in Table 5. In some embodiments, the presence of one or more biomarkers comprises the presence of a variation (e.g., polymorphism or mutation) of one or more genes listed in Table 5 (e.g., a variation (e.g., polymorphism or mutation) in Table 5). In some embodiments, the variation (e.g., polymorphism or mutation) is a somatic variation (e.g., polymorphism or mutation).
In some embodiments of any of the methods, the one or more biomarkers comprise one or more genes selected from the group consisting of KRAS, TP53, APC, PIK3CA, SMAD4, FBXW7, CSMD1, NRXN1, DNAH5, MRVI1, TRPS1, DMD, KIF2B, ATM, FAM5C, EVC2, OR2W3, SIN3A, SMARCA5, NCOR1, JARID2, TCF12, TCF7L2, PHF2, SOS2, RASGRF2, ARHGAP10, ARHGEF33, Rab40c, TET2, TET3, EP400, MLL, TMPRSS11A, ERBB3, EPHB4, EFNB3, EPHA1, TYRO3, TIE1, FLT, RIOK3, PRKCB, MUSK, MAP2K7, MAP4K5, PTPRN2, GPR4, GPR98, TOPORS, and SCN10A. In some embodiments, the one or more biomarkers comprise one or more genes selected from the group consisting of CSMD1, NRXN1, DNAH5, MRVI1, TRPS1, DMD, KIF2B, ATM, FAM5C, EVC2, OR2W3, TMPRSS11A, and SCN10A. In some embodiments, the one or more biomarkers comprise RAB40C, TCF12, C20orf132, GRIN3A, and/or SOS2. In some embodiments, the one or more biomarkers comprise ETV4, GRIND2D, FOXQ1, and/or CLDN1. In some embodiments, the one or more biomarkers comprise MRPL33. In some embodiments In some embodiments, the one or more biomarkers comprise one or more transcriptional regulators (e.g., TCF12, TCF7L2 and/or PHF2) In some embodiments, the one or more biomarkers comprise one or more Ras/Rho related regulators (e.g., SOS1 (e.g., R547W, T614M R854*, G1129V), SOS2 (e.g., R225*, R854C, and Q1296H) RASGRF2, ARHGAP10, ARHGEF33 and/or Rab40c (e.g., G251S)). In some embodiments, the one or more biomarkers comprise one or more chromatin modifying enzymes (e.g., TET1, TET2, TET3, EP400 and/or MLL). In some embodiments, the one or more chromatin modifying enzymes are TET1 and/or TET3. In some embodiments, the one or more chromatin modifying enzymes are TET1 (e.g., R81H, E417A, K540T, K792T, S879L, S1012*, Q1322*, C1482Y, A1896V, and A2129V), TET2 (e.g., K108T, T1181, S289L, F373L, K1056N, Y1169*, A1497V, and V1857M), and/or TET3 (e.g., T165M, A874T, M977V, G1398R, and R1576Q/W). In some embodiments, the one or more biomarkers comprise one or more receptor tyrosine kinases (e.g., ERBB3, EPHB4, EFNB3, EPHA1, TYRO3, TIE1 and FLT4). In some embodiments, the one or more biomarkers comprise one or more kinases (e.g., RIOK3, PRKCB, MUSK, MAP2K7 and MAP4K5). In some embodiments, the one or more biomarkers comprise one or more protein phosphatase (e.g., PTPRN2). In some embodiments, the one or more biomarkers comprise one or more GPRCs (e.g., GPR4 and/or GPR98). In some embodiments, the one or more biomarkers comprise one or more E3-ligase (e.g., TOPORS). In some embodiments, the presence of the one or more biomarkers comprise presence of a variation (e.g., polymorphism or mutation) of the one or more biomarkers listed in Table 2, 3, 4, and/or 5 (e.g., a variation (e.g., polymorphism or mutation) in Table 2, 3, 4, and/or 5). In some embodiments, the variation (e.g., polymorphism or mutation) comprise a somatic variation (e.g., polymorphism or mutation).
In some embodiments of any of the methods, the one or more biomarkers comprise one or more RSPO (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4). In some embodiments, presence of the one or more biomarkers is indicated by the presence of elevated expression levels (e.g., compared to reference) of one or more RSPO (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4). In some embodiments, the one or more biomarkers comprises RSPO1. In some embodiments, the one or more biomarkers comprises RSPO2. In some embodiments, the one or more biomarkers comprises RSPO3. In some embodiments, the one or more biomarkers comprises RSPO4.
In some embodiments of any of the methods, the one or more biomarkers comprise one or more genes listed in Table 6. In some embodiments, presence of the one or more biomarkers is indicated by the presence of elevated expression levels (e.g., compared to reference) of one or more genes listed in Table 6. In some embodiments, the one or more biomarkers comprise FOXA1, CLND1, and/or IGF2. In some embodiments, presence of the one or more biomarkers is indicated by presence of elevated expression levels (e.g., compared to reference) of FOXA1, CLND1, and/or IGF2. In some embodiments, the one or more biomarkers comprise a differentially expressed signaling pathway including, but not limited to, Calcium Signaling, cAMP-mediated signaling, Glutamate Receptor Signaling, Amyotrophic Lateral Sclerosis Signaling, Nitrogen Metabolism, Axonal Guidance Signaling, Role of IL-17A in Psoriasis, Serotonin Receptor Signaling, Airway Pathology in Chronic Obstructive Pulmonary Disease, Protein Kinase A Signaling, Bladder Cancer Signaling, HIF1α Signaling, Cardiac β-adrenergic Signaling, Synaptic Long Term Potentiation, Atherosclerosis Signaling, Circadian Rhythm Signaling, CREB Signaling in Neurons, G-Protein Coupled Receptor Signaling, Leukocyte Extravasation Signaling, Complement System, Eicosanoid Signaling, Tyrosine Metabolism, Cysteine Metabolism, Synaptic Long Term Depression, Role of IL-17A in Arthritis, Cellular Effects of Sildenafil (Viagra), Neuropathic Pain Signaling In Dorsal Horn Neurons, D-arginine and D-ornithine Metabolism, Role of IL-17F in Allergic Inflammatory Airway Diseases, Thyroid Cancer Signaling, Hepatic Fibrosis/Hepatic Stellate Cell Activation, Dopamine Receptor Signaling, Role of NANOG in Mammalian Embryonic Stem Cell Pluripotency, Chondroitin Sulfate Biosynthesis, Endothelin-1 Signaling, Keratan Sulfate Biosynthesis, Phototransduction Pathway, Wnt/β-catenin Signaling, Chemokine Signaling, Alanine and Aspartate Metabolism, Glycosphingolipid Biosynthesis—Neolactoseries, Bile Acid Biosynthesis, Role of Macrophages, Fibroblasts and Endothelial Cells in Rheumatoid Arthritis, α-Adrenergic Signaling, Taurine and Hypotaurine Metabolism, LPS/IL-1 Mediated Inhibition of RXR Function, Colorectal Cancer Metastasis Signaling, CCR3 Signaling in Eosinophils, and/or O-Glycan Biosynthesis.
In some embodiments of any of the methods, the one or more biomarkers comprise one or more genes listed in Table 7. In some embodiments, presence of the one or more biomarkers is indicated by the presence of elevated gene copy number (e.g., compared to reference) of one or more genes listed in Table 7. In some embodiments, the one or more biomarkers comprise IGF2, KRAS, and/or MYC. In some embodiments, presence of the one or more biomarkers is indicated by the presence of elevated gene copy number (e.g., compared to reference) of IGF2, KRAS, and/or MYC. In some embodiments, presence of the one or more biomarkers is indicated by the presence of reduced gene copy number (e.g., compared to reference) of one or more genes listed in Table 7. In some embodiments, the one or more biomarkers comprise FHIT, APC, and/or SMAD4. In some embodiments, presence of the one or more biomarkers is indicated by the presence of reduced gene copy number (e.g., compared to reference) of FHIT, APC, and/or SMAD4. In some embodiments, presence of the one or more biomarkers is indicated by the presence of elevated copy number (e.g., compared to reference) of chromosome 20q. In some embodiments, presence of the one or more biomarkers is indicated by the presence of reduced copy number (e.g., compared to reference) of chromosome 18q.
In some embodiments of any of the methods, the one or more biomarkers comprise one or more genes listed in Table 9. In some embodiments, presence of the one or more biomarkers is indicated by the presence of a variation (e.g., polymorphism or mutation) of one or more genes listed in Table 9 (e.g., a variation (e.g., polymorphism or mutation) in Table 9) and/or alternative splicing (e.g., compared to reference) of one or more genes listed in Table 9. In some embodiments, the one or more biomarkers comprise TP53, NOTCH2, MRPL33, and/or EIF5B. In some embodiments, the one or more biomarkers is MRPL33. In some embodiments, presence of the one or more biomarkers is indicated by the presence of a variation (e.g., polymorphism or mutation) of TP53, NOTCH2, MRPL33, and/or EIF5B (e.g., a variation (e.g., polymorphism or mutation) in Table 9) and/or alternative splicing (e.g., compared to reference) of TP53, NOTCH2, MRPL33, and/or EIF5B.
In some embodiments of any of the methods, the one or more biomarkers comprise a translocation (e.g., rearrangement and/or fusion) of one or more genes listed in Table 10. In some embodiments, the presence of one or more biomarkers comprises the presence of a translocation (e.g., rearrangement and/or fusion) of one or more genes listed in Table 10 (e.g., a translocation (e.g., rearrangement and/or fusion) in Table 10). In some embodiments of any of the methods, the translocation (e.g., rearrangement and/or fusion) is a PVT1 translocation (e.g., rearrangement and/or fusion). In some embodiments, the PVT1 translocation (e.g., rearrangement and/or fusion) comprises PVT1 and MYC. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises PVT1 and IncDNA. In some embodiments of any of the methods, the translocation (e.g., rearrangement and/or fusion) is an R-spondin translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO1 translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO2 translocation (e.g., rearrangement and/or fusion). In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E and RSPO2. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises SEQ ID NO:71. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is detectable by primers which include SEQ ID NO:12, 41, and/or 42. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is driven by the EIF3E promoter. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is driven by the RSPO2 promoter. In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO3 translocation (e.g., rearrangement and/or fusion). In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK and RSPO3. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises SEQ ID NO:72 and/or SEQ ID NO:73. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is detectable by primers which include SEQ ID NO:13, 14, 43, and/or 44. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is driven by the PTPRK promoter. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is driven by the RSPO3 promoter. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises the PTPRK secretion signal sequence (and/or does not comprise the RSPO3 secretion signal sequence). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO4 translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) results in elevated expression levels of R-spondin (e.g., compared to a reference without the R-spondin translocation). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) results in elevated activity and/or activation of R-spondin (e.g., compared to a reference without the R-spondin translocation). In some embodiments, the presence of one or more biomarkers comprises an R-spondin translocation (e.g., rearrangement and/or fusion), such as a translocation (e.g., rearrangement and/or fusion) in Table 10, and KRAS and/or BRAF. In some embodiments, the presence of one or more biomarkers is presence of an R-spondin translocation (e.g., rearrangement and/or fusion), such as a translocation (e.g., rearrangement and/or fusion) in Table 10, and a variation (e.g., polymorphism or mutation) KRAS and/or BRAF. In some embodiments, the presence of one or more biomarkers is presence of an R-spondin translocation (e.g., rearrangement and/or fusion), such as a translocation (e.g., rearrangement and/or fusion) in Table 10, and the absence of one or more biomarkers is absence of a variation (e.g., polymorphism or mutation) CTNNB1 and/or APC.
In some embodiments of any of the translocation (e.g., rearrangement and/or fusion), the translocation (e.g., rearrangement and/or fusion) is a somatic translocation (e.g., rearrangement and/or fusion). In some embodiments, the translocation (e.g., rearrangement and/or fusion) is an intra-chromosomal translocation (e.g., rearrangement and/or fusion). In some embodiments, the translocation (e.g., rearrangement and/or fusion) is an inter-chromosomal translocation (e.g., rearrangement and/or fusion). In some embodiments, the translocation (e.g., rearrangement and/or fusion) is an inversion. In some embodiments, the translocation (e.g., rearrangement and/or fusion) is a deletion. In some embodiments, the translocation (e.g., rearrangement and/or fusion) is a functional translocation fusion polynucleotide (e.g., functional R-spondin-translocation fusion polynucleotide) and/or functional translocation fusion polypeptide (e.g., functional R-spondin-translocation fusion polypeptide). In some embodiments, the functional translocation fusion polypeptide (e.g., functional R-spondin-translocation fusion polypeptide) activates a pathway known to be modulated by one of the tranlocated genes (e.g., wnt signaling pathway). In some embodiments, the pathway is canonical wnt signaling pathway. In some embodiments, the pathway is noncanonical wnt signaling pathway. In some embodiments, the Methods of determining pathway activation are known in the art and include luciferase reporter assays as described herein.
Examples of cancers and cancer cells include, but are not limited to, carcinoma, lymphoma, blastoma (including medulloblastoma and retinoblastoma), sarcoma (including liposarcoma and synovial cell sarcoma), neuroendocrine tumors (including carcinoid tumors, gastrinoma, and islet cell cancer), mesothelioma, schwannoma (including acoustic neuroma), meningioma, adenocarcinoma, melanoma, and leukemia or lymphoid malignancies. More particular examples of such cancers include squamous cell cancer (e.g., epithelial squamous cell cancer), lung cancer including small-cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung and squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer (including metastatic breast cancer), colon cancer, rectal cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, testicular cancer, esophageal cancer, tumors of the biliary tract, as well as head and neck cancer. In some embodiments, the cancer is colorectal cancer. In some embodiments, the cancer is colon cancer. In some embodiments, the cancer is rectal cancer.
Presence and/or expression levels/amount of a biomarker (e.g., R-spondin translocation) can be determined qualitatively and/or quantitatively based on any suitable criterion known in the art, including but not limited to DNA, mRNA, cDNA, proteins, protein fragments and/or gene copy number. In certain embodiments, presence and/or expression levels/amount of a biomarker in a first sample is increased as compared to presence/absence and/or expression levels/amount in a second sample. In certain embodiments, presence/absence and/or expression levels/amount of a biomarker in a first sample is decreased as compared to presence and/or expression levels/amount in a second sample. In certain embodiments, the second sample is a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue. Additional disclosures for determining presence/absence and/or expression levels/amount of a gene are described herein.
In some embodiments of any of the methods, elevated expression refers to an overall increase of about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or greater, in the level of biomarker (e.g., protein or nucleic acid (e.g., gene or mRNA)), detected by standard art known methods such as those described herein, as compared to a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue. In certain embodiments, the elevated expression refers to the increase in expression level/amount of a biomarker in the sample wherein the increase is at least about any of 1.5×, 1.75×, 2×, 3×, 4×, 5×, 6×, 7×, 8×, 9×, 10×, 25×, 50×, 75×, or 100× the expression level/amount of the respective biomarker in a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue. In some embodiments, elevated expression refers to an overall increase of greater than about 1.5 fold, about 1.75 fold, about 2 fold, about 2.25 fold, about 2.5 fold, about 2.75 fold, about 3.0 fold, or about 3.25 fold as compared to a reference sample, reference cell, reference tissue, control sample, control cell, control tissue, or internal control (e.g., housekeeping gene).
In some embodiments of any of the methods, reduced expression refers to an overall reduction of about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or greater, in the level of biomarker (e.g., protein or nucleic acid (e.g., gene or mRNA)), detected by standard art known methods such as those described herein, as compared to a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue. In certain embodiments, reduced expression refers to the decrease in expression level/amount of a biomarker in the sample wherein the decrease is at least about any of 0.9×, 0.8×, 0.7×, 0.6×, 0.5×, 0.4×, 0.3×, 0.2×, 0.1×, 0.05×, or 0.01× the expression level/amount of the respective biomarker in a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue.
Presence and/or expression level/amount of various biomarkers in a sample can be analyzed by a number of methodologies, many of which are known in the art and understood by the skilled artisan, including, but not limited to, immunohistochemical (“IHC”), Western blot analysis, immunoprecipitation, molecular binding assays, ELISA, ELIFA, fluorescence activated cell sorting (“FACS”), MassARRAY, proteomics, quantitative blood based assays (as for example Serum ELISA), biochemical enzymatic activity assays, in situ hybridization, Southern analysis, Northern analysis, whole genome sequencing, polymerase chain reaction (“PCR”) including quantitative real time PCR (“qRT-PCR”) and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like), RNA-Seq, FISH, microarray analysis, gene expression profiling, and/or serial analysis of gene expression (“SAGE”), as well as any one of the wide variety of assays that can be performed by protein, gene, and/or tissue array analysis. Typical protocols for evaluating the status of genes and gene products are found, for example in Ausubel et al., eds., 1995, Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4 (Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Multiplexed immunoassays such as those available from Rules Based Medicine or Meso Scale Discovery (“MSD”) may also be used.
In some embodiments, presence and/or expression level/amount of a biomarker is determined using a method comprising: (a) performing gene expression profiling, PCR (such as rtPCR), RNA-seq, microarray analysis, SAGE, MassARRAY technique, or FISH on a sample (such as a subject cancer sample); and b) determining presence and/or expression level/amount of a biomarker in the sample. In some embodiments, the microarray method comprises the use of a microarray chip having one or more nucleic acid molecules that can hybridize under stringent conditions to a nucleic acid molecule encoding a gene mentioned above or having one or more polypeptides (such as peptides or antibodies) that can bind to one or more of the proteins encoded by the genes mentioned above. In one embodiment, the PCR method is qRT-PCR. In one embodiment, the PCR method is multiplex-PCR. In some embodiments, gene expression is measured by microarray. In some embodiments, gene expression is measured by qRT-PCR. In some embodiments, expression is measured by multiplex-PCR.
Methods for the evaluation of mRNAs in cells are well known and include, for example, hybridization assays using complementary DNA probes (such as in situ hybridization using labeled riboprobes specific for the one or more genes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR using complementary primers specific for one or more of the genes, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like).
Samples from mammals can be conveniently assayed for mRNAs using Northern, dot blot or PCR analysis. In addition, such methods can include one or more steps that allow one to determine the levels of target mRNA in a biological sample (e.g., by simultaneously examining the levels a comparative control mRNA sequence of a “housekeeping” gene such as an actin family member). Optionally, the sequence of the amplified target cDNA can be determined.
Optional methods of the invention include protocols which examine or detect mRNAs, such as target mRNAs, in a tissue or cell sample by microarray technologies. Using nucleic acid microarrays, test and control mRNA samples from test and control tissue samples are reverse transcribed and labeled to generate cDNA probes. The probes are then hybridized to an array of nucleic acids immobilized on a solid support. The array is configured such that the sequence and position of each member of the array is known. For example, a selection of genes whose expression correlates with increased or reduced clinical benefit of anti-angiogenic therapy may be arrayed on a solid support. Hybridization of a labeled probe with a particular array member indicates that the sample from which the probe was derived expresses that gene.
According to some embodiments, presence and/or expression level/amount is measured by observing protein expression levels of an aforementioned gene. In certain embodiments, the method comprises contacting the biological sample with antibodies to a biomarker (e.g., anti-R-spondin translocation antibodies) described herein under conditions permissive for binding of the biomarker, and detecting whether a complex is formed between the antibodies and biomarker. Such method may be an in vitro or in vivo method. In one embodiment, an antibody is used to select subjects eligible for therapy with wnt pathway antagonist, in particular R-spondin-translocation antagonist, e.g., a biomarker for selection of individuals.
In certain embodiments, the presence and/or expression level/amount of biomarker proteins in a sample is examined using IHC and staining protocols. IHC staining of tissue sections has been shown to be a reliable method of determining or detecting presence of proteins in a sample. In one aspect, expression level of biomarker is determined using a method comprising: (a) performing IHC analysis of a sample (such as a subject cancer sample) with an antibody; and b) determining expression level of a biomarker in the sample. In some embodiments, IHC staining intensity is determined relative to a reference value.
IHC may be performed in combination with additional techniques such as morphological staining and/or fluorescence in-situ hybridization. Two general methods of IHC are available; direct and indirect assays. According to the first assay, binding of antibody to the target antigen is determined directly. This direct assay uses a labeled reagent, such as a fluorescent tag or an enzyme-labeled primary antibody, which can be visualized without further antibody interaction. In a typical indirect assay, unconjugated primary antibody binds to the antigen and then a labeled secondary antibody binds to the primary antibody. Where the secondary antibody is conjugated to an enzymatic label, a chromogenic or fluorogenic substrate is added to provide visualization of the antigen. Signal amplification occurs because several secondary antibodies may react with different epitopes on the primary antibody.
The primary and/or secondary antibody used for IHC typically will be labeled with a detectable moiety. Numerous labels are available which can be generally grouped into the following categories: (a) Radioisotopes, such as 35S, 14C, 125I, 3H, and 131I; (b) colloidal gold particles; (c) fluorescent labels including, but are not limited to, rare earth chelates (europium chelates), Texas Red, rhodamine, fluorescein, dansyl, Lissamine, umbelliferone, phycocrytherin, phycocyanin, or commercially available fluorophores such SPECTRUM ORANGE7 and SPECTRUM GREEN7 and/or derivatives of any one or more of the above; (d) various enzyme-substrate labels are available and U.S. Pat. No. 4,275,149 provides a review of some of these. Examples of enzymatic labels include luciferases (e.g., firefly luciferase and bacterial luciferase; U.S. Pat. No. 4,737,456), luciferin, 2,3-dihydrophthalazinediones, malate dehydrogenase, urease, peroxidase such as horseradish peroxidase (HRPO), alkaline phosphatase, β-galactosidase, glucoamylase, lysozyme, saccharide oxidases (e.g., glucose oxidase, galactose oxidase, and glucose-6-phosphate dehydrogenase), heterocyclic oxidases (such as uricase and xanthine oxidase), lactoperoxidase, microperoxidase, and the like.
Examples of enzyme-substrate combinations include, for example, horseradish peroxidase (HRPO) with hydrogen peroxidase as a substrate; alkaline phosphatase (AP) with para-Nitrophenyl phosphate as chromogenic substrate; and β-D-galactosidase (β-D-Gal) with a chromogenic substrate (e.g., p-nitrophenyl-β-D-galactosidase) or fluorogenic substrate (e.g., 4-methylumbelliferyl-β-D-galactosidase). For a general review of these, see U.S. Pat. Nos. 4,275,149 and 4,318,980.
Specimens thus prepared may be mounted and coverslipped. Slide evaluation is then determined, e.g., using a microscope, and staining intensity criteria, routinely used in the art, may be employed. In some embodiments, a staining pattern score of about 1+ or higher is diagnostic and/or prognostic. In certain embodiments, a staining pattern score of about 2+ or higher in an IHC assay is diagnostic and/or prognostic. In other embodiments, a staining pattern score of about 3 or higher is diagnostic and/or prognostic. In one embodiment, it is understood that when cells and/or tissue from a tumor or colon adenoma are examined using IHC, staining is generally determined or assessed in tumor cell and/or tissue (as opposed to stromal or surrounding tissue that may be present in the sample).
In alternative methods, the sample may be contacted with an antibody specific for said biomarker (e.g., anti-R-spondin translocation antibody) under conditions sufficient for an antibody-biomarker complex to form, and then detecting said complex. The presence of the biomarker may be detected in a number of ways, such as by Western blotting and ELISA procedures for assaying a wide variety of tissues and samples, including plasma or serum. A wide range of immunoassay techniques using such an assay format are available, see, e.g., U.S. Pat. Nos. 4,016,043, 4,424,279 and 4,018,653. These include both single-site and two-site or “sandwich” assays of the non-competitive types, as well as in the traditional competitive binding assays. These assays also include direct binding of a labeled antibody to a target biomarker.
Presence and/or expression level/amount of a selected biomarker in a tissue or cell sample may also be examined by way of functional or activity-based assays. For instance, if the biomarker is an enzyme, one may conduct assays known in the art to determine or detect the presence of the given enzymatic activity in the tissue or cell sample.
In certain embodiments, the samples are normalized for both differences in the amount of the biomarker assayed and variability in the quality of the samples used, and variability between assay runs. Such normalization may be accomplished by detecting and incorporating the expression of certain normalizing biomarkers, including well known housekeeping genes, such as ACTB. Alternatively, normalization can be based on the mean or median signal of all of the assayed genes or a large subset thereof (global normalization approach). On a gene-by-gene basis, measured normalized amount of a subject tumor mRNA or protein is compared to the amount found in a reference set. Normalized expression levels for each mRNA or protein per tested tumor per subject can be expressed as a percentage of the expression level measured in the reference set. The presence and/or expression level/amount measured in a particular subject sample to be analyzed will fall at some percentile within this range, which can be determined by methods well known in the art.
In certain embodiments, relative expression level of a gene is determined as follows:
Relative expression gene1 sample1=2 exp (Ct housekeeping gene−Ct gene1) with Ct determined in a sample.
Relative expression gene1 reference RNA=2 exp (Ct housekeeping gene−Ct gene1) with Ct determined in the reference sample.
Normalized relative expression gene1 sample1=(relative expression gene1 sample1/relative expression gene1 reference RNA)×100
Ct is the threshold cycle. The Ct is the cycle number at which the fluorescence generated within a reaction crosses the threshold line.
All experiments are normalized to a reference RNA, which is a comprehensive mix of RNA from various tissue sources (e.g., reference RNA #636538 from Clontech, Mountain View, Calif.). Identical reference RNA is included in each qRT-PCR run, allowing comparison of results between different experimental runs.
In one embodiment, the sample is a clinical sample. In another embodiment, the sample is used in a diagnostic assay. In some embodiments, the sample is obtained from a primary or metastatic tumor. Tissue biopsy is often used to obtain a representative piece of tumor tissue. Alternatively, tumor cells can be obtained indirectly in the form of tissues or fluids that are known or thought to contain the tumor cells of interest. For instance, samples of lung cancer lesions may be obtained by resection, bronchoscopy, fine needle aspiration, bronchial brushings, or from sputum, pleural fluid or blood. Genes or gene products can be detected from cancer or tumor tissue or from other body samples such as urine, sputum, serum or plasma. The same techniques discussed above for detection of target genes or gene products in cancerous samples can be applied to other body samples. Cancer cells may be sloughed off from cancer lesions and appear in such body samples. By screening such body samples, a simple early diagnosis can be achieved for these cancers. In addition, the progress of therapy can be monitored more easily by testing such body samples for target genes or gene products.
In certain embodiments, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is a single sample or combined multiple samples from the same subject or individual that are obtained at one or more different time points than when the test sample is obtained. For example, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is obtained at an earlier time point from the same subject or individual than when the test sample is obtained. Such reference sample, reference cell, reference tissue, control sample, control cell, or control tissue may be useful if the reference sample is obtained during initial diagnosis of cancer and the test sample is later obtained when the cancer becomes metastatic.
In certain embodiments, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is a combined multiple samples from one or more healthy individuals who are not the subject or individual. In certain embodiments, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is a combined multiple samples from one or more individuals with a disease or disorder (e.g., cancer) who are not the subject or individual. In certain embodiments, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is pooled RNA samples from normal tissues or pooled plasma or serum samples from one or more individuals who are not the subject or individual. In certain embodiments, a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is pooled RNA samples from tumor tissues or pooled plasma or serum samples from one or more individuals with a disease or disorder (e.g., cancer) who are not the subject or individual.
In some embodiments of any of the methods, the win pathway antagonist is an R-spondin antagonist (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4 antagonist). In some embodiments of any of the methods, the R-spondin antagonist in particular R-spondin-translocation antagonist is an antibody, binding polypeptide, binding small molecule, or polynucleotide. In some embodiments, the R-spondin antagonist in particular R-spondin-translocation antagonist is an antibody. In some embodiments, the antibody is a monoclonal antibody. In some embodiments, the antibody is a human, humanized, or chimeric antibody. In some embodiments, the antibody is an antibody fragment and the antibody fragment binds wnt pathway polypeptide in particular R-spondin antagonist and/or R-spondin-translocation fusion polypeptide.
In some embodiments of any of the methods, the individual according to any of the above embodiments may be a human.
In some embodiments of any of the methods, the method comprises administering to an individual having such cancer an effective amount of a wnt pathway antagonist in particular R-spondin-translocation antagonist. In one such embodiment, the method further comprises administering to the individual an effective amount of at least one additional therapeutic agent, as described below. In some embodiments, the individual may be a human.
The wnt pathway antagonist, in particular R-spondin-translocation antagonist, described herein can be used either alone or in combination with other agents in a therapy. For instance, a wnt pathway antagonist, in particular R-spondin-translocation antagonist, described herein may be co-administered with at least one additional therapeutic agent including another wnt pathway antagonist. In certain embodiments, an additional therapeutic agent is a chemotherapeutic agent.
Such combination therapies noted above encompass combined administration (where two or more therapeutic agents are included in the same or separate formulations), and separate administration, in which case, administration of the wnt pathway antagonist, in particular R-spondin-translocation antagonist, can occur prior to, simultaneously, and/or following, administration of the additional therapeutic agent and/or adjuvant. Wnt pathway antagonist, in particular R-spondin-translocation antagonist, can also be used in combination with radiation therapy.
A wnt pathway antagonist, in particular R-spondin-translocation antagonist (e.g., an antibody, binding polypeptide, and/or small molecule) described herein (and any additional therapeutic agent) can be administered by any suitable means, including parenteral, intrapulmonary, and intranasal, and, if desired for local treatment, intralesional administration. Parenteral infusions include intramuscular, intravenous, intraarterial, intraperitoneal, or subcutaneous administration. Dosing can be by any suitable route, e.g., by injections, such as intravenous or subcutaneous injections, depending in part on whether the administration is brief or chronic. Various dosing schedules including but not limited to single or multiple administrations over various time-points, bolus administration, and pulse infusion are contemplated herein.
Wnt pathway antagonist, in particular R-spondin antagonist (e.g., an antibody, binding polypeptide, and/or small molecule) described herein may be formulated, dosed, and administered in a fashion consistent with good medical practice. Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners. The wnt pathway antagonist, in particular R-spondin antagonist, need not be, but is optionally formulated with one or more agents currently used to prevent or treat the disorder in question. The effective amount of such other agents depends on the amount of the wnt pathway antagonist, in particular R-spondin antagonist, present in the formulation, the type of disorder or treatment, and other factors discussed above. These are generally used in the same dosages and with administration routes as described herein, or about from 1 to 99% of the dosages described herein, or in any dosage and by any route that is empirically/clinically determined to be appropriate.
For the prevention or treatment of disease, the appropriate dosage of a wnt pathway antagonist, in particular R-spondin antagonist, described herein (when used alone or in combination with one or more other additional therapeutic agents) will depend on the type of disease to be treated, the severity and course of the disease, whether the wnt pathway antagonist, in particular R-spondin antagonist, is administered for preventive or therapeutic purposes, previous therapy, the subject's clinical history and response to the wnt pathway antagonist, and the discretion of the attending physician. The wnt pathway antagonist, in particular R-spondin antagonist, is suitably administered to the individual at one time or over a series of treatments. One typical daily dosage might range from about 1 μg/kg to 100 mg/kg or more, depending on the factors mentioned above. For repeated administrations over several days or longer, depending on the condition, the treatment would generally be sustained until a desired suppression of disease symptoms occurs. Such doses may be administered intermittently, e.g., every week or every three weeks (e.g., such that the individual receives from about two to about twenty, or e.g., about six doses of the wnt pathway antagonist). An initial higher loading dose, followed by one or more lower doses may be administered. An exemplary dosing regimen comprises administering. However, other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays.
It is understood that any of the above formulations or therapeutic methods may be carried out using an immunoconjugate of the invention in place of or in addition to the wnt pathway antagonist, in particular R-spondin antagonist.
Provided herein are wnt pathway antagonists useful in the methods described herein. In some embodiments, the wnt pathway antagonists are an antibody, binding polypeptide, binding small molecule, and/or polynucleotide. In some embodiments, the wnt pathway antagonists are canonical wnt pathway antagonists. In some embodiments, the win pathway antagonists are non-canonical wnt pathway antagonists.
In some embodiments, the wnt pathway antagonists are R-spondin antagonists. In some embodiments, the R-spondin antagonists are R-spondin-translocation antagonists. In some embodiments, the R-spondin antagonist inhibits LPR6 mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and LRP6. In some embodiments, the R-spondin antagonist inhibits LGR5 mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and LGR5. In some embodiments, the R-spondin antagonist inhibits KRM mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and KRM. In some embodiments, the R-spondin antagonist inhibits syndecan (e.g., syndecan 4) mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and syndecan (e.g., syndecan 4). Examples of R-spondin antagonists include, but are not limited to, those described in WO 2008/046649, WO 2008/020942, WO 2007/013666, WO 2005/040418, WO 2009/005809, U.S. Pat. Nos. 8,088,374, 7,541,431, WO 2011/076932, and/or US 2009/0074782, which are incorporated by reference in their entirety.
A wnt signaling pathway component or wnt pathway polypeptide is a component that transduces a signal originating from an interaction between a Wnt protein and an Fz receptor. As the wnt signaling pathway is complex, and involves extensive feedback regulation. Example of wnt signaling pathway components include Wnt (e.g., WNT1, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B, WNT10A, WNT10B, WNT11, WNT16), Frizzled (e.g., Frz 1-10), RSPO (e.g., RSPO1, RSPO2, RSPO3, and/or RSPO4), LGR (e.g., LGR5), WTX, WISP (e.g., WISP1, WISP2, and/or WISP3), βTrCp, STRA6, the membrane associated proteins LRP (e.g., LRP5 and/or LRP6), Axin, and Dishevelled, the extracellular Wnt interactive proteins sFRP, WIF-1, the LRP inactivating proteins Dkk and Krn, the cytoplasmic protein β-catenin, members of the β-catenin “degradation complex” APC, GSK3β, CKIα and PP2A, the nuclear transport proteins APC, pygopus and bcl9/legless, and the transcription factors TCF/LEF, Groucho and various histone acetylases such as CBP/p300 and Brg-1.
In one aspect, provided herein isolated antibodies that bind to a wnt pathway polypeptide. In any of the above embodiments, an antibody is humanized In a further aspect of the invention, an anti-wnt pathway antibody according to any of the above embodiments is a monoclonal antibody, including a chimeric, humanized or human antibody. In one embodiment, an anti-wnt pathway antibody is an antibody fragment, e.g., an Fv, Fab, Fab′, scFv, diabody, or F(ab′)2 fragment. In another embodiment, the antibody is a full length antibody, e.g., an intact IgG1″ antibody or other antibody class or isotype as defined herein.
In some embodiments of any of the antibodies, the anti-win pathway antibody is an anti-LRP6 antibody. Examples of anti-LRP6 antibodies include, but are not limited to, the anti-LRP6 antibodies described in U.S. Patent Application No. 2011/0256127, which is incorporated by reference in its entirety. In some embodiments, the anti-LRP6 antibody inhibits signaling induced by a first Wnt isoform and potentiates signaling induced by a second Wnt isoform. In some embodiments, the first Wnt isoform is selected from the group consisting of Wnt3 and Wnt3a and the second Wnt isoform is selected from the group consisting of Wnt 1, 2, 2b, 4, 6, 7a, 7b, 8a, 9a, 9b, 10a, and 10b. In some embodiments, the first Wnt isoform is selected from the group consisting of Wnt 1, 2, 2b, 6, 8a, 9a, 9b, and 10b and the second Wnt isoform is selected from the group consisting of Wnt3 and Wnt3a.
In some embodiments of any of the antibodies, the anti-wnt pathway antibody is an anti-Frizzled antibody. Examples of anti-Frizzled antibodies include, but are not limited to, the anti-Frizzled antibodies described in U.S. Pat. No. 7,947,277, which is incorporated by reference in its entirety.
In some embodiments of any of the antibodies, the anti-wnt pathway antibody is an anti-STRA6 antibody. Examples of anti-STRA6 antibodies include, but are not limited to, the anti-STRA6 antibodies described in U.S. Pat. Nos. 7,173,115, 7,741,439, and/or 7,855,278, which are incorporated by reference in their entirety.
In some embodiments of any of the antibodies, the anti-wnt pathway antibody is an anti-S100-like cytokine polypeptide antibody. In some embodiments, the anti-S100-like cytokine polypeptide antibody is an anti-S100-A14 antibody. Examples of anti-S100-like cytokine polypeptide antibodies include, but are not limited to, the anti-S100-like cytokine polypeptide antibodies described in U.S. Pat. Nos. 7,566,536 and/or 7,005,499, which are incorporated by reference in their entirety.
In some embodiments of any of the antibodies, the anti-wnt pathway antibody is an anti-R-spondin antibody. In some embodiment, the R-spondin is RSPO1. In some embodiment, the R-spondin is RSPO2. In some embodiment, the R-spondin is RSPO3. In some embodiment, the R-spondin is RSPO4. In some embodiments, the R-spondin antagonist inhibits LPR6 mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and LRP6. In some embodiments, the R-spondin antagonist inhibits LGRS mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and LGR5. In some embodiments, the R-spondin antagonist inhibits LGR4 mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and LGR4. In some embodiments, the R-spondin antagonist inhibits ZNRF3 and/or RNF43 mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and ZNRF3 and/or RNF43. In some embodiments, the R-spondin antagonist inhibits KRM mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and KRM. In some embodiments, the R-spondin antagonist inhibits syndecan (e.g., syndecan 4) mediated wnt signaling. In some embodiments, the R-spondin antagonist inhibits and/or blocks the interaction of R-spondin and syndecan (e.g., syndecan 4). Examples of R-spondin antibodies include, but are not limited to, any antibody disclosed in US 2009/0074782, U.S. Pat. Nos. 8,088,374, 8,158,757, 8,1587,58 and/or US Biological R9417-50C, which are incorporated by reference in their entirety.
In some embodiments, the anti-R-spondin antibody binds to an R-spondin-translocation fusion polypeptide. In some embodiments, the antibodies that bind to an R-spondin-translocation fusion polypeptide specifically bind an R-spondin-translocation fusion polypeptide, but do not substantially bind wild-type R-spondin and/or a second gene of the translocation. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO1-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO2-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO3-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO4-translocation fusion polypeptide. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E and RSPO2. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2-translocation fusion polypeptide comprises SEQ ID NO:71. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK and RSPO3. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polypeptide comprises SEQ ID NO:72 and/or SEQ ID NO:73.
In a further aspect, an anti-wnt pathway antibody, in particular, an anti-R-spondin-translocation antibody, according to any of the above embodiments may incorporate any of the features, singly or in combination, as described in Sections below:
1. Antibody Affinity
In certain embodiments, an antibody provided herein has a dissociation constant (Kd) of ≤1 μM. In one embodiment, Kd is measured by a radiolabeled antigen binding assay (RIA) performed with the Fab version of an antibody of interest and its antigen as described by the following assay. Solution binding affinity of Fabs for antigen is measured by equilibrating Fab with a minimal concentration of (125I)-labeled antigen in the presence of a titration series of unlabeled antigen, then capturing bound antigen with an anti-Fab antibody-coated plate (see, e.g., Chen et al., J. Mol. Biol. 293:865-881(1999)). To establish conditions for the assay, MICROTITER® multi-well plates (Thermo Scientific) are coated overnight with 5 μg/ml of a capturing anti-Fab antibody (Cappel Labs) in 50 mM sodium carbonate (pH 9.6), and subsequently blocked with 2% (w/v) bovine serum albumin in PBS for two to five hours at room temperature (approximately 23° C.). In a non-adsorbent plate (Nunc #269620), 100 pM or 26 pM [125I]-antigen are mixed with serial dilutions of a Fab of interest (e.g., consistent with assessment of the anti-VEGF antibody, Fab-12, in Presta et al., Cancer Res. 57:4593-4599 (1997)). The Fab of interest is then incubated overnight; however, the incubation may continue for a longer period (e.g., about 65 hours) to ensure that equilibrium is reached. Thereafter, the mixtures are transferred to the capture plate for incubation at room temperature (e.g., for one hour). The solution is then removed and the plate washed eight times with 0.1% polysorbate 20 (TWEEN-20®) in PBS. When the plates have dried, 150 μl/well of scintillant (MICROSCINT-20™; Packard) is added, and the plates are counted on a TOPCOUNT™ gamma counter (Packard) for ten minutes. Concentrations of each Fab that give less than or equal to 20% of maximal binding are chosen for use in competitive binding assays.
According to another embodiment, Kd is measured using surface plasmon resonance assays using a BIACORE®-2000 or a BIACORE ®-3000 (BIAcore, Inc., Piscataway, N.J.) at 25° C. with immobilized antigen CM5 chips at ˜10 response units (RU). Briefly, carboxymethylated dextran biosensor chips (CM5, BIACORE, Inc.) are activated with N-ethyl-N′-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) according to the supplier's instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8, to 5 μg/ml (˜0.2 μM) before injection at a flow rate of 5 μl/minute to achieve approximately 10 response units (RU) of coupled protein. Following the injection of antigen, 1 M ethanolamine is injected to block unreacted groups. For kinetics measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05% polysorbate 20 (TWEEN-20™) surfactant (PBST) at 25° C. at a flow rate of approximately 25 μl/min. Association rates (kon) and dissociation rates (koff) are calculated using a simple one-to-one Langmuir binding model (BIACORE® Evaluation Software version 3.2) by simultaneously fitting the association and dissociation sensorgrams. The equilibrium dissociation constant (Kd) is calculated as the ratio koff/kon. See, e.g., Chen et al., J. Mol. Biol. 293:865-881 (1999). If the on-rate exceeds 106M−1s−1 by the surface plasmon resonance assay above, then the on-rate can be determined by using a fluorescent quenching technique that measures the increase or decrease in fluorescence emission intensity (excitation=295 nm; emission=340 nm, 16 nm band-pass) at 25° C. of a 20 nM anti-antigen antibody (Fab form) in PBS, pH 7.2, in the presence of increasing concentrations of antigen as measured in a spectrometer, such as a stop-flow equipped spectrophometer (Aviv Instruments) or a 8000-series SLM-AMINCO™ spectrophotometer (ThermoSpectronic) with a stirred cuvette.
2. Antibody Fragments
In certain embodiments, an antibody provided herein is an antibody fragment. Antibody fragments include, but are not limited to, Fab, Fab′, Fab′-SH, F(ab′)2, Fv, and scFv fragments, and other fragments described below. For a review of certain antibody fragments, see Hudson et al., Nat. Med. 9:129-134 (2003). For a review of scFv fragments, see, e.g., Pluckthün, in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., (Springer-Verlag, New York), pp. 269-315 (1994); see also WO 93/16185; and U.S. Pat. Nos. 5,571,894 and 5,587,458. For discussion of Fab and F(ab′)2 fragments comprising salvage receptor binding epitope residues and having increased in vivo half-life, see U.S. Pat. No. 5,869,046.
Diabodies are antibody fragments with two antigen-binding sites that may be bivalent or bispecific. See, for example, EP 404,097; WO 1993/01161; Hudson et al., Nat. Med. 9:129-134 (2003); and Hollinger et al., Proc. Natl. Acad. Sci. USA 90: 6444-6448 (1993). Triabodies and tetrabodies are also described in Hudson et al., Nat. Med. 9:129-134 (2003).
Single-domain antibodies are antibody fragments comprising all or a portion of the heavy chain variable domain or all or a portion of the light chain variable domain of an antibody. In certain embodiments, a single-domain antibody is a human single-domain antibody (Domantis, Inc., Waltham, Mass.; see, e.g., U.S. Pat. No. 6,248,516 B1).
Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells (e.g., E. coli or phage), as described herein.
3. Chimeric and Humanized Antibodies
In certain embodiments, an antibody provided herein is a chimeric antibody. Certain chimeric antibodies are described, e.g., in U.S. Pat. No. 4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA, 81:6851-6855 (1984)). In one example, a chimeric antibody comprises a non-human variable region (e.g., a variable region derived from a mouse, rat, hamster, rabbit, or non-human primate, such as a monkey) and a human constant region. In a further example, a chimeric antibody is a “class switched” antibody in which the class or subclass has been changed from that of the parent antibody. Chimeric antibodies include antigen-binding fragments thereof.
In certain embodiments, a chimeric antibody is a humanized antibody. Typically, a non-human antibody is humanized to reduce immunogenicity to humans, while retaining the specificity and affinity of the parental non-human antibody. Generally, a humanized antibody comprises one or more variable domains in which HVRs, e.g., CDRs, (or portions thereof) are derived from a non-human antibody, and FRs (or portions thereof) are derived from human antibody sequences. A humanized antibody optionally will also comprise at least a portion of a human constant region. In some embodiments, some FR residues in a humanized antibody are substituted with corresponding residues from a non-human antibody (e.g., the antibody from which the HVR residues are derived), e.g., to restore or improve antibody specificity or affinity.
Humanized antibodies and methods of making them are reviewed, e.g., in Almagro and Fransson, Front. Biosci. 13:1619-1633 (2008), and are further described, e.g., in Riechmann et al., Nature 332:323-329 (1988); Queen et al., Proc. Nat'l Acad. Sci. USA 86:10029-10033 (1989); U.S. Pat. Nos. 5,821,337, 7,527,791, 6,982,321, and 7,087,409; Kashmiri et al., Methods 36:25-34 (2005) (describing SDR (a-CDR) grafting); Padlan, Mol. Immunol. 28:489-498 (1991) (describing “resurfacing”); Dall'Acqua et al., Methods 36:43-60 (2005) (describing “FR shuffling”); and Osbourn et al., Methods 36:61-68 (2005) and Klimka et al., Br. J. Cancer, 83:252-260 (2000) (describing the “guided selection” approach to FR shuffling).
Human framework regions that may be used for humanization include but are not limited to: framework regions selected using the “best-fit” method (see, e.g., Sims et al., J. Immunol. 151:2296 (1993)); framework regions derived from the consensus sequence of human antibodies of a particular subgroup of light or heavy chain variable regions (see, e.g., Carter et al., Proc. Natl. Acad. Sci. USA, 89:4285 (1992); and Presta et al., J. Immunol., 151:2623 (1993)); human mature (somatically mutated) framework regions or human germline framework regions (see, e.g., Almagro and Fransson, Front. Biosci. 13:1619-1633 (2008)); and framework regions derived from screening FR libraries (see, e.g., Baca et al., J. Biol. Chem. 272:10678-10684 (1997) and Rosok et al., J. Biol. Chem. 271:22611-22618 (1996)).
4. Human Antibodies
In certain embodiments, an antibody provided herein is a human antibody. Human antibodies can be produced using various techniques known in the art. Human antibodies are described generally in van Dijk and van de Winkel, Curr. Opin. Pharmacol. 5: 368-74 (2001) and Lonberg, Curr. Opin. Immunol. 20:450-459 (2008).
Human antibodies may be prepared by administering an immunogen to a transgenic animal that has been modified to produce intact human antibodies or intact antibodies with human variable regions in response to antigenic challenge. Such animals typically contain all or a portion of the human immunoglobulin loci, which replace the endogenous immunoglobulin loci, or which are present extrachromosomally or integrated randomly into the animal's chromosomes. In such transgenic mice, the endogenous immunoglobulin loci have generally been inactivated. For review of methods for obtaining human antibodies from transgenic animals, see Lonberg, Nat. Biotech. 23:1117-1125 (2005). See also, e.g., U.S. Pat. Nos. 6,075,181 and 6,150,584 describing XENOMOUSE™ technology; U.S. Pat. No. 5,770,429 describing HuMab® technology; U.S. Pat. No. 7,041,870 describing K-M MOUSE® technology, and U.S. Patent Application Publication No. US 2007/0061900, describing VelociMouse® technology). Human variable regions from intact antibodies generated by such animals may be further modified, e.g., by combining with a different human constant region.
Human antibodies can also be made by hybridoma-based methods. Human myeloma and mouse-human heteromyeloma cell lines for the production of human monoclonal antibodies have been described. (See, e.g., Kozbor J. Immunol., 133: 3001 (1984); and Boerner et al., J. Immunol., 147: 86 (1991).) Human antibodies generated via human B-cell hybridoma technology are also described in Li et al., Proc. Natl. Acad. Sci. USA, 103:3557-3562 (2006). Additional methods include those described, for example, in U.S. Pat. No. 7,189,826 (describing production of monoclonal human IgM antibodies from hybridoma cell lines) and Ni, Xiandai Mianyixne, 26(4):265-268 (2006) (describing human-human hybridomas). Human hybridoma technology (Trioma technology) is also described in Vollmers and Brandlein, Histology and Histopathology, 20(3):927-937 (2005) and Vollmers and Brandlein, Methods and Findings in Experimental and Clin. Pharma., 27(3):185-91 (2005).
Human antibodies may also be generated by isolating Fv clone variable domain sequences selected from human-derived phage display libraries. Such variable domain sequences may then be combined with a desired human constant domain. Techniques for selecting human antibodies from antibody libraries are described below.
5. Library Derived Antibodies
Antibodies of the invention may be isolated by screening combinatorial libraries for antibodies with the desired activity or activities. For example, a variety of methods are known in the art for generating phage display libraries and screening such libraries for antibodies possessing the desired binding characteristics. Such methods are reviewed, e.g., in Hoogenboom et al., in M
In certain phage display methods, repertoires of VH and VL genes are separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be screened for antigen-binding phage as described in Winter et al., Ann. Rev. Immunol., 12: 433-455 (1994). Phage typically display antibody fragments, either as single-chain Fv (scFv) fragments or as Fab fragments. Libraries from immunized sources provide high-affinity antibodies to the immunogen without the requirement of constructing hybridomas. Alternatively, the naive repertoire can be cloned (e.g., from human) to provide a single source of antibodies to a wide range of non-self and also self antigens without any immunization as described by Griffiths et al., EMBO J, 12: 725-734 (1993). Finally, naive libraries can also be made synthetically by cloning unrearranged V-gene segments from stem cells, and using PCR primers containing random sequence to encode the highly variable CDR3 regions and to accomplish rearrangement in vitro, as described by Hoogenboom and Winter, J. Mol. Biol., 227: 381-388 (1992). Patent publications describing human antibody phage libraries include, for example: U.S. Pat. No. 5,750,373, and US Patent Publication Nos. 2005/0079574, 2005/0119455, 2005/0266000, 2007/0117126, 2007/0160598, 2007/0237764, 2007/0292936, and 2009/0002360.
Antibodies or antibody fragments isolated from human antibody libraries are considered human antibodies or human antibody fragments herein.
6. Multispecific Antibodies
In certain embodiments, an antibody provided herein is a multispecific antibody, e.g., a bispecific antibody. Multispecific antibodies are monoclonal antibodies that have binding specificities for at least two different sites. In certain embodiments, one of the binding specificities is for wnt pathway polypeptide such as an R-spondin-translocation fusion polypeptide and the other is for any other antigen. In certain embodiments, bispecific antibodies may bind to two different epitopes of wnt pathway polypeptide such as an R-spondin-translocation fusion polypeptide. Bispecific antibodies may also be used to localize cytotoxic agents to cells which express wnt pathway polypeptide such as an R-spondin-translocation fusion polypeptide. Bispecific antibodies can be prepared as full length antibodies or antibody fragments.
Techniques for making multispecific antibodies include, but are not limited to, recombinant co-expression of two immunoglobulin heavy chain-light chain pairs having different specificities (see Milstein and Cuello, Nature 305: 537 (1983)), WO 93/08829, and Traunecker et al., EMBO J. 10: 3655 (1991)), and “knob-in-hole” engineering (see, e.g., U.S. Pat. No. 5,731,168). Multi-specific antibodies may also be made by engineering electrostatic steering effects for making antibody Fc-heterodimeric molecules (WO 2009/089004A1); cross-linking two or more antibodies or fragments (see, e.g., U.S. Pat. No. 4,676,980, and Brennan et al., Science, 229: 81 (1985)); using leucine zippers to produce bi-specific antibodies (see, e.g., Kostelny et al., J. Immunol., 148(5):1547-1553 (1992)); using “diabody” technology for making bispecific antibody fragments (see, e.g., Hollinger et al., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993)); and using single-chain Fv (sFv) dimers (see, e.g., Gruber et al., J. Immunol., 152:5368 (1994)); and preparing trispecific antibodies as described, e.g., in Tutt et al., J. Immunol. 147: 60 (1991).
Engineered antibodies with three or more functional antigen binding sites, including “Octopus antibodies,” are also included herein (see, e.g., US 2006/0025576).
The antibody or fragment herein also includes a “Dual Acting FAb” or “DAF” comprising an antigen binding site that binds to a wnt pathway polypeptide such as an R-spondin-translocation fusion polypeptide as well as another, different antigen (see, US 2008/0069820, for example).
7. Antibody Variants
a) Glycosylation Variants
In certain embodiments, an antibody provided herein is altered to increase or decrease the extent to which the antibody is glycosylated. Addition or deletion of glycosylation sites to an antibody may be conveniently accomplished by altering the amino acid sequence such that one or more glycosylation sites is created or removed.
Where the antibody comprises an Fc region, the carbohydrate attached thereto may be altered. Native antibodies produced by mammalian cells typically comprise a branched, biantennary oligosaccharide that is generally attached by an N-linkage to Asn297 of the CH2 domain of the Fc region. See, e.g., Wright et al., TIBTECH 15:26-32 (1997). The oligosaccharide may include various carbohydrates, e g., mannose, N-acetyl glucosamine (GlcNAc), galactose, and sialic acid, as well as a fucose attached to a GlcNAc in the “stem” of the biantennary oligosaccharide structure. In some embodiments, modifications of the oligosaccharide in an antibody of the invention may be made in order to create antibody variants with certain improved properties.
In one embodiment, antibody variants are provided having a carbohydrate structure that lacks fucose attached (directly or indirectly) to an Fc region. For example, the amount of fucose in such antibody may be from 1% to 80%, from 1% to 65%, from 5% to 65% or from 20% to 40%. The amount of fucose is determined by calculating the average amount of fucose within the sugar chain at Asn297, relative to the sum of all glycostructures attached to Asn 297 (e.g., complex, hybrid and high mannose structures) as measured by MALDI-TOF mass spectrometry, as described in WO 2008/077546, for example. Asn297 refers to the asparagine residue located at about position 297 in the Fc region (Eu numbering of Fc region residues); however, Asn297 may also be located about ±3 amino acids upstream or downstream of position 297, i.e., between positions 294 and 300, due to minor sequence variations in antibodies. Such fucosylation variants may have improved ADCC function. See, e.g., US Patent Publication Nos. US 2003/0157108 (Presta, L.); US 2004/0093621 (Kyowa Hakko Kogyo Co., Ltd). Examples of publications related to “defucosylated” or “fucose-deficient” antibody variants include: US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614; US 2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US 2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO 2005/035586; WO 2005/035778; W02005/053742; WO2002/031140; Okazaki et al., J. Mol. Biol. 336:1239-1249 (2004); Yamane-Ohnuki et al., Biotech. Bioeng. 87: 614 (2004). Examples of cell lines capable of producing defucosylated antibodies include Lec13 CHO cells deficient in protein fucosylation (Ripka et al., Arch. Biochem. Biophys. 249:533-545 (1986); US 2003/0157108, Presta, L; and WO 2004/056312, Adams et al., especially at Example 11), and knockout cell lines, such as alpha-1,6-fucosyltransferase gene, FUT8, knockout CHO cells (see, e.g., Yamane-Ohnuki et al., Biotech. Bioeng. 87: 614 (2004); Kanda, Y. et al., Biotechnol. Bioeng., 94(4):680-688 (2006); and WO2003/085107).
Antibodies variants are further provided with bisected oligosaccharides, e.g., in which a biantennary oligosaccharide attached to the Fc region of the antibody is bisected by GlcNAc. Such antibody variants may have reduced fucosylation and/or improved ADCC function. Examples of such antibody variants are described, e.g., in WO 2003/011878 (Jean-Mairet et al.); U.S. Pat. No. 6,602,684 (Umana et al.); and US 2005/0123546 (Umana et al.). Antibody variants with at least one galactose residue in the oligosaccharide attached to the Fc region are also provided. Such antibody variants may have improved CDC function. Such antibody variants are described, e.g., in WO 1997/30087 (Patel et al.); WO 1998/58964 (Raju, S.); and WO 1999/22764 (Raju, S.).
b) Fc Region Variants
In certain embodiments, one or more amino acid modifications may be introduced into the Fc region of an antibody provided herein, thereby generating an Fc region variant. The Fc region variant may comprise a human Fc region sequence (e.g., a human IgG1, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g., a substitution) at one or more amino acid positions.
In certain embodiments, the invention contemplates an antibody variant that possesses some but not all effector functions, which make it a desirable candidate for applications in which the half life of the antibody in vivo is important yet certain effector functions (such as complement and ADCC) are unnecessary or deleterious. In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/depletion of CDC and/or ADCC activities. For example, Fc receptor (FcR) binding assays can be conducted to ensure that the antibody lacks FcγR binding (hence likely lacking ADCC activity), but retains FcRn binding ability. The primary cells for mediating ADCC, NK cells, express Fc(RIII only, whereas monocytes express Fc(RI, Fc(RII and Fc(RIII. FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991). Non-limiting examples of in vitro assays to assess ADCC activity of a molecule of interest is described in U.S. Pat. No. 5,500,362 (see, e.g., Hellstrom, I. et al., Proc. Nat'l Acad. Sci. USA 83:7059-7063 (1986)) and Hellstrom, I et al., Proc. Nat'l Acad. Sci. USA 82:1499-1502 (1985); U.S. Pat. No. 5,821,337 (see Bruggemann, M. et al., J. Exp. Med. 166:1351-1361 (1987)). Alternatively, non-radioactive assays methods may be employed (see, for example, ACTI™ non-radioactive cytotoxicity assay for flow cytometry (CellTechnology, Inc. Mountain View, Calif.; and CytoTox 96® non-radioactive cytotoxicity assay (Promega, Madison, Wis.). Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al., Proc. Natl. Acad. Sci. USA 95:652-656 (1998). C1q binding assays may also be carried out to confirm that the antibody is unable to bind C1q and hence lacks CDC activity. See, e.g., C1q and C3c binding ELISA in WO 2006/029879 and WO 2005/100402. To assess complement activation, a CDC assay may be performed (see, for example, Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996); Cragg, M. S. et al., Blood 101:1045-1052 (2003); and Cragg, M. S. and M. J. Glennie, Blood 103:2738-2743 (2004)). FcRn binding and in vivo clearance/half life determinations can also be performed using methods known in the art (see, e.g., Petkova, S. B. et al., Int I. Immunol. 18(12):1759-1769 (2006)).
Antibodies with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Pat. No. 6,737,056). Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called “DANA” Fc mutant with substitution of residues 265 and 297 to alanine (U.S. Pat. No. 7,332,581).
Certain antibody variants with improved or diminished binding to FcRs are described. (See, e.g., U.S. Pat. No. 6,737,056; WO 2004/056312, and Shields et al., J. Biol. Chem. 9(2): 6591-6604 (2001).) In certain embodiments, an antibody variant comprises an Fc region with one or more amino acid substitutions which improve ADCC, e.g., substitutions at positions 298, 333, and/or 334 of the Fc region (EU numbering of residues). In some embodiments, alterations are made in the Fc region that result in altered (i.e., either improved or diminished) C1q binding and/or Complement Dependent Cytotoxicity (CDC), e.g., as described in U.S. Pat. No. 6,194,551, WO 99/51642, and Idusogie et al., J. Immunol. 164: 4178-4184 (2000).
Antibodies with increased half lives and improved binding to the neonatal Fc receptor (FcRn), which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al., J. Immunol. 24:249 (1994)), are described in US2005/0014934A1 (Hinton et al.). Those antibodies comprise an Fc region with one or more substitutions therein which improve binding of the Fc region to FcRn. Such Fc variants include those with substitutions at one or more of Fc region residues: 238, 256, 265, 272, 286, 303, 305, 307, 311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, 413, 424 or 434, e.g., substitution of Fc region residue 434 (U.S. Pat. No. 7,371,826). See also Duncan & Winter, Nature 322:738-40 (1988); U.S. Pat. Nos. 5,648,260; 5,624,821; and WO 94/29351 concerning other examples of Fc region variants.
c) Cysteine Engineered Antibody Variants
In certain embodiments, it may be desirable to create cysteine engineered antibodies, e.g., “thioMAbs,” in which one or more residues of an antibody are substituted with cysteine residues. In particular embodiments, the substituted residues occur at accessible sites of the antibody. By substituting those residues with cysteine, reactive thiol groups are thereby positioned at accessible sites of the antibody and may be used to conjugate the antibody to other moieties, such as drug moieties or linker-drug moieties, to create an immunoconjugate, as described further herein. In certain embodiments, any one or more of the following residues may be substituted with cysteine: V205 (Kabat numbering) of the light chain; A118 (EU numbering) of the heavy chain; and S400 (EU numbering) of the heavy chain Fc region. Cysteine engineered antibodies may be generated as described, e.g., in U.S. Pat. No. 7,521,541.
Further provided herein are immunoconjugates comprising an anti-wnt pathway antibody such as an R-spondin-translocation fusion polypeptide herein conjugated to one or more cytotoxic agents, such as chemotherapeutic agents or drugs, growth inhibitory agents, toxins (e.g., protein toxins, enzymatically active toxins of bacterial, fungal, plant, or animal origin, or fragments thereof), or radioactive isotopes.
In one embodiment, an immunoconjugate is an antibody-drug conjugate (ADC) in which an antibody is conjugated to one or more drugs, including but not limited to a maytansinoid (see U.S. Pat. Nos. 5,208,020, 5,416,064 and European Patent EP 0 425 235 B1); an auristatin such as monomethylauristatin drug moieties DE and DF (MMAE and MMAF) (see U.S. Pat. Nos. 5,635,483 and 5,780,588, and 7,498,298); a dolastatin; a calicheamicin or derivative thereof (see U.S. Pat. Nos. 5,712,374, 5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001, and 5,877,296; Hinman et al., Cancer Res. 53:3336-3342 (1993); and Lode et al., Cancer Res. 58:2925-2928 (1998)); an anthracycline such as daunomycin or doxorubicin (see Kratz et al., Current Med. Chem. 13:477-523 (2006); Jeffrey et al., Bioorganic & Med. Chem. Letters 16:358-362 (2006); Torgov et al., Bioconj. Chem. 16:717-721 (2005); Nagy et al., Proc. Natl. Acad. Sci. USA 97:829-834 (2000); Dubowchik et al., Bioorg. & Med. Chem. Letters 12:1529-1532 (2002); King et al., J. Med. Chem. 45:4336-4343 (2002); and U.S. Pat. No. 6,630,579); methotrexate; vindesine; a taxane such as docetaxel, paclitaxel, larotaxel, tesetaxel, and ortataxel; a trichothecene; and CC1065.
In another embodiment, an immunoconjugate comprises an antibody as described herein conjugated to an enzymatically active toxin or fragment thereof, including but not limited to diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), Momordica charantia inhibitor, curcin, crotin, Sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes.
In another embodiment, an immunoconjugate comprises an antibody as described herein conjugated to a radioactive atom to form a radioconjugate. A variety of radioactive isotopes are available for the production of radioconjugates. Examples include At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212 and radioactive isotopes of Lu. When the radioconjugate is used for detection, it may comprise a radioactive atom for scintigraphic studies, for example Tc99 or I123, or a spin label for nuclear magnetic resonance (NMR) imaging (also known as magnetic resonance imaging, MRI), such as iodine-123 again, iodine-131, indium-111, fluorine-19, carbon-13, nitrogen-15, oxygen-17, gadolinium, manganese or iron.
Conjugates of an antibody and cytotoxic agent may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science 238:1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See WO94/11026. The linker may be a “cleavable linker” facilitating release of a cytotoxic drug in the cell. For example, an acid-labile linker, peptidase-sensitive linker, photolabile linker, dimethyl linker or disulfide-containing linker (Chari et al., Cancer Res. 52:127-131 (1992); U.S. Pat. No. 5,208,020) may be used.
The immunuoconjugates or ADCs herein expressly contemplate, but are not limited to such conjugates prepared with cross-linker reagents including, but not limited to, BMPS, EMCS, GMBS, HBVS, LC-SMCC, MBS, MPBH, SBAP, SIA, SIAB, SMCC, SMPB, SMPH, sulfo-EMCS, sulfo-GMBS, sulfo-KMUS, sulfo-MBS, sulfo-SIAB, sulfo-SMCC, and sulfo-SMPB, and SVSB (succinimidyl-(4-vinylsulfone)benzoate) which are commercially available (e.g., from Pierce Biotechnology, Inc., Rockford, Ill., U.S.A).
Provided herein are wnt pathway binding polypeptide antagonists for use as a wnt pathway antagonist in any of the methods described herein. Wnt pathway binding polypeptide antagonists are polypeptides that bind, preferably specifically, to a wnt pathway polypeptide.
In some embodiments of any of the wnt pathway binding polypeptide antagonists, the wnt pathway binding polypeptide antagonist is a chimeric polypeptide. In some embodiments, the wnt pathway binding polypeptide antagonist comprises (a) a Frizzled domain component, and (b) a Fc domain. For example, any wnt pathway antagonists described in U.S. Pat. No. 7,947,277, which is incorporated by reference in its entirety.
In some embodiments of any of the wnt pathway binding polypeptide antagonists, the wnt pathway binding polypeptide antagonist is a polypeptide that binds specifically to Dvl PDZ, wherein said polypeptide comprises a C-terminal region comprising a sequence with Gly at position −2, Trp or Tyr at position '1, Phe or Leu at position 0, and a hydrophobic or aromatic residue at position −3, wherein amino acid numbering is based on the C-terminal residue being in position 0. In some embodiments, position −6 is Trp. In some embodiments, position −1 is Trp. In some embodiments of any of the wnt pathway binding polypeptide antagonists, the wnt pathway binding polypeptide antagonist is a polypeptide that binds specifically to Dvl PDZ at a binding affinity of IC50=1.5 uM or better. In some embodiments, the polypeptide inhibits Dvl PDZ interaction with its endogenous binding partner. In some embodiments, the polypeptide inhibits endogenous Dvl-mediated Wnt signaling. In some embodiments, a polypeptide comprising a C-terminus consisting of KWYGWL (SEQ ID NO: 80). In some embodiments, the polypeptide comprises the amino acid sequence X1-X2-W-X3-D-X4-P, and wherein X1 is L or V, X2 is L, X3 is S or T, and X4 is I, F or L. In some embodiments, the polypeptide comprises the amino acid sequence GEIVLWSDIPG (SEQ ID NO:81). In some embodiments, the polypeptide is any polypeptide described in U.S. Pat. Nos. 7,977,064 and/or 7,695,928, which are incorporated by reference in their entirety.
In some embodiments of any of the wnt pathway binding polypeptide antagonists, the binding polypeptide binds WISP. In some embodiments, the WISP is WISP1, WISP2, and/or WISP3. In some embodiments, the polypeptide is any polypeptide described in U.S. Pat. Nos. 6,387,657, 7,455,834, 7,732,567, 7,687,460, and/or 7,101,850 and/or U.S. Patent Application No. 2006/0292150, which are incorporated by reference in their entirety.
In some embodiments of any of the wnt pathway binding polypeptide antagonists, the binding polypeptide binds a S100-like cytokine polypeptide. In some embodiments, the S100-like cytokine polypeptide is a S100-A14 polypeptide. In some embodiments, the polypeptide is any polypeptide described in U.S. Pat. Nos. 7,566,536 and/or 7,005,499, which are incorporated by reference in their entirety.
In some embodiments of any of the wnt pathway binding polypeptide antagonists, the wnt pathway binding polypeptide antagonist is a polypeptide that binds specifically to STRA6. In some embodiments, the polypeptide is any polypeptide described in U.S. Pat. Nos. 7,173,115, 7,741,439, and/or 7,855,278, which are incorporated by reference in their entirety.
In some embodiments of any of the wnt pathway binding polypeptide antagonists, the binding polypeptide binds R-spondin polypeptide. In some embodiment, the R-spondin polypeptide is RSPO1 polypeptide. In some embodiment, the R-spondin polypeptide is RSPO2 polypeptide. In some embodiment, the R-spondin polypeptide is RSPO3 polypeptide. In some embodiment, the R-spondin polypeptide is RSPO4 polypeptide.
In some embodiments of any of the binding polypeptides, the wnt pathway binding polypeptide antagonists bind to an R-spondin-translocation fusion polypeptide. In some embodiments, the binding polypeptide specifically bind an R-spondin-translocation fusion polypeptide, but do not substantially bind wild-type R-spondin and/or a second gene of the translocation. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO1-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO2-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO3-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO4-translocation fusion polypeptide. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E and RSPO2. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2-translocation fusion polypeptide comprises SEQ ID NO:71. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK and RSPO3. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polypeptide comprises SEQ ID NO:72 and/or SEQ ID NO:73.
Binding polypeptides may be chemically synthesized using known polypeptide synthesis methodology or may be prepared and purified using recombinant technology. Binding polypeptides are usually at least about 5 amino acids in length, alternatively at least about 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 amino acids in length or more, wherein such binding polypeptides that are capable of binding, preferably specifically, to a target, wnt pathway polypeptide, as described herein. Binding polypeptides may be identified without undue experimentation using well known techniques. In this regard, it is noted that techniques for screening polypeptide libraries for binding polypeptides that are capable of specifically binding to a polypeptide target are well known in the art (see, e.g., U.S. Pat. Nos. 5,556,762, 5,750,373, 4,708,871, 4,833,092, 5,223,409, 5,403,484, 5,571,689, 5,663,143; PCT Publication Nos. WO 84/03506 and WO84/03564; Geysen et al., Proc. Natl. Acad. Sci. U.S.A., 81:3998-4002 (1984); Geysen et al., Proc. Natl. Acad. Sci. U.S.A., 82:178-182 (1985); Geysen et al., in Synthetic Peptides as Antigens, 130-149 (1986); Geysen et al., J. Immunol. Meth., 102:259-274 (1987); Schoofs et al., J. Immunol., 140:611-616 (1988), Cwirla, S. E. et al., (1990) Proc. Natl. Acad. Sci. USA, 87:6378; Lowman, H. B. et al., (1991) Biochemistry, 30:10832; Clackson, T. et al., (1991) Nature, 352: 624; Marks, J. D. et al., (1991), J. Mol. Biol., 222:581; Kang, A. S. et al., (1991) Proc. Natl. Acad. Sci. USA, 88:8363, and Smith, G. P. (1991) Current Opin. Biotechnol., 2:668).
In this regard, bacteriophage (phage) display is one well known technique which allows one to screen large polypeptide libraries to identify member(s) of those libraries which are capable of specifically binding to a target polypeptide, win pathway polypeptide. Phage display is a technique by which variant polypeptides are displayed as fusion proteins to the coat protein on the surface of bacteriophage particles (Scott, J. K. and Smith, G. P. (1990) Science, 249: 386). The utility of phage display lies in the fact that large libraries of selectively randomized protein variants (or randomly cloned cDNAs) can be rapidly and efficiently sorted for those sequences that bind to a target molecule with high affinity. Display of peptide (Cwirla, S. E. et al., (1990) Proc. Natl. Acad. Sci. USA, 87:6378) or protein (Lowman, H. B. et al., (1991) Biochemistry, 30:10832; Clackson, T. et al., (1991) Nature, 352: 624; Marks, J. D. et al., (1991), J. Mol. Biol., 222:581; Kang, A. S. et al., (1991) Proc. Natl. Acad. Sci. USA, 88:8363) libraries on phage have been used for screening millions of polypeptides or oligopeptides for ones with specific binding properties (Smith, G. P. (1991) Current Opin. Biotechnol., 2:668). Sorting phage libraries of random mutants requires a strategy for constructing and propagating a large number of variants, a procedure for affinity purification using the target receptor, and a means of evaluating the results of binding enrichments. U.S. Pat. Nos. 5,223,409, 5,403,484, 5,571,689, and 5,663,143.
Although most phage display methods have used filamentous phage, lambdoid phage display systems (WO 95/34683; U.S. Pat. No. 5,627,024), T4 phage display systems (Ren et al., Gene, 215: 439 (1998); Zhu et al., Cancer Research, 58(15): 3209-3214 (1998); Jiang et al., Infection & Immunity, 65(11): 4770-4777 (1997); Ren et al., Gene, 195(2):303-311 (1997); Ren, Protein Sci., 5: 1833 (1996); Efimov et al., Virus Genes, 10: 173 (1995)) and T7 phage display systems (Smith and Scott, Methods in Enzymology, 217: 228-257 (1993); U.S. Pat. No. 5,766,905) are also known.
Additional improvements enhance the ability of display systems to screen peptide libraries for binding to selected target molecules and to display functional proteins with the potential of screening these proteins for desired properties. Combinatorial reaction devices for phage display reactions have been developed (WO 98/14277) and phage display libraries have been used to analyze and control bimolecular interactions (WO 98/20169; WO 98/20159) and properties of constrained helical peptides (WO 98/20036). WO 97/35196 describes a method of isolating an affinity ligand in which a phage display library is contacted with one solution in which the ligand will bind to a target molecule and a second solution in which the affinity ligand will not bind to the target molecule, to selectively isolate binding ligands. WO 97/46251 describes a method of biopanning a random phage display library with an affinity purified antibody and then isolating binding phage, followed by a micropanning process using microplate wells to isolate high affinity binding phage. The use of Staphylococcus aureus protein A as an affinity tag has also been reported (Li et al., (1998) Mol Biotech., 9:187). WO 97/47314 describes the use of substrate subtraction libraries to distinguish enzyme specificities using a combinatorial library which may be a phage display library. A method for selecting enzymes suitable for use in detergents using phage display is described in WO 97/09446. Additional methods of selecting specific binding proteins are described in U.S. Pat. Nos. 5,498,538, 5,432,018, and WO 98/15833.
Methods of generating peptide libraries and screening these libraries are also disclosed in U.S. Pat. Nos. 5,723,286, 5,432,018, 5,580,717, 5,427,908, 5,498,530, 5,770,434, 5,734,018, 5,698,426, 5,763,192, and 5,723,323.
Provided herein are wnt pathway small molecule antagonists for use as a wnt pathway antagonist in any of the methods described herein. In some embodiments, the wnt pathway antagonist is a canonical wnt pathway antagonist. In some embodiments, the wnt pathway antagonist is a non-canonical wnt pathway antagonist.
In some embodiments of any of the small molecules, the wnt pathway small molecule antagonist is an R-spondin small molecule antagonist (e.g., RSPO1, 2, 3, and/or 4 small molecule antagonist). In some embodiment, the R-spondin small molecule antagonist is RSPO1-translocation small molecule antagonist. In some embodiment, the R-spondin small molecule antagonist is RSPO2-translocation small molecule antagonist. In some embodiment, the R-spondin small molecule antagonist is RSPO3-translocation antagonist. In some embodiment, the R-spondin small molecule antagonist is RSPO4-translocation small molecule antagonist.
In some embodiments of any of the small molecules, the small molecule binds to an R-spondin-translocation fusion polypeptide. In some embodiments, small molecule specifically binds an R-spondin-translocation fusion polypeptide, but do not substantially bind wild-type R-spondin and/or a second gene of the translocation. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO1-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO2-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO3-translocation fusion polypeptide. In some embodiments, the R-spondin-translocation fusion polypeptide is RSPO4-translocation fusion polypeptide. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E and RSPO2. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2-translocation fusion polypeptide comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2-translocation fusion polypeptide comprises SEQ ID NO:71. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK and RSPO3. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polypeptide comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polypeptide comprises SEQ ID NO:72 and/or SEQ ID NO:73.
Small molecules are preferably organic molecules other than binding polypeptides or antibodies as defined herein that bind, preferably specifically, to wnt pathway polypeptide as described herein. Organic small molecules may be identified and chemically synthesized using known methodology (see, e.g., PCT Publication Nos. WO00/00823 and WO00/39585). Organic small molecules are usually less than about 2000 Daltons in size, alternatively less than about 1500, 750, 500, 250 or 200 Daltons in size, wherein such organic small molecules that are capable of binding, preferably specifically, to a polypeptide as described herein may be identified without undue experimentation using well known techniques. In this regard, it is noted that techniques for screening organic small molecule libraries for molecules that are capable of binding to a polypeptide target are well known in the art (see, e.g., PCT Publication Nos. WO00/00823 and WO00/39585). Organic small molecules may be, for example, aldehydes, ketones, oximes, hydrazones, semicarbazones, carbazides, primary amines, secondary amines, tertiary amines, N-substituted hydrazines, hydrazides, alcohols, ethers, thiols, thioethers, disulfides, carboxylic acids, esters, amides, ureas, carbamates, carbonates, ketals, thioketals, acetals, thioacetals, aryl halides, aryl sulfonates, alkyl halides, alkyl sulfonates, aromatic compounds, heterocyclic compounds, anilines, alkenes, alkynes, diols, amino alcohols, oxazolidines, oxazolines, thiazolidines, thiazolines, enamines, sulfonamides, epoxides, aziridines, isocyanates, sulfonyl chlorides, diazo compounds, acid chlorides, or the like.
Provided herein are wnt pathway polynucleotide antagonists for use as a wnt pathway antagonist in any of the methods described herein. The polynucleotide may be an antisense nucleic acid and/or a ribozyme. The antisense nucleic acids comprise a sequence complementary to at least a portion of an RNA transcript of a wnt pathway gene. However, absolute complementarity, although preferred, is not required. In some embodiments, the wnt pathway antagonist is a canonical wnt pathway antagonist. In some embodiments, the wnt pathway antagonist is a non-canonical wnt pathway antagonist. In some embodiments, wnt pathway polynucleotide is R-spondin. In some embodiments, the R-spondin is RSPO1. In some embodiments, the R-spondin is RSPO2. In some embodiments, the R-spondin is RSPO3. In some embodiments, the R-spondin is RSPO4. Examples of polynucleotide antagonists include those described in WO 2005/040418 such as TCCCATTTGCAAGGGTTGT (SEQ ID NO: 82) and/or AGCTGACTGTGATACCTGT(SEQ ID NO: 83).
In some embodiments of any of the polynucleotides, the polynucleotide binds to an R-spondin-translocation fusion polynucleotide. In some embodiments, polynucleotide specifically binds an R-spondin-translocation fusion polynucleotide, but do not substantially bind wild-type R-spondin and/or a second gene of the translocation. In some embodiments, the R-spondin-translocation fusion polynucleotide is RSPO1-translocation fusion polynucleotide. In some embodiments, the R-spondin-translocation fusion polynucleotide is RSPO2-translocation fusion polynucleotide. In some embodiments, the R-spondin-translocation fusion polynucleotide is RSPO3-translocation fusion polynucleotide. In some embodiments, the R-spondin-translocation fusion polynucleotide is RSPO4-translocation fusion polynucleotide. In some embodiments, the RSPO2-translocation fusion polynucleotide comprises EIF3E and RSPO2. In some embodiments, the RSPO2-translocation fusion polynucleotide comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2-translocation fusion polynucleotide comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2-translocation fusion polynucleotide comprises SEQ ID NO:71. In some embodiments, the RSPO3-translocation fusion polynucleotide comprises PTPRK and RSPO3. In some embodiments, the RSPO3-translocation fusion polynucleotide comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polynucleotide comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3-translocation fusion polynucleotide comprises SEQ ID NO:72 and/or SEQ ID NO:73.
A sequence “complementary to at least a portion of an RNA,” referred to herein, means a sequence having sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex; in the case of double stranded win pathway antisense nucleic acids, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed. The ability to hybridize will depend on both the degree of complementarity and the length of the antisense nucleic acid. Generally, the larger the hybridizing nucleic acid, the more base mismatches with an wnt pathway RNA it may contain and still form a stable duplex (or triplex as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.
Polynucleotides that are complementary to the 5′ end of the message, e.g., the 5′ untranslated sequence up to and including the AUG initiation codon, should work most efficiently at inhibiting translation. However, sequences complementary to the 3′ untranslated sequences of mRNAs have been shown to be effective at inhibiting translation of mRNAs as well. See generally, Wagner, R., 1994, Nature 372:333-335. Thus, oligonucleotides complementary to either the 5′- or 3′-non-translated, non-coding regions of the wnt pathway gene, could be used in an antisense approach to inhibit translation of endogenous wnt pathway mRNA. Polynucleotides complementary to the 5′ untranslated region of the mRNA should include the complement of the AUG start codon. Antisense polynucleotides complementary to mRNA coding regions are less efficient inhibitors of translation but could be used in accordance with the invention. Whether designed to hybridize to the 5′-, 3′- or coding region of wnt pathway mRNA, antisense nucleic acids should be at least six nucleotides in length, and are preferably oligonucleotides ranging from 6 to about 50 nucleotides in length. In specific aspects the oligonucleotide is at least 10 nucleotides, at least 17 nucleotides, at least 25 nucleotides or at least 50 nucleotides.
In one embodiment, the wnt pathway antisense nucleic acid of the invention is produced intracellularly by transcription from an exogenous sequence. For example, a vector or a portion thereof, is transcribed, producing an antisense nucleic acid (RNA) of the wnt pathway gene. Such a vector would contain a sequence encoding the wnt pathway antisense nucleic acid. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA. Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others know in the art, used for replication and expression in vertebrate cells. Expression of the sequence encoding wnt pathway, or fragments thereof, can be by any promoter known in the art to act in vertebrate, preferably human cells. Such promoters can be inducible or constitutive. Such promoters include, but are not limited to, the SV40 early promoter region (Bernoist and Chambon, Nature 29:304-310 (1981), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto et al., Cell 22:787-797 (1980), the herpes thymidine promoter (Wagner et al., Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445 (1981), the regulatory sequences of the metallothionein gene (Brinster et al., Nature 296:39-42 (1982)), etc.
In certain embodiments, amino acid sequence variants of the antibodies and/or the binding polypeptides provided herein are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of the antibody and/or binding polypeptide. Amino acid sequence variants of an antibody and/or binding polypeptides may be prepared by introducing appropriate modifications into the nucleotide sequence encoding the antibody and/or binding polypeptide, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of residues within the amino acid sequences of the antibody and/or binding polypeptide. Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics, e.g., target-binding.
In certain embodiments, antibody variants and/or binding polypeptide variants having one or more amino acid substitutions are provided. Sites of interest for substitutional mutagenesis include the HVRs and FRs. Conservative substitutions are shown in Table 1 under the heading of “conservative substitutions.” More substantial changes are provided in Table 1 under the heading of “exemplary substitutions,” and as further described below in reference to amino acid side chain classes. Amino acid substitutions may be introduced into an antibody and/or binding polypeptide of interest and the products screened for a desired activity, e.g., retained/improved antigen binding, decreased immunogenicity, or improved ADCC or CDC.
Amino acids may be grouped according to common side-chain properties:
(1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile;
(2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln;
(3) acidic: Asp, Glu;
(4) basic: His, Lys, Arg;
(5) residues that influence chain orientation: Gly, Pro;
(6) aromatic: Trp, Tyr, Phe.
Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
One type of substitutional variant involves substituting one or more hypervariable region residues of a parent antibody (e.g., a humanized or human antibody). Generally, the resulting variant(s) selected for further study will have modifications (e.g., improvements) in certain biological properties (e.g., increased affinity, reduced immunogenicity) relative to the parent antibody and/or will have substantially retained certain biological properties of the parent antibody. An exemplary substitutional variant is an affinity matured antibody, which may be conveniently generated, e.g., using phage display-based affinity maturation techniques such as those described herein. Briefly, one or more HVR residues are mutated and the variant antibodies displayed on phage and screened for a particular biological activity (e.g., binding affinity).
Alterations (e.g., substitutions) may be made in HVRs, e.g., to improve antibody affinity. Such alterations may be made in HVR “hotspots,” i.e., residues encoded by codons that undergo mutation at high frequency during the somatic maturation process (see, e.g., Chowdhury, Methods Mol. Biol. 207:179-196 (2008)), and/or SDRs (a-CDRs), with the resulting variant VH or VL being tested for binding affinity. Affinity maturation by constructing and reselecting from secondary libraries has been described, e.g., in Hoogenboom et al., in M
In certain embodiments, substitutions, insertions, or deletions may occur within one or more HVRs so long as such alterations do not substantially reduce the ability of the antibody to bind antigen. For example, conservative alterations (e.g., conservative substitutions as provided herein) that do not substantially reduce binding affinity may be made in HVRs. Such alterations may be outside of HVR “hotspots” or SDRs. In certain embodiments of the variant VH and VL sequences provided above, each HVR either is unaltered, or contains no more than one, two or three amino acid substitutions.
A useful method for identification of residues or regions of the antibody and/or the binding polypeptide that may be targeted for mutagenesis is called “alanine scanning mutagenesis” as described by Cunningham and Wells (1989) Science, 244:1081-1085. In this method, a residue or group of target residues (e.g., charged residues such as arg, asp, his, lys, and glu) are identified and replaced by a neutral or negatively charged amino acid (e.g., alanine or polyalanine) to determine whether the interaction of the antibody with antigen is affected. Further substitutions may be introduced at the amino acid locations demonstrating functional sensitivity to the initial substitutions. Alternatively, or additionally, a crystal structure of an antigen-antibody complex to identify contact points between the antibody and antigen. Such contact residues and neighboring residues may be targeted or eliminated as candidates for substitution. Variants may be screened to determine whether they contain the desired properties.
Amino acid sequence insertions include amino- and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues. Examples of terminal insertions include an antibody with an N-terminal methionyl residue. Other insertional variants of the antibody molecule include the fusion to the N- or C-terminus of the antibody to an enzyme (e.g., for ADEPT) or a polypeptide which increases the serum half-life of the antibody.
In certain embodiments, an antibody and/or binding polypeptide provided herein may be further modified to contain additional nonproteinaceous moieties that are known in the art and readily available. The moieties suitable for derivatization of the antibody and/or binding polypeptide include but are not limited to water soluble polymers. Non-limiting examples of water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly-1,3-dioxolane, poly-1,3,6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof. Polyethylene glycol propionaldehyde may have advantages in manufacturing due to its stability in water. The polymer may be of any molecular weight, and may be branched or unbranched. The number of polymers attached to the antibody and/or binding polypeptide may vary, and if more than one polymer is attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody and/or binding polypeptide to be improved, whether the antibody derivative and/or binding polypeptide derivative will be used in a therapy under defined conditions, etc.
In another embodiment, conjugates of an antibody and/or binding polypeptide to nonproteinaceous moiety that may be selectively heated by exposure to radiation are provided. In one embodiment, the nonproteinaceous moiety is a carbon nanotube (Kam et al., Proc. Natl. Acad. Sci. USA 102: 11600-11605 (2005)). The radiation may be of any wavelength, and includes, but is not limited to, wavelengths that do not harm ordinary cells, but which heat the nonproteinaceous moiety to a temperature at which cells proximal to the antibody and/or binding polypeptide-nonproteinaceous moiety are killed.
Antibodies and/or binding polypeptides may be produced using recombinant methods and compositions, e.g., as described in U.S. Pat. No. 4,816,567. In one embodiment, isolated nucleic acid encoding an anti-wnt pathway antibody. Such nucleic acid may encode an amino acid sequence comprising the VL and/or an amino acid sequence comprising the VH of the antibody (e.g., the light and/or heavy chains of the antibody). In a further embodiment, one or more vectors (e.g., expression vectors) comprising such nucleic acid encoding the antibody and/or binding polypeptide are provided. In a further embodiment, a host cell comprising such nucleic acid is provided. In one such embodiment, a host cell comprises (e.g., has been transformed with): (1) a vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and an amino acid sequence comprising the VH of the antibody, or (2) a first vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and a second vector comprising a nucleic acid that encodes an amino acid sequence comprising the VH of the antibody. In one embodiment, the host cell is eukaryotic, e.g., a Chinese Hamster Ovary (CHO) cell or lymphoid cell (e.g., Y0, NS0, Sp20 cell). In one embodiment, a method of making an antibody such as an anti-wnt pathway antibody and/or binding polypeptide is provided, wherein the method comprises culturing a host cell comprising a nucleic acid encoding the antibody and/or binding polypeptide, as provided above, under conditions suitable for expression of the antibody and/or binding polypeptide, and optionally recovering the antibody and/or polypeptide from the host cell (or host cell culture medium).
For recombinant production of an antibody such as an anti-wnt pathway antibody and/or a binding polypeptide, nucleic acid encoding the antibody and/or the binding polypeptide, e.g., as described above, is isolated and inserted into one or more vectors for further cloning and/or expression in a host cell. Such nucleic acid may be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody).
Suitable host cells for cloning or expression of vectors include prokaryotic or eukaryotic cells described herein. For example, antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed. For expression of antibody fragments and polypeptides in bacteria, see, e.g., U.S. Pat. Nos. 5,648,237, 5,789,199, and 5,840,523. (See also Charlton, M
In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for vectors, including fungi and yeast strains whose glycosylation pathways have been “humanized,” resulting in the production of an antibody with a partially or fully human glycosylation pattern. See Gerngross, Nat. Biotech. 22:1409-1414 (2004), and Li et al., Nat. Biotech. 24:210-215 (2006).
Suitable host cells for the expression of glycosylated antibody and/or glycosylated binding polypeptides are also derived from multicellular organisms (invertebrates and vertebrates). Examples of invertebrate cells include plant and insect cells. Numerous baculoviral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells.
Plant cell cultures can also be utilized as hosts. See, e.g., U.S. Pat. Nos. 5,959,177, 6,040,498, 6,420,548, 7,125,978, and 6,417,429 (describing PLANTIBODIES™ technology for producing antibodies in transgenic plants).
Vertebrate cells may also be used as hosts. For example, mammalian cell lines that are adapted to grow in suspension may be useful. Other examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293 cells as described, e.g., in Graham et al., J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK); mouse sertoli cells (TM4 cells as described, e.g., in Mather, Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (CV1); African green monkey kidney cells (VERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); human lung cells (W138); human liver cells (Hep G2); mouse mammary tumor (MMT 060562); TRI cells, as described, e.g., in Mather et al., Annals N.Y. Acad. Sci. 383:44-68 (1982); MRC 5 cells; and FS4 cells. Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including DHFR− CHO cells (Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216 (1980)); and myeloma cell lines such as Y0, NS0 and Sp2/0. For a review of certain mammalian host cell lines suitable for antibody production and/or binding polypeptide production, see, e.g., Yazaki and Wu, M
While the description relates primarily to production of antibodies and/or binding polypeptides by culturing cells transformed or transfected with a vector containing antibody- and binding polypeptide-encoding nucleic acid. It is, of course, contemplated that alternative methods, which are well known in the art, may be employed to prepare antibodies and/or binding polypeptides. For instance, the appropriate amino acid sequence, or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques [see, e.g., Stewart et al., Solid-Phase Peptide Synthesis, W.H. Freeman Co., San Francisco, Calif. (1969); Merrifield, J. Am. Chem. Soc., 85:2149-2154 (1963)]. In vitro protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be accomplished, for instance, using an Applied Biosystems Peptide Synthesizer (Foster City, Calif.) using manufacturer's instructions. Various portions of the antibody and/or binding polypeptide may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the desired antibody and/or binding polypeptide.
IV. Methods of Screening and/or Identifying Wnt Pathway Antagonists with Desired Function
Techniques for generating wnt pathway antagonists such as antibodies, binding polypeptides, and/or small molecules have been described above. Additional wnt pathway antagonists such as anti-wnt pathway antibodies, binding polypeptides, small molecules, and/or polynucleotides provided herein may be identified, screened for, or characterized for their physical/chemical properties and/or biological activities by various assays known in the art.
Provided herein are methods of screening for and/or identifying a wnt pathway antagonist which inhibits wnt pathway signaling, induces cancer cell cycle arrest, inhibits cancer cell proliferation, and/or promotes cancer cell death said method comprising: (a) contacting (i) a cancer cell, cancer tissue, and/or cancer sample, wherein the cancer cell, cancer tissue, and/or cancer comprises one or more biomarkers, and (ii) a reference cancer cell, reference cancer tissue, and/or reference cancer sample with a wnt pathway candidate antagonist, (b) determining the level of wnt pathway signaling, distribution of cell cycle stage, level of cell proliferation, and/or level of cancer cell death, whereby decreased level of wnt pathway signaling, a difference in distribution of cell cycle stage, decreased level of cell proliferation, and/or increased level of cancer cell death between the cancer cell, cancer tissue, and/or cancer sample, wherein the cancer cell, cancer tissue, and/or cancer comprises one or more biomarkers, and reference cancer cell, reference cancer tissue, and/or reference cancer sample identifies the wnt pathway candidate antagonist as an wnt pathway antagonist which inhibits wnt pathway signaling, induces cancer cell cycle arrest, inhibits cancer cell proliferation, and/or promotes cancer cell cancer death. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist.
Further provided herein are methods of screening for and/or identifying a wnt pathway antagonist which inhibits wnt pathway signaling, induces cancer cell cycle arrest, inhibits cancer cell proliferation, and/or promotes cancer cell death said method comprising: (a) contacting a cancer cell, cancer tissue, and/or cancer sample, wherein the cancer cell, cancer tissue, and/or cancer comprises one or more biomarkers with a wnt pathway candidate antagonist, (b) determining the level of wnt pathway signaling, distribution of cell cycle stage, level of cell proliferation, and/or level of cancer cell death to the cancer cell, cancer tissue, and/or cancer sample in the absence of the wnt pathway candidate antagonist, whereby decreased level of win pathway signaling, a difference in distribution of cell cycle stage, decreased level of cell proliferation, and/or increased level of cancer cell death between the cancer cell, cancer tissue, and/or cancer sample in the presence of the wnt pathway candidate antagonist and the cancer cell, cancer tissue, and/or cancer sample in the absence of the wnt pathway candidate antagonist identifies the wnt pathway candidate antagonist as an wnt pathway antagonist which inhibits wnt pathway signaling, induces cancer cell cycle arrest, inhibits cancer cell proliferation, and/or promotes cancer cell cancer death. In some embodiments, the wnt pathway antagonist is an R-spondin antagonist.
In some embodiments of any of the methods, the one or more biomarkers is a translocation (e.g., rearrangement and/or fusion) of one or more genes listed in Table 9. In some embodiments of any of the methods, the translocation (e.g., rearrangement and/or fusion) is an R-spondin translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO1 translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO2 translocation (e.g., rearrangement and/or fusion). In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E and RSPO2. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises SEQ ID NO:71 In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is detectable by primers which include SEQ ID NO:12, 41, and/or 42. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is driven by the EIF3E promoter. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is driven by the RSPO2 promoter. In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO3 translocation (e.g., rearrangement and/or fusion). In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK and RSPO3. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises SEQ ID NO:72 and/or SEQ ID NO:73. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is detectable by primers which include SEQ ID NO:13, 14, 43, and/or 44. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is driven by the PTPRK promoter. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is driven by the RSPO3 promoter. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises the PTPRK secretion signal sequence (and/or does not comprise the RSPO3 secretion signal sequence). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO4 translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) results in elevated expression levels of R-spondin (e.g., compared to a reference without the R-spondin translocation. In some embodiments, the one or more biomarkers is an R-spondin translocation (e.g., rearrangement and/or fusion) and KRAS and/or BRAF. In some embodiments, the presence of one or more biomarkers is presence of an R-spondin translocation (e.g., rearrangement and/or fusion) and a variation (e.g., polymorphism or mutation) KRAS and/or BRAF. In some embodiments, the presence of one or more biomarkers is presence of an R-spondin translocation (e.g., rearrangement and/or fusion) and the absence of one or more biomarkers is absence of a variation (e.g., polymorphism or mutation) CTNNB1 and/or APC.
Methods of determining the level of win pathway signaling are known in the art and are described in the Examples herein. In some embodiments, the levels of wnt pathway signaling are determined using a luciferase reporter assay as described in the Examples. In some embodiments, the wnt pathway antagonist inhibits wnt pathway signaling by reducing the level of wnt pathway signaling by about any of 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100%.
The growth inhibitory effects of a wnt pathway antagonist described herein may be assessed by methods known in the art, e.g., using cells which express wnt pathway either endogenously or following transfection with the respective gene(s). For example, appropriate tumor cell lines, and wnt pathway polypeptide-transfected cells may be treated with a wnt pathway antagonist described herein at various concentrations for a few days (e.g., 2-7) days and stained with crystal violet or MTT or analyzed by some other colorimetric assay. Another method of measuring proliferation would be by comparing 3H-thymidine uptake by the cells treated in the presence or absence an antibody, binding polypeptide, small molecule, and/or polynucleotides of the invention. After treatment, the cells are harvested and the amount of radioactivity incorporated into the DNA quantitated in a scintillation counter. Appropriate positive controls include treatment of a selected cell line with a growth inhibitory antibody known to inhibit growth of that cell line. Growth inhibition of tumor cells in vivo can be determined in various ways known in the art.
Methods of determining the distribution of cell cycle stage, level of cell proliferation, and/or level of cell death are known in the art. In some embodiments, cancer cell cycle arrest is arrest in G1.
In some embodiments, the wnt pathway antagonist will inhibit cancer cell proliferation of the cancer cell, cancer tissue, or cancer sample in vitro or in vivo by about 25-100% compared to the untreated cancer cell, cancer tissue, or cancer sample, more preferably, by about 30-100%, and even more preferably by about 50-100% or about 70-100%. For example, growth inhibition can be measured at a wnt pathway antagonist concentration of about 0.5 to about 30 μg/ml or about 0.5 nM to about 200 nM in cell culture, where the growth inhibition is determined 1-10 days after exposure of the tumor cells to the wnt pathway candidate antagonist. The wnt pathway antagonist is growth inhibitory in vivo if administration of the wnt pathway candidate antagonist at about 1 μg/kg to about 100 mg/kg body weight results in reduction in tumor size or reduction of tumor cell proliferation within about 5 days to 3 months from the first administration of the wnt pathway candidate antagonist, preferably within about 5 to 30 days.
To select for a writ pathway antagonists which induces cancer cell death, loss of membrane integrity as indicated by, e.g., propidium iodide (PI), trypan blue or 7AAD uptake may be assessed relative to a reference. API uptake assay can be performed in the absence of complement and immune effector cells. wnt pathway-expressing tumor cells are incubated with medium alone or medium containing the appropriate a wnt pathway antagonist. The cells are incubated for a 3-day time period. Following each treatment, cells are washed and aliquoted into 35 mm strainer-capped 12×75 tubes (1 ml per tube, 3 tubes per treatment group) for removal of cell clumps. Tubes then receive PI (10 μg/ml). Samples may be analyzed using a FACSCAN® flow cytometer and FACSCONVERT® CellQuest software (Becton Dickinson). Those wnt pathway antagonists that induce statistically significant levels of cell death as determined by PI uptake may be selected as cell death-inducing antibodies, binding polypeptides, small molecules, and/or polynucleotides.
To screen for wnt pathway antagonists which bind to an epitope on or interact with a polypeptide bound by an antibody of interest, a routine cross-blocking assay such as that described in Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, Ed Harlow and David Lane (1988), can be performed. This assay can be used to determine if a candidate wnt pathway antagonist binds the same site or epitope as a known antibody. Alternatively, or additionally, epitope mapping can be performed by methods known in the art. For example, the antibody and/or binding polypeptide sequence can be mutagenized such as by alanine scanning, to identify contact residues. The mutant antibody is initially tested for binding with polyclonal antibody and/or binding polypeptide to ensure proper folding. In a different method, peptides corresponding to different regions of a polypeptide can be used in competition assays with the candidate antibodies and/or polypeptides or with a candidate antibody and/or binding polypeptide and an antibody with a characterized or known epitope.
In some embodiments of any of the methods of screening and/or identifying, the wnt pathway candidate antagonist is an antibody, binding polypeptide, small molecule, or polynucleotide. In some embodiments, the wnt pathway candidate antagonist is an antibody. In some embodiments, the wnt pathway antagonist (e.g., R-spondin-translocation antagonist) antagonist is a small molecule.
In one aspect, a wnt pathway antagonist is tested for its antigen binding activity, e.g., by known methods such as ELISA, Western blot, etc.
Pharmaceutical formulations of a wnt pathway antagonist as described herein are prepared by mixing such antibody having the desired degree of purity with one or more optional pharmaceutically acceptable carriers (R
Exemplary lyophilized formulations are described in U.S. Pat. No. 6,267,958. Aqueous antibody formulations include those described in U.S. Pat. No. 6,171,586 and WO 2006/044908, the latter formulations including a histidine-acetate buffer.
The formulation herein may also contain more than one active ingredients as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. Such active ingredients are suitably present in combination in amounts that are effective for the purpose intended.
Active ingredients may be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions. Such techniques are disclosed in R
Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the wnt pathway antagonist, which matrices are in the form of shaped articles, e.g., films, or microcapsules.
The formulations to be used for in vivo administration are generally sterile. Sterility may be readily accomplished, e.g., by filtration through sterile filtration membranes.
In another aspect of the invention, an article of manufacture containing materials useful for the treatment, prevention and/or diagnosis of the disorders described above is provided. The article of manufacture comprises a container and a label or package insert on or associated with the container. Suitable containers include, for example, bottles, vials, syringes, IV solution bags, etc. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition which is by itself or combined with another composition effective for treating, preventing and/or diagnosing the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). At least one active agent in the composition is a wnt pathway antagonist (e.g., R-spondin antagonist, e.g., R-spondin-translocation antagonist) described herein. The label or package insert indicates that the composition is used for treating the condition of choice. Moreover, the article of manufacture may comprise (a) a first container with a composition contained therein, wherein the composition comprises a wnt pathway antagonist (e.g., R-spondin antagonist, e.g., R-spondin-translocation antagonist); and (b) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
In some embodiments, the article of manufacture comprises a container, a label on said container, and a composition contained within said container; wherein the composition includes one or more reagents (e.g., primary antibodies that bind to one or more biomarkers or probes and/or primers to one or more of the biomarkers described herein), the label on the container indicating that the composition can be used to evaluate the presence of one or more biomarkers in a sample, and instructions for using the reagents for evaluating the presence of one or more biomarkers in a sample. The article of manufacture can further comprise a set of instructions and materials for preparing the sample and utilizing the reagents. In some embodiments, the article of manufacture may include reagents such as both a primary and secondary antibody, wherein the secondary antibody is conjugated to a label, e.g., an enzymatic label. In some embodiments, the article of manufacture one or more probes and/or primers to one or more of the biomarkers described herein.
In some embodiments of any of the articles of manufacture, the one or more biomarkers comprises a translocation (e.g., rearrangement and/or fusion) of one or more genes listed in Table 9. In some embodiments of any of the articles of manufacture, the translocation (e.g., rearrangement and/or fusion) is an R-spondin translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO1 translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO2 translocation (e.g., rearrangement and/or fusion). In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E and RSPO2. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E exon 1 and RSPO2 exon 2. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises EIF3E exon 1 and RSPO2 exon 3. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) comprises SEQ ID NO:71. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is detectable by primers which include SEQ ID NO:12, 41, and/or 42. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is driven by the EIF3E promoter. In some embodiments, the RSPO2 translocation (e.g., rearrangement and/or fusion) is driven by the RSPO2 promoter. In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO3 translocation (e.g., rearrangement and/or fusion). In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK and RSPO3. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK exon 1 and RSPO3 exon 2. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises PTPRK exon 7 and RSPO3 exon 2. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises SEQ ID NO:72 and/or SEQ ID NO:73. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is detectable by primers which include SEQ ID NO:13, 14, 43, and/or 44. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is driven by the PTPRK promoter. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) is driven by the RSPO3 promoter. In some embodiments, the RSPO3 translocation (e.g., rearrangement and/or fusion) comprises the PTPRK secretion signal sequence (and/or does not comprise the RSPO3 secretion signal sequence). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) is a RSPO4 translocation (e.g., rearrangement and/or fusion). In some embodiments, the R-spondin translocation (e.g., rearrangement and/or fusion) results in elevated expression levels of R-spondin (e.g., compared to a reference without the R-spondin translocation. In some embodiments, the one or more biomarkers is an R-spondin translocation (e.g., rearrangement and/or fusion) and KRAS and/or BRAF. In some embodiments, the presence of one or more biomarkers is presence of an R-spondin translocation (e.g., rearrangement and/or fusion) and a variation (e.g., polymorphism or mutation) KRAS and/or BRAF. In some embodiments, the presence of one or more biomarkers is presence of an R-spondin translocation (e.g., rearrangement and/or fusion) and the absence of one or more biomarkers is absence of a variation (e.g., polymorphism or mutation) CTNNB1 and/or APC.
In some embodiments of any of the articles of manufacture, the articles of manufacture comprise primers. In some embodiments, the primers are any of SEQ ID NO:12, 13, 14, 41, 42, 43, and/or 44.
In some embodiments of any of the article of manufacture, the wnt pathway antagonist (e.g., R-spondin-translocation antagonist) is an antibody, binding polypeptide, small molecule, or polynucleotide. In some embodiments, the wnt pathway antagonist (e.g., R-spondin-translocation antagonist) is a small molecule. In some embodiments, the wnt pathway antagonist (e.g., R-spondin-translocation antagonist) is an antibody. In some embodiments, the antibody is a monoclonal antibody. In some embodiments, the antibody is a human, humanized, or chimeric antibody. In some embodiments, the antibody is an antibody fragment and the antibody fragment binds wnt pathway polypeptide (e.g., R-spondin-translocation fusion polypeptide).
The article of manufacture in this embodiment of the invention may further comprise a package insert indicating that the compositions can be used to treat a particular condition. Alternatively, or additionally, the article of manufacture may further comprise a second (or third) container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
Other optional components in the article of manufacture include one or more buffers (e.g., block buffer, wash buffer, substrate buffer, etc), other reagents such as substrate (e.g., chromogen) which is chemically altered by an enzymatic label, epitope retrieval solution, control samples (positive and/or negative controls), control slide(s) etc.
It is understood that any of the above articles of manufacture may include an immunoconjugate described herein in place of or in addition to a wnt pathway antagonist.
The following are examples of methods and compositions of the invention. It is understood that various other embodiments may be practiced, given the general description provided above.
Samples, DNA and RNA Preps and MSI Testing
Patient-matched fresh frozen primary colon tumors and normal tissue samples were obtained from commercial sources subjected to genomic analysis described below. All tumor and normal tissue were subject to pathology review. From a set of 90 samples 74 tumor pairs were identified for further analysis. Tumor DNA and RNA were extracted using Qiagen AllPrep DNA/RNA kit (Qiagen, CA). Tumor samples were assessed for microsatellite instability using an MSI detection kit (Promega, WI).
Exome Capture and Sequencing
Seventy two tumor samples and matched normal tissues were analyzed by exome sequencing. Exome capture was performed using SeqCap EZ human exome library v2.0 (Nimblegen, WI) consisting of 2.1 million empirically optimized long oligonucleotides that target 30,000 coding genes (300,000 exons, total size 36.5 Mb). The library was capable of capturing a total of 44.1 Mb of the genome, including genes and exons represented in RefSeq (January 2010), CCDS (September 2009) and miRBase (v.14, September 2009). Exome capture libraries generated were sequenced on HiSeq 2000 (Illumina, CA). One lane of 2×75 bp paired-end data was collected for each sample.
RNA-seq
RNA from 68 colon tumor and matched normal sample pairs was used to generate RNA-seq libraries using TruSeq RNA Sample Preparation kit (Illumina, CA). RNA-seq libraries were multiplex (two per lane) and sequenced on HiSeq 2000 as per manufacturer's recommendation (Illumina, CA). ˜30 million 2×75 bp paired-end sequencing reads per sample were generated.
Sequence Data Processing
All short read data was evaluated for quality control using the Bioconductor ShortRead package. Morgan, M. et al., Bioinformafics 25, 2607-2608 (2009). To confirm that all samples were identified correctly, all exome and RNA-seq data variants that overlapped with the Illuman 2.5 M array data were compared and checked for consistency. An all by all germline variant comparison was also done between all samples to check that all pairs were correctly matched between the tumor and normal and correspondingly did not match with any other patient pair above a cutoff of 90%.
Variant Calling
Sequencing reads were mapped to UCSC human genome (GRCh37/hg19) using BWA software set to default parameters. Li, H. & Durbin, R. Bioinformatics 25, 1754-1760 (2009). Local realignment, duplicate marking and raw variant calling were performed as described previously. DePristo, M. A. et al., Nat. Genet. 43, 491-498 (2011). Known germline variations represented in dbSNP Build 131 ENREF 4 (Sherry, S. T. et al., Nucleic Acids Res 29, 308-311 (2001)), but not represented in COSMIC ENREF 5 (Forbes, S. A. et al., Nucleic Acids Res. 38, D652-657 (2010)), were additionally filtered out. In addition variants that were present in both the tumor and normal samples were removed as germline variations. Remaining variations present in the tumor sample, but absent in the matched normal were predicted to be somatic. Predicted somatic variations were additionally filtered to include only positions with a minimum of 10× coverage in both the tumor and matched normal as well as an observed variant allele frequency of <3% in the matched normal and a significant difference in variant allele counts using Fisher's exact test. To evaluate the performance of this algorithm, 807 protein-altering variants were randomly selected and validated them using Sequenom (San Diego, Calif.) nucleic acid technology as described previously. Kan, Z. et al., Nature 466, 869-873 (2010). Of these, 93% (753) validated as cancer specific with the invalidated variants being equally split between not being seen in the tumor and also being seen in the adjacent normal (germline). Indels were called using the GATK Indel Genotyper Version 2 which reads both the tumor and normal BAM file for a given pair. DePristo, M. A. et al., Nat. Genet. 43, 491-498 (2011).
In order to identify variants grossly violating a binomial assumption, or variant calls affected by a specific mapper, Sequenom validated variants were additionally included using the following algorithm. Reads were mapped to UCSC human genome (GRCh37/hg19) using GSNAP. Wu, T. D. & Nacu, S. Bioinformatics 26, 873-881 (2010). Variants seen at least twice at a given position and greater than 10% allele frequency were selected. These variants were additionally filtered for significant biases in strand and position using Fisher's exact test. In addition variants that did not have adequate coverage in the adjacent normal as determined as at least a 1% chance of being missed using a beta-binomial distribution at a normal allele frequency of 12.5% were excluded. All novel protein-altering variants included in the second algorithm were validated by Sequenom, which resulted in a total of 515 additional variants. The effect of all non-synonymous somatic mutations on gene function was predicted using SIFT (Ng, P. C. & Henikoff, S. Genome Res 12, 436-446 (2002)) and PolyPhen ENREF 9 (Ramensky, V., Bork, P. & Sunyaev, S. Nucleic Acids Res 30, 3894-3900 (2002)). All variants were annotated using Ensembl (release 59, www.ensembl.org).
Validation of Somatic Mutations and Indels
Single base pair extension followed by nucleic acid mass spectrometry (Sequenom, CA) was used as described previously to validate the predicted somatic mutations. Tumor and matched normal DNA was whole genome amplified and using the REPLI-g Whole Genome Amplification Midi Kit (Qiagen, CA) and cleaned up as per manufacturer's recommendations and used. Variants found as expected in the tumor but absent in the normal were designated somatic. Those that were present in both tumor and normal were classified as germline. Variants that could not be validated in tumor or normal were designated as failed. For indel validation, primers for PCR were designed that will generate an amplicon of ˜300 bp that contained the indel region. The region was PCR amplified in both tumor and matched normal sample using Phusion (NEB, MA) as per manufacturer's instructions. The PCR fragments were then purified on a gel an isolated the relevant bands and Sanger sequenced them. The sequencing trace files were analyzed using Mutation Surveyor (SoftGenetics, PA). Indels that were present in the tumor and absent in the normal were designated somatic and are reported in Table 3.
Mutational Significance
Mutational significance of genes was evaluated using a previously described method ENREF 10. Briefly this method can identify genes that have statistically significant more protein-altering mutations than what would be expected based on a calculated background mutation rate. The background mutation rate was calculated for six different nucleotide mutation categories (A,C,G,T,CG1,CG2) in which there was sufficient coverage (≥10×) in both the tumor and matched normal sample. A nonsynonymous to synonymous ratio, ri, was calculated using a simulation of mutating all protein coding nucleotides and seeing if the resulting change would result in a synonymous or nonsynonymous change. The background mutation rate, fi, was determined by multiplying the number of synonymous somatic variants by ri and normalizing by the total number of protein-coding nucleotides. The number of expected mutations for a given gene was determined as the number of protein-coding bases multiplied by fi and integrated across all mutation categories. A p-value was calculated using a Poisson probability function given the expected and observed number of mutations for each gene. P values were corrected for multiple testing using the Benjamini Hochberg method and the resulting q-values were converted to q-scores by taking the negative log 10 of the q-values. Given that different mutation rates existed for the MSI and MSS samples, qscores were calculated separately for each with the two hypermutated samples being removed completely. In order to not underestimate the background mutation rates, the seven samples with less than 50% tumor content were excluded from the analysis. Pathway mutational significance was also calculated as previously described, with the exception that the BioCara Pathway database used used which was downloaded as part of MSigDB (Subramanian A. et al., Proc. of the Natl Acad. Of Sci. USA 102, 15545-15550 (2005)).
Whole Genome Sequencing and Analysis
Paired-end DNA-Seq reads were aligned to GRCh37 using BWA. Further processing of the alignments to obtain mutation calls was similar to the exome sequencing analysis using the GATK pipeline. Copy-number was calculated by computing the number of reads in 10 kb non-overlapping bins and taking the ratio tumor/normal of these counts. Chromosomal breakpoints were predicted using breakdancer. Chen, K. et al., Nat. Methods 6, 677-681 (2009). Genome plots were created using Circos (Krzywinski, M. et al., Genome Res. 19, 1639-1459 (2009)).
RNA-Seq Data Analysis
RNA-Seq reads were aligned to the human genome version GRCh37 using GSNAP (Wu, T. D. & Nacu, S. Bioinformatics 26, 873-881 (2010). Expression counts per gene were obtained by counting the number of reads aligning concordant and uniquely to each gene locus as defined by CCDS. The gene counts were then normalized for library size and subsequently variance stabilized using the DESeq Bioconductor software package. Anders, S. & Huber, W. Genome Biology 11, R106 (2010). Differential gene expression was computed by pairwise t-tests on the variance stabilized counts followed by correction for multiple testing using the Benjamini & Hochberg method.
SNP Array Data Generation and Analysis
Illumina HumanOmni2.5_4v1 arrays were used to assay 74 colon tumors and matched normals for genotype, DNA copy and LOH at ˜2.5 million SNP positions. These samples all passed our quality control metrics for sample identity and data quality (see below). A subset of 2295239 high-quality SNPs was selected for all analyses.
After making modifications to permit use with Illumina array data, the PICNIC (Greenman, C. D. et al., Biostatistics 11, 164-175 (2010)) algorithm was applied to estimate total copy number and allele-specific copy number/LOH. Modification included replacement of the segment initialization component with the CBS algorithm (Venkatraman, E. S. & Olshen, A. B. Bioinformatics 23, 657-663 (2007)), and adjustment of the prior distribution for background raw copy number signal (abjusted mean of 0.7393 and a standard deviation of 0.05). For the preprocessing required by PICNIC's hidden Markov model (HMM), a Bayesiaan model to estimate cluster centroids for each SNP. For SNP k and genotype g, observed data in normal sample were modeled as following a bivariate Gaussian distribution. Cluster centers for the three diploid genotypes were modeled jointly by a 6-dimensional Gaussian distribution with mean treated as a hyperparameter and set empirically based on a training set of 156 normal samples. Cluster center and within-genotype covariance matrices were modeled as inverse Wishart with scale matrix hyperparameters also set empirically and with degrees of freedom manually tuned to provide satisfactory results for a wide range of probe behavior and minor allele frequencies. Finally, signal for SNP k (for the A and B alleles separately) was transformed with a non-linear function: y=αkxγ
Sample identity was verified using genotype concordance between all samples. Pairs of tumors from the same patient were expected to have >90% concordance and all other pairs were expected to have <80% concordance. Samples failing those criteria were excluded from all analyses. Following modified PICNIC, the quality of the overall HMM fit was assessed by measuring the root mean squared error (RMSE) between the raw and HMM-fitted value for each SNP. Samples with and RMSE>1.5 were excluded from all analyses. Finally to account for two commonly observed artifacts, fitted copy number values were set to “NA” for singletons with fitted copy number 0 or when the observed and fitted means differed by more tha 2 for regions of inferred copy gain.
Recurrent DNA Copy Number Gain and Loss
Genomic regions with recurrent DNA copy gain and loss were identified using GISTIC, version 2.0. Mermel, C. H. et al., Genome Biology 12, R41 (2011). Segmented integer total copy number values obtained from PICNIC, c, were converted to loge ratio values, y, as y=log2(c+0.1)−1. Cutoffs of +/−0.2 were used to categorize loge ratio values as gain or loss, respectively. A minimum segment length of 20 SNPs and a loge ratio “cap” value of 3 were used.
Fusion Detection and Validation
Putative fusions were identified using a computational pipeline developed called GSTRUCT-fusions. The pipeline was based on a generate-and-test strategy that is fundamentally similar to methodology reported previously for finding readthrough fusions. Nacu, S. et al., BMC Med Genomics 4, 11 (2011). Paired-end reads were aligned using our alignment program GSNAP. Nacu, S. et al., BMC Med Genomics 4, 11 (2011). GSNAP has the ability to detect splices representing translocations, inversions, and other distant fusions within a single read end.
These distant splices provided one set of candidate fusions for the subsequent testing stage. The other set of candidate fusions derived from unpaired unique alignments, where each end of the paired-end read aligned uniquely to a different chromosome, and also from paired, but discordant unique alignments, where each end aligned uniquely to the same chromosome, but with an apparent genomic distance that exceeded 200,000 bp or with genomic orientations that suggested an inversion or scrambling event.
Candidate fusions were then filtered against known transcripts from RefSeq, aligned to the genome using GMAP. Wu, T. D. & Watanabe, C. K. Bioinformatics 21, 1859-1875 (2005). Both fragments flanking a distant splice, or both ends of an unpaired or discordant paired-end alignment, were required to map to known exon regions. This filtering step eliminated approximately 90% of the candidates. Candidate inversions and deletions were further eliminated that suggested rearrangements of the same gene, as well as apparent readthrough fusion events involving adjacent genes in the genome, which our previous research indicated were likely to have a transcriptional rather than genomic origin.
For the remaining candidate fusion events, artificial exon-exon junctions consisting of the exons distal to the supported donor exon and the exons proximal to the supported acceptor exon were constructed. The exons included in the proximal and distal computations were limited so that the cumulative length along each gene was within an estimated maximum insert length of 200 bp. As a control, all exon-exon junctions consisting of combinations of exons within the same gene were constructed for all genes contributing to a candidate fusion event.
In the testing stage of our pipeline, we constructed a genomic index from the artificial exon-exon junctions and controls using the GMAP_BUILD program included as part of the GMAP and GSNAP package. This genomic index and the GSNAP program with splice detection turned off were used to re-align the original read ends that were not concordant to the genome. Reads were extracted that aligned to an intergenic junction corresponding to a candidate fusion, but not to a control intragenic junction.
The results of the re-alignment were filtered to require that each candidate fusion have at least one read with an overhang of 20 bp. Each candidate fusion was also required to have at least 10 supporting reads. For each remaining candidate fusion, the two component genes were aligned against each other using GMAP and eliminated the fusion if the alignment had any region containing 60 matches in a window of 75 bp. The exon-exon junction were also aligned against each of the component genes using GMAP and eliminated the fusion if the alignment had coverage greater than 90% of the junction and identity greater than 95%.
Validation of gene fusions was done using reverse transcription (RT)-PCR approach using both colon tumor and matched normal samples. 500 ng of total RNA was reverse transcribed to cDNA with a High Capacity cDNA Reverse Transcription kit (Life Technologies, CA) following manufacturer's instructions. 50 ng of cDNA was amplified in a 25 μl reaction containing 400 pM of each primer, 300 μM of each deoxynucleoside triphosphates and 2.5 units of LongAmp Taq DNA polymerase (New England Biolabs, MA). PCR was performed with an initial denaturation at 95° C. for 3 minutes followed by 35 cycles of 95° C. for 10 seconds, 56° C. for 1 minute and 68° C. for 30 seconds and a final extension step at 68° C. for 10 minutes. 3 μl of PCR product was run on 1.2% agarose gel to identify samples containing gene fusion. Specific PCR products were purified with either a QIAquick PCR Purification kit or Gel Extraction kit (Qiagen, CA). The purified DNA was either sequenced directly with PCR primers specific to each fusion or cloned into TOPO cloning vector pCR2.1 (Life Technologies, CA) prior to Sanger sequencing. The clones were sequenced using Sanger sequencing on a ABI3730xl (Life Technologies, CA) as per manufacturer instructions. The Sanger sequencing trace files were analyzed using Sequencher (Gene Cordes Corp., MI).
RSPO Fusion Activity Testing
Eukaryotic expression plasmid pRK5E driving the expression of c-terminal FLAG tag EIF3E, PTPKR (amino acids 1-387), RSPO2, RSPO3, EIF3E(e1)-RSPO2(e2), PTPRK(e1)-RSPO3(e2), PTPRK(e7)-RSPO3(e2) was generated using standard PCR and cloning strategies.
Cells, Conditioned Media, Immunoprecipitation and Western Blot
HEK 293T, human embryonic kidney cells, were maintained in DMEM supplemented with 10% FBS. For expression analysis and condition media generation 3×105 HEK29T cells were plated in 6-well plates in 1.5 ml DMEM containing 10% FBS. Cells were transfected with 1 μg of DNA using
Luciferase Reporter Assays
HEK 293T cells were plated at a density of 50,000 cells/ml in 90 μl of media containing 2.5% FBS per well of a 96-well plate. After 24 hours, cells were transfected using
Immunoprecipitation and Western Blot
To confirm that the RSPO wild type and RSPO fusion proteins were secreted, FLAG tagged proteins were immunoprecipitated from the media using anti-FLAG-M2 antibody coupled beads (Sigma, MO), boiled in SDS-PAGE loading buffer, resolved on a 4-20% SDS-PAGE (Invitrogen, Carlsbad, Calif.) and transferred onto a nitrocellulose membrane. RSPO and other FLAG tagged proteins expressed in cells were detected from cell lysates using western blot as described before (Bijay p85 paper). Briefly, immunoprecipitated proteins and proteins from cell lysates were detected by Western blot using FLAG-HRP-conjugated antibody and chemiluminescences Super signal West Dura chemiluminescence detection substrate (Thermo Fisher Scientific, IL).
Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics. In these examples, a systematically analysis of over 70 pairs of primary human colon cancers was undertaken by applying next generation sequencing to characterize their exomes, transcirptomes and copy number alterations. 36,303 protein altering somatic changes were identified that include several new recurrent mutations in Wnt pathway genes like TCF12 and TCF7L2, chromatin remodeling proteins such as TET2 and TET3 and receptor tyrosine kinases including ERBB3. The analysis for significant cancer genes identified 18 candidates, including cell cycle checkpoint kinase ATM. The copy number and RNA-seq data analysis identified amplifications and corresponding overexpression of IGF2 in a subset of colon tumors. Further, using RNA-seq data multiple fusion transcripts were identified including recurrent gene fusions of the R-spondin genes RSPO2 and RSPO3, occurring in 10% of the samples. The RSPO fusion proteins were demonstrated to be biologically active and potentiate Wnt signaling. The RSPO fusions aremutually exclusive with APC mutations indicating that they likely play a role in activating Wnt signaling and tumorigenesis. The R-spondin gene fusions and several other gene mutations identified in these examples provide new opportunities for therapeutic intervention in colon cancer.
74 primary colon tumors and their matched adjacent normal samples were characterized. Whole-exome sequencing for 72 (15 MSI and 57 MSS) of the 74 colon tumor and adjacent normal sample pairs to assess the mutational spectra was performed. These 74 tumor/normal pairs were also analyzed on Illumina 2.5M array to assess chromosomal copy number changes. RNA-seq data for 68 tumor/normal pairs was also obtained. Finally, the genome of an MSI and MSS tumor/normal pair at 30× coverage from this set of samples was sequenced and analyzed.
Exons were captured using Nimblegen SeqCap EZ human exome library v2.0 and sequenced on HiSeq 2000 (Illumina, CA) to generate 75 bp paired-end sequencing reads. The targeted regions had a mean coverage of 179× with 97.4% bases covered at ≥10 times. 95,075 somatic mutations in the 72 colon tumor samples analyzed were identified of which 36,303 were protein-altering. Two MSS samples showed an unusually large number of mutations (24,830 and 5,780 mutations of which 9,479 and 2,332 were protein-altering mutations respectively). These were designated as hypermutated samples and were not considered for calculating the background mutation rate. 52,312 somatic mutations in the 15 MSI samples (18,436 missense, 929 nonsense, 22 stop lost, 436 essential splice site, 363 protein-altering indels, 8,065 synonymous, 16,675 intronic and 7,386 others) and 12,153 somatic mutations in the 55 MSS samples (3,922 missense, 289 nonsense, 6 stop lost, 69 essential splice site, 20 protein-altering indels 1,584 synonymous, 4,375 intronic and 1,888 others) studied (Table 2 and 3) were found. About 98% (35,524/36,303) of the protein altering single nucleotide variants reported in these examples are novel and have not been reported in COSMIC ENREF 7 v54 (Forbes, S. A. et al., Nucleic Acids Res. 38:D652-657 (2010)). Thirty seven percent of the somatic mutations reported were validated using RNA-seq data or mass spectrometry genotyping with a validation rate of 93% (Table 2). All the indels reported were confirmed somatic using Sanger sequencing (Table 3-Somatic Indels). A mean non-synonymous mutation rate of 2.8/Mb (31-149 coding region mutations in the 55 samples) in the MSS samples and 40/Mb (764-3113 coding region mutations in the 15 samples) in the MSI samples was observed, consistent with the MMR defect in the later.
The analysis of the base level transitions and transversions at mutated sites revealed that in CRCs C to T transitions to be predominant, regardless of the MMR status, both in the whole exome and whole genome analysis. This was consistent with previous mutation reports (Wood, L. D. et al., Science 318:1108-1113 (2007); Sjoblom, T. et al., Science 314:268-274 (2006); Bass, A. J. et al., Nat. Genet. 43:964-968 (2011)). The two hyper mutated tumors samples examined also showed higher proportion of C to A and T to G transversions, consistent with the much higher mutation rate observed for these samples.
Consistent with the exome mutation data, the MSS whole genome analyzed showed 17,651 mutations compared to the 97,968 mutations observed in the MSI whole genome. The average whole genome mutation rate was 6.2/Mb and 34.5/Mb for the MSS and MSI genome respectively. A mutation rate of 4.0-9.8/Mb was previously reported for MSS CRC genomes (Bass, A. J. et al., Nat. Genet. 43:964-968 (2011)).
The mutation analysis identified protein altering somatic single nucleotide variants in 12,956 genes including 3,257 in the MSS samples, 9,851 in the MSI samples and 6,891 in the two hyper mutated samples. Among the frequently mutated class of proteins are human kinases including RTKs, G-protein coupled receptors, and nuclear hormone receptors. In an effort to understand the impact of the mutations on gene function SIFT ENREF 10 (Ng, P. C. & Henikoff, S., Genome Res 12:436-446 (2002)), Polyphen ENREF 11 (Ramensky, V. et al., Nucleic Acids Res 30:3894-3900 (2002)) and mCluster (Yue, P. et al., Hum. Mutat. 31:264-271 (2010)) was applied and 36.7% of the mutations were found likely to have a functional consequence, in contrast to 12% for germline variants from the normal samples, based on at least two of the three methods (Table 2).
To further understand the relevance of the mutated genes, a previously described q-score metric was applied to rank significantly mutated cancer genes ENREF 13 (Kan, Z. et al., Nature 466:869-873 (2010)). In MSS samples, 18 significant cancer genes (q-score>=1; ≤10% false discovery rate) were identified (KRAS, TP53, APC, PIK3CA, SMAD4, FBXW7, CSMD1, NRXN1, DNAH5, MRVI1, TRPS1, DMD, KIF2B, ATM, FAM5C, EVC2, OR2W3, TMPRSS11A, and SCN10A). The significantly mutated MSS colon cancer genes included previously reported genes including KRAS, APC, TP53, SMAD4, FBXW7, and PIK3CA and several new genes including the cell cycle checkpoint gene ATM. Genes like KRAS and TP53 were among the top mutated MSI colon cancer genes, however, none of the genes achieved statistical significance due to the limited number of MSI samples analyzed.
In an effort to establish the relevance of the mutated genes, the mutated genes were compared against 399 candidate colon cancer genes identified in screens involving mouse models of cancer (Starr, T. K. et al., Science 323, 1747-1750 (2009); March, H. N. et al., Nat. Genet. 43, 1202-1209 (2011)). Of the 399 genes mutations were found in 327. When the data sets were analyzed via an alternative method, of the 432 genes, mutations were found in 356. The frequently mutated genes in the data set that overlapped with mouse colon cancer model hits included KRAS, APC, SMAD4, FBXW7 and EP400. Additionally, genes involved in chromatin remodeling like SIN3A, SMARCA5 and NCOR1 and histone modifying enzyme JARID2 found in the mouse CRC screen (Starr, T. K. et al., Science 323, 1747-1750 (2009); March, H. N. et al., Nat. Genet. 43, 1202-1209 (2011)) were also mutated in our exome screen. Further, TCF12, identified in the mouse colon cancer model screen, was mutated in 5 (Q179*, G444*, and R603W/Q) of our samples (7%) and contained a hotspot mutation at R603 (3 of 5 mutations; R603W/Q). This hotspot mutation within the TCF12 helix-loop-helix domain will likely abolish its ability to bind DNA, suggesting a loss-function mutation. Interestingly, all of the TCF12 mutations were identified in MSI samples. The TCF12 transcription factor has been previously implicated in colon cancer metastasis ENREF 14 (Lee, C. C. et al., J. of Biol. Chem. 287:2798-2809 (2011)). The presence of hotspots in this gene and its identification in mouse CRC model screen indicates that it likely functions as a CRC driver gene.
Mutational hotspots, where the same position in a gene was mutated across independent samples, are indicative of functionally relevant driver cancer gene. In this study, 270 genes were identified with hotspot mutation (Table 4). Seventy of these genes were not previously reported in COSMIC ENREF 7. Comparison of our mutations with those reported in COSMIC identified an additional 245 hotspot mutations in 166 genes (Table 5). Utilizing an alternative data analysis method, 274 genes were identified with hotspot mutations with forty of these genes not previously in COSMI and an additional 435 hotspot mutations in 361 genes. Genes with novel hotspot mutations include transcriptional regulators (TCF12, TCF7L2 and PHF2), Ras/Rho related regulators (SOS1 (e.g., R547W, T614M R854*, G1129V), SOS2 (e.g., R225*, R854C, and Q1296H), RASGRF2, ARHGAP10, ARHGEF33 and Rab40c (e.g., G251S)), chromatin modifying enzymes (TET2, TET3, EP400 and MLL), glutamate receptors (GRIN3A and GRM8), receptor tyrosine kinases (ERBB3, EPHB4, EFNB3, EPHA1, TYRO3, TIE1 and FLT4), other kinases (RIOK3, PRKCB , MUSK, MAP2K7 and MAP4K5), protein phosphatase (PTPRN2), GPRCs (GPR4 and GPR98) and E3-ligase (TOPORS). Of further interest in this gene set are TET2 and TET3, both of which encode methylcytosine dioxygenase involved in DNA methylation ENREF 15 (Mohr, F. et al., Exp. Hematol. 39:272-281 (2011)). While mutations in TET2 have been reported in myeloid cancers, thus far mutations in TET3 or TET1 have not been reported in solid tumors, especially, in CRC ENREF 15 (Mohr, F. et al., Exp. Hematol. 39:272-281 (2011)). All the three family members TET1 (e.g., R81H, E417A, K540T, K792T, S879L, S1012*, Q1322*, C1482Y, A1896V, and A2129V), TET2 (e.g., K108T, T1181, S289L, F373L, K1056N, Y1169*, A1497V, and V1857M), and TET3 (e.g., T165M, A874T, M977V, G1398R, and R1576Q/W) are mutated in these examples.
The RNA-seq data was used to compute differentially expressed genes between tumor and normal samples (Table 6). The top differentially overexpressed genes include FOXQ1 and CLND1 which have both been implicated in tumorigenesis (Kaneda, H. et al., Cancer Res. 70:2053-2063 (2010)). Importantly, in analyzing the RNA-seq data, IGF2 upregulation was identified in 12% (8/68) of the colon tumors examined A majority (7/8) of the tumors with IGF2 overexpression also showed focal amplification of the IGF2 locus as measured by Illumina 2.5M array. Overall the differentially expressed genes affect multiple signaling pathways including Calcium Signaling, cAMP-mediated signaling, Glutamate Receptor Signaling, Amyotrophic Lateral Sclerosis Signaling, Nitrogen Metabolism, Axonal Guidance Signaling, Role of IL-17A in Psoriasis, Serotonin Receptor Signaling, Airway Pathology in Chronic Obstructive Pulmonary Disease, Protein Kinase A Signaling, Bladder Cancer Signaling, HIF1α Signaling, Cardiac β-adrenergic Signaling, Synaptic Long Term Potentiation, Atherosclerosis Signaling, Circadian Rhythm Signaling, CREB Signaling in Neurons, G-Protein Coupled Receptor Signaling, Leukocyte Extravasation Signaling, Complement System, Eicosanoid Signaling, Tyrosine Metabolism, Cysteine Metabolism, Synaptic Long Term Depression, Role of IL-17A in Arthritis, Cellular Effects of Sildenafil (Viagra), Neuropathic Pain Signaling In Dorsal Horn Neurons, D-arginine and D-ornithine Metabolism, Role of IL-17F in Allergic Inflammatory Airway Diseases, Thyroid Cancer Signaling, Hepatic Fibrosis/Hepatic Stellate Cell Activation, Dopamine Receptor Signaling, Role of NANOG in Mammalian Embryonic Stem Cell Pluripotency, Chondroitin Sulfate Biosynthesis, Endothelin-1 Signaling, Keratan Sulfate Biosynthesis, Phototransduction Pathway, Wnt/β-catenin Signaling, Chemokine Signaling, Alanine and Aspartate Metabolism, Glycosphingolipid Biosynthesis—Neolactoseries, Bile Acid Biosynthesis, Role of Macrophages, Fibroblasts and Endothelial Cells in Rheumatoid Arthritis, α-Adrenergic Signaling, Taurine and Hypotaurine Metabolism, LPS/IL-1 Mediated Inhibition of RXR Function, Colorectal Cancer Metastasis Signaling, CCR3 Signaling in Eosinophils, and O-Glycan Biosynthesis.
Copy number alterations in 74 tumor/normal pairs were assessed by applying GISTIC to the PICNIC segmented copy number data. In addition to the IGF2 amplifications, known amplifications were found involving KRAS (13%; 10/74) and MYC (31%; 23/74) located in a broad amplicon on chromosome 8q (Table 7). Focal deletion involving FHIT, a tumor suppressor was observed in 21% (16/74) of the samples (Table 8). FHIT, which encodes a diadenosine 5′,5′″-P1,P3-triphosphate hydrolase involved in purine metabolism, has previously been reported to be lost in other cancers ENREF 18 (Pichiorri, F. et al., Future Oncol. 4:815-824 (2008)). Deletion of APC (18%; 14/74) and SMAD4 (29%; 22/74) was also observed. Finally, chromosome 20q was found to be frequently gained and in contrast, 18q to be lost.
When copy number alterations were analyzed using PICNIC probe-level copy number calling, CBS segmentation of the copy number tumor/normal ratios and GISTIC on these tumor/normal ratios, the top set of genes with copy number alterations were similar though the percentages varied slightly. Known amplifications involving KRAS (13%; 10/74) and MYC (23%; 17/74) located in a broad amplicon on chromosome 8q. Deletion involving FHIT, a tumor suppressor was observed in 30% (22/74) of the samples. Deletion of APC (8%; 6/74), PTEN (4%, 3/74) and SMAD3 (9%, 10/74). SMAD4 and SMAD2 are both altered in 27% (20/74) of the samples and are located within 3 Mb from each other on 18q which is frequently lost.
Besides assessing expression, the RNA-seq data can be exploited to examine splicing patterns. Among the mutated genes there are several that carry somatic mutations in canonical splice sites that will likely affect their splicing. 112 genes were found with canonical splice site mutations that show evidence for splicing defects based on RNA-seq data. The affected genes include TP53, NOTCH2 and EIF5B (Table 9). RNA-seq data was also used to analyze tumor specific expression of certain exons in gene coding regions. Two novel tumor specific exons upstream of the first 5′annotated exon of a mitochondrial large subunit MRPL33 gene were identified (
RNA-seq data was next used to identify intra- and inter-chromosomal rearrangements such as gene fusions that occur in cancer genomes ENREF 9 (Ozsolak, F. & Milos, P. M. Nature Rev Genet. 12:87-98 (2011)). In mapping the paired-end RNA-seq data, 36 somatic gene fusions, including two recurrent ones, were indentified in the analyzed CRC transcriptomes. The somatic nature of the fusions was established by confirming it presence in the tumors and absence in corresponding matched normal using RT-PCR. Further, all fusions reported in these examples were Sanger sequenced and validated (Table 10). The majority of predicted somatic fusions identified were intra-chromosomal (89%; 32/36).
The recurrent fusions identified in these examples involve the R-spondin family members, RSPO2 (3%; 2/68) and RSPO3 (8%; 5/68;
RSPO3 translocations were observed in 5 of 68 tumors and they involve PTPRK (protein tyrosine kinase receptor kappa) as its 5′ partner. WGS reads from the 5 tumors expressing the RSPO3fusions showed rearrangements involving a simple (3 samples) or a complex (2 samples) inversion that places RSPO3 in proximity to PTPRK on the same strand as PTPRK on chromosome 6q. Two different RSPO3 fusion variants were identified consisting either of exon 1 (e 1) or exon 7 (e7) of PTPRK and exon 2 (e2) of RSPO3 (
To determine if the predicted R-spondin fusion proteins were functional, expression constructs containing a C-terminal flag tag were generated and tested their expression following transfecting into mammalian 293T cells. Western blot analysis of the conditioned media showed that the fusion proteins were expressed and secreted (
To further characterize the RSPO gene fusions, RSPO gene fusions were analyzed in the context of mutations and other alterations that occur in components of cellular signaling pathways including the Wnt signaling cascade (
In these examples, an in-depth extensive genomic analysis of human primary colon tumors was reported. In sequencing and analyzing human CRC exomes and transcriptomes, multiple new recurrent somatic mutations were found. Many of the significantly mutated genes in these examples (APC, KRAS, PIK3CA, SMAD4, FBXW7, TP53, TCF7L2) agree with the previous findings. In addition, multiple mutations in 111 out of the 140 genes they highlighted in their study were reported. Further, 11 additional significant colon cancer genes including ATM and TMPRSS11A have been identified that have not been previously reported. The examples identified multiple hotspot containing genes including TCF12 and ERBB3. The ERBB3 oncogenic mutants identified here potentially provide new opportunities for therapeutic intervention in CRC. Combined analysis of expression and copy number data identified IGF2 overexpression in a subset of our human CRC samples.
Finally, using RNA-seq data, new recurrent fusions involving R-spondins have been identified that occur at a frequency of approximately 10%. The fusions results in functional R-spondin proteins that potentiate Wnt signaling. R-spondins provide attractive targets for antibody based therapy in colon cancer patients that harbor them. Besides directly targeting R-spondins, other therapeutic strategies that block Wnt signaling will likely be effective against tumors positive for R-spondin fusions.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, the descriptions and examples should not be construed as limiting the scope of the invention. The disclosures of all patent and scientific literature cited herein are expressly incorporated in their entirety by reference.
This application is a continuation application of U.S. patent application Ser. No. 13/764,631, filed on Feb. 11, 2013, which claims benefit under 35 U.S.C. § 119 to U.S. Patent Application No. 61/597,746, filed on Feb. 11, 2012 and 61/674,763 filed on Jul. 23, 2012, the entire contents of which are incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 61674763 | Jul 2012 | US | |
| 61597746 | Feb 2012 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 13764631 | Feb 2013 | US |
| Child | 16895395 | US |
