US20170174753A1 - Method for treating breast cancer - Google Patents

Method for treating breast cancer Download PDF

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US20170174753A1
US20170174753A1 US14/364,937 US201314364937A US2017174753A1 US 20170174753 A1 US20170174753 A1 US 20170174753A1 US 201314364937 A US201314364937 A US 201314364937A US 2017174753 A1 US2017174753 A1 US 2017174753A1
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seq
set forth
variable region
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heavy chain
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Gilles Bernard Tremblay
Anna N. Moraitis
Mario Filion
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ADC Therapeutics SA
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Alethia Biotherapeutics Inc
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    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
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Definitions

  • human epidermal growth factor receptor 2 HER2
  • FISH fluorescence in situ hybridization
  • TNBC triple-negative breast cancer
  • TNBC basal-like cancer
  • cytotoxic agents in the adjuvant setting as well as in the neoadjuvant setting when administered agents such as 5-fluorouracil, doxorubicin and cyclophosphamide (Rouzier et al. 2005).
  • agents such as 5-fluorouracil, doxorubicin and cyclophosphamide
  • Other agents that have shown some efficacy include platinum based compounds such as cisplatin and anti-tubulin compounds such as taxanes (Santana-Davila and Perez, 2010).
  • PARP1 is an enzyme that participates in the repair of DNA single-strand breaks by associating with corrupted DNA strands and mediating the recruitment of enzymes needed to repair single-strand breaks (de Ruijter et al., 2011).
  • PARP1 activity has been to inhibit PARP1 activity as a means of allowing cancer cells to accumulate more DNA single-strand breaks, which ultimately leads to genetic instability, mitotic arrest and apoptosis.
  • Kidney associated antigen 1 (KAAG1), the protein sequence which is identified herein as SEQ ID NO.:2, was originally cloned from a cDNA library derived from a histocompatibility leukocyte antigen-B7 renal carcinoma cell line as an antigenic peptide presented to cytotoxic T lymphocytes (Van den Eynde et al., 1999; Genebank accesssion no. Q9UBP8, the cDNA sequence is represented by nucleotides 738-992 of SEQ ID NO.:1). The locus containing KAAG1 was found to encode two genes transcribed in both directions on opposite strands. The sense strand was found to encode a transcript that encodes a protein termed DCDC2.
  • KAAG1 antisense transcript was tumor specific and exhibited very little expression in normal tissues whereas the DCDC2 sense transcript was ubiquitously expressed (Van den Eynde et al., 1999).
  • the expression of the KAAG1 transcript in cancer, and in particular ovarian cancer, renal cancer, lung cancer, colon cancer, breast cancer and melanoma was disclosed in international application No. PCT/CA2007/001134 published on Dec. 27, 2007 under No. WO 2007/147265.
  • Van den Eynde et al. also observed RNA expression in renal carcinomas, colorectal carcinomas, melanomas, sarcomas, leukemias, brain tumors, thyroid tumors, mammary carcinomas, prostatic carcinomas, oesophageal carcinomas, bladder tumor, lung carcinomas and head and neck tumors.
  • VMP/DCDC2/KAAG1 locus was associated with dyslexia (Schumacher et al., 2006; Cope et al., 2005).
  • DCDC2 marker pointed to the DCDC2 marker as the culprit in dyslexic patients since the function of this protein in cortical neuron migration was in accordance with symptoms of these patients who often display abnormal neuronal migration and maturation (Schumacher et al., 2006).
  • the Applicant has obtained a panel of antibodies and antigen binding fragment that bind to the KAAG1 protein. These antibodies or antigen binding fragments were shown to target three regions of the protein; amino acids 1 to 35, amino acids 36 to 60 amino acids 61 to 84. The Applicant found that antibodies targeting a region between amino acids 30 to 84 were the most advantageous for therapeutic purposes as they recognized KAAG1 located at the surface of tumor cells. The Applicant has shown that some of these antibodies and antigen binding fragments can mediate antibody-dependent cell cytotoxicity and/or are internalized by tumor cells, which makes them good candidates to deliver a payload to tumor cells.
  • the Applicant has also generated chimeric and humanized antibodies based on selected antibody candidates and has shown that these antibodies can inhibit tumor cell formation and invasion (see PCT/CA2009/001586 published on Jun. 3, 2010 under No. WO2010/060186 and PCT/CA2010/001785 published on May 12, 2011 under No. WO2011/054112). Finally, the Applicant found that these antibodies could be used for the treatment and diagnosis of ovarian cancer, skin cancer, renal cancer, colorectal cancer, sarcoma, leukemia, brain tumor, thyroid tumor, breast cancer, prostate cancer, oesophageal tumor, bladder tumor, lung tumor and head and neck tumor and metastatic form of these cancers.
  • the Applicant has now come to the unexpected discovery that breast cancer cells lacking ER protein expression, PgR protein expression and/or showing absence of HER2 protein over-expression (i.e., triple-negative breast cancer cells, basal-like) can be efficiently targeted with an antibody or antigen binding fragment that specifically binds to KAAG1.
  • Anti-KAAG1 antibodies may thus be used for the, detection and therapeutic treatment of breast cancer cells that are negative for at least one of these markers.
  • FIG. 1 a is an amino acid sequence alignment of the 3A4 variable domains of the murine and humanized light chains.
  • the light chain has two humanized variants (Lh1 an Lh2).
  • the CDRs are shown in bold and indicted by CDRL1, CDRL2 and CDRL3.
  • Back mutations in the human framework regions that are murine amino acids are underlined in the humanized sequences.
  • FIG. 1 b is an amino acid sequence alignment of the 3A4 variable domains of the murine and humanized heavy chains.
  • the heavy chain has four humanized variants (Hh1 to Hh4).
  • the CDRs are shown in bold and indicted by CDRH1, CDRH2 and CDRH3.
  • Back mutations in the human framework regions that are murine amino acids are underlined in the humanized sequences.
  • FIG. 3 a represents plasmid map of pKCR5-3A4-HC-Variant 1.
  • the heavy chains of the humanized 3A4 variants were cloned in the same manner into the HindIII site of pK-CR5. Consequently the resulting plasmids are identical to pKCR5-3A4-HC variant 1 except for the sequence of the heavy chain immunoglobulin variable domain.
  • FIG. 3 b represents plasmid map of pMPG-CR5-3A4-LC-Variant 1.
  • the light chains of the humanized variants 1 and 2 of 3A4 antibody were cloned in the same manner into the BamHI site of pMPG-CR5. Consequently, the resulting plasmid is identical to pMPG-CR5-3A4-LC-Variant 1, except for the sequence of the light chain immunoglobulin variable domain.
  • FIG. 4 represents an analysis of antibody production after transient transfection in CHO cells.
  • Supernatant (13 days post-transfection) of CHOcTA cells transfected with the different combinations of light and heavy chains of humanized 3A4 antibody were analyzed by western blot. Quantification of antibody produced in the supernatants was determined after scanning the bands of the western blot against dilution of a known standard (human purified IgG antibody). Mr molecular weight marker (kDa).
  • FIG. 5 is a graph of a Superdex G75 gel filtration of recombinant KAAG1 sample.
  • KAAG1 was injected over the gel filtration and separated at 0.4 ml/min. The largest peak between fractions 15-19.
  • FIG. 6 is a Table listing the rate and affinity constants for the murine and humanized variants of the 3A4 antibody.
  • FIG. 7 a is an histogram illustrating the association rates (K a ) of the humanized antibodies.
  • FIG. 7 b is an histogram illustrating the dissociation rates (K d ) of the humanized antibodies.
  • FIG. 7 c is an histogram illustrating the affinity constants (K D ) of the humanized antibodies.
  • FIG. 8 a illustrates humanized 3A4 variants binding to KAAG1 in an ELISA. This figure shows the comparative binding of 3A4 humanized antibody variants and the murine 3A4. Concentration-dependent binding profiles of the humanized heavy chains (Hh1, Hh2, Hh3 and Hh4) assembled with the Lh1 light chain variant.
  • FIG. 8 b illustrates humanized 3A4 variants binding to KAAG1 in an ELISA. This figure shows the comparative binding of 3A4 humanized antibody variants and the murine 3A4. Concentration-dependent binding profiles of the humanized heavy chains (Hh1, Hh2, Hh3 and Hh4) assembled with the Lh2 light chain variant.
  • FIG. 9 illustrates humanized 3A4 variants binding to KAAG1 on the surface of cancer cells. This illustration shows the comparative binding activity of the humanized and the murine 3A4 antibodies on the unpermeabilized SKOV-3 ovarian cancer cells.
  • FIG. 10 shows a scan of a tissue microarray containing 139 biopsy samples obtained from breast cancer patients. The samples were blotted with the 3A4 anti-KAAG1 antibody and showed that the vast majority of the breast tumors expressed very high level of KAAG1 antigen. The confirmed TNBC samples are marked with an asterisk.
  • FIG. 11 shows the results of flow cytometry performed using MDA-MB-231, MDA-MB-436, MDA-MB-468, BT-20, BT-549, T47D, MCF-7 and 293-6E cell lines incubated with the 3A4 anti-KAAG1 antibody (blue bars of the histogram) compared with a control IgG (red bars).
  • This is a representative results from an experiment that was performed in triplicate.
  • the TNBC cell lines are marked with an asterisk.
  • FIG. 12 represents the detection of the KAAG1 antigen on the surface of MDA-MB-231 cells by flow cytometry with the 3A4 anti-KAAG1 antibody.
  • the fluorescence signal decreases with time when the cells were incubated at 37° C., which suggests that the KAAG1/antibody complex was internalized during the incubation when the cells were incubated with 3A4.
  • FIG. 13 represents the detection of the KAAG1 antigen on the surface of MDA-MB-436 cells by flow cytometry with the 3A4 anti-KAAG1 antibody.
  • the fluorescence signal decreases with time when the cells were incubated at 37° C., which suggests that the KAAG1/antibody complex was internalized during the incubation when the cells were incubated with 3A4.
  • FIG. 14 represents the detection of the KAAG1 antigen on the surface of BT-20 cells by flow cytometry with the 3A4 anti-KAAG1 antibody.
  • the fluorescence signal decreases with time when the cells were incubated at 37° C., which suggests that the KAAG1/antibody complex was internalized during the incubation when the cells were incubated with 3A4.
  • FIG. 15 represents the detection of the KAAG1 antigen on the surface of T47D cells by flow cytometry with the 3A4 anti-KAAG1 antibody.
  • the fluorescence signal decreases with time when the cells were incubated at 37° C., which suggests that the KAAG1/antibody complex was internalized during the incubation when the cells were incubated with 3A4.
  • FIG. 16 represents immunofluorescence data performed on live MDA-MB-231 cells with the 3A4 anti-KAAG1 antibody and the anti-LAMP1 antibody.
  • the immunofluorescence signal associated with the anti-KAAG1 antibody is shown in the left panel, the immunofluorescence signal associated LAMP1 is shown in the middle panel and the merging of both images is shown in the right panel.
  • FIG. 17 represents immunofluorescence data performed on live MDA-MB-231 cells with the 3A4 anti-KAAG1 antibody and the anti-LAMP1 antibody.
  • the immunofluorescence signal associated with the anti-KAAG1 antibody is shown in the left panel
  • the immunofluorescence signal associated LAMP1 is shown in the middle panel
  • the merging of both images is shown in the right panel.
  • the present invention provides a method of treating or detecting cancer or cancer cells (in vitro or in vivo) in an individual in need.
  • methods of treatment or detection may be carried out with an antibody capable of binding to KAAG1 or an antigen binding fragment thereof.
  • the individual in need may comprise, for example, an individual having or suspected of having cancer.
  • Such individual may have a cancer or cancer cells originating from a breast carcinoma.
  • the cancer or cancer cells may more particularly originate from a breast carcinoma characterized as being triple-negative or basal-like.
  • the individuals who may benefit from methods of treatment or detection described herein may include those suffering from breast carcinoma.
  • the breast carcinoma may comprise tumors cells showing a decrease or a lost in the expression of the estrogen receptor.
  • the breast carcinoma may comprise tumor cells showing a decrease or a lost in the expression of the progesterone receptor.
  • the breast carcinoma may comprise tumor cells showing a decrease or a lost in the expression of Her2.
  • the breast carcinoma may comprise tumor cells showing a decrease or a lost in Her2 overexpression.
  • the breast carcinoma may comprise tumor cells showing either 1) a decrease or a loss in expression of the estrogen receptor and the progesterone receptor, 2) a decrease or a loss in expression of the estrogen receptor and a decrease or a loss of Her2 overexpression, 3) a decrease or a loss in expression of the progesterone receptor and a decrease or a loss of Her2 overexpression or 4) a decrease or a loss in expression of the estrogen receptor, a decrease or a loss in expression of the progesterone receptor and a decrease or a loss of Her2 overexpression.
  • the breast carcinoma may comprise tumor cells showing either 1) a loss in expression of the estrogen receptor and the progesterone receptor, 2) a loss in expression of the estrogen receptor and a loss of Her2 expression, 3) a loss in expression of the progesterone receptor and a loss of Her2 expression or 4) a loss in expression of the estrogen receptor, a loss in expression of the progesterone receptor and a loss of Her2 expression.
  • the individual may carry breast cancer cells that are characterized as being triple-negative or may have a tumor categorized as being a triple-negative breast cancer.
  • the individual may carry breast cancer cells that are characterized as basal-like, or may have a tumor categorized as being a basal-like breast cancer.
  • an anti-KAAG1 Other individuals who would benefit from treatment with an anti-KAAG1 include those having carcinoma comprising tumors cells exhibiting an epithelial-to-mesenchymal transition (EMT) phenotype.
  • EMT epithelial-to-mesenchymal transition
  • EMT EMT
  • cytokeratin and ⁇ -catenin in the membrane
  • Snail Slug
  • Twist ZEB1, ZEB2, N-cadherin
  • vimentin ⁇ -smooth muscle actin
  • matrix metalloproteinases etc.
  • An EMT phenotype may also be distinguished by an increased capacity for migration, invasion of by resistance to anoikis/apoptosis. Cells that are undergoing epithelial-to-mesenchymal transition may thus be detected by a reduction of epithelial markers and apparition of mesenchymal markers or EMT phenotypes.
  • the method may thus comprise, for example, administering an antibody or antigen binding fragment which is capable of specific binding to KAAG1 to an individual in need.
  • the individual in need is preferentially selected on the basis of their tumor lacking ER expression, PgR expression and/or by the absence of HER2 protein over-expression. Clinical testing for these markers is usually performed using histopathologic methods (immunohistochemistry, FISH, etc.) and/or by gene expression studies (see for example Dent et al, 2007, Bernstein and Lacey, 2011).
  • the individual in need may thus be an individual who has received a diagnosis of triple-negative breast cancer or basal-like breast cancer.
  • the individual in need may be an individual which is unresponsive to hormonal therapy and/or to transtuzumab therapy (or other anti-Her2 antibodies).
  • the individual in need may be an individual carrying tumor cells that have the ability of undergoing epithelial-to-mesenchymal transition or that have acquired a mesenchymal phenotype.
  • the present invention thus provides a method of treating triple-negative breast cancer or basal-like breast cancer by administering an inhibitor of KAAG1 activity or expression to an individual in need.
  • the KAAG1 inhibitor may thus comprise an antibody described herein or an antigen binding fragment thereof.
  • the KAAG1 inhibitor may comprise a nucleotide sequence complementary to SEQ ID NO.:1 or to a fragment thereof. More particularly, the KAAG1 inhibitor may comprise a nucleotide sequence complementary to nucleotides 738 to 992 (inclusively) of SEQ ID NO.:1 or to a fragment thereof.
  • the inhibitor may include at least 10 consecutive nucleotides (at least 15, at least 20) which are complementary to SEQ ID NO.:1 or to nucleotides 738 to 992 (inclusively) of SEQ ID NO.:1. More particular type of KAAG1 inhibitor includes a siRNA which inhibit expression of SEQ ID NO.:1.
  • Suitable antibodies or antigen binding fragments include those that are capable of binding to KAAG1 at the surface of tumor cells. Such antibodies or antigen binding fragments thereof may preferentially bind an epitope included within amino acids 30 to 84 of KAAG1 inclusively.
  • antibodies or antigen binding fragments thereof may bind an epitope located within amino acids 36 to 60 (inclusively) or within amino acids 61 to 84 (inclusively) of KAAG1.
  • the epitope may particularly be located or comprised within amino acids 50 to 70, 50 to 65, 51 to 65, 52 to 65, 53 to 65, 54 to 65, 54 to 64, 54 to 63, 54 to 62, 54 to 61, 54 to 60, 50 to 62; 50 to 61, or 50 to 60 (inclusively or exclusively).
  • the antibody or antigen binding fragment may bind an epitope comprised within amino acids 50 to 70 of KAAG1.
  • the antibody or antigen binding fragment may bind an epitope comprised within amino acids 50 to 62 of KAAG1.
  • the antibody or antigen binding fragment may bind an epitope comprised within amino acids 54 to 65 of KAAG1.
  • Suitable antibodies for therapeutic treatment include for example, those which mediate antibody-dependent cell cytotoxicity.
  • Suitable antibodies for therapeutic treatment include those that are conjugated with a therapeutic moiety.
  • the antibody may be, for example, a monoclonal antibody, a chimeric antibody, a humanized antibody a human antibody or an antigen binding fragment thereof.
  • the present invention encompass administering an antibody or antigen binding fragment to an individual having a breast cancer characterized as being “triple negative breast cancer” or “basal-like breast cancer”.
  • Base-like breast cancer may include for example, a subtype of breast cancer comprising a heterogenous group of tumors characterized by the absence of or low levels of expression of estrogen receptors, very low prevalence of Her2 overexpression and expression of genes usually found in the basal or myoepithelial cells of the human breast. Such expression may be determined by microarray analysis.
  • “Triple-negative breast cancer” may include for example, a tumor characterized by lack of estrogen receptor (ER), progesterone receptor (PR) and Her2 expression. Some investigators accept tumors as being negative for expression of ER or PR only if less than 1% of the cells are positive for ER or PR expression; others consider tumors to be negative for ER or PR expression when up to 10% of cells are positive for expression. Different definitions of HER2-negativity have been used. The two most frequently adopted include tumors with immunohistochemical scores of 0/1+ or 2+ that are lacking HER2 gene amplification after in situ hybridization. Such expression may be especially determined by immunohistochemical staining.
  • the method of treatment includes administering a KAAG1 inhibitor to an individual in need.
  • KAAG1 inhibitor includes, for example, an antibody or antigen binding fragment thereof which specifically binds to KAAG1.
  • the most potent antibodies or antigen binding fragments may be those having a high affinity for KAAG1. It is also likely that the most potent antibodies or antigen binding fragments may be those that are internalized within a cells compartment such as, for example, a lysosome or an endosome.
  • the present invention especially encompasses antibodies or antigen binding fragments having a high affinity for KAAG1.
  • Suitable antibodies or antigen binding fragments include those that are capable of binding to KAAG1 at the surface of tumor cells with a high affinity. Such high affinity antibodies or antigen binding fragments thereof may preferentially bind an epitope included within amino acids 30 to 84 of KAAG1 inclusively.
  • high affinity antibodies or antigen binding fragments thereof may bind an epitope located within amino acids 36 to 60 (inclusively) or within amino acids 61 to 84 (inclusively) of KAAG1.
  • the high affinity antibodies or antigen binding fragments may bind, for example, an epitope may particularly be located or comprised within amino acids 50 to 70, 50 to 65, 51 to 65, 52 to 65, 53 to 65, 54 to 65, 54 to 64, 54 to 63, 54 to 62, 54 to 61, 54 to 60, 50 to 62; 50 to 61, or 50 to 60 (inclusively or exclusively).
  • the high affinity antibody or antigen binding fragment may bind an epitope comprised within amino acids 50 to 70 of KAAG1.
  • the high affinity antibody or antigen binding fragment may bind an epitope comprised within amino acids 50 to 62 of KAAG1.
  • the high affinity antibody or antigen binding fragment may bind an epitope comprised within amino acids 54 to 65 of KAAG1.
  • Preferred antibodies including high affinity antibodies are those than may be internalized in a cell or cell compartment (e.g., lysosomes or endosomes).
  • the ability of antibodies to be internalized may be determined by method known in the art such as for example and without limitation, by immunofluorescence studies similar to those performed herein.
  • Antibodies having CDRs identical to those of the 3A4 antibodies are particularly encompassed by the present invention.
  • antibodies having a light chain variable region and/or heavy chain variable region consensus sequences set forth in any of SEQ ID NOs.:186 to 188 and 191 to 193 and specific sequences set forth in SEQ ID No.:46, 48, 189, 190, or 194 to 198 are encompassed by the present invention.
  • antibodies having a light chain variable region and/or heavy chain variable region consensus sequences set forth in any of SEQ ID NO.: 188 and 196 or specific sequences set forth in SEQ ID NO.:46, 48, 189, 190, or 194 to 198 are particularly contemplated.
  • the antibodies or antigen binding fragments thereof may preferably be conjugated with a therapeutic moiety.
  • the antibodies or antigen binding fragments thereof may have a human constant region.
  • the antibodies or antigen binding fragments thereof may have a human IgG1 constant region.
  • the antibodies or antigen binding fragments thereof may have an IgG2 constant region.
  • the method of the present invention may also include administering a KAAG1 inhibitor such as an antibody (e.g., conjugated with a therapeutic moiety) or antigen binding fragment in combination with an anticancer agent such as for example, a small molecule drug, an antibody or antigen binding fragment binding to a target other than KAAG1, a chemotherapeutic or a cytotoxic agent.
  • a KAAG1 inhibitor such as an antibody (e.g., conjugated with a therapeutic moiety) or antigen binding fragment in combination with an anticancer agent such as for example, a small molecule drug, an antibody or antigen binding fragment binding to a target other than KAAG1, a chemotherapeutic or a cytotoxic agent.
  • an anticancer agent such as for example, a small molecule drug, an antibody or antigen binding fragment binding to a target other than KAAG1, a chemotherapeutic or a cytotoxic agent.
  • anticancer agent such as for example, doxorubicin, taxanes
  • KAAG1 inhibitors such as antisense-based therapeutics (siRNA, antisenses, ribozymes, etc.).
  • antibody or antigen binding fragment or similar terms such as “antibodies and antigen binding fragments” encompasses, for example “variant antibody or antigen binding fragment” such as, for example, “humanized antibody or antigen binding fragment”.
  • antibody refers to intact antibody, monoclonal or polyclonal antibodies.
  • antibody also encompasses multispecific antibodies such as bispecific antibodies.
  • Human antibodies are usually made of two light chains and two heavy chains each comprising variable regions and constant regions.
  • the light chain variable region comprises 3 CDRs, identified herein as CDRL1, CDRL2 and CDRL3 flanked by framework regions.
  • the heavy chain variable region comprises 3 CDRs, identified herein as CDRH1, CDRH2 and CDRH3 flanked by framework regions.
  • antigen-binding fragment refers to one or more fragments of an antibody that retain the ability to bind to an antigen (e.g., KAAG1, secreted form of KAAG1 or variants thereof). It has been shown that the antigen-binding function of an antibody can be performed by fragments of an intact antibody.
  • an antigen e.g., KAAG1, secreted form of KAAG1 or variants thereof. It has been shown that the antigen-binding function of an antibody can be performed by fragments of an intact antibody.
  • binding fragments encompassed within the term “antigen-binding fragment” of an antibody include (i) a Fab fragment, a monovalent fragment consisting of the V L , V H , C L and C H1 domains; (ii) a F(ab′) 2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the V H and C H1 domains; (iv) a Fv fragment consisting of the V L and V H domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341:544-546), which consists of a V H domain; and (vi) an isolated complementarity determining region (CDR), e.g., V H CDR3.
  • CDR complementarity determining region
  • the two domains of the Fv fragment, V L and V H are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single polypeptide chain in which the V L and V H regions pair to form monovalent molecules (known as single chain Fv (scFv); see e.g., Bird et al. (1988) Science 242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883).
  • single chain Fv single chain Fv
  • Such single chain antibodies are also intended to be encompassed within the term “antigen-binding fragment” of an antibody.
  • the antigen-binding fragments include binding-domain immunoglobulin fusion proteins comprising (i) a binding domain polypeptide (such as a heavy chain variable region, a light chain variable region, or a heavy chain variable region fused to a light chain variable region via a linker peptide) that is fused to an immunoglobulin hinge region polypeptide, (ii) an immunoglobulin heavy chain CH2 constant region fused to the hinge region, and (iii) an immunoglobulin heavy chain CH3 constant region fused to the CH2 constant region.
  • the hinge region may be modified by replacing one or more cysteine residues with serine residues so as to prevent dimerization.
  • binding-domain immunoglobulin fusion proteins are further disclosed in US 2003/0118592 and US 2003/0133939. These antibody fragments are obtained using conventional techniques known to those with skill in the art, and the fragments are screened for utility in the same manner as are intact antibodies.
  • a typical antigen binding site is comprised of the variable regions formed by the pairing of a light chain immunoglobulin and a heavy chain immunoglobulin.
  • the structure of the antibody variable regions is very consistent and exhibits very similar structures.
  • These variable regions are typically comprised of relatively homologous framework regions (FR) interspaced with three hypervariable regions termed Complementarity Determining Regions (CDRs).
  • CDRs Complementarity Determining Regions
  • the overall binding activity of the antigen binding fragment is often dictated by the sequence of the CDRs.
  • the FRs often play a role in the proper positioning and alignment in three dimensions of the CDRs for optimal antigen binding.
  • high affinity refers to an affinity of 10 nM or less.
  • high affinity especially includes antibodies having an affinity of 5 nM or less.
  • high affinity even more particularly includes antibodies having an affinity of 1 nM or less, or 0.1 nM or less.
  • Antibodies and/or antigen binding fragments of the present invention may originate, for example, from a mouse, a rat or any other mammal or from other sources such as through recombinant DNA technologies.
  • An-KAAG1 antibodies were initially isolated from Fab libraries for their specificity towards the antigen of interest. Exemplary methods on how to convert Fab into full immunoglobulins are provided herein.
  • variable regions described herein may be fused with constant regions of a desired species thereby allowing recognition of the antibody by effector cells of the desired species.
  • the constant region may originate, for example, from an IgG1, IgG2, IgG3, or IgG4 subtype. Cloning or synthesizing a constant region in frame with a variable region is well within the scope of a person of skill in the art and may be performed, for example, by recombinant DNA technology.
  • antibodies that bind to KAAG1 may be of the IgG1, IgG2, IgG3, or IgG4 subtype. More specific embodiments of the invention relates to an antibody of the IgG1 subtype or especially human IgG1 subtype. Other specific embodiments of the invention relates to an antibody of the IgG2 subtype or especially of the human IgG2 subtype.
  • the antibody may be a humanized antibody of the IgG1 subtype subtype or especially human IgG1 subtype.
  • the antibody may be a humanized antibody of the IgG2 subtype or especially of the human IgG2 subtype.
  • the antibody may be, for example, biologically active in mediating antibody-dependent cellular cytotoxicity (ADCC), complement-mediated cytotoxicity (CMC), or associated with immune complexes.
  • ADCC antibody-dependent cellular cytotoxicity
  • CMC complement-mediated cytotoxicity
  • the typical ADCC involves activation of natural killer (NK) cells and is reliant on the recognition of antibody-coated cells by Fc receptors on the surface of the NK cells.
  • the Fc receptors recognize the Fc domain of antibodies such as is present on IgG1, which bind to the surface of a target cell, in particular a cancerous cell that expresses an antigen, such as KAAG1.
  • IgG1 natural killer
  • KAAG1 antigen
  • the present invention described a collection of antibodies that bind to KAAG1 or to a KAAG1 variant.
  • the antibodies may be selected from the group consisting of polyclonal antibodies, monoclonal antibodies such as chimeric or humanized antibodies, antibody fragments such as antigen binding fragments, single chain antibodies, domain antibodies, and polypeptides with an antigen binding region.
  • the isolated antibody or antigen binding fragment of the present invention may be capable of inducing killing (elimination, destruction, lysis) of KAAG1-expressing tumor cells or KAAG1 variant-expressing tumor cells (e.g., in an ADCC-dependent manner).
  • the isolated antibody or antigen binding fragment of the present invention may especially be characterized by its capacity of reducing spreading of tumor cells expressing KAAG1 or a KAAG1 variant.
  • the isolated antibody or antigen binding fragment of the present invention may be characterized by its capacity of decreasing or impairing formation of tumors expressing KAAG1 or a KAAG1 variant.
  • the isolated antibody or antigen binding fragment may comprise amino acids of a constant region, which may originate, for example, from a human antibody.
  • the isolated antibody or antigen binding fragment may comprise framework amino acids of a human antibody.
  • the 3D3, 3A4, 3G10 and 3C4 were selected for in vitro and/or in vivo biological testing.
  • the 3A4 antibody appeared to have the best characteristics.
  • the 3A4 antibody when conjugated with a therapeutic moiety e.g. a cytotoxic agent
  • a therapeutic moiety e.g. a cytotoxic agent
  • the antibody or antigen binding fragment may comprise any individual CDR or a combination of CDR1, CDR2 and/or CDR3 of the light chain variable region.
  • the CDR3 may more particularly be selected.
  • Combination may include for example, CDRL1 and CDRL3; CDRL1 and CDRL2; CDRL2 and CDRL3 and; CDRL1, CDRL2 and CDRL3.
  • the antibody or antigen binding fragment may comprise any individual CDR or a combination of CDR1, CDR2 and/or CDR3 of the heavy chain variable region.
  • the CDR3 may more particularly be selected.
  • Combination may include for example, CDRH1 and CDRH3; CDRH1 and CDRH2; CDRH2 and CDRH3 and; CDRH1, CDRH2 and CDRH3.
  • the antibody or antigen binding fragment may comprise at least two CDRs of a CDRL1, a CDRL2 or a CDRL3.
  • the antibody or antigen binding fragment may comprise one CDRL1, one CDRL2 and one CDRL3.
  • the antibody or antigen binding fragment may comprise:
  • the antibody or antigen binding fragment may more preferably comprise one CDRL1, one CDRL2 and one CDRL3.
  • the antibody or antigen binding fragment may also more preferably comprise one CDRH1, one CDRH2 and one CDRH3.
  • an antibody or antigen-binding fragment may be reconstituted by screening a library of complementary variable regions using methods known in the art (Portolano et al. The Journal of Immunology (1993) 150:880-887, Clarkson et al., Nature (1991) 352:624-628).
  • Exemplary embodiments of the present invention encompass antibodies or antigen binding fragments having the CDRs of the light chain and/or heavy chains of the 3D3, 3A4, 3C4, 3G10, 3A2, 3F6, 3E8, 3E10, 3A9, 3B1, 3G5, 3B2, 368, 3G8, 3F7, 3E9, 3G12, 3C3, 3E12, 4A2, 3F10, 3F4, 3611, 3D1, 3C2, 3E6 or 3H3 antibodies. More particular embodiments of the invention include antibodies or antigen binding fragments having the CDRs of the light chain and/or heavy chains of the 3D3, 3A4, 3C4 or 3G10 antibodies.
  • inventions include antibodies or antigen binding fragments having the CDRs of the light chain and/or heavy chains of the 3A4 antibody.
  • the invention thus encompassed any monoclonal, chimeric, human, or humanized antibody comprising one or more CDRs of the 3A4 antibody.
  • Antibodies or antigen binding fragments that may be used in methods of the present invention include those having CDRs of the 3A4 antibody and may comprise, for example, a CDRH1 as set forth in SEQ ID NO.:49, a CDRH2 as set forth in SEQ ID NO.:50 or in SEQ ID NO.:212, a CDRH3 as set forth in SEQ ID NO.:51, a CDRL1 as set forth in SEQ ID NO.: 52, a CDRL2 as set forth in SEQ ID NO.:53 and a CDRL3 as set forth in SEQ ID NO.: 54.
  • the present invention therefore encompass, antibodies and antigen binding fragment which are capable of specific binding to KAAG1 and which may comprise sequences selected from the group consisting of:
  • exemplary embodiments of the invention encompass antibodies or antigen binding fragments having the light chain and/or heavy chains of the 3D3, 3A4, 3C4, 3G10, 3A2, 3F6, 3E8, 3E10, 3A9, 361, 3G5, 3B2, 368, 3G8, 3F7, 3E9, 3G12, 3C3, 3E12, 4A2, 3F10, 3F4, 3611, 3D1, 3C2, 3E6 or 3H3 antibodies. More particular embodiments of the invention include antibodies or antigen binding fragments having the light chain and/or heavy chains of the 3D3, 3A4, 3C4 or 3G10 antibodies. Even more particular embodiments of the invention include antibodies or antigen binding fragments having the light chain and/or heavy chains of the 3A4 antibody (humanized and non-humanized).
  • the present invention therefore encompass, antibodies and antigen binding fragment which are capable of specific binding to KAAG1 and which may comprise sequences selected from the group consisting of:
  • the framework region of the heavy and/or light chains described herein may be derived from one or more of the framework regions illustrated in the antibodies described herein.
  • the antibody or antigen binding fragments may thus comprise one or more of the CDRs described herein (e.g., selected from the specific CDRs or consensus CDRs of SEQ ID NO.:72 to 88 or CDR variants of SEQ ID NO.:89-102) and framework regions originating from those described herein.
  • the expected CDRs are shown in bold, while the framework regions are not.
  • Table 1 refers to the complete sequences of light and heavy chain of some of the anti-KAAG1 antibodies which were selected for biological testing.
  • 3D3 antibody interacts with a KAAG1 epitope spanned by amino acids 36-60, inclusively.
  • the 3G10 and 3A4 antibodies interact with a KAAG1 epitope spanned by amino acids 61-84, inclusively and the 3C4 antibody interacts with a KAAG1 epitope spanned by amino acids 1-35.
  • the 3G10 and 3A4 binds a similar region, the 3G10 antibody does not bind to KAAG1 as efficiently as the 3A4 antibody.
  • the light chain variable region of the specific combination provided above may be changed for any other light chain variable region.
  • the heavy chain variable region of the specific combination provided above may be changed for any other heavy chain variable region.
  • SEQ ID NOs. 103-154 correspond to the light chain and heavy chain variable regions of other antibodies which were shown to bind KAAG1.
  • the present invention also encompasses variants of the antibodies or antigen binding fragments described herein.
  • Variant antibodies or antigen binding fragments included are those having a variation in the amino acid sequence.
  • variant antibodies or antigen binding fragments included are those having at least one variant CDR (two, three, four, five or six variant CDRs, etc. or even twelve variant CDRs), a variant light chain variable region, a variant heavy chain variable region, a variant light chain and/or a variant heavy chain.
  • variant antibodies or antigen binding fragments included in the present invention are those having, for example, similar or improved binding affinity in comparison with the original antibody or antigen binding fragment.
  • variant applies to any of the sequence described herein and includes for example, a variant CDR (either CDRL1, CDRL2, CDRL3, CDRH1, CDRH2 and/or CDRH3), a variant light chain variable region, a variant heavy chain variable region, a variant light chain, a variant heavy chain, a variant antibody, a variant antigen binding fragment and a KAAG1 variant.
  • CDRs hypervariable regions
  • modifications in the framework region or even in the constant region are also contemplated.
  • Exemplary embodiments of CDR variants are provided in SEQ ID NOs.: 72-102.
  • Conservative substitutions may be made by exchanging an amino acid (of a CDR, variable chain, antibody, etc.) from one of the groups listed below (group 1 to 6) for another amino acid of the same group.
  • variants may be generated by substitutional mutagenesis and retain the biological activity of the polypeptides of the present invention. These variants have at least one amino acid residue in the amino acid sequence removed and a different residue inserted in its place.
  • one site of interest for substitutional mutagenesis may include a site in which particular residues obtained from various species are identical. Examples of substitutions identified as “conservative substitutions” are shown in Table 1A. If such substitutions result in a change not desired, then other type of substitutions, denominated “exemplary substitutions” in Table 1A, or as further described herein in reference to amino acid classes, are introduced and the products screened.
  • Substantial modifications in function or immunological identity are accomplished by selecting substitutions that differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation. (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
  • Naturally occurring residues are divided into groups based on common side chain properties:
  • group 1 hydrophobic: norleucine, methionine (Met), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile) (group 2) neutral hydrophilic: Cysteine (Cys), Serine (Ser), Threonine (Thr) (group 3) acidic: Aspartic acid (Asp), Glutamic acid (Glu) (group 4) basic: Asparagine (Asn), Glutamine (Gln), Histidine (His), Lysine (Lys), Arginine (Arg) (group 5) residues that influence chain orientation: Glycine (Gly), Proline (Pro); and (group 6) aromatic: Tryptophan (Trp), Tyrosine (Tyr), Phenylalanine (Phe)
  • Non-conservative substitutions will entail exchanging a member of one of these classes for another.
  • Variation in the amino acid sequence of the variant antibody or antigen binding fragment may include an amino acid addition, deletion, insertion, substitution etc., one or more modification in the backbone or side-chain of one or more amino acid, or an addition of a group or another molecule to one or more amino acids (side-chains or backbone).
  • Variant antibody or antigen binding fragment may have substantial sequence similarity and/or sequence identity in its amino acid sequence in comparison with that the original antibody or antigen binding fragment amino acid sequence.
  • the degree of similarity between two sequences is based upon the percentage of identities (identical amino acids) and of conservative substitution.
  • Blast2 sequence program Tropiana A. Tatusova, Thomas L. Madden (1999), “Blast 2 sequences—a new tool for comparing protein and nucleotide sequences”, FEMS Microbiol Lett. 174:247-250
  • blastp program BLOSUM62 matrix (open gap 11 and extension gap penalty 1; gapx dropoff 50, expect 10.0, word size 3) and activated filters.
  • Percent identity will therefore be indicative of amino acids which are identical in comparison with the original peptide and which may occupy the same or similar position.
  • Percent similarity will be indicative of amino acids that are identical and those that are replaced with conservative amino acid substitution in comparison with the original peptide at the same or similar position.
  • Variants of the present invention therefore comprise those which may have at least 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with an original sequence or a portion of an original sequence.
  • Exemplary embodiments of variants are those having at least 81% sequence identity to a sequence described herein and 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence similarity with an original sequence or a portion of an original sequence.
  • variants are those having at least 82% sequence identity to a sequence described herein and 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence similarity with an original sequence or a portion of an original sequence.
  • variants are those having at least 85% sequence identity to a sequence described herein and 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence similarity with an original sequence or a portion of an original sequence.
  • variants are those having at least 90% sequence identity to a sequence described herein and 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence similarity with an original sequence or a portion of an original sequence.
  • Additional exemplary embodiments of variants are those having at least 95% sequence identity to a sequence described herein and 95%, 96%, 97%, 98%, 99% or 100% sequence similarity with an original sequence or a portion of an original sequence.
  • variants are those having at least 97% sequence identity to a sequence described herein and 97%, 98%, 99% or 100% sequence similarity with an original sequence or a portion of an original sequence.
  • Table 1B illustrating exemplary embodiments of individual variants encompassed by the present invention and comprising the specified % sequence identity and % sequence similarity. Each “X” is to be construed as defining a given variant.
  • the present invention encompasses CDRs, light chain variable regions, heavy chain variable regions, light chains, heavy chains, antibodies and/or antigen binding fragments which comprise at least 70% identity or at least 80% identity with the sequence described herein.
  • the present invention therefore encompass, antibodies and antigen binding fragment which are capable of specific binding to KAAG1 and which may comprise sequences selected from the group consisting of:
  • the variant antibodies or antigen binding fragments may comprise CDRs that are identical to those of the corresponding light chain and/or heavy chain variable region.
  • the variant antibodies or antigen binding fragments may comprise variant CDR(s).
  • exemplary embodiments of a variant antibody or antigen binding fragment of the present invention are those comprising a light chain variable region comprising a sequence which is at least 70%, 75%, 80% identical to SEQ ID NOs.:16, 20, 24, 103, 106 or 121.
  • the CDRs of such variant may be identical to those of the corresponding non-variant (wild type sequence) antibody or antigen binding fragment or may vary by 1-3 amino acids.
  • variant antibody light chain variable region encompasses a light chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:16 and having for example from 1 to 22 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:16.
  • a SEQ ID NO.:16 variant is provided in SEQ ID NO.:168.
  • An exemplary embodiment of a variant antibody light chain variable region encompasses a light chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:20 and having for example from 1 to 22 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:20.
  • An exemplary embodiment of a variant antibody light chain variable region encompasses a light chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:24 and having for example from 1 to 21 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:24.
  • a SEQ ID NO.:24 variant is provided in SEQ ID NO.:172.
  • An exemplary embodiment of a variant antibody light chain variable region encompasses a light chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:103 and having for example from 1 to 22 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:103.
  • An exemplary embodiment of a variant antibody light chain variable region encompasses a light chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:106 and having for example from 1 to 22 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:106.
  • An exemplary embodiment of a variant antibody light chain variable region encompasses a light chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:121 and having for example from 1 to 21 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:121.
  • the variant antibody light chain variable region may comprise amino acid deletions or additions (in combination or not with amino acid substitutions). Often 1, 2, 3, 4 or 5 amino acid deletions or additions may be tolerated.
  • variant antibody or antigen binding fragment of the present invention are those comprising a heavy chain variable region comprising a sequence which is at least 70%, 75%, 80% identical to 18, 22, 26, 126, 138 or 145.
  • the CDRs of such variant may be identical to those of the corresponding non-variant (wild type sequence) antibody or antigen binding fragment or may vary by 1-3 amino acids.
  • An exemplary embodiment of a variant antibody heavy chain variable region encompasses a heavy chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:18 and having, for example, from 1 to 22 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:18.
  • a SEQ ID NO.:18 variant is provided in SEQ ID NO.:169.
  • An exemplary embodiment of a variant antibody heavy chain variable region encompasses a heavy chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:22 and having, for example, from 1 to 23 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:22.
  • An exemplary embodiment of a variant antibody heavy chain variable region encompasses a heavy chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:26 and having, for example, from 1 to 23 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:26.
  • a SEQ ID NO.:26 variant is provided in SEQ ID NO.:173.
  • An exemplary embodiment of a variant antibody heavy chain variable region encompasses a heavy chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:126 and having, for example, from 1 to 23 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:126.
  • An exemplary embodiment of a variant antibody heavy chain variable region encompasses a heavy chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:145 and having, for example, from 1 to 23 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:145.
  • An exemplary embodiment of a variant antibody heavy chain variable region encompasses a heavy chain variable region having CDR amino acid sequences that are 100% identical to the CDR amino acid sequence of SEQ ID NO.:138 and having, for example, from 1 to 22 amino acid modifications (e.g., conservative or non-conservative amino acid substitutions) in its framework region in comparison with the framework region of SEQ ID NO.:138.
  • the variant antibody heavy chain variable region may comprise amino acid deletions or additions (in combination or not with amino acid substitutions). Often 1, 2, 3, 4 or 5 amino acid deletions or additions may be tolerated.
  • polypeptides, antibodies or antigen binding fragments comprising variable chains having at least one conservative amino acid substitution in at least one of the CDRs described herein (in comparison with the original CDR).
  • the present invention also encompasses are polypeptides, antibodies or antigen binding fragments comprising variable chains having at least one conservative amino acid substitution in at least two of the CDRs (in comparison with the original CDRs).
  • the present invention also encompasses are polypeptides, antibodies or antigen binding fragments comprising variable chains having at least one conservative amino acid substitution in the 3 CDRs (in comparison with the original CDRs).
  • the present invention also encompasses are polypeptides, antibodies or antigen binding fragments comprising variable chains having at least two conservative amino acid substitutions in at least one of the CDRs (in comparison with the original CDRs).
  • the present invention also encompasses are polypeptides, antibodies or antigen binding fragments comprising variable chains having at least two conservative amino acid substitutions in at least two of the CDRs (in comparison with the original CDRs).
  • the present invention also encompasses are polypeptides, antibodies or antigen binding fragments comprising variable chains having at least two conservative amino acid substitutions in the 3 CDRs (in comparison with the original CDRs).
  • the present invention therefore provides in an exemplary embodiment, an isolated antibody or antigen binding fragment comprising a light chain variable region having;
  • the present invention therefore provides in an exemplary embodiment, an isolated antibody or antigen binding fragment comprising a heavy chain variable region having;
  • the antibody may comprise a CDRL1 sequence comprising or consisting of formula:
  • X 1a may be a basic amino acid
  • X 2a may be a basic amino acid
  • X 3a may be H, Y or N;
  • X 4a may be S, T, N or R;
  • X 5a may be absent, S or N;
  • X 6a may be D, F or N;
  • X 7a may be G or Q
  • X 8a may be K, L or N;
  • X 9a may be T or N
  • X 10a may be an aromatic amino acid, and
  • X 11a may be A, N, E or Y.
  • X 1a may be K or R.
  • X 2a may be Q or K.
  • X 3 may be N or H.
  • X 10a may be Y or F.
  • CDRL1 of SEQ ID NO.:72 where: X 1a is K; X 2a is Q; X 3a is N; X 3a is H; X 4a is S; X 4a is T; X 5a is S; X 5a is absent; X 6a is N; X 7a is Q; X 7a is G; X 8a is K; X 9a is N; X 9a is T; X 10a is Y; or X 11a is A.
  • the antibody may comprise a CDRL1 sequence comprising or consisting of formula:
  • X 1b may be an hydrophobic amino acid
  • X 2b may be G or H
  • X 3b may be T, N or R;
  • X 4b may be F, Y or A;
  • X 5b may be an hydrophobic amino acid, and
  • X 6b may be N or A.
  • X 1b may be V or I.
  • X 5b may be V or L.
  • CDRL1 are provided in SEQ ID NOs. 89 and 90.
  • the antibody may comprise a CDRL2 sequence comprising or consisting of formula:
  • X 1c is A or G
  • X 2c is R or T, and
  • X 3c is E, K or A.
  • X 1c may be A and X 2c may be T.
  • X 1c may be A and X 2c may be R.
  • the antibody may comprise a CDRL2 sequence comprising or consisting of formula:
  • X 1d may be L or K
  • X 2d may be a basic amino acid
  • X 3d may be L or R and
  • X 4d may be D or F.
  • X 2d may be K or N.
  • the antibody may comprise a CDRL2 sequence comprising or consisting of formula:
  • X 1e may be a basic amino acid, and
  • X 2e may be D or A.
  • X 1e may be R or H.
  • CDRL2 are provided in SEQ ID NOs.: 91-93.
  • the antibody may comprise a CDRL3 sequence comprising or consisting of formula:
  • X 1f may be Q or L
  • X 2f may be an aromatic amino acid
  • X 3f may be D, F or Y;
  • X 4f may be E, A, N or S, and
  • X 5f may be I, F or T.
  • X 2f may be Y or H.
  • X 3f may be Y or D.
  • X 5f may be I or T.
  • the antibody may comprise a CDRL3 sequence comprising or consisting of formula:
  • X 1g may be an aromatic amino acid
  • X 2g may be N or S, and
  • X 3g may be I or T.
  • X 1g may be F or Y
  • the antibody may comprise a CDRL3 sequence comprising or consisting of formula:
  • X 1h may be an aromatic amino acid
  • X 2h may be a neutral hydrophilic amino acid
  • X 3h may be F or V, and
  • X 4h may be R or L.
  • X 1h may be W or F.
  • X 2h may be S or T.
  • CDRL3 are provided in SEQ ID NOs. 94 and 95.
  • the antibody may comprise a CDRH1 sequence comprising or consisting of formula:
  • X 1i may be T, I or K;
  • X 2i may be a neutral hydrophilic amino acid
  • X 3i may be an acidic amino acid
  • X 4i may be E, N or D, and
  • X 5i may be hydrophobic amino acid.
  • X 2i may be T or S.
  • X 3i may be D or E.
  • X 4i may be N or E.
  • X 5i may be M, I or v.
  • CDRH1 of SEQ ID NO.:80 where X 2i is T; X 3i is D; X 4i is E; X 5i is I or X 5i is M.
  • CDRH1 is provided in SEQ ID NOs.: 96 and 97.
  • the antibody may comprise a CDRH2 sequence comprising or consisting of formula:
  • X 1j may be V or G
  • X 2j may be a hydrophobic amino acid
  • X 3j may be A, G or E;
  • X 4j may be R, G, D, A, S, N or V, and;
  • X 5j may be a hydrophobic amino acid.
  • X 2j may be I or L.
  • X 5j may be A or V.
  • CDRH2 of SEQ ID NO.:81 where X 1j is V; X 2j is I; X 3j is E; X 4j is D or X 5j is A.
  • the antibody may comprise a CDRH2 sequence comprising or consisting of formula:
  • X 1k may be an hydrophobic amino acid
  • X 2k may be A, E or G;
  • X 3k may be R, G, A, S, N V or D.
  • X 1k may be L or I.
  • the antibody may comprise a CDRH2 sequence comprising or consisting of formula:
  • X1 l may be S or N;
  • X 2l may be an aromatic amino acid
  • X 3l may be D, E or N;
  • X4 l may be a D or H
  • X 5l may be Y, S or N;
  • X 6l may be D, E or N.
  • X 3l may be D or N.
  • X 6l may be D or N.
  • CDRH2 of SEQ ID NO.:83 where X 2l is F or Y, X 3l is N, X 4l is D or X 6l is N.
  • the antibody may comprise a CDRH2 sequence comprising or consisting of formula:
  • X 1m may be N or Y, and
  • X 2m may be E, D or N.
  • X 2m may be D or N.
  • the antibody may comprise a CDRH2 sequence comprising or consisting of formula:
  • X 1n may be N or Y
  • X 2n may be G or T and
  • X 3n may be I or T.
  • CDRH2 are provided in SEQ ID NOs. 98 and 99.
  • the antibody may comprise a CDRH3 sequence comprising or consisting of formula:
  • X 1o may be G or S
  • X 2o may be Y or H, and
  • X 3o may be A or S.
  • the antibody may comprise a CDRH3 sequence comprising or consisting of formula:
  • X 1p may be G or S and
  • X 2p may be absent or M.
  • the antibody may comprise a CDRH3 sequence comprising or consisting of formula:
  • X 1q may be R or W
  • X 2q may be an aromatic amino acid and
  • X 3q may be a basic amino acid
  • X 2q may be W or F.
  • X 3q may be Q or N.
  • Variant antibodies or antigen binding fragments encompassed by the present invention include those that may comprise an insertion, a deletion or an amino acid substitution (conservative or non-conservative). These variants may have at least one amino acid residue in its amino acid sequence removed and a different residue inserted in its place.
  • Exemplary embodiments of variant antibodies and antigen binding fragments of the present invention are a group of antibodies and antigen binding fragments capable of binding to KAAG1 and characterized herein as being humanized.
  • the humanized antibodies and antigen binding fragments of the present invention includes more particularly, humanized 3D3, 3A4 or 3C4 antibodies and antigen binding fragments.
  • the humanized 3D3, 3A4 or 3C4 antibodies have at least one amino acid difference in a framework region in comparison with the monoclonal 3D3, 3A4 or 3C4 antibody.
  • Humanized 3A4 antibodies having CDRs identical to those of the monoclonal 3A4 antibody (VL: SEQ ID NO.:48, VH: SEQ ID NO.:46) were generated and tested. These humanized antibodies comprise up to 11 amino acid substitutions (from one to eleven) in the variable light chain framework region and up to 23 amino acid substitutions (from one to twenty-three) in the variable heavy chain framework region in comparison with the monoclonal 3A4 antibody. The applicant has shown that these humanized 3A4 antibodies bind to KAAG1 as efficiently as the monoclonal 3A4 antibody.
  • variant antibody or antigen binding fragments include those having a light chain variable region as set forth in SEQ ID NO.:186:
  • amino acids identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:48.
  • the amino acid substitution may be, for example, an amino acid found at a corresponding position of a natural human antibody or a human antibody consensus.
  • the amino acid substitution may be, for example conservative.
  • variant antibody or antigen binding fragment include those having a light chain variable region as set forth in SEQ ID NO.:187:
  • X e2 may be A or P;
  • X e3 may be neutral hydrophilic amino acid
  • X e4 may be L or P;
  • X e5 may be an acidic amino acid
  • X e6 may be Q or P
  • X e7 may be a basic amino acid
  • X e8 may be a hydrophobic amino acid
  • X e9 may be A or Q
  • X e10 may be a basic amino acid; or Wherein X e11 may be a hydrophobic amino acid, wherein at least one of the amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:48.
  • variant antibody or antigen binding fragment include those having a light chain variable region as set forth in SEQ ID NO.:188:
  • X E1 may be V or I
  • X E2 may be A or P
  • X E3 may be S or T
  • X E4 may be L or P
  • X E5 may be D or E
  • X E6 may be Q or P
  • X E7 may be K or Q
  • X E8 may be L or V
  • X E9 may be A or Q
  • X E10 may be R or K or
  • X E11 may be L or I
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:48.
  • the light chain variable domain variant may have a sequence as set forth in SEQ ID NO.:189 or 190:
  • SEQ ID NO.: 189 DIVMTQTPLSLPVTPGEPASISCRSSQSLLHSNGNTYLEWYLQKPGQSPQ LLIYTVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVP LTFGQGTKLEIK.
  • SEQ ID NO.: 190 DVVMTQTPLSLPVTPGEPASISCRSSQSLLHSNGNTYLEWYLQKPGQSPK LLIYTVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVP LTFGQGTKLEIK.
  • variant antibody or antigen binding fragments include those having a heavy chain variable region as set forth in SEQ ID NO.:191.
  • amino acid substitution may be, for example, an amino acid found at a corresponding position of a natural human antibody or a human antibody consensus.
  • the amino acid substitution may be, for example conservative.
  • variant antibody or antigen binding fragment include those having a heavy chain variable region as set forth in SEQ ID NO.:192:
  • X bf2 may be P or A
  • X f3 may be a hydrophobic amino acid
  • X f4 may be V or K
  • X f5 may be a hydrophobic amino acid
  • X f6 may be a basic amino acid
  • X f7 may be S or A
  • X f8 may be H or P
  • X f9 may be a basic amino acid
  • X f10 may be S or G
  • X f11 may be a hydrophobic amino acid
  • X f12 may be a basic amino acid
  • X f13 may be a hydrophobic amino acid
  • X f14 may be I or T
  • X f15 may be a hydrophobic amino acid
  • X f16 may be a hydrophobic amino acid
  • X f17 may be K or T
  • X f18 may be a neutral hydrophilic amino acid
  • X f19 may be Q or E;
  • X f20 may be N or S
  • X f21 may be T or R;
  • X f22 may be a neutral hydrophilic amino acid
  • X f23 may be S or L
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:46.
  • variant antibody or antigen binding fragment include those having a heavy chain variable region as set forth in SEQ ID NO.:193:
  • X F1 may be I or V
  • X F2 may be P or A
  • X F3 may be M or V
  • X F4 may be V or K
  • X F5 may be M or V
  • X F6 may be K or R
  • X F7 may be S or A
  • X F8 may be H or P
  • X F9 may be K or Q
  • X F10 may be S or G
  • X F11 may be I or M
  • X F12 may be K or R
  • X F13 may be A or V
  • X F14 may be I or T
  • X F15 may be L or I
  • X F16 may be V or A
  • X F17 may be K or T
  • X F18 may be S or T
  • X F19 may be Q or E;
  • X F20 may be N or S
  • X F21 may be T or R
  • X F22 may be S or T;
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:46.
  • the heavy chain variable domain variant may have a sequence as set forth in any one of SEQ ID NO. 194 to 197:
  • SEQ ID NO.: 194 QVQLVQSGAEVKKPGASVKVSCKASGYTFTDDYMSWVRQAPGQGLEWMGD INPYNGDTNYNQKFKGRVTITADTSTSTAYMELSSLRSEDTAVYYCARDP GAMDYWGQGTLVTVSS.
  • SEQ ID NO.: 195 QIQLVQSGAEVKKPGASVKVSCKASGYTFTDDYMSWVRQAPGQGLEWMGD INPYNGDTNYNQKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARDP GAMDYWGQGTLVTVSS.
  • the humanized 3D3 antibody may have a light chain variable region of formula:
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:16.
  • the amino acid substitution may be, for example conservative.
  • the humanized 3D3 antibody may have a light chain variable region of formula:
  • the humanized 3D3 antibody may have a light chain variable region of formula:
  • X a1 may be, for example, D or S;
  • X a2 may be, for example, L or I;
  • X a3 may be, for example, E or Q;
  • X a4 may be, for example, R or K;
  • X a5 may be, for example, A or V;
  • X a6 may be, for example, I or M;
  • X a7 may be, for example, P or S;
  • X a8 may be, for example, V or I;
  • X a9 may be, for example, S or I;
  • X a10 may be, for example, L or V;
  • X a11 may be, for example, V or L;
  • X a12 may be, for example, V or D;
  • X a13 may be, for example, Y or F;
  • X a14 may be, for example, Q or A and
  • X a15 is for example, I or L.
  • the humanized 3D3 antibody may have a heavy chain variable region of formula:
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:18.
  • the amino acid substitution may be, for example conservative.
  • the humanized 3D3 antibody may have a heavy chain variable region of formula:
  • the humanized 3D3 antibody may have a heavy chain variable region of formula:
  • X b1 may be, for example, V or Q;
  • X b2 may be, for example, G or V;
  • X b3 may be, for example, V or L;
  • X b4 may be, for example, K or V;
  • X b5 may be, for example, K or R;
  • X b6 may be, for example, K or T;
  • X b7 may be, for example, V or L;
  • X b8 may be, for example, R or K;
  • X b9 may be, for example, A or T;
  • X b10 may be, for example, G or V;
  • X b11 may be, for example, Q or H;
  • X b12 may be, for example, M or I;
  • X b13 may be, for example, R or K;
  • X b14 may be, for example, V or A;
  • X b15 may be, for example, I or L;
  • X b16 may be, for example, T or I;
  • X b17 may be, for example, T or S;
  • X b18 may be, for example, T or S;
  • X b19 may be, for example, L or T;
  • X b20 may be, for example, V or L.
  • the humanized 3C4 antibody may have a light chain variable region of formula:
  • the humanized 3C4 antibody may have a light chain variable region of formula:
  • the humanized 3C4 antibody may have a light chain variable region of formula:
  • X c1 may be, for example, T or S;
  • X c2 may be, for example, L or M;
  • X c3 may be, for example, S or Y;
  • X c4 may be, for example, V or L;
  • X c5 may be, for example, D or E;
  • X c6 may be, for example, A or S;
  • X c7 may be, for example, T or Q;
  • X c8 may be, for example, T or S;
  • X c9 may be, for example, Q or E;
  • X c10 may be, for example, P or F;
  • X c11 may be, for example, F or L;
  • X c12 may be, for example, A or G;
  • X c13 may be, for example, T or I;
  • X c14 may be, for example, Q or A;
  • X c15 may be, for example, I or L and;
  • X c16 may be, for example, K or R.
  • the humanized 3C4 antibody may have a heavy chain variable region of formula:
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:26.
  • the amino acid substitution may be, for example conservative.
  • the humanized 3C4 antibody may have a heavy chain variable region of formula:
  • the humanized 3C4 antibody may have a heavy chain variable region of formula:
  • X d1 may be, for example, G or D;
  • X d2 may be, for example, T or S;
  • X d3 may be, for example, S or T;
  • X d4 may be, for example, H or F;
  • X d5 may be, for example, K or N;
  • X d6 may be, for example, G or K;
  • X d7 may be, for example, I or M;
  • X d8 may be, for example, V or I;
  • X d9 may be, for example, T or S;
  • X d10 may be, for example, S or T;
  • X d11 may be, for example, S or F;
  • X d12 may be, for example, K or Q;
  • X d13 may be, for example, S or N;
  • X d14 may be, for example, A or T;
  • X d15 may be, for example, A or E;
  • X d16 may be, for example, V or T and;
  • an antibody or antigen binding fragment thereof capable of specific binding to Kidney associated antigen 1 (KAAG1) which may have a light chain variable region at least 70% identical to SEQ ID NO.:16 and/or a heavy chain variable region at least 70% identical to SEQ ID NO.:18.
  • the antibody or antigen binding fragment thereof may also comprise at least one amino acid substitution in comparison with SEQ ID NO.:16 or SEQ ID NO.:18.
  • the present invention also provides in another aspect, an antibody or antigen binding fragment thereof which may have a light chain variable region at least 70% identical to SEQ ID NO.:24 and/or a heavy chain variable region at least 70% identical to SEQ ID NO.:26.
  • the antibody or antigen binding fragment thereof may also comprise at least one amino acid substitution in comparison with SEQ ID NO.:24 or SEQ ID NO.:26.
  • the present invention also provides in another aspect, an antibody or antigen binding fragment thereof which may have a light chain variable region at least 70% identical to SEQ ID NO.:48 and/or a heavy chain variable region at least 70% identical to SEQ ID NO.:46.
  • the antibody or antigen binding fragment thereof may also comprise at least one amino acid substitution in comparison with SEQ ID NO.:48 or SEQ ID NO.:46.
  • the amino acid substitution may be outside of a complementarity determining region (CDR).
  • CDR complementarity determining region
  • An antibody or antigen binding fragment having such an amino acid sequence encompasses, for example, a humanized antibody or antigen binding fragment.
  • the term “from one to twenty-five” includes every individual values and ranges such as for example, 1, 2, 3, and up to 25; 1 to 25; 1 to 24, 1 to 23, 1 to 22, 1 to 21, 1 to 20, 1 to 19; 1 to 18; 1 to 17; 1 to 16; 1 to 15 and so on; 2 to 25, 2 to 24, 2 to 23, 2 to 22, 2 to 21, 2 to 20; 2 to 19; 2 to 18; 2 to 17 and so on; 3 to 25, 3 to 24, 3 to 23, 3 to 22, 3 to 21, 3 to 20; 3 to 19; 3 to 18 and so on; 4 to 25, 4 to 24, 4 to 23, 4 to 22, 4 to 21, 4 to 20; 4 to 19; 4 to 18; 4 to 17; 4 to 16 and so on; 5 to 25, 5 to 24, 5 to 23, 5 to 22, 5 to 21, 5 to 20; 5 to 19; 5 to 18; 5 to 17 and so on, etc.
  • the term “from one to twenty-three” includes every individual values and ranges such as for example, 1, 2, 3, and up to 23; 1 to 23, 1 to 22, 1 to 21, 1 to 20, 1 to 19; 1 to 18; 1 to 17; 1 to 16; 1 to 15 and so on; 2 to 23, 2 to 22, 2 to 21, 2 to 20; 2 to 19; 2 to 18; 2 to 17 and so on; 3 to 23, 3 to 22, 3 to 21, 3 to 20; 3 to 19; 3 to 18 and so on; 4 to 23, 4 to 22, 4 to 21, 4 to 20; 4 to 19; 4 to 18; 4 to 17; 4 to 16 and so on; 5 to 25, 5 to 24, 5 to 23, 5 to 22, 5 to 21, 5 to 20; 5 to 19; 5 to 18; 5 to 17 and so on, etc.
  • the term “from one to twenty” includes every individual values and ranges such as for example, 1, 2, 3, and up to 20; 1 to 20; 1 to 19; 1 to 18; 1 to 17; 1 to 16; 1 to 15 and so on; 2 to 20; 2 to 19; 2 to 18; 2 to 17 and so on; 3 to 20; 3 to 19; 3 to 18 and so on; 4 to 20; 4 to 19; 4 to 18; 4 to 17; 4 to 16 and so on; 5 to 20; 5 to 19; 5 to 18; 5 to 17 and so on, etc.
  • the term “from one to fifteen” includes every individual values and ranges such as for example, 1, 2, 3, and up to 15; 1 to 15; 1 to 14; 1 to 13; 1 to 12; 1 to 11; 1 to 10 and so on; 2 to 15; 2 to 14; 2 to 13; 2 to 12 and so on; 3 to 15; 3 to 14; 3 to 13 and so on; 4 to 15; 4 to 14; 4 to 13; 4 to 12; 4 to 11 and so on; 5 to 15; 5 to 14; 5 to 13; 5 to 12 and so on, etc.
  • the term “from one to eleven” includes every individual values and ranges such as for example, 1, 2, 3, and up to 11; 1 to 11; 1 to 10, 1 to 9, 1 to 8, 1 to 7, and so on; 2 to 11; 2 to 10; 2 to 9; 2 to 8 and so on; 3 to 11; 3 to 10; 3 to 9 and so on; 4 to 11; 4 to 10; 4 to 9; 4 to 8; 4 to 7 and so on; 5 to 11; 5 to 10; 5 to 9; 5 to 8 and so on, etc.
  • the number of amino acid substitutions that may be accommodated in a humanized light chain variable region derived from SEQ ID NO.:16 may be for example, from 1 to 15 amino acid substitutions.
  • the number of amino acid substitutions that may be accommodated in a humanized heavy chain variable region derived from SEQ ID NO.:18 may be for example, from 1 to 20 amino acid substitutions. In some instances, when considering a humanized version of SEQ ID NO.:18, it may be useful to have at least three amino acid substitutions.
  • the number of amino acid substitutions that may be accommodated in a humanized light chain variable region derived from SEQ ID NO.:24 may be for example, from 1 to 16 amino acid substitutions.
  • the number of amino acid substitutions that may be accommodated in a humanized heavy chain variable region of SEQ ID NO.:26 may be for example, from 1 to 17 amino acid substitutions.
  • the number of amino acid substitutions that may be accommodated in a humanized light chain variable region derived from SEQ ID NO.:48 may be for example, from 1 to 11 amino acid substitutions.
  • the number of amino acid substitutions that may be accommodated in a humanized heavy chain variable region of SEQ ID NO.:46 may be for example, from 1 to 23 amino acid substitutions.
  • the one to twenty amino acid substitutions may be for example, in the light chain variable region.
  • the one to twenty amino acid substitutions may be for example, in the heavy chain variable region.
  • a humanized antibody or antigen binding fragment may therefore have a light chain variable region having up to twenty amino acid substitutions in comparison with SEQ ID NO.:16 or SEQ ID NO.:24 and may have a heavy chain variable region having up to twenty amino acid substitutions in comparison with SEQ ID NO.:18 or SEQ ID NO.:26.
  • a humanized antibody or antigen binding fragment may therefore have a light chain variable region having up to twenty-five amino acid substitutions in comparison with SEQ ID NO.:48 and may have a heavy chain variable region having up to twenty-five amino acid substitutions in comparison with SEQ ID NO.:46.
  • each one of the light chain variable regions may independently have up to twenty-five, twenty-four, twenty-three, twenty-two, twenty-one, twenty, nineteen, eighteen, seventeen, sixteen, fifteen, fourteen, thirteen, twelve, eleven, ten, nine, eight, seven, six, five, four, three, two, one amino acid substitutions and each one of the heavy chain variable regions may have up to twenty-five, twenty-four, twenty-three, twenty-two, twenty-one, twenty, nineteen, eighteen, seventeen, sixteen, fifteen, fourteen, thirteen, twelve, eleven, ten, nine, eight, seven, six, five, four, three, two, one amino acid substitutions.
  • amino acid substitutions may be conservative or non-conservative. In an exemplary embodiment the amino acid substitutions may be conservative.
  • the humanized antibody or antigen binding fragment of the invention may also have a light chain variable region and/or heavy chain variable region showing a deletion in comparison with SEQ ID NO.:16, SEQ ID NO.:18, SEQ ID NO.:189, SEQ ID NO.:190, SEQ ID NO.:194, SEQ ID NO.:195, SEQ ID NO.:196, SEQ ID NO.:197, SEQ ID NO.:24 and/or SEQ ID NO.:26.
  • Such deletion may be found, for example, at an amino- or carboxy-terminus of the light chain variable region and/or heavy chain variable region.
  • Another exemplary embodiment of the humanized antibody or antigen binding fragment of the present invention includes for example, an antibody or antigen binding fragment having a light chain variable region which may comprise at least 90 consecutive amino acids of any of SEQ ID NO.:186, SEQ ID NO.:187, SEQ ID NO.:188, SEQ ID NO.:189 or SEQ ID NO.:190.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:186” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, or at least 112 consecutive amino acids”.
  • amino acids of SEQ ID NO.:186 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:186 and especially those sequences which include the 3 CDRs of SEQ ID NO.:186, such as, for example a sequence comprising amino acids 6 to 108, 5 to 109, 13 to 103, 14 to 111 of SEQ ID NO.:186 and so on.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:187” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, or at least 112 consecutive amino acids”.
  • amino acids of SEQ ID NO.:187 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:187 and especially those sequences which include the 3 CDRs of SEQ ID NO.:187, such as, for example a sequence comprising amino acids 7 to 109, 12 to 104, 22 to 113, 18 to 112 of SEQ ID NO.:187 and so on.
  • the antibody or antigen binding fragment of the present invention may have, for example, a light chain variable region as set forth in SEQ ID NO.:189 or 190.
  • the humanized antibody or antigen binding fragment of the invention includes (or further includes) for example, a heavy chain variable region which may comprise at least 90 consecutive amino acids of any of SEQ ID NOs.:191, 192, 193, 194, 195, 196 or 197.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:191” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115 or at least 116 consecutive amino acids”.
  • amino acids of SEQ ID NO.:191 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:191 and especially those sequences which include the 3 CDRs of SEQ ID NO.:191, such as, for example a sequence comprising amino acids 1 to 106, 2 to 112, 11 to 113, 7 to 102 of SEQ ID NO.:191 and so on.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:192” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115 or at least 116 consecutive amino acids”.
  • amino acids of SEQ ID NO.:192 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:192 and especially those sequences which include the 3 CDRs of SEQ ID NO.:192, for example a sequence comprising amino acids 6 to 109, 8 to 113, 1 to 102, 2 to 105 of SEQ ID NO.:192 and so on.
  • the antibody or antigen binding fragment of the present invention may have, for example, a heavy chain variable region as set forth in SEQ ID NO.:194, 195, 196 or 197.
  • the antibody or antigen binding fragment may comprise, for example,
  • the light chain variable region may comprise at least 90 consecutive amino acids of SEQ ID NO.:189 or 190 and the heavy chain variable region may comprise at least 90 consecutive amino acids of SEQ ID NO.:194, 195, 196 or 197.
  • the light chain variable region may be as set forth in SEQ ID NO.:189 and the heavy chain variable region may be as set forth in SEQ ID NO.:194.
  • the light chain variable region may be as set forth in SEQ ID NO.:189 and the heavy chain variable region may be as set forth in SEQ ID NO.:195.
  • the light chain variable region may be as set forth in SEQ ID NO.:189 and the heavy chain variable region may be as set forth in SEQ ID NO.:196.
  • the light chain variable region may be as set forth in SEQ ID NO.:189 and the heavy chain variable region may be as set forth in SEQ ID NO.:197.
  • the light chain variable region may be as set forth in SEQ ID NO.:190 and the heavy chain variable region may be as set forth in SEQ ID NO.:194.
  • the light chain variable region may be as set forth in SEQ ID NO.:190 and the heavy chain variable region may be as set forth in SEQ ID NO.:195.
  • the light chain variable region may be as set forth in SEQ ID NO.:190 and the heavy chain variable region may be as set forth in SEQ ID NO.:196.
  • the light chain variable region may be as set forth in SEQ ID NO.:190 and the heavy chain variable region may be as set forth in SEQ ID NO.:197.
  • Another exemplary embodiment of the humanized antibody or antigen binding fragment of the present invention includes for example, an antibody or antigen binding fragment having a light chain variable region which may comprise at least 90 consecutive amino acids of any of SEQ ID NO.:174, SEQ ID NO.:175, SEQ ID NO.:176 or SEQ ID NO.:168.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:174” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112 or at least 113 consecutive amino acids”.
  • amino acids of SEQ ID NO.:174 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:174 and especially those sequences which include the 3 CDRs of SEQ ID NO.:174, such as, for example a sequence comprising amino acids 6 to 108, 5 to 109, 13 to 103, 14 to 111 of SEQ ID NO.:174 and so on.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:175” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112 or at least 113 consecutive amino acids”.
  • amino acids of SEQ ID NO.:175 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:175 and especially those sequences which include the 3 CDRs of SEQ ID NO.:175, such as, for example a sequence comprising amino acids 7 to 109, 12 to 104, 22 to 113, 18 to 112 of SEQ ID NO.:175 and so on.
  • the antibody or antigen binding fragment of the present invention may have, for example, a light chain variable region as set forth in SEQ ID NO.:168.
  • the humanized antibody or antigen binding fragment of the invention includes (or further includes) for example, a heavy chain variable region which may comprise at least 90 consecutive amino acids of any of SEQ ID NOs.:177, 178, 179 or 169.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:177” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112 or at least 113 consecutive amino acids”.
  • amino acids of SEQ ID NO.:177 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:177 and especially those sequences which include the 3 CDRs of SEQ ID NO.:177, such as, for example a sequence comprising amino acids 1 to 106, 2 to 112, 11 to 113, 7 to 102 of SEQ ID NO.:177 and so on.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:178” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112 or at least 113 consecutive amino acids”.
  • amino acids of SEQ ID NO.:178 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:178 and especially those sequences which include the 3 CDRs of SEQ ID NO.:178, for example a sequence comprising amino acids 6 to 109, 8 to 113, 1 to 102, 2 to 105 of SEQ ID NO.:178 and so on.
  • the antibody or antigen binding fragment of the present invention may have, for example, a heavy chain variable region as set forth in SEQ ID NO.:169.
  • the antibody or antigen binding fragment may comprise, for example,
  • the light chain variable region may comprise at least 90 consecutive amino acids of SEQ ID NO.:168 and the heavy chain variable region may comprise at least 90 consecutive amino acids of SEQ ID NO.:169.
  • the light chain variable region may be as set forth in SEQ ID NO.:168 and the heavy chain variable region may be as set forth in SEQ ID NO.:169.
  • humanized antibodies or antigen binding fragments of the invention are those which may comprise a light chain variable region which may comprise at least 90 consecutive amino acids of any of SEQ ID Nos. 180, 181, 182 or 172.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:180” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106 or at least 107, consecutive amino acids”.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:180” encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:180 and especially those sequences which include the 3 CDRs of SEQ ID NO.:180, for example a sequence comprising amino acids 6 to 102, 11 to 106, 1 to 106, 3 to 95, 5 to 95 of SEQ ID NO.:180 and so on.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:181” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106 or at least 107, consecutive amino acids”.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:181” encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:181 and especially those sequences which include the 3 CDRs of SEQ ID NO.:181, for example a sequence comprising amino acids 9 to 106, 10 to 101, 1 to 98, 3 to 99, 7 to 107 of SEQ ID NO.:181 and so on.
  • the antibody or antigen binding fragment of the present invention may have, for example, a light chain variable region as set forth in SEQ ID NO.:172.
  • the humanized antibody or antigen binding fragment of the invention includes (or further includes) for example, a heavy chain variable region which may comprise at least 90 consecutive amino acids of any of SEQ ID NOs.:183, 184, 185 or 173.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:183” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115 or at least 116 consecutive amino acids”.
  • amino acids of SEQ ID NO.:183 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:183 and especially those sequences which include the 3 CDRs of SEQ ID NO.:183, such as, for example a sequence comprising amino acids 6 to 111, 1 to 106, 2 to 104, 5 to 106, 10 to 107 of SEQ ID NO.:183 and so on.
  • the term “at least 90 consecutive amino acids of SEQ ID NO.:185” also includes the terms “at least 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115 or at least 116 consecutive amino acids”.
  • amino acids of SEQ ID NO.:185 encompasses any possible sequence of at least 90 consecutive amino acids found in SEQ ID NO.:185 and especially those sequences which include the 3 CDRs of SEQ ID NO.:185, such as, for example a sequence comprising amino acids 3 to 107, 1 to 115, 1 to 110, 22 to 116, 20 to 115 of SEQ ID NO.:185 and so on.
  • the antibody or antigen binding fragment of the present invention may have, for example, a heavy chain variable region as set forth in SEQ ID NO.:173.
  • the antibody or antigen binding fragment may comprise, for example,
  • the light chain variable region may have at least 90 consecutive amino acids of SEQ ID NO.:172 and the heavy chain variable region may have at least 90 consecutive amino acids of SEQ ID NO.:173.
  • the light chain variable region may be as set forth in SEQ ID NO.:172 and the heavy chain variable region may be as set forth in SEQ ID NO.:173.
  • the antibody or antigen binding fragment of the present invention may have a light chain variable region and/or heavy chain variable region as described above and may further comprise amino acids of a constant region, such as, for example, amino acids of a constant region of a human antibody.
  • the antibody or antigen binding fragment of the present invention may comprise, for example, a human IgG1 constant region.
  • the antigen binding fragment may be, for example, a scFv, a Fab, a Fab′ or a (Fab) 2 .
  • anti-KAAG1 antibodies that are disclosed herein can be made by a variety of methods familiar to those skilled in the art, such as hybridoma methodology or by recombinant DNA methods.
  • the anti-KAAG1 antibodies may be produced by the conventional hybridoma technology, where a mouse is immunized with an antigen, spleen cells isolated and fused with myeloma cells lacking HGPRT expression and hybrid cells selected by hypoxanthine, aminopterin and thymine (HAT) containing media.
  • HAT hypoxanthine, aminopterin and thymine
  • the anti-KAAG1 antibodies may be produced by recombinant DNA methods.
  • nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein or any other may be inserted into an expression vector, i.e., a vector that contains the elements for transcriptional and translational control of the inserted coding sequence in a particular host.
  • These elements may include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5′ and 3′ un-translated regions.
  • Methods that are well known to those skilled in the art may be used to construct such expression vectors. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination.
  • a variety of expression vector/host cell systems known to those of skill in the art may be utilized to express a polypeptide or RNA derived from nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein.
  • These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with baculovirus vectors; plant cell systems transformed with viral or bacterial expression vectors; or animal cell systems.
  • microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors
  • yeast transformed with yeast expression vectors insect cell systems infected with baculovirus vectors
  • plant cell systems transformed with viral or bacterial expression vectors or animal cell systems.
  • stable expression in cell lines may be effected.
  • nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein may be transformed into cell lines using expression vectors that may contain viral origins of replication and/or endogenous expression elements and a selectable or visible marker gene on the same or on a separate vector.
  • the invention is not to be limited by the vector or host cell employed.
  • the nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein may each be ligated into a separate expression vector and each chain expressed separately.
  • both the light and heavy chains able to encode any one of a light and heavy immunoglobulin chains described herein may be ligated into a single expression vector and expressed simultaneously.
  • RNA and/or polypeptide may be expressed from a vector comprising nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein using an in vitro transcription system or a coupled in vitro transcription/translation system respectively.
  • host cells that contain nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein and/or that express a polypeptide encoded by the nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein, or a portion thereof, may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA/DNA or DNA/RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques that include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or amino acid sequences.
  • Immunological methods for detecting and measuring the expression of polypeptides using either specific polyclonal or monoclonal antibodies are known in the art. Examples of such techniques include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), and fluorescence activated cell sorting (FACS). Those of skill in the art may readily adapt these methodologies to the present invention.
  • ELISAs enzyme-linked immunosorbent assays
  • RIAs radioimmunoassays
  • FACS fluorescence activated cell sorting
  • Host cells comprising nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein may thus be cultured under conditions for the transcription of the corresponding RNA (mRNA, siRNA, shRNA etc.) and/or the expression of the polypeptide from cell culture.
  • the polypeptide produced by a cell may be secreted or may be retained intracellularly depending on the sequence and/or the vector used.
  • expression vectors containing nucleotide sequences able to encode any one of a light and heavy immunoglobulin chains described herein may be designed to contain signal sequences that direct secretion of the polypeptide through a prokaryotic or eukaryotic cell membrane.
  • nucleotide sequences of the present invention may be engineered using methods generally known in the art in order to alter the nucleotide sequences for a variety of purposes including, but not limited to, modification of the cloning, processing, and/or expression of the gene product.
  • DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences.
  • oligonucleotide-mediated site-directed mutagenesis may be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so forth.
  • a host cell strain may be chosen for its ability to modulate expression of the inserted sequences or to process the expressed polypeptide in the desired fashion.
  • modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation.
  • anti-KAAG1 antibodies that contain particular glycosylation structures or patterns may be desired.
  • Post-translational processing which cleaves a “prepro” form of the polypeptide, may also be used to specify protein targeting, folding, and/or activity.
  • Different host cells that have specific cellular machinery and characteristic mechanisms for post-translational activities e.g., CHO, HeLa, MDCK, HEK293, and W138
  • ATCC American Type Culture Collection
  • nucleic acid sequences may be ligated to a heterologous sequence resulting in translation of a fusion polypeptide containing heterologous polypeptide moieties in any of the aforementioned host systems.
  • heterologous polypeptide moieties may facilitate purification of fusion polypeptides using commercially available affinity matrices.
  • Such moieties include, but are not limited to, glutathione S-transferase (GST), maltose binding protein, thioredoxin, calmodulin binding peptide, 6-His (His), FLAG, c-myc, hemaglutinin (HA), and antibody epitopes such as monoclonal antibody epitopes.
  • GST glutathione S-transferase
  • thioredoxin calmodulin binding peptide
  • 6-His His
  • FLAG c-myc
  • HA hemaglutinin
  • antibody epitopes such as monoclonal antibody epitopes.
  • the present invention relates to a polynucleotide which may comprise a nucleotide sequence encoding a fusion protein.
  • the fusion protein may comprise a fusion partner (e.g., HA, Fc, etc.) fused to the polypeptide (e.g., complete light chain, complete heavy chain, variable regions, CDRs etc.) described herein.
  • nucleic acid and polypeptide sequences may be synthesized, in whole or in part, using chemical or enzymatic methods well known in the art.
  • peptide synthesis may be performed using various solid-phase techniques and machines such as the ABI 431A Peptide synthesizer (PE Biosystems) may be used to automate synthesis.
  • the amino acid sequence may be altered during synthesis and/or combined with sequences from other proteins to produce a variant protein.
  • the antibody or antigen binding fragment of the present invention may be conjugated with a detectable moiety (i.e., for detection or diagnostic purposes) or with a therapeutic moiety (for therapeutic purposes)
  • a “detectable moiety” is a moiety detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical and/or other physical means.
  • a detectable moiety may be coupled either directly and/or indirectly (for example via a linkage, such as, without limitation, a DOTA or NHS linkage) to antibodies and antigen binding fragments thereof of the present invention using methods well known in the art.
  • a wide variety of detectable moieties may be used, with the choice depending on the sensitivity required, ease of conjugation, stability requirements and available instrumentation.
  • a suitable detectable moiety include, but is not limited to, a fluorescent label, a radioactive label (for example, without limitation, 125 I, In 111 , Tc 99 , I 131 and including positron emitting isotopes for PET scanner etc), a nuclear magnetic resonance active label, a luminiscent label, a chemiluminescent label, a chromophore label, an enzyme label (for example and without limitation horseradish peroxidase, alkaline phosphatase, etc.), quantum dots and/or a nanoparticle.
  • Detectable moiety may cause and/or produce a detectable signal thereby allowing for a signal from the detectable moiety to be detected.
  • the antibody or antigen binding fragment thereof may be coupled (modified) with a therapeutic moiety (e.g., drug, cytotoxic moiety).
  • a therapeutic moiety e.g., drug, cytotoxic moiety
  • the anti-KAAG1 antibodies and antigen binding fragments may comprise an inhibitor, a chemotherapeutic or cytotoxic agent.
  • the antibody and antigen binding fragments may be conjugated to the chemotherapeutic or cytotoxic agent.
  • chemotherapeutic or cytotoxic agents include, but are not limited to, Yttrium-90, Scandium-47, Rhenium-186, Iodine-131, Iodine-125, and many others recognized by those skilled in the art (e.g., lutetium (e.g., Lu 177 ), bismuth (e.g., Bi 213 ), copper (e.g., Cu 67 )).
  • the chemotherapeutic or cytotoxic agent may comprise, without limitation, 5-fluorouracil, adriamycin, irinotecan, platinum-based compounds such as cisplatin and anti-tubulin or anti-mitotic compounds such as, taxanes, doxorubicin and cyclophosphamide, pseudomonas endotoxin, ricin and other toxins.
  • Suitable antibody drug conjugates are selected amongst those having an IC 50 in the range of 0.001 nM to 150 nM, 0.001 nM to 100 nM, 0.001 nM to 50 nM, 0.001 nM to 20 nM or 0.001 nM to 10 nM (inclusively). The cytotoxic drug used for conjugation is thus selected on the basis of these criteria.
  • the antibody or antigen binding fragment of the present invention may be used in combination with a second molecule (e.g., a secondary antibody, etc.) which is able to specifically bind to the antibody or antigen binding fragment of the present invention and which may carry a desirable detectable, diagnostic or therapeutic moiety.
  • a second molecule e.g., a secondary antibody, etc.
  • compositions of the anti-KAAG1 antibodies or antigen binding fragments are also encompassed by the present invention.
  • the pharmaceutical composition may comprise an anti-KAAG1 antibody or an antigen binding fragment and may also contain a pharmaceutically acceptable carrier.
  • compositions which may comprise the antibody or antigen binding fragment described herein and a carrier.
  • the present invention also relates to a pharmaceutical composition which may comprise the antibody or antigen binding fragment described herein and a pharmaceutically acceptable carrier.
  • a pharmaceutical composition may contain pharmaceutically acceptable carriers comprising water, PBS, salt solutions, gelatins, oils, alcohols, and other excipients and auxiliaries that facilitate processing of the active compounds into preparations that may be used pharmaceutically. In other instances, such preparations may be sterilized.
  • compositions means therapeutically effective amounts of the agent together with pharmaceutically acceptable diluents, preservatives, solubilizers, emulsifiers, adjuvant and/or carriers.
  • a “therapeutically effective amount” as used herein refers to that amount which provides a therapeutic effect for a given condition and administration regimen.
  • Such compositions are liquids or lyophilized or otherwise dried formulations and include diluents of various buffer content (e.g., Tris-HCl., acetate, phosphate), pH and ionic strength, additives such as albumin or gelatin to prevent absorption to surfaces, detergents (e.g., Tween 20, Tween 80, Pluronic F68, bile acid salts).
  • Solubilizing agents e.g., glycerol, polyethylene glycerol
  • anti-oxidants e.g., ascorbic acid, sodium metabisulfite
  • preservatives e.g., thimerosal, benzyl alcohol, parabens
  • bulking substances or tonicity modifiers e.g., lactose, mannitol
  • covalent attachment of polymers such as polyethylene glycol to the protein, complexation with metal ions, or incorporation of the material into or onto particulate preparations of polymeric compounds such as polylactic acid, polyglycolic acid, hydrogels, etc, or onto liposomes, microemulsions, micelles, unilamellar or multilamellar vesicles, erythrocyte ghosts, or spheroplasts.
  • Controlled or sustained release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils).
  • particulate compositions coated with polymers e.g., poloxamers or poloxamines.
  • Other embodiments of the compositions of the invention incorporate particulate forms protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal, oral, vaginal, rectal routes.
  • the pharmaceutical composition is administered parenterally, paracancerally, transmucosally, transdermally, intramuscularly, intravenously, intradermally, subcutaneously, intraperitonealy, intraventricularly, intracranially and intratumorally.
  • pharmaceutically acceptable carrier or “pharmaceutical carrier” are known in the art and include, but are not limited to, 0.01-0.1 M or 0.05 M phosphate buffer or 0.8% saline. Additionally, such pharmaceutically acceptable carriers may be aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.
  • Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's orfixed oils.
  • Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers such as those based on Ringer's dextrose, and the like. Preservatives and other additives may also be present, such as, for example, antimicrobials, antioxidants, collating agents, inert gases and the like.
  • the therapeutically effective dose may be estimated initially either in cell culture assays or in animal models such as mice, rats, rabbits, dogs, or pigs. An animal model may also be used to determine the concentration range and route of administration. Such information may then be used to determine useful doses and routes for administration in humans. These techniques are well known to one skilled in the art and a therapeutically effective dose refers to that amount of active ingredient that ameliorates the symptoms or condition. Therapeutic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or with experimental animals, such as by calculating and contrasting the ED 50 (the dose therapeutically effective in 50% of the population) and LD 50 (the dose lethal to 50% of the population) statistics. Any of the therapeutic compositions described above may be applied to any subject in need of such therapy, including, but not limited to, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and humans.
  • compositions utilized in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means.
  • treatment refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder.
  • Those in need of treatment include those already having the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented.
  • the present invention provides in one aspect thereof, a method of treating an individual having or suspected of having breast cancer with an antibody or antigen binding fragment which is capable of specific binding to KAAG1.
  • the individual may have a breast cancer that is negative for the estrogen receptor expression, the progesterone receptor expression and/or Her2 expression (or overexpression).
  • the individual may have a breast cancer that has low expression for at least one of estrogen receptor, progesterone receptor and/or Her2.
  • the tumor may be negative for (or have low expression of) both estrogen receptor expression and progesterone receptor expression.
  • the individual may have a breast cancer that is characterized as being triple-negative or basal-like.
  • Yet other aspects of the invention relate to the use of the isolated antibody or antigen binding fragment described herein in the treatment or diagnosis of breast cancer characterized by a lack of estrogen receptor expression, progesterone receptor expression and/or Her2 overexpression or by low expression of at least one of these three markers.
  • the method may comprise, for example, administering an antibody or antigen binding fragment which is capable of specific binding to KAAG1 to an individual in need.
  • the individual in need is preferentially selected on the basis of a lack of ER expression, PgR expression and/or by the absence of HER2 protein over-expression.
  • Clinical testing for these markers is usually performed using histopathologic methods (immunohistochemistry, FISH, etc.) and/or by gene expression studies (see for example Dent et al, 2007, Bernstein and Lacey, 2011).
  • the individual in need may thus be an individual who has received a diagnosis of triple-negative breast cancer or basal-like breast cancer.
  • the present invention thus particularly relates to the therapeutic treatment of individual having triple-negative breast cancer or basal-like cancer with an anti-KAAG1 antibody.
  • Suitable antibodies or antigen binding fragments include those that are capable of specific binding to KAAG1 at the surface of tumor cells. Such antibodies may preferentially bind an epitope included within amino acids 30 to 84 of KAAG1 inclusively (e.g., within amino acids 36 to 60 (inclusively) or within amino acids 61 to 84 (inclusively) of KAAG1).
  • Suitable antibodies may be those which mediate antibody-dependent cell cytotoxicity and those that are conjugated with a therapeutic moiety.
  • the antibody may be, for example, a monoclonal antibody, a chimeric antibody or a humanized antibody or an antigen binding fragment thereof.
  • the method of the present invention may include administering the antibody or antigen binding fragment in combination with an inhibitor, a chemotherapeutic or a cytotoxic agent.
  • KAAG1 inhibitors such as antisense-based therapeutics (siRNA, antisenses, ribozymes, etc.).
  • the present invention thus provides a method of treating triple-negative breast cancer or basal-like breast cancer by administering an inhibitor of KAAG1 activity or expression to an individual in need.
  • the inhibitor may comprise a nucleotide sequence complementary to SEQ ID NO.:1 or to a fragment thereof. More particularly, the inhibitor may comprise a nucleotide sequence complementary to nucleotides 738 to 992 (inclusively) of SEQ ID NO.:1 or to a fragment thereof.
  • the inhibitor may include at least 10 consecutive nucleotides (at least 15, at least 20) which are complementary to SEQ ID NO.:1 or to nucleotides 738 to 992 (inclusively) of SEQ ID NO.:1.
  • the anti-KAAG1 antibodies and fragments may interact with cancer cells that express KAAG1 and induce an immunological reaction by mediating ADCC. In other instances, the anti-KAAG1 antibodies and fragments may block the interaction of KAAG1 with its protein partners.
  • the anti-KAAG1 antibodies and antigen binding fragments thereof may be administered concurrently with other treatments given for the same condition (inhibitors, chemotherapeutics or cytotoxic agents).
  • the antibodies may be administered with a PARP1 inhibitor, a EGFR inhibitor, anti-mitotics (eg., taxanes), platinum-based agents (eg., cisplatin), DNA damaging agents (eg. Doxorubicin) and other anti-cancer therapies that are known to those skilled in the art.
  • the anti-KAAG1 antibodies and antigen binding fragments thereof may be administered with other therapeutic antibodies. These include, but are not limited to, antibodies that target EGFR, CD-20, and Her2.
  • the present invention relates in a further aspect thereof to a method for inhibiting the growth of KAAG1-expressing cell that are estrogen receptor-negative (ER ⁇ ), progesterone receptor negative (PgR ⁇ ) and/or that lacks Her2 overexpression (Her2 ⁇ ), the method may comprise contacting the cell with an effective amount of the antibody or antigen binding fragment described herein.
  • ER ⁇ estrogen receptor-negative
  • PgR ⁇ progesterone receptor negative
  • Her2 ⁇ Her2 overexpression
  • the present invention also encompasses method of treating cancer or inhibiting the growth of a KAAG1 expressing cells that are estrogen receptor-negative (ER ⁇ ), progesterone receptor negative (PgR ⁇ ) and/or that lacks Her2 overexpression (Her2 ⁇ ), in a mammal, the method may comprise administering the antibody or antigen binding fragment described herein to a mammal in need.
  • ER ⁇ estrogen receptor-negative
  • PgR ⁇ progesterone receptor negative
  • Her2 ⁇ Her2 overexpression
  • the present invention provides method of treatment, diagnostic methods and method of detection using the antibody or antigen binding fragment of the present invention and the use of these antibodies or antigen binding fragment in the manufacture of a pharmaceutical composition or drug for such purposes.
  • Method of treatment encompassed by the present invention includes administering an antibody or antigen binding fragment described herein to a mammal in need, and especially to a patient having or susceptible of having a cancer characterized as being estrogen receptor-negative (ER ⁇ ), progesterone receptor negative (PgR ⁇ ) and/or that lacks Her2 overexpression (Her2 ⁇ ),
  • ER ⁇ estrogen receptor-negative
  • PgR ⁇ progesterone receptor negative
  • Her2 ⁇ Her2 overexpression
  • the invention also provides in further aspects, methods for reducing tumor spread, tumor invasion, tumor formation or for inducing tumor lysis, which may comprise administering an isolated antibody or antigen binding fragment to a mammal in need.
  • the invention therefore relates to the use of the isolated antibody or antigen binding fragment described herein in the (manufacture of a pharmaceutical composition for) treatment of cancer, reduction of tumor spread, tumor invasion, tumor formation or for inducing tumor lysis of KAAG1-expressing tumor cells that are estrogen receptor-negative (ER ⁇ ), progesterone receptor negative (PgR ⁇ ) and/or that lacks Her2 overexpression (Her2 ⁇ ).
  • ER ⁇ estrogen receptor-negative
  • PgR ⁇ progesterone receptor negative
  • Her2 ⁇ Her2 overexpression
  • the antibody or antigen binding fragment may more particularly be applicable for malignant tumor including, for example, a malignant tumor having the ability to metastasize and/or tumor cells characterized by anchorage-independent growth.
  • the antibody or antigen binding fragment of the present invention may also be used in the diagnosis of cancer.
  • the diagnosis of cancer may be performed in vivo by administering the antibody or antigen binding fragment of the present invention to a mammal having or suspected of having a cancer.
  • the diagnosis may also be performed ex vivo by contacting a sample obtained from the mammal with the antibody or antigen binding fragment and determining the presence or absence of cells (tumor cells) expressing KAAG1 or a KAAG1 variant.
  • the present invention also encompasses method of detecting cancer or detecting a KAAG1 expressing cells that are estrogen receptor-negative (ER ⁇ ), progesterone receptor negative (PgR ⁇ ) and/or that lacks Her2 overexpression (Her2 ⁇ ), in a mammal, the method may comprise administering the antibody or antigen binding fragment described herein to a mammal in need.
  • ER ⁇ estrogen receptor-negative
  • PgR ⁇ progesterone receptor negative
  • Her2 ⁇ Her2 overexpression
  • the present invention relates in another aspect thereof to a method for detecting a cell expressing KAAG1 or a KAAG1 variant, the method may comprise contacting the cell with an antibody or antigen binding fragment described herein and detecting a complex formed by the antibody and the KAAG1- or KAAG1 variant-expressing cell.
  • exemplary embodiments of antibodies or antigen binding fragments used in detection methods are those which are capable of binding to the extracellular region of KAAG1.
  • antibodies or antigen binding fragments used in detection methods are those which bind to KAAG1 or KAAG1 variant expressed at the surface of tumor cells that are estrogen receptor-negative (ER ⁇ ), progesterone receptor negative (PgR ⁇ ) and/or that lacks Her2 overexpression (Her2 ⁇ ).
  • ER ⁇ estrogen receptor-negative
  • PgR ⁇ progesterone receptor negative
  • Her2 ⁇ Her2 overexpression
  • Another aspect of the invention relates a method for detecting KAAG1 (SEQ ID NO.:2), a KAAG1 variant having at least 80% sequence identity with SEQ ID NO.:2 or a secreted form of circulating form of KAAG1 or KAAG1 variant, the method may comprise contacting a cell expressing KAAG1 or the KAAG1 variant or a sample (biopsy, serum, plasma, urine etc.) comprising or suspected of comprising KAAG1 or the KAAG1 variant with the antibody or antigen binding fragments described herein and measuring binding.
  • a sample biopsy, serum, plasma, urine etc.
  • the sample may originate from a mammal (e.g., a human) which may have cancer (e.g., breast cancer that is characterized as being estrogen receptor-negative (ER ⁇ ), progesterone receptor negative (PgR ⁇ ) and/or that lacks Her2 overexpression (Her2 ⁇ ), such as basal-like breast cancer or triple-negative breast cancer) or may be suspected of having cancer.
  • a mammal e.g., a human
  • cancer e.g., breast cancer that is characterized as being estrogen receptor-negative (ER ⁇ ), progesterone receptor negative (PgR ⁇ ) and/or that lacks Her2 overexpression (Her2 ⁇ ), such as basal-like breast cancer or triple-negative breast cancer
  • the sample may be a tissue sample obtained from the mammal or a cell culture supernatant.
  • the sample may be a serum sample, a plasma sample, a blood sample or ascitic fluid obtained from the mammal.
  • the antibody or antigen binding fragment described herein may advantageously detect a secreted or circulating form (circulating in blood) of KAAG1.
  • the method may comprise quantifying the complex formed by the antibody or antigen binding fragment bound to KAAG1 or to the KAAG1 variant.
  • the binding of an antibody to an antigen will cause an increase in the expected molecular weight of the antigen.
  • a physical change therefore occurs upon specific binding of the antibody or antigen binding fragment and the antigen.
  • Such changes may be detected using, for example, electrophoresis followed by Western blot and coloration of the gel or blot, mass spectrometry, HPLC coupled with a computer or else.
  • Apparatus capable of computing a shift in molecular weight are known in the art and include for example, PhosphorimagerTM.
  • the antigen-antibody complex may be detected by the fluorescence emitted by the label, radiation emission of the label, enzymatic activity of a label provided with its substrate or else.
  • Detection and/or measurement of binding between an antibody or antigen binding fragment and an antigen may be performed by various methods known in the art. Binding between an antibody or antigen binding fragment and an antigen may be monitored with an apparatus capable of detecting the signal emitted by the detectable label (radiation emission, fluorescence, color change etc.). Such apparatus provides data which indicates that binding as occurred and may also provide indication as to the amount of antibody bound to the antigen. The apparatus (usually coupled with a computer) may also be capable of calculating the difference between a background signal (e.g., signal obtained in the absence of antigen-antibody binding) or background noise and the signal obtained upon specific antibody-antigen binding. Such apparatuses may thus provide the user with indications and conclusions as to whether the antigen has been detected or not.
  • a background signal e.g., signal obtained in the absence of antigen-antibody binding
  • background noise e.g., signal obtained upon specific antibody-antigen binding
  • kits which may include one or more container containing one or more antibodies or antigen binding fragments described herein.
  • Antibodies are usually made in cells allowing expression of the light chain and heavy chain expressed from a vector(s) comprising a nucleic acid sequence encoding the light chain and/or heavy chain.
  • the present therefore encompasses nucleic acids capable of encoding any of the CDRs, light chain variable regions, heavy chain variable regions, light chains, heavy chains described herein.
  • the present invention therefore relates in a further aspect to a nucleic acid encoding a light chain variable region and/or a heavy chain variable region of an antibody which is capable of specific binding to KAAG1.
  • nucleic acids encompassed by the present invention includes a nucleic acid selected from the group consisting of a nucleic acid having at least 70% sequence identity (i.e., at least 75%, at least 80% sequence identity) with any one of SEQ ID NOs.:3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 45 and 47, fragments (e.g., of at least 10, at least 15, at least 20 consecutive nucleotides) and complement thereof.
  • the nucleic acid may especially encode a light chain variable region and/or heavy chain variable region of an antibody which may be capable of inducing killing (elimination, destruction, lysis) of KAAG1- or KAAG1 variant-expressing tumor cells.
  • the nucleic acid may especially encode a light chain variable region and/or heavy chain variable region of an antibody which may be capable of reducing spreading of KAAG1- or KAAG1 variant-expressing tumor cells.
  • the nucleic acid may particularly encode a light chain variable region and/or heavy chain variable region of an antibody which may be capable of decreasing or impairing formation of KAAG1- or KAAG1 variant-expressing tumors.
  • the nucleic acid may encode a light chain variable region which may comprise at least two CDRs of a CDRL1, a CDRL2 or a CDRL3.
  • the nucleic acid may encode a light chain variable region which may comprise one CDRL1, one CDRL2 and one CDRL3.
  • the present invention also relates to a nucleic acid encoding a heavy chain variable region comprising:
  • the nucleic acid may encode a heavy chain variable region which may comprise at least two CDRs of a CDRH1, a CDRH2 or a CDRH3.
  • the nucleic acid may encode a heavy chain variable region which may comprise one CDRH1, one CDRH2 and one CDRH3.
  • nucleic acids encoding antibody variants having at least one conservative amino acid substitution are also encompassed by the present invention.
  • the nucleic acid may encode a CDR comprising at least one conservative amino acid substitution.
  • the nucleic acid may encode a CDR comprising at least one conservative amino acid substitution in at least two of the CDRs.
  • the nucleic acid may encode a CDR comprising at least one conservative amino acid substitution in the 3 CDRs.
  • the nucleic acid may encode a CDR comprising at least two conservative amino acid substitutions in at least one of the CDRs.
  • the nucleic acid may encode a CDR comprising at least two conservative amino acid substitutions in at least two of the CDRs.
  • the nucleic acid may encode a CDR comprising at least two conservative amino acid substitutions in the 3 CDRs.
  • nucleic acid encoding a light chain variable region having at least 70%, 75%, 80% sequence identity with a sequence selected from the group consisting of SEQ ID NO.:16, SEQ ID NO.:20, SEQ ID NO.:24, SEQ ID NO.:103, SEQ ID NO.:104, SEQ ID NO.:105, SEQ ID NO.:106, SEQ ID NO.:107, SEQ ID NO.:108, SEQ ID NO.:109, SEQ ID NO.:110, SEQ ID NO.:111, SEQ ID NO.:112, SEQ ID NO.:113, SEQ ID NO.:114, SEQ ID NO.:115, SEQ ID NO.:116, SEQ ID NO.:117, SEQ ID NO.:118, SEQ ID NO.:119, SEQ ID NO.:120, SEQ ID NO.:121, SEQ ID NO.:122, SEQ ID NO.:123, SEQ ID NO.:124 and SEQ ID NO.:125.
  • nucleic acid encoding a heavy chain variable region having at least 70%. 75%, 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO.:18, SEQ ID NO.:22, SEQ ID NO.:26, SEQ ID NO.:126, SEQ ID NO.:127, SEQ ID NO.:128, SEQ ID NO.:129, SEQ ID NO.:130, SEQ ID NO.:131, SEQ ID NO.:132, SEQ ID NO.:133, SEQ ID NO.:134, SEQ ID NO.:135, SEQ ID NO.:136, SEQ ID NO.:137, SEQ ID NO.:138, SEQ ID NO.:139, SEQ ID NO.:140, SEQ ID NO.:141, SEQ ID NO.:142, SEQ ID NO.:143, SEQ ID NO.:144, SEQ ID NO.:145, SEQ ID NO.:146 and SEQ ID NO.:147.
  • the present invention relates to a vector comprising the nucleic acids described herein.
  • the vector may be an expression vector.
  • Vector that contains the elements for transcriptional and translational control of the inserted coding sequence in a particular host are known in the art. These elements may include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5′ and 3′ un-translated regions. Methods that are well known to those skilled in the art may be used to construct such expression vectors. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination.
  • the present invention relates to an isolated cell that may comprise the nucleic acid described herein.
  • the isolated cell may comprise a nucleic acid encoding a light chain variable region and a nucleic acid encoding a heavy chain variable region either on separate vectors or on the same vector.
  • the isolated cell may also comprise a nucleic acid encoding a light chain and a nucleic acid encoding a heavy chain either on separate vectors or on the same vector.
  • the cell may be capable of expressing, assembling and/or secreting an antibody or antigen binding fragment thereof.
  • the present invention provides a cell which may comprise and/or may express the antibody described herein.
  • the cell may comprise a nucleic acid encoding a light chain variable region and a nucleic acid encoding a heavy chain variable region.
  • the cell may be capable of expressing, assembling and/or secreting an antibody or antigen binding fragment thereof.
  • This example discloses the methods used to convert the Fabs into full IgG1 chimeric monoclonal antibodies.
  • Fabs may be limited with respect to conducting meaningful in vitro and in vivo studies to validate the biological function of the antigen.
  • the expression vectors for both the light and heavy immunoglobulin chains were constructed such that i) the original bacterial signal peptide sequences upstream of the Fab expression vectors were replaced by mammalian signal peptides and ii) the light and heavy chain constant regions in the mouse antibodies were replaced with human constant regions.
  • the methods to accomplish this transfer utilized standard molecular biology techniques that are familiar to those skilled in the art.
  • Light chain expression vector an existing mammalian expression plasmid, called pTTVH8G (Durocher et al., 2002), designed to be used in the 293E transient transfection system was modified to accommodate the mouse light chain variable region.
  • the resulting mouse-human chimeric light chain contained a mouse variable region followed by the human kappa constant domain.
  • the cDNA sequence encoding the human kappa constant domain was amplified by PCR with primers OGS1773 and OGS1774 (SEQ ID NOS:55 and 56, respectively).
  • the nucleotide sequence and the corresponding amino acid sequence for the human kappa constant region are shown in SEQ ID NOS: 57 and 58, respectively.
  • pTTVH8G immediately downstream of the signal peptide sequence of human VEGF A (NM_003376). This cloning step also positioned unique restriction endonuclease sites that permitted the precise positioning of the cDNAs encoding the mouse light chain variable regions.
  • the sequence of the final expression plasmid, called pTTVK1, is shown in SEQ ID NO.:59.
  • PCR primers specific for the light chain variable regions of antibodies 3D3, 3G10, 3C4 and 3A4 were designed that incorporated, at their 5′-end, a sequence identical to the last 20 base pairs of the VEGF A signal peptide.
  • the sequences of these primers are shown in SEQ ID NOS:60, 61, 62 and 213.
  • the same reverse primer was used to amplify all three light chain variable regions of 3D3, 3G10 and 3C4 since the extreme 3′-ends were identical.
  • This primer (SEQ ID NO.:63) incorporated, at its 3′-end, a sequence identical to the first 20 base pairs of the human kappa constant domain.
  • Primer SE ID NO.:214 was used to amplify the 3A4 light chain variable region. Both the PCR fragments and the digested pTTVK1 were treated with the 3′-5′ exonuclease activity of T4 DNA polymerase resulting in complimentary ends that were joined by annealing. The annealing reactions were transformed into competent E. coli and the expression plasmids were verified by sequencing to ensure that the mouse light chain variable regions were properly inserted into the pTTVK1 expression vector. Those skilled in the art will readily recognize that the method used for construction of the light chain expression plasmids applies to all anti-KAAG1 antibodies contained in the original Fab library.
  • Heavy chain expression vector the expression vector that produced the heavy chain immunoglobulins was designed in a similar manner to the pTTVK1 described above for production of the light chain immunoglobulins. Plasmid pYD11 (Durocher et al., 2002), which contains the human IgGK signal peptide sequence as well as the CH2 and CH3 regions of the human Fc domain of IgG1, was modified by ligating the cDNA sequence encoding the human constant CH1 region.
  • PCR primers OGS1769 and OGS1770 (SEQ ID NOS:64 and 65), designed to contain unique restriction endonuclease sites, were used to amplify the human IgG1 CH1 region containing the nucleotide sequence and corresponding amino acid sequence shown in SEQ ID NOS:66 and 67.
  • the modified plasmid (SEQ ID NO.:68) was designated pYD15.
  • PCR primers specific for the heavy chain variable regions of antibodies 3D3, 3G10, 3C4 and 3A4 were designed that incorporated, at their 5′-end, a sequence identical to the last 20 base pairs of the IgGK signal peptide.
  • the sequences of these primers are shown in SEQ ID NOS:69 (3D3 and 3G10 have the same 5′-end sequence), SEQ ID NO.: 70 or SEQ ID NO.:215 for 3A4.
  • the same reverse primer was used to amplify all three heavy chain variable regions of 3D3, 3C4 and 3G10 since the extreme 3′-ends were identical.
  • This primer (SEQ ID NO.:71) incorporated, at its 3′-end, a sequence identical to the first 20 base pairs of the human CH1 constant domain.
  • SEQ ID NO.:216 was used for the 3A4 heavy chain variable region.
  • Both the PCR fragments and the digested pYD15 were treated with the 3′-5′ exonuclease activity of T4 DNA polymerase resulting in complimentary ends that were joined by annealing.
  • the annealing reactions were transformed into competent E. coli and the expression plasmids were verified by sequencing to ensure that the mouse heavy chain variable regions were properly inserted into the pYD15 expression vector.
  • the method used for construction of the heavy chain expression plasmids applies to all anti-KAAG1 antibodies contained in the original Fab library.
  • human IgG1s in 293E cells The expression vectors prepared above that encoded the light and heavy chain immunoglobulins were expressed in 293E cells using the transient transfection system (Durocher et al., 2002). Other methods of transient or stable expression may be used. The ratio of light to heavy chain was optimized in order to achieve the most yield of antibody in the tissue culture medium and it was found to be 9:1 (L:H). The ability of the anti-KAAG1 antibodies (monoclonal, chimeric or humanized) to bind to recombinant Fc-KAAG1 was measured by ELISA and compared with the original mouse Fabs.
  • Humanization of the 3A4 antibody light chain variable region involved 11 mutations to its proposed humanized framework for 100% framework humanization. Humanization of the 3A4 antibody heavy chain variable region involved 23 mutations to its proposed humanized framework for 100% framework humanization.
  • These 100% humanized variable region sequences are labelled Lvh1 and Hvh1, respectively (SEQ ID NOs:189 and 194). Additional humanized sequences were also designed in which several residues from the 3A4 mouse sequences were retained based on careful structural and comparative sequence analyses that indicate a high probability of altering antigen-binding affinity if mutations are to be introduced at these positions. These sequences of the variable regions are labelled Lvh2, Hvh2, Hvh3 and Hvh4 (SEQ ID NOs: 190, 195, 196 and 197).
  • the two humanized light chain variants are identified herein as Lh1 (SEQ ID NO.: 199) and Lh2 (SEQ ID NO.:200).
  • the four humanized heavy chain variants are identified herein as Hh1 (SEQ ID NO.:202), Hh2 (SEQ ID NO.:203), Hh3 (SEQ ID NO.:204) and Hh4 (SEQ ID NO.:205).
  • the two humanized light chain and 4 humanized heavy chain can be assembled into 8 humanized antibodies (Lh1Hh1, Lh1Hh2, Lh1Hh3, Lh1Hh4, Lh2Hh1, Lh2Hh2, Lh2Hh3, and Lh2Hh4).
  • FIGS. 2 a and 2 b is an alignment of the murine light chain variable region with the 100% humanized light chain variable region and the murine heavy chain variable region with the 100% humanized heavy chain variable region respectively. This figure illustrates the amino acids that are preserved and those that have been chosen for substitution.
  • the purpose of these investigations is to determine the kinetics parameters of anti-clusterin antibodies.
  • humanization of the 3A4 anti-KAAG1 monoclonal antibody affects the kinetics parameters of its binding to human KAAG1.
  • a kinetic analysis method was developed using the ProteOn XPR36 instrument from BioRad. Human KAAG1 was immobilized on a sensor chip. Full length antibodies or Fab fragments were injected and allowed to interact with the immobilized KAAG1.
  • the heavy and light chains of the chimeric antibody were amplified by PCR from the original murine immunoglobulin chains using the following oligonucleotide primer pairs: heavy chain, 5′-oligo encoded by SEQ ID NO: 206 and 3′-oligo encoded by SEQ ID NO:207; light chain, 5′-oligo encoded by SEQ ID NO: 208 and 3′-oligo encoded by SEQ ID NO:209.
  • the resulting PCR products were digested by Hind III and cloned into pK-CR5 (SEQ ID NO:210) previously digested with Hind III.
  • the fragments coding for the humanized heavy chain region of the antibody 3A4 were ordered from GenScript (Piscataway, USA).
  • the DNA fragments including the kozak and stop codon sequences were digested with HindIII and cloned into the HindIII site of plasmid pK-CR5 previously dephosphorylated with calf intestinal phosphatase (NEB) to prevent recircularization.
  • FIG. 3 a shows the map of the plasmid pK-CR5-3A4-HC-variant1. All heavy chain variants of the humanized 3A4 were constructed in a similar manner.
  • the fragments coding for the human light chain regions of the antibody 3A4 were ordered from GenScript.
  • the DNA fragments including the kozak and stop codon sequences was digested with BamHI and cloned into the BamHI site of plasmid pMPG-CR5 (SEQ ID NO:211) previously dephosphorylated with calf intestinal phosphatase (NEB) to prevent recircularization.
  • FIG. 3 b shows the map of the plasmid pMPG-CR5-3A4-LC-variant1. All light chain variants of the humanized 3A4 were constructed in a similar manner.
  • Plasmid DNA was isolated from small cultures of E. coli using the Mini-Prep kit (Qiagen Inc, Mississauga, ON) according to the manufacturer's recommendation. Briefly, 2 ml of LB medium containing 100 ⁇ g/ml of ampicillin were inoculated with a single colony picked after ligation and transformation. The cultures were incubated at 37° C. overnight with vigorous shaking (250 RPM). The plasmid was then isolated from 1.5 ml of culture using the protocols, buffers, and columns provided by the kit. The DNA was eluted using 50 ⁇ l of sterile water. Plasmid DNA was isolated from large culture of E.
  • Plasmid Plus Maxi kit Qiagen Inc, Mississauga, ON
  • 200 mL of LB medium containing 100 ⁇ g/mL ampicillin were inoculated with a single fresh colony of E. coli and incubated overnight at 37° C. with vigorous shaking (250 RPM).
  • the bacteria 130 mL of culture for the heavy chain and 180 mL of culture for the light chain
  • the pure plasmids was resuspended in sterile 50 mM Tris, pH8 and quantified by measuring the optical density at 260 nm. Before transfection the purified plasmid were sterilized by extraction with phenol/chloroform followed by ethanol precipitation. The plasmid were resuspended in sterile 50 mM Tris, pH 8 and quantified by optical density at 260 nm.
  • the cells were washed with PBS and resuspended at a concentration of 4.0 ⁇ 10 6 cell/ml in growth medium (CD-CHO, Invitrogen) without dextran sulfate for 3 h in suspension culture.
  • CD-CHO growth medium
  • For each plasmid combination 45 ml of cells were transfected by adding slowly 5 ml of CDCHO medium supplemented with 10 ⁇ g/ml of each plasmid and 50 ⁇ g/ml of polyethylenimine (PEI Max; Polysciences). The final concentration was 1 ⁇ g/ml of each plasmid and 5 ⁇ g/ml of PEI. After 2 h, the cells were transferred at 30° C.
  • CHO cells (CHOcTA) were transfected with plasmids encoding the different variants of humanized heavy and light chains of the 3A4 antibody regulated by the CR5 promoter. Transfection with different combinations of light and heavy chains was performed. As control, cells were also transfected with plasmids encoding the chimeric/murine antibody.
  • the membrane was blocked for 1 h in 0.15% Tween 20, 5% skimmed milk in PBS and incubated for 1 hr with an Goat anti-Human IgG (H+L) conjugated to Cy5 (Jackson, Cat#109-176-099).
  • the signal was revealed and quantified by scanning with the Typhoon Trio+ scanner (GE Healthcare).
  • Typhoon Trio+ scanner GE Healthcare
  • GLM sensorchips the Biorad ProteOn amine coupling kit (EDC, sNHS and ethanolamine), and 10 mM sodium acetate buffers were purchased from Bio-Rad Laboratories (Mississauga, ON). HEPES buffer, EDTA, and NaCl were purchased from from Sigma-Aldrich (Oakville, ON). Ten percent Tween 20 solution was purchased from Teknova (Hollister, Calif.). The goat anti-human IgG Fc fragment specific antibody was purchased from Jackson ImmunoResearch. The gel filtration column Superdex 75 10/300 GL was purchased from GE Healthcare.
  • FIG. 5 represents the profile of the gel filtration of KAAG1. A small peak of potential aggregate is eluting at around 11 ml. The protein eluting at 13 ml was used as analyte for the SPR assay (fractions 15-19).
  • the screening of the 3A4 variants for binding to KAAG1 occurred in two steps: an indirect capture of 3A4 variants from cell supernatant onto the anti-human IgG Fc fragment specific surface in the ligand direction (vertical) followed by a KAAG1 injection in the analyte direction. Firstly, one buffer injection for 30 s at 100 uL/min in the ligand direction was used to stabilize the baseline. For each 3A4 capture, unpurified 3A4 variants in cell-culture media were diluted to 4% in HBST, or approximately 1.25 ⁇ g/mL of purifed 3A4 in HBST was used.
  • 3A4 variants Four to five 3A4 variants along with wild-type 3A4 were simultaneously injected in individual ligand channels for 240 s at flow 25 ⁇ L/min. This resulted in a saturating 3A4 capture of approximately 400-700 RUs onto the anti-human IgG Fc fragment specific surface. The first ligand channel was left empty to use as a blank control if required. This 3A4 capture step was immediately followed by two buffer injections in the analyte direction to stabilize the baseline, and then the gel filtration purified KAAG1 was injected.
  • KAAG1 concentrations (8, 2.66, 0.89, 0.29, and 0.098 nM) and buffer control were simultaneously injected in individual analyte channels at 50 ⁇ L/min for 120 s with a 600s dissociation phase, resulting in a set of binding sensorgrams with a buffer reference for each of the captured 3A4 variants.
  • the anti-human IgG Fc fragment specific-3A4 complexes were regenerated by a 18 s pulse of 0.85% phosphoric acid for 18 s at 100 ⁇ L/min to prepare the anti-human IgG Fc fragment specific surface for the next injection cycle.
  • FIG. 6 summarizes the association (k a , 1/Ms) and dissociation (k d , 1/s) rate constants as well as affinity (K D , M) constants for the interaction of KAAG1 with purified murine 3A4, murine 3A4 transiently expressed as a chimeric and transiently expressed humanized variants. These constants are graphically represented in FIG. 7 a - c .
  • the association rate constant is very similar for the pure parental, chimeric and humanized 3A4 variants ( FIG. 7 a ).
  • the dissociation rate constants is similar for the transiently express chimeric as compared to the pure parental 3A4 with suggest that the transfection procedure did not alter the parameters of the interaction of KAAG1 with the antibody ( FIG. 7 b ).
  • all humanized variants seem to have a slightly altered off rate, i.e. quicker dissociation rate ( FIG. 7 b ). This is reflected in the affinity constants ( FIG. 7 c ).
  • ELISA methods were also used to compare the binding activity of the humanized 3A4 variants to the murine 3A4 antibody.
  • Recombinant human KAAG1 was coated in 96-well plates O/N, washed and incubated for 1 h at RT with increasing quantities of murine or humanized 3A4 variants.
  • an anti-human antibody conjugated to HRP was added to the wells and the bound 3A4 antibody was measured calorimetrically at Abs 450 . As shown in FIG.
  • the humanized variants (Lh1Hh1, Lh1Hh2, Lh1Hh3 and Lh1Hh4) displayed very similar binding to KAAG1 when compared to the murine 3A4 (LcHc), which has a high affinity of 0.016 nM.
  • LcHc murine 3A4
  • FIG. 8 a shows the results when the heavy chain variants were assembled with Lh2 variant of the 3A4 humanized light chain. In this instance, there was a difference in the binding of the variants.
  • Lh2hh4 was the variant with the closest profile compared to the murine 3A4.
  • SKOV-3 ovarian cancer cells which we had previously showed were efficiently bound by 3A4 by flow cytometry, were incubated with the eight humanized variants and the original murine antibody. Briefly, SKOV-3 cells were detached from the plate with EDTA and incubated on ice with either 3.0 mg/ml, 0.3 mg/ml or 0.3 mg/ml of the antibodies for 1 h. After three washing steps, the cells were incubated with the secondary antibody, anti-human IgG-conjugated to FITC for 1 h on ice.
  • This example describes the use of anti-KAAG1 antibodies for detecting the expression of KAAG1 in TNBC.
  • Tissue microarrays were obtained that contained 139 breast tumor samples generated from patient biopsies. Paraffin-embedded epithelial breast tumor samples were placed on glass slides and fixed for 15 min at 50° C. Deparaffinization was conducted by treating 2 ⁇ with xylene followed by dehydration in successive 5 min washes in 100%, 80%, and 70% ethanol. The slides were washed 3 ⁇ in PBS for 5 min and treated with antigen retrieval solution (1 mM EDTA, pH 8.0) to unmask the antigen.
  • antigen retrieval solution (1 mM EDTA, pH 8.0
  • Endogenous peroxide reactive species were removed by incubating slides with H 2 O 2 in methanol and blocking was performed by incubating the slides with serum-free blocking solution (Santa Cruz Biotech) for 5 min at room temperature.
  • the primary antibody (anti-KAAG1 3A4) was added for 1 h at room temperature.
  • KAAG1-reactive antigen was detected by incubating with biotin-conjugated mouse anti-kappa followed by streptavidin-HRP tertiary antibody. Positive staining was revealed by treating the slides with DAB-hydrogen peroxide substrate for less than 5 min and subsequently counterstained with hematoxylin.
  • the KAAG1 protein was found to be expressed at very high levels in the vast majority of breast tumor samples.
  • FIG. 10 A representative array containing 139 tumors is depicted in FIG. 10 .
  • 15/20 biopsy samples confirmed to be TNBC ( FIG. 10 , samples identified by an asterisk) were stained strongly for KAAG1 expression with the 3A4 antibody.
  • these immunohistochemical studies illustrate the utility of detecting KAAG1 in breast cancer, in particular TNBC, with the monoclonal antibodies.
  • This example describes the use of anti-KAAG1 antibodies for detecting the expression of KAAG1 in TNBC cell lines.
  • the cells were harvested using 5 mM EDTA, counted with a hemocytometer, and resuspended in FCM buffer (0.5% BSA, 0.01% goat serum in 1 ⁇ PBS) at a cell density of 2 ⁇ 10 6 cells/ml.
  • Chimeric 3A4 anti-KAAG1 antibody or a control IgG were added to 100 ⁇ l of cells at a final concentration of 0.5 ⁇ g/ml and incubated on ice for 1 h.
  • the cells were washed in cold FCM buffer to remove unbound antibodies, resuspended in 100 ⁇ l FCM buffer containing anti-human IgG conjugated to FITC secondary antibody (diluted 1:200) and incubated on ice for 45 min.
  • the cells were resuspended in 300 ⁇ l FCM buffer and analyzed with a flow cytometer. 10 ⁇ g/ml propidium iodide was added to each sample to allow for gating of dead cells.
  • MFI mean fluorescence intensity
  • FIG. 11 where the mean fluorescence intensity (MFI) fold Induction represents the geometric mean value of the signal obtained when the cells were incubated with 3A4 antibody over that of the negative human IgG control, which was arbitrarily set to 1.
  • Incubation of the antibodies with the control 293-6EHEK-293 cells resulted in fluorescence signals that were similar to the signal obtained when the cells were incubated in the absence of the primary antibody.
  • the KAAG1 antigen was detected by 3A4 on the surface of cancer cells using flow cytometry.
  • molecular events that can occur upon binding of an antibody to its target on the surface of cells. These include i) blocking accessibility to another cell-surface antigen/receptor or a ligand, ii) formation of a relatively stable antibody-antigen complex to allow cells to be targeted via ADCC or CDC, iii) signalling events can occur as exemplified by agonistic antibodies, iv) the complex can be internalized, or v) the complex can be shed from the cell surface.
  • To address this question we examined the behavior of the 3A4 antibody-KAAG1 complex on the surface of the cells.
  • the ovarian cancer cell line, SKOV3, was used as a positive control in this experiment since it was successfully used in previous internalization experiments (see PCT/CA2009/001586).
  • MDA-MB-231 TNBC cells were plated, washed, and incubated with 0.5 ⁇ g/ml chimeric 3A4 antibody as described in Example 3. After washing, complete medium was added and the cells placed at 37° C. for up to 60 minutes. The cells were removed at the indicated times (see FIG. 12 ), rapidly cooled, prepared for flow cytometry with FITC-conjugated anti-human IgG and the results were expressed as the percentage of mean fluorescence intensity remaining on the cell surface compared with the signal at time 0 minutes (see FIG.
  • MDA-MB-231 cells were seeded on cover slips and once the cells were properly adhered, fresh medium was added containing the 3A4 anti-KAAG1 chimeric antibody at 10 ug/ml and incubating at 37 C for 4 h. The cells were washed in PBS then fixed in 4% paraformaldehyde (in PBS) for 20 min. After washing, the cells were permeabilized with 0.1% Triton X-100 in PBS for 5 min. Blocking was performed with 1.5% dry milk in PBS for 1 h.
  • Lysosomal-associated membrane protein 1 (LAMP1, Chang et al., 2002) was detected by incubating with anti-LAMP1 (Santa Cruz, sc-18821, diluted 1:100) in 1.5% milk in PBS for 2 h. After washing in PBS, the secondary antibodies were added together in 1.5% milk and incubated for 1 h.
  • the secondary antibody was a Rhodamine Red-X conjugated donkey anti-human IgG (H+L) diluted 1:300.
  • the anti-LAMP1 antibody the secondary antibody was a DyLight488-conjugated goat anti-mouse IgG (H+L) diluted 1:300. Both secondary antibodies were from Jackson ImmunoResearch.
  • the coverslips were washed in PBS and mounted in ProLong Gold antifade reagent with DAPI.
  • the 3A4 antibody was able to be detected in complexes predominantly near the peri-nuclear area (arrows, see red staining in the left panel in FIG. 16 ), which is typical of endosomal-lysosomal-based internalization pathways.
  • This observation was further confirmed when a lysosomal marker, LAMP1 was visualized and was found to be also expressed in these areas (arrows, see green staining in the middle panel in FIG. 16 ).
  • ADCs antibody drug conjugates
  • cytotoxic drug may become active once internalized in the cells.
  • 3A4 ADCs The ability of the 3A4 ADCs to detect KAAG1 on the surface of TNBC cells was determined using flow cytometry using the methods described herein. Briefly, unconjugated 3A4, 3A4-ADC1, 3A4-ADC2 and a control IgG were incubated in the presence of MDA-231 TNBC cells, which are KAAG1 positive. Results indicated that the conjugation of 3A4 with either drug did not affect its binding to triple negative breast cancer cells such as MDA-231 (data not shown).
  • MDA-231 or TOV-112D cells were cultured as described above in previous examples. The cells were seeded at 3000 cells/well in 96-well plates in 200 ⁇ l of media per well overnight at 37° C., in 5% CO 2 . The next day, media was replaced with fresh media containing antibodies, at concentrations ranging from 0.122 nM to 500 nM, and incubated at 37° C. for 72 h. All conditions were performed in triplicate wells.
  • the number of surviving cells was determined by performing a cellular proliferation assay, using CellTiter 96 Aqueous One Solution (Promega, Madison, Wis.), following manufacturer's protocol. Following the collection of the raw data, the results were expressed as the percentage survival compared to the number of cells in the wells treated with PBS, which was set to 100%. Results indicated that the unconjugated 3A4 did not affect the proliferation of MDA-231 cells at all concentrations tested. In contrast, the 3A4 ADCs tested showed significant cytotoxicity.
  • 3A4 antibody conjugates may be used as an alternative treatment for patients having triple negative breast cancer or basal-like breast cancer. Similar results are expected for conjugates based on humanized 3A4 antibodies.
  • 105- 3E8 light chain variable region DAVMTQIPLTLSVTIGQPASISC KSSQSLLHSDGKTYLN WLLQRPGQSPKRLIY LVSKLDS GVPD RFTGSGSGTDFTLKISRVEAEDLGVYYC WQGTHFPRT FGGGTKLEIK SEQ ID NO.
  • 106- 3E10 light chain variable region DIVMTQAAPSVPVTPGESVSISC RSSKSLLHSNGNTYLY WFLQRPGQSPQLLIY RMSNLAS GVPD RFSGSGSGTAFTLRISRVEAEDVGVYYC MQHLEYPYT FGGGTKLEIK SEQ ID NO.
  • HQVQVQQPGAELVRPGASVTLSCKAS GYIFTDYEVH WVRQRPVHGLEWIG VIDPETGDTA YNQKF KGKATLTADKSSSTAYMELSSLTAEDSAVYYC IGYADY WGQGTTLTVSS SEQ ID NO. 130- 3B1 heavy chain variable region HQVQLQQPGAELVRPGASVTLSCKAS GYTFTDYEIH WVKQTPVHGLEWIG VIDPETGGTA YNQKF KGKATLTTDKSSSTAYMELRSLTSEDSAVYYC MGYSDY WGQGTTLTVSS SEQ ID NO.
  • HQVQLQQSGAELVRPGASVTLSCKAS GYTFSDYEMH WVKQTPVHGLEWIG GIDPETGDTV YNQKF KGKATLTADKSSSTAYMELSSLTSEDSAVYYC ISYAMDY WGQGTSVTVSS SEQ ID NO.
  • X a1 may be a hydrophobic amino acid
  • X a2 may be A or P;
  • X a3 may be neutral hydrophilic amino acid
  • X a4 may be L or P;
  • X a5 may be an acidic amino acid
  • X a6 may be Q or P
  • X a7 may be a basic amino acid
  • X a8 may be a hydrophobic amino acid
  • X a9 may be A or Q
  • X a10 may be a basic amino acid; or Wherein X a11 may be a hydrophobic amino acid, wherein at least one of the amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:48.
  • X A1 may be V or I
  • X A2 may be A or P
  • X A3 may be S or T
  • X A4 may be L or P
  • X A5 may be D or E
  • X A6 may be Q or P
  • X A7 may be K or Q
  • X A8 may be L or V
  • X A9 may be A or Q
  • X A10 may be R or K or
  • X A11 may be L or I
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:48.
  • X b1 may be a hydrophobic amino acid
  • X b2 may be P or A
  • X b3 may be a hydrophobic amino acid
  • X b4 may be V or K
  • X b5 may be a hydrophobic amino acid
  • X b6 may be a basic amino acid
  • X b7 may be S or A;
  • X b8 may be H or P
  • X b9 may be a basic amino acid
  • X b10 may be S or G;
  • X b11 may be a hydrophobic amino acid
  • X b12 may be a basic amino acid
  • X b13 may be a hydrophobic amino acid
  • X b14 may be I or T;
  • X b15 may be a hydrophobic amino acid
  • X b16 may be a hydrophobic amino acid
  • X b17 may be K or T;
  • X b18 may be a neutral hydrophilic amino acid
  • X b19 may be Q or E;
  • X b20 may be N or S
  • X b21 may be T or R;
  • X b22 may be a neutral hydrophilic amino acid
  • X b23 may be S or L
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:46.
  • X B1 may be I or V
  • X B2 may be P or A
  • X B3 may be M or V;
  • X B4 may be V or K
  • X B5 may be M or V;
  • X B6 may be K or R
  • X B7 may be S or A
  • X B8 may be H or P
  • X B9 may be K or Q
  • X B10 may be S or G
  • X B11 may be I or M
  • X B12 may be K or R
  • X B13 may be A or V
  • X B14 may be I or T
  • X B15 may be L or I
  • X B16 may be V or A
  • X B17 may be K or T
  • X B18 may be S or T
  • X B19 may be Q or E;
  • X B20 may be N or S
  • X B21 may be T or R
  • X B22 may be S or T;
  • X B23 may be S or L
  • amino acid identified by X is an amino acid substitution (conservative or non-conservative) in comparison with a corresponding amino acid in the polypeptide set forth in SEQ ID NO.:46.

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