# Patent

## Title
Anti-c-met antibodies

## Abstract

The present invention relates to antibodies, or antigen-binding fragments thereof, that bind to the extracellular domain of human c-Met, compositions and kits comprising such c-Met antibodies, or antigen-binding fragments thereof, and methods of using the same for detection of human c-Met that aid in identifying patients with tumors expressing or overexpressing human Met and/or improving their treatment response with anti-c-Met therapeutics.

## Background
The present invention relates to the field of medicine. More particularly, the present invention relates to antibodies, or antigen-binding fragments thereof, that bind human c-Met (also known as MET) to form a detectable c-Met/anti-c-Met antibody complex useful in diagnostic techniques that require labeling, marking, or identifying human c-Met, such as imaging, prognostic or predictive applications that aid in identifying patients with tumors expressing or overexpressing human c-Met protein and/or improving their treatment response with anti-c-Met therapeutics.
The protein c-Met is a member of the receptor tyrosine kinase superfamily, and the receptor for hepatocyte growth factor (HGF), also known as scatter factor (SF). The mature human c-Met protein is composed of a completely extracellular alpha subunit, a beta subunit comprised of an extracellular ligand binding domain, a single transmembrane domain, and a cytoplasmic tyrosine kinase domain.
Activation of human c-Met by HGF has been shown to enhance characteristics that are associated with an invasive cell phenotype: proliferation, migration, morphogenesis, survival, and protease synthesis. The human c-Met signaling pathway is one of the most frequently dysregulated pathways in human cancers, and is implicated in virtually all types of solid tumors. The stimulation, overexpression, or mutation of human c-Met is observed in many types of cancers, including colon, breast, ovary, lung, liver, prostate, pancreas, bile ducts, brain, thyroid, kidney, gastric, as well as melanomas and sarcomas. These biochemical and genetic abnormalities of the HGF/c-Met signaling axis are correlated with poor clinical outcomes and drug resistance in cancer patients.
Due to the role of the human c-Met signaling pathway in regulating initial steps of tumor formation and subsequent disease dissemination, human c-Met is considered to be an attractive target for cancer therapy with small molecule and antibody antagonists of HGF or c-Met in development. Given the small molecule and antibody antagonists to human c-Met that are in development, diagnostic antibodies are needed for the analysis of patient cancers for human c-Met.
PCT International Publication WO2009/029591 discloses a monoclonal antibody, designated MET4, that is reported to bind the ECD of human c-Met, and to be capable of staining c-Met in formalin fixed and paraffin embedded (FFPE) tumor tissues.
For evaluation of the level of expression or overexpression of human c-Met in the tumor cells of a cancer patient, either before, during, or after treatment with small molecule or antibody antagonists to human c-Met, there is a need for alternative human c-Met diagnostic antibodies that can specifically bind to an ECD of membrane localized human c-Met. Further, for evaluation of the level of expression or overexpression of human c-Met in the tumor cells of a cancer patient undergoing treatment with a therapeutic anti-c-Met agent, there is a need for human c-Met diagnostic antibodies that can specifically bind to human c-Met when the c-Met is already bound to a therapeutic anti-c-Met agent.
For a human c-Met diagnostic antibody, specificity and selectivity to human c-Met are also extremely important. Avoidance of cross-reactivity with closely related receptor tyrosine kinase family members of c-Met, such as human RON (also known as MST1R) is critical for a human c-Met diagnostic antibody. Therefore, there is also a need for human c-Met diagnostic antibodies that can specifically and selectively (e.g., without significant binding to human RON) bind to membrane localized human c-Met.
Accordingly, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 comprises the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 comprises the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 comprises the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 comprises the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 comprises the polypeptide of GFHPGNSGTNYNQKFKG (SEQ ID NO: 5) or GFHPRNSGTNYNQKFKG (SEQ ID NO: 6), and the HCDR3 comprises the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).
In an embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 comprises the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 comprises the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 comprises the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 comprises the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 comprises the polypeptide of GFHPGNSGTNYNQKFKG (SEQ ID NO: 5), and the HCDR3 comprises the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).
In an embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 comprises the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 comprises the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 comprises the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 comprises the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 comprises the polypeptide of GFHPRNSGTNYNQKFKG (SEQ ID NO: 6), and the HCDR3 comprises the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).
In an embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 is the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 is the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 is the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 is the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 is the polypeptide of GFHPGNSGTNYNQKFKG (SEQ ID NO: 5) or GFHPRNSGTNYNQKFKG (SEQ ID NO: 6), and the HCDR3 is the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).
In an embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 is the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 is the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 is the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 is the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 is the polypeptide of GFHPGNSGTNYNQKFKG (SEQ ID NO: 5), and the HCDR3 is the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).
In an embodiment, the present invention provides an antibody that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 is the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 is the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 is the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 is the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 is the polypeptide of GFHPGNSGTNYNQKFKG (SEQ ID NO: 5), and the HCDR3 is the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).
In an embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 is the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 is the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 is the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 is the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 is the polypeptide of GFHPRNSGTNYNQKFKG (SEQ ID NO: 6), and the HCDR3 is the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).
In an embodiment, the present invention provides an antibody that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 is the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 is the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 is the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 is the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 is the polypeptide of GFHPRNSGTNYNQKFKG (SEQ ID NO: 6), and the HCDR3 is the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).
In an embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising an LCVR and an HCVR, wherein the LCVR is the polypeptide of SEQ ID NO: 8, and the HCVR is the polypeptide of SEQ ID NO: 9 or SEQ ID NO: 10. In a further embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising an LCVR and an HCVR, wherein the LCVR is the polypeptide of SEQ ID NO: 8, and the HCVR is the polypeptide of SEQ ID NO: 9. In another embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising an LCVR and an HCVR, wherein the LCVR is the polypeptide of SEQ ID NO: 8, and the HCVR is the polypeptide of SEQ ID NO: 10.
In an embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain (LC) and a heavy chain (HC), wherein the LC is the polypeptide of SEQ ID NO: 11, and the HC is the polypeptide of SEQ ID NO: 12 or SEQ ID NO: 13. In a further embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain (LC) and a heavy chain (HC), wherein the LC is the polypeptide of SEQ ID NO: 11, and the HC is the polypeptide of SEQ ID NO: 12. In another embodiment, the present invention provides an antibody, or antigen-binding fragment thereof, that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising a light chain (LC) and a heavy chain (HC), wherein the LC is the polypeptide of SEQ ID NO: 11, and the HC is the polypeptide of SEQ ID NO: 13.
In an embodiment, the present invention provides an antibody that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 12. In an embodiment, the present invention provides an antibody that specifically binds to the ECD of human c-Met (SEQ ID NO: 24), comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 13.
The present invention provides compositions comprising an antibody, or antigen-binding fragment thereof, of the present invention, and an acceptable carrier, diluent, or excipient. More particularly, the compositions of the present invention further comprise one or more additional diagnostic agents.
The present invention provides a kit comprising an antibody, or antigen-binding fragment thereof, of the present invention. In an embodiment, the kit of the present invention further comprises a container comprising a secondary antibody that specifically binds to the antibody of the present invention. In a further embodiment, the kit of the present invention further comprises a container comprising a secondary antibody that specifically binds to the antibody of the present invention. Preferably, the secondary antibody is an anti-mouse IgG antibody such as an anti-mouse IgG1 antibody.
In an embodiment, the present invention provides a method of detecting human c-Met expressed or overexpressed by a human cell, comprising: (a) contacting the cell in vitro with an antibody, or antigen-binding fragment thereof, of the present invention; (b) removing any unbound or non-specifically bound antibody, or antigen-binding fragment thereof; and (c) detecting, and optionally quantifying the amount of antibody, or antigen-binding fragment thereof which is specifically bound to the ECD of human c-Met (SEQ ID NO: 24). In a further embodiment, the present invention provides a method of detecting human c-Met expressed or overexpressed by a human cell, comprising: (a) contacting the cell in vitro with an antibody, or antigen-binding fragment thereof, of the present invention; (b) removing any unbound or non-specifically bound antibody, or antigen-binding fragment thereof; and (c) detecting, and optionally quantifying the amount of antibody, or antigen-binding fragment thereof which is specifically bound to the ECD of human c-Met (SEQ ID NO: 24), wherein the human cell is formalin-fixed and paraffin-embedded. In a further embodiment, the present invention provides a method of detecting human c-Met expressed or overexpressed by a human cell, comprising: (a) contacting the cell in vitro with an antibody, or antigen-binding fragment thereof, of the present invention; (b) removing any unbound or non-specifically bound antibody, or antigen-binding fragment thereof; and (c) detecting, and optionally quantifying the amount of antibody, or antigen-binding fragment thereof, which is specifically bound to the ECD of human c-Met (SEQ ID NO: 24), and wherein the detecting is performed by direct or indirect immunohistochemistry (IHC).
In an embodiment, the present invention provides a method of determining or monitoring the response to administration of an anti-c-Met therapeutic agent in a patient, comprising: (a) measuring the amount of human c-Met with an antibody, or antigen-binding fragment thereof, of the present invention, in a first sample isolated from the patient prior to administration of the anti-c-Met therapeutic agent; (b) measuring the amount of human c-Met with an antibody, or antigen-binding fragment thereof, of the present invention in a second sample isolated from the patient after administration of the anti-c-Met therapeutic agent; (c) determining whether there has been a decrease of human c-Met in the second sample compared to the first sample, wherein a decrease in human c-Met indicates that the patient is responding to the anti-c-Met therapeutic agent.
In an embodiment, the present invention provides a method of determining or monitoring the response to administration of an anti-c-Met therapeutic agent in a patient, comprising: (a) measuring the amount of human c-Met with an antibody, or antigen-binding fragment thereof, of the present invention, in a first sample isolated from the patient prior to administration of the anti-c-Met therapeutic agent; (b) measuring the amount of human c-Met with an antibody, or antigen-binding fragment thereof, of the present invention in a second sample isolated from the patient after administration of the anti-c-Met therapeutic agent; (c) determining whether there has been a decrease of human c-Met in the second sample compared to the first sample, wherein a decrease in human c-Met indicates that the patient is responding to the anti-c-Met therapeutic agent, and wherein the anti-c-Met therapeutic agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22.
In an embodiment, the present invention provides a method of determining or monitoring the response to administration of an anti-c-Met therapeutic agent in a patient, comprising: (a) measuring the amount of human c-Met with an antibody, or antigen-binding fragment thereof, of the present invention, in a first sample isolated from the patient prior to administration of the anti-c-Met therapeutic agent; (b) measuring the amount of human c-Met with an antibody, or antigen-binding fragment thereof, of the present invention in a second sample isolated from the patient after administration of the anti-c-Met therapeutic agent; (c) determining whether there has been a decrease of human c-Met in the second sample compared to the first sample, wherein a decrease in human c-Met indicates that the patient is responding to the anti-c-Met therapeutic agent, and wherein the anti-c-Met therapeutic agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine.
In an embodiment, the present invention provides an antibody of the present invention, for use in diagnosis, prognosis and/or prediction of a cancer treatment response with an anti-c-Met therapeutic antibody or small molecule c-Met therapeutic compound.
In an embodiment, the present invention provides use of an antibody, or antigen-binding fragment thereof, of the present invention, for:
(a) detecting, and optionally quantifying human c-Met in or on a human cell;
(b) detecting, and optionally quantifying human c-Met expressing or overexpressing tumor cells in a patient;
(c) detecting and, optionally, quantifying human c-Met expressing or overexpressing circulating tumor cells in a blood sample of a patient;
(d) detecting and, optionally, quantifying human c-Met expressing or overexpressing tumor cells in a bodily fluid from a cancer patient;
(e) assessing whether an individual has cancer of a tissue or organ wherein human c-Met is expressed or overexpressed;
(f) selecting a patient having a tumor suitable for treatment with an anti-c-Met therapeutic agent; or
(g) determining response to treatment with an anti-c-Met therapeutic agent.
In a further embodiment, the present invention provides use of an antibody, or antigen-binding fragment thereof, of the present invention, wherein the detection, and, optionally, the quantification of human c-Met is performed by IHC. In a further embodiment, the present invention provides use of an antibody, or antigen-binding fragment thereof, of the present invention, wherein the anti-c-Met agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22, or wherein the anti-c-Met agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine.
In an embodiment, the present invention provides a method of selecting a patient, having a tumor in which human c-Met is expressed or overexpressed, for treatment with an anti-c-Met therapeutic antibody or small molecule c-Met therapeutic compound, comprising: (a) contacting a sample of the tumor with an antibody, or antigen-binding fragment thereof, of the present invention; (b) removing any unbound or non-specifically bound antibody, or antigen-binding fragment thereof; and (c) detecting and, optionally, quantifying the amount of antibody, or antigen-binding fragment thereof, which is specifically bound to the ECD of human c-Met, wherein the presence of the antibody, or antigen-binding fragment thereof, specifically bound to the ECD of human c-Met identifies the patient as being appropriate for treatment with the anti-c-Met therapeutic antibody or small molecule c-Met therapeutic compound.
In an embodiment, the present invention provides a method of predicting a patient's response to administration of an anti-c-Met therapeutic antibody or small molecule c-Met therapeutic compound, comprising: (a) contacting a sample of a tumor from the patient with an antibody, or antigen-binding fragment thereof, of the present invention; (b) removing any unbound or non-specifically bound antibody, or antigen-binding fragment thereof; and (c) detecting and, optionally, quantifying the amount of antibody, or antigen-binding fragment thereof, which is specifically bound to the ECD of human c-Met, wherein the presence of the antibody, or antigen-binding fragment thereof, specifically bound to the ECD of human c-Met indicates that the patient will likely respond to the administration of an anti-c-Met therapeutic antibody or small molecule c-Met therapeutic compound.
In an embodiment, the present invention provides a method of treating cancer, comprising: (a) selecting a patient in need of treatment thereof, wherein the patient has a tumor in which human c-Met is expressed or overexpressed as determined by detecting human c-Met with an antibody, or antigen-binding fragment thereof, of the present invention; and (b) treating the patient with an anti-c-Met therapeutic agent, wherein the anti-c-Met therapeutic agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22, or wherein the anti-c-Met agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine. In various embodiments of the methods of the present invention, the cancer being treated is gastric cancer, non-small cell lung cancer, colon, cholangiocarcinoma, head and neck cancer, or kidney cancer. In various embodiments of the methods of the present invention, the detecting human c-Met is with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 12, or with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 13.
In an embodiment, the present invention provides a method of treating cancer in a patient, comprising testing for the presence of human c-Met in a biological sample from the patient and administering a therapeutically effective amount of an anti-c-Met therapeutic agent to the patient if the sample tests positive for human c-Met as determined by detection with an antibody, or antigen-binding fragment thereof, of the present invention, and wherein the anti-c-Met therapeutic agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22, or wherein the anti-c-Met agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine. In various embodiments of the methods of the present invention, the cancer being treated is gastric cancer, non-small cell lung cancer, colon, cholangiocarcinoma, head and neck cancer, or kidney cancer. In various embodiments of the methods of the present invention, the detecting human c-Met is with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 12, or with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 13. In various embodiments of the methods of the present invention, the biological sample is formalin-fixed and paraffin-embedded.
In an embodiment, the present invention provides a method of treating cancer in a patient, comprising administering a therapeutically effective amount of an anti-c-Met therapeutic agent to the patient provided that the patient is selected for treatment if a biological sample from the patient tests positive for human c-Met as determined by detection with an antibody, or antigen-binding fragment thereof, of the present invention, and wherein the anti-c-Met therapeutic agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22, or wherein the anti-c-Met agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine. In various embodiments of the methods of the present invention, the cancer being treated is gastric cancer, non-small cell lung cancer, colon, cholangiocarcinoma, head and neck cancer, or kidney cancer. In various embodiments of the methods of the present invention, the detecting human c-Met is with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 12, or with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 13. In various embodiments of the methods of the present invention, the biological sample is formalin-fixed and paraffin-embedded.
In an embodiment, the present invention provides an anti-c-Met therapeutic agent, for use in the treatment of cancer comprising (a) selecting a patient in need of treatment thereof, wherein the patient has a tumor in which human c-Met is expressed or overexpressed as determined by detecting human c-Met with an antibody, or antigen-binding fragment thereof, of the present invention, and (b) treating the patient with the anti-c-Met therapeutic agent, wherein the anti-c-met therapeutic agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22, or wherein the anti-c-Met therapeutic agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine. In various embodiments of the present invention for use in the treatment of cancer, the cancer is gastric cancer, non-small cell lung cancer, colon, cholangiocarcinoma, head and neck cancer, or kidney cancer. In various embodiments of the present invention for use in the treatment of cancer, human c-Met is detected with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 12, or with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 13.
In an embodiment, the present invention provides an anti-c-Met therapeutic agent, for use in treating cancer, comprising performing an in vitro assay using a biological sample from a patient, determining the presence of human c-Met by detection with an antibody, or antigen-binding fragment thereof, of the present invention, and administering a therapeutically effective amount of the anti-c-Met therapeutic agent to the patient if human c-Met is present, wherein the anti-c-Met therapeutic agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22, or wherein the anti-c-Met therapeutic agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine. In various embodiments of the present invention for use in the treatment of cancer, the cancer is gastric cancer, non-small cell lung cancer, colon, cholangiocarcinoma, head and neck cancer, or kidney cancer. In various embodiments of the present invention for use in the treatment of cancer, human c-Met is detected with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 12, or with an antibody comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 13.
In various embodiments of the methods of the present invention, the detection of binding of an antibody, or antigen-binding fragment thereof, of the present invention to the ECD of human c-Met is performed by immunoassay techniques, such as IHC, flow cytometry, western blotting, or ELISA. More preferably, the detection of binding of an antibody, or antigen-binding fragment thereof, of the present invention to the ECD of human c-Met is performed by IHC.
In further embodiments of this aspect of the invention, the human cell can be formalin fixed and paraffin-embedded, and the detecting can be performed by direct or indirect IHC. Indirect IHC can comprise the use of a secondary, enzyme-conjugated monoclonal antibody or antigen-binding fragment thereof that binds the c-Met or competing monoclonal antibody or antigen-binding fragment thereof, and c-Met can be detected by the use of a chromogenic substrate of the enzyme.
In another embodiment, the antibodies, or antigen-binding fragments thereof, of the present invention may be used to detect circulating tumor cells (CTCs). CTCs are tumor cells that are shed from tumors, survive within the bloodstream during transit and initiate a new growth in distant sites. Detecting CTCs is useful as CTCs can be found in patients before a tumor is detected. CTCs are also found in a significant proportion of patients when a carcinoma recurs, and CTCs persist in some patients after removal of the primary tumor. Evidence suggests that CTCs are derived from clones in the primary tumor as well as metastatic tumors and that they may reflect the tumor burden at all stages of tumor progression. Thus, in addition to a potential role in early diagnosis and prognostication, CTCs may play a major role in characterizing genetic and phenotypic changes with tumor progression, thereby helping to guide targeted therapy. More particularly, the antibodies, or antigen-binding fragments thereof, of the present invention may be useful in assays that can capture, identify, and/or quantify CTCs such as, e.g., the CellSearch® CTC Test (Veridex LLC, San Diego, Calif.), Magnetic Activated Cell Sorting System (MACS®, Miltenyi Biotec GmbH, Germany), Dynal Magnetic Beads® (Invitrogen), EasySep® (Stem Cell Technologies, Vancouver Canada), CTC Chips (On-Q-ity, Waltham, Mass.), or any other test known in the art for the isolation and detection of CTCs such as those described in Sleijfer, et al. Circulating tumour cell detection on its way to routine diagnostic implementation? Eur J Cancer, 43 (18):2645-50 (2007); Lacroix M., Significance, detection and markers of disseminated breast cancer cells. Endocr Relat Cancer., 13 (4):1033-67 (2006); and Pantel, et al., Detection, clinical relevance and specific biological properties of disseminating tumour cells. Nat Rev Cancer, 8 (5):329-40 (2008)). Presently, CellSearch® CTC is the only diagnostic test approved by the USFDA as an automated test to detect and enumerate circulating tumor cells (Fed. Reg. 69(91):26036-38 (2004). Results from CellSearch® tests have been used to monitor disease progression and therapeutic efficacy in metastatic prostate (Danila, et al., Circulating tumor cell number and prognosis in progressive castration-resistant prostate cancer. Clin Cancer Res., 13(23):7053-58 (2007)), colorectal (Cohen, et al., Isolation and characterization of circulating tumor cells in patients with metastatic colorectal cancer. Clin Colorectal Cancer 6 (2):125-32 (2006)), and breast (Cristofanilli, et al. Circulating tumor cells, disease progression, and survival in metastatic breast cancer. N Engl J Med., 351(8):781-91 (2004)) cancer. An antibody, or antigen-binding fragment thereof, of the present invention, e.g., Antibody I or II, described herein and in particular in Table 1 below, can be used in such methods, e.g., CellSearch® tests, and in some cases performed at the start of therapy and any time during the course of treatment for a c-Met-mediated-cancer. Preferably, an antibody, or antigen-binding fragment thereof, of the present invention may be used in such methods along with antibodies specific for other polypeptides including, but not limited to, EPCAM, DAPI, CD45, and/or cytokeratin (including, but not limited to, cytokeratin 7, 8, 18, and/or 19). Information generated from such testing may be useful for its prognostic value by allowing, e.g., monitoring of disease progression and therapeutic efficacy and may allow earlier (and ongoing) treatment decisions. Further, by permitting simultaneous binding of a detectably labeled antibody, or antigen-binding fragment thereof, of the present invention and a therapeutic anti-c-Met antibody (such as disclosed in WO/2010/059654) a break in treatment with a therapeutic anti-c-Met antibody, i.e., “washing out” the therapeutic antibody to allow the diagnostic antibody to bind c-Met, is not required. Consequently, an antibody, or antigen-binding fragment thereof, of the invention permits uninterrupted therapeutic treatment concomitantly with diagnostic monitoring, as necessary.
As used herein, “c-Met” or “human c-Met” refers to human c-Met; the structure of c-Met is depicted schematically as:




    
    
        SEMA: Sema domain
        PSI: Plexin, Semaphorins, and Integrins domain
        IPT: 4 Immunoglobulins, Plexins, and Transcription (IPT) factor domains
        TM: Transmembrane region
        JM: Juxtamembrane domain
        KD: Kinase domain
    
    


For the human c-Met ECD, the mature protein is the polypeptide of SEQ ID NO: 24. The SEMA domain consists of approximately 500 amino acid residues at the N-terminus of human c-Met, and contains the α-chain (amino acid residues 1-283 of SEQ ID NO: 24, i.e., (SEQ ID NO: 25) and part of the β-chain (amino acid residues 284-495 of SEQ ID NO: 24, i.e., (SEQ ID NO: 26)).
In an embodiment, an antibody, or antigen-binding fragment thereof, of the present invention specifically binds to the ECD of human c-Met. In another embodiment, an antibody, or antigen-binding fragment thereof, of the present invention specifically binds to the IPT domain. In a further embodiment, an antibody, or antigen-binding fragment thereof, of the present invention specifically binds within amino acids 517-538, inclusive, of the mature human c-Met ECD (SEQ ID NO: 24).
The general structure of an “antibody” is very well-known in the art. For an antibody of the IgG type, there are four amino acid chains (two “heavy” chains and two “light” chains) that are cross-linked via intra- and inter-chain disulfide bonds. When expressed in certain biological systems, antibodies having unmodified human Fc sequences are glycosylated in the Fc region. Antibodies may be glycosylated at other positions as well. One of skill in the art will appreciate that antibodies of the present invention may contain such glycosylation. The subunit structures and three-dimensional configurations of antibodies are well known in the art. Each heavy chain is comprised of an N-terminal heavy chain variable region (“HCVR”) and a heavy chain constant region (“HCCR”). The heavy chain constant region is comprised of three domains (CH1, CH2, and CH3) for IgG, IgD, and IgA; and 4 domains (CH1, CH2, CH3, and CH4) for IgM and IgE. Each light chain is comprised of a light chain variable region (“LCVR”) and a light chain constant region (“LCCR”). The variable regions of each light/heavy chain pair form the antibody binding site.
An antibody, or antigen-binding fragment thereof, of the present invention can be produced using techniques well known in the art, e.g., recombinant technologies, phage display technologies, synthetic technologies, or combinations of such technologies or other technologies readily known in the art. Methods for producing and purifying antibodies and antigen-binding fragments are well known in the art and can be found, for example, in Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., chapters 5-8 and 15, ISBN 0-87969-314-2.
An antibody, or antigen-binding fragment thereof, of the present invention is an engineered antibody that has been designed to have frameworks, hinge regions, and constant regions of human origin that are identical with or substantially identical (substantially human) with frameworks and constant regions derived from human genomic sequences. Fully human frameworks, hinge regions, and constant regions are those human germline sequences as well as sequences with naturally-occurring somatic mutations and/or those with engineered mutations. An antibody, or antigen-binding fragment thereof, of the present invention may comprise framework, hinge, or constant regions derived from a fully human framework, hinge, or constant region containing one or more amino acid substitutions, deletions, or additions therein. Further, an antibody, or antigen-binding fragment thereof, of the present invention is substantially non-immunogenic in humans.
The antibodies, or antigen-binding fragments thereof, of the present invention may be useful as diagnostics to aid in identification of cancer patients with tumor cells expressing relatively high levels of c-Met. Furthermore, such antibodies, or antigen-binding fragments thereof, may be used to monitor and, optionally, optimize a cancer patient's treatment with c-Met targeted therapeutic agents, such as the small molecule c-Met therapeutic compounds described in WO2010/011538 and U.S. patent application Ser. No. 13/188,496, for example, Structures 1 and 2 hereafter, as well as anti-c-Met therapeutic antibodies, such as those described in WO2010/059654 and WO2006/015371, including, but not limited to, C8-H241 and MetMAb. More specifically, the antibodies, or antigen-binding fragments thereof, of the present invention may be used to monitor, and optionally optimize, a cancer patient's treatment with the anti-c-Met therapeutic antibody C8-H241 (Chemical Abstracts Service (CAS) #1365287-97-3). The anti-c-Met antibody C8-H241 comprises two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22. Alternatively, the anti-c-Met therapeutic antibody comprises two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 21. More specifically, the antibodies, or antigen-binding fragments thereof, of the present invention may be used to monitor, and optionally optimize, a cancer patient's treatment with the anti-c-Met therapeutic antibody MetMAb. As used herein, “MetMAb” is intended to mean a humanized one-armed 5D5 (OA-5D5; onartuzumab, CAS #1133766-06-9) antibody having the light chain as shown in SEQ ID NO: 27 and the heavy chain as shown in SEQ ID NO: 28. MetMAb may be produced in mammalian cells or E. coli; mammalian cells may include HEK 293 EBNA cells. More specifically, the antibodies, or antigen-binding fragments thereof, of the present invention may be used to monitor, and, optionally, optimize, a cancer patient's treatment with the small molecule c-Met therapeutic compounds shown below as Structure 1 and Structure 2, or pharmaceutically acceptable salts thereof.
Structure 1: N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide




Structure 2: 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine




The phrase “specifically binds” as used herein in reference to the affinity of a c-Met antibody, or antigen-binding fragment thereof, for the ECD of human c-Met is intended to mean, unless indicated otherwise, a KD of less than about 1×10−8 M, preferably, less than about 1×10−9 M as determined by common methods known in the art, including by use of a surface plasmon resonance (SPR) biosensor at 25° C. essentially as described herein. The term “selective” used herein in reference to an antibody, or antigen-binding fragment thereof, of the present invention refers to an antibody, or antigen-binding fragment thereof, that binds the ECD of human c-Met with a KD about 1000-, 500-, 200-, 100-, 50-, 10-, or about 5-fold lower than the antibody, or antigen-binding fragment thereof, binds at least one member of the human tyrosine kinase family, including, but not limited to, human RON, as measured by surface plasmon resonance at 25° C. Additionally, or alternatively, a c-Met selective antibody, or antigen-binding fragment thereof, of the present invention binds to the ECD of human c-Met but does not bind or only minimally binds to at least one member of the human tyrosine kinase family, including, but not limited to human RON, when assayed by the immunoassay methods described in Examples 3-7 herein below.
Human c-Met is overexpressed in or on a human cell, CTC, or tumor tissue sample when the quantity of human c-Met is determined to be significantly greater for the human cell, CTC, or tumor tissue sample than the quantity of human c-Met in normal human cells or non-tumor human tissue.
The antibodies, or antigen-binding fragments thereof, disclosed herein are useful for detecting expression, overexpression, or the level of human c-Met present in or on cells, or in or on cells in tissues, organs, bodily fluids, etc., and in diagnostic, prognostic, and/or patient monitoring procedures. The term “bodily fluid” refers to any fluid or other material derived from the body of a normal or diseased subject, such as blood, serum, plasma, lymph, bone marrow, urine, saliva, tears, cerebrospinal fluid, milk, amniotic fluid, bile, urine, bronchial fluid, ascites fluid, pus, and any other biological product. Also included within the meaning of this term is an organ or tissue extract, and a culture fluid in which any cells or tissue preparation from a subject have been incubated.
There are well-known methods in the art that a skilled artisan may use to form stable, detectable antigen-antibody complexes (see, e.g., Antibodies, A Laboratory Manual by Harlow and Lane (current edition), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., for conditions permitting formation of detectable antigen/antibody complexes). In particular, WO 2010/059654 describes exemplary conditions which may permit binding of the antibodies, or antigen-binding fragments thereof, of the present invention including, but not limited to, the antibodies referred to herein as Antibody I and Antibody II. A composition comprising an antibody, or antigen-binding fragment thereof, of the present invention bound to the ECD of human c-Met may also be detected, labeled, and/or identified using methods taught herein or generally known in the art, including, but not limited to, such methods disclosed in Harlow and Lane, ibid, or WO 2010/059654.
A particular protein such as human c-Met can be measured by a variety of immunoassay methods including, e.g., without limitation, competitive and noncompetitive assay systems using techniques such as, e.g., without limitation, western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, and protein A immunoassays. For a review of immunological and immunoassay procedures in general, see Stites and Terr (eds.) (1991) Basic and Clinical Immunology (7th ed.). Moreover, the immunoassays of the invention can be performed in many configurations, which are reviewed extensively in Maggio (ed.) (1980) Enzyme Immunoassay CRC Press, Boca Raton, Fla.; Gosling J P 2000 Immunoassays: A Practical Approach (Practical Approach Series) Oxford Univ Press; Diamandis & Christopoulus, 1996 Immunoassay Academic Press, San Diego, Calif.; Tijan (1985) “Practice and Theory of Enzyme Immunoassays,” Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers B.V., Amsterdam; Wild, D. (Ed.), 2001 The Immunoassay Handbook (2nd edition) Nature Pub Group; James T. Wu, 2000 Quantitative Immunoassay: A Practical Guide for Assay Establishment, Troubleshooting, and Clinical Application, Amer Assn for Clinical Chemistry, Brousseau & Beaudet (Eds.) Manual of Immunological Methods CRC Press Boca Raton, Fla.; and Harlow and Lane Antibodies, A Laboratory Manual, supra. See also Chan (ed.) (1987) Immunoassay: A Practical Guide Academic Press, Orlando, Fla.; Price and Newman (eds.) (1991) Principles and Practice of Immunoassays Stockton Press, NY; and Ngo (ed.) (1988) Non-isotopic Immunoassays Plenum Press, NY.
Immunoassays can be performed by a variety of art-known methods. In brief, immunoassays to measure the human c-Met ECD can be either competitive or noncompetitive binding assays. In competitive binding assays, the sample to be analyzed competes with a labeled analyte for specific binding sites on a capture agent bound to a solid surface. Preferably, the capture agent is an antibody specifically reactive with the human c-Met ECD as described herein. The concentration of labeled analyte bound to the capture agent is inversely proportional to the amount of free analyte present in the sample.
In a competitive binding immunoassay, the target protein present in the sample (i.e., the human c-Met ECD) competes with labeled protein for binding to an antibody of the present invention. The antibody of the present invention may be bound to a solid surface to effect separation of bound-labeled protein from the unbound-labeled protein. Alternately, the competitive binding assay may be conducted in liquid phase and a variety of techniques known in the art may be used to separate the bound-labeled protein from the unbound-labeled protein. Following separation, the amount of bound labeled protein is determined. The amount of protein present in the sample is inversely proportional to the amount of labeled protein binding.
Alternatively, a homogeneous immunoassay may be performed in which a separation step is not needed. In these immunoassays, the label on the protein is altered by the binding of the protein to its specific binding composition. This alteration in the labeled protein results in a decrease or increase in the signal emitted by label, so that measurement of the label at the end of the immunoassay allows for detection or quantitation of the protein.
Competitive assays are also particularly useful, where the cells are contacted and incubated with a labeled antibody having known binding affinity to the protein, such as a 125I-labeled antibody, and a test sample whose binding affinity to the binding composition is being measured. The bound and free-labeled binding compositions are then separated to assess the degree of protein binding. The amount of test compound bound is inversely proportional to the amount of labeled binding partner binding to the known source. Any one of numerous techniques can be used to separate bound from free protein to assess the degree of protein binding. This separation step could typically involve a procedure such as adhesion to filters followed by washing, adhesion to plastic followed by washing, or centrifugation of the cell membranes. Viable cells could also be used to screen for the effects of drugs on a human c-Met mediated function (e.g., second messenger levels, such as, e.g., cell proliferation; inositol phosphate pool changes, transcription using a luciferase-type assay; and others). Some detection methods allow for elimination of a separation step, e.g., a proximity-sensitive detection system.
Qualitative or quantitative analysis of human c-Met may also be determined by a variety of noncompetitive immunoassay methods using the antibodies, or antigen-binding fragments thereof, of the present invention. For example, a two-site, solid phase sandwich immunoassay may be used. In this type of assay, an antibody is attached to a solid support. A second protein-binding composition, which may also be an antibody, and which specifically bind the protein at a different site, is labeled. After binding at both sites on the protein has occurred, the unbound-labeled binding composition is removed and the amount of labeled binding composition bound to the solid phase is measured. The amount of labeled binding composition bound is directly proportional to the amount of protein in the sample.


EXAMPLE 1
Antibody Expression and Purification
The polypeptides of the variable regions of the heavy chain and light chain, the complete heavy chain and light chain amino acid sequences of Antibody I and II, and the nucleotide sequences encoding the same, are listed below in the section entitled “Amino Acid and Nucleotide Sequences.” In addition, the light chain and heavy chain CDR polypeptides are shown in Table 1.
The antibodies, or antigen-binding fragments thereof, of the present invention, including, but not limited to, Antibodies I and II, may be transiently expressed in HEK293 EBNA cells (Edge BioSystems, #90500130) using standard transfection procedures. Transfected cells are cultured in standard serum-free medium containing geneticin (G418) and tobramycin for 48 to 120 hours at 37° C. after transfection. The antibody may be purified on a 60 ml rProtein A Sepharose column (Amersham Biosciences; #17-1279-04) by following well-known procedures and/or the manufacturer's instructions, and further concentrated and purified by size exclusion chromatography (XK50/60 Superdex200, Pharmacia) with phosphate buffered saline (PBS), pH 7.4, as the mobile phase. Next, the antibody preparation may be filtered using a Millex-GV, PVDF membrane, 0.22 μmm, (Millipore; #SLGV033RS) and stored at 4 to 8° C.







TABLE 1





SEQ ID NOs



















Anti-
Light
Heavy




body
Chain
Chain
LCVR
HCVR





I
11
12
8
9


II
11
13
8
10













Anti-





body
LCDR1
LCDR2
LCDR3





I
RASENIYSYLA
VYNAKPLAE
CQHHYGTPFT



(SEQ ID NO: 1)
(SEQ ID NO: 2)
(SEQ ID NO: 3)


 


II
RASENIYSYLA
VYNAKPLAE
CQHHYGTPFT



(SEQ ID NO: 1)
(SEQ ID NO: 2)
(SEQ ID NO: 3)





Anti-





body 
HCDR1
HCDR2
HCDR3





I
KASGYSFTSYWMY
GFHPGNSGTNYNQ
TRGYYYDGSFTY



(SEQ ID NO: 4)
KFKG
(SEQ ID NO: 7)




(SEQ ID NO: 5)



 


II
KASGYSFTSYWMY
GFHPRNSGTNYNQ
TRGYYYDGSFTY



(SEQ ID NO: 4)
KFKG
(SEQ ID NO: 7)




(SEQ ID NO: 6)









EXAMPLE 2
Binding Kinetics and Affinity of Antibodies I and II
The binding kinetics and affinity of an antibody, or antigen-binding fragment thereof, of the present invention to human c-Met ECD may be determined by use of a surface plasmon resonance biosensor such as a BIAcore® 2000, BIAcore® 3000, or a BIAcore® T100 (GE Health Care, Piscataway, N.J.) according to methods known in the art. Except as noted, all reagents and materials may be purchased from GE Healthcare, and measurements may be performed at 25° C. The BIAcore® instrument may be primed with HBS-EP+ running buffer (10 mM N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid (HEPES) pH 7.4, 150 mM NaCl, 3 mM EDTA, 0.05% surfactant P20; #BR-1006-69) and analysis temperature set at 25° C. A CMS chip containing immobilized goat anti-mouse Fc antibody (generated using standard NHS-EDC amine coupling) on all four flow cells may be used to employ a capture methodology. The antibodies, or antigen-binding fragments thereof, of the present invention may be prepared at 5 microgram/mL by dilution into HBS-EP+ running buffer. The c-Met-ECD with Fc and Flis tag (c-Met-ECD-Fc-Flis) can be expressed from CHO cells and purified for this analysis (SEQ ID NO: 23). Human c-Met-ECD-Fc-Flis may be prepared at a final concentrations ranging from 200 nM to 1.56 nM (with 2 fold dilutions) by dilution into HBS-EP+ running buffer. Each analysis cycle may consist of (1) capturing samples of the antibodies, or antigen-binding fragments thereof, of the present invention on flow cells 2, 3, and 4, (2) injection of 250 microliter (300 sec) of human c-Met-ECD over all flow cells at 50 microliter/min, (3) return to HBS-EP+ running buffer flow for 20 min to monitor dissociation phase, (4) regeneration of chip surfaces with a 30 microliter (36 sec) injection of glycine, pH 1.5, (5) equilibration of chip surfaces with a 50 microliter (60 sec) injection of HBS-EP+ running buffer. Data may be processed using standard double-referencing and fit to a 1:1 binding model using BIAcore® 2000 Evaluation software, version 4.1, to determine the association rate (kon, M−1s−1 units), dissociation rate (koff, s−1 units), and Rmax (RU units). The equilibrium dissociation constant (KD) may be calculated from the relationship KD=koff/kon, and is in molar units.
In experiments performed essentially as described in this Example 2, Antibodies I and II bind human c-Met-ECD with very high binding affinity (KD) (see Table 2). Antibody II binds c-Met-ECD with greater than 5× binding affinity compared to Antibody I.







TABLE 2







Antibodies I and II Binding Kinetics and Affinity 


to human c-Met-ECD-Fc-Flis














kon
koff
KD





Avg +/− SD
Avg +/− SD
Avg +/− SD




Antibody
M−1 s−1 (105)
s−1 (10−4)
nM
n







I
1.23 ± 0.06
3.02 ± 0.01
2.47 ± 0.14
2



II
1.25 ± 0.06
0.46 ± 0.02
0.37 ± 0.04
2










EXAMPLE 3
Antibodies I and II Simultaneously Bind ECD of Human c-Met with C8-H241
Surface Plasmon Resonance
To determine if an antibody, or antigen-binding fragment thereof, of the present invention can bind the ECD of human c-Met at the same time as an anti-c-Met therapeutic antibody (such as, e.g., C8-H241, disclosed in WO/2010/059654), a binding experiment may be performed using a surface plasmon resonance biosensor such as a BIAcore® 2000, BIAcore® 3000, or a BIAcore® T100 (GE Health Care, Piscataway, N.J.) according to methods known in the art. Except as noted, all reagents and materials may be purchased from BIAcore®. The c-Met-ECD with Fc and Flis tag (c-Met-ECD-Fc-Flis) can be expressed from CHO cells and purified for this analysis (SEQ ID NO: 23). All measurements may be performed at 25° C. HBS-EP+ buffer (10 mM HEPES pH 7.4, 150 mM NaCl, 3 mM EDTA, 0.05% surfactant P20; #BR-1006-69) can be used as the running buffer and sample buffer. Mouse IgG1 anti-polyhistidine antibody (R&D systems, Mab050) may be immobilized on flow cells 1 to 4 of a CMS sensor chip at a level of 7000 response units (Rus) using an amine coupling kit to capture human c-Met-ECD-Fc-Flis. Human c-Met-ECD-Fc-Flis may be first injected to flow cell 2. An antibody, or antigen-binding fragment thereof, of the present invention may be initially injected at 50 nM to fully saturate the c-Met-ECD-Fc-Flis on the chip surface. C8-H241 may then be injected immediately. Binding response units may be used to calculate binding stoichiometry. To show that simultaneous binding is independent of the addition order of the two antibodies, binding order may be reversed or alternated several times in the course of the experiment.
In experiments performed essentially as described in this Example 3, each c-Met-ECD-Fc-Flis binds 1.1 of Antibody I and 0.8 of C8-H241 (human IgG4 subtype) anti-c-Met antibodies. For Antibody II, each c-Met-ECD-Fc-Flis binds 1.5 of Antibody II and 0.9 of C8-H241 (CAS #1365287-97-3) anti-c-Met antibodies. All combinations of order addition show that Antibodies I and II can bind to cMet-ECD-Fc-Flis in the presence of C8-H241. These data show that Antibodies I and II and mAb C8-H241 (human IgG4 subtype) can simultaneously bind human c-Met-ECD-Fc-Flis, indicating that Antibody I and Antibody II could be used to detect c-Met levels in patient samples while treatment with C8-H241 is on-going, without requiring a wash-out period.
FACS
An in vitro assay designed to measure cell surface c-Met receptor may be conducted to determine if the antibodies of the present invention are capable of staining human c-Met on the cell surface while C8-H241 is also bound. Fluorescence-activated cell sorting (FACS) analysis may be used to demonstrate that c-Met antibody C8-H241 and an antibody of the present invention bind simultaneously to cell surface c-Met.
C8-H241 c-Met antibody may be labeled with an Alexa Fluor 488 Monoclonal Antibody Labeling Kit (Molecular Probes, Eugene, Oreg., #A-20181). Human gastric tumor MKN45 cells (Japan Health Sciences Foundation, Health Science Research Resource Bank, #JCRB0254) may be cultured in RPMI-1640 (Invitrogen, #11835), 10% (v/v) FBS (Invitrogen, #10082); 2 mM L-glutamine (Invitrogen, #25030); 100 U/500 mL penicillin G, and 100 micrograms/500 mL streptomycin (Invitrogen, #15140). The MKN45 cells from a T75 flask may be dissociated with 5 mL of enzyme-free cell dissociation solution (Chemicon, #S-014-B). The cells may be collected into centrifuge tubes after being incubated for 5 minutes at room temperature, and washed once in culture medium followed by an additional wash in binding buffer (Dulbecco's phosphate buffered saline (DPBS) with 1% (w/v) BSA and 0.1% (w/v) sodium azide). 100 microliters of binding buffer containing 5 microgram/mL of the anti-c-Met antibody, or antigen-binding fragment thereof, of the invention may be added to the cells. The cells may be incubated for 30 minutes and then washed with 1 mL of binding buffer. 100 microliters of binding buffer containing 5 microgram/mL of Alexa Fluor 647 (Invitrogen, #A21236) labeled anti-mIgG may then be added and incubated for 30 minutes on ice. Then 10 microliters of 50 microgram/mL Alexa Fluor 488 labeled C8-H241 (final concentration of 5 microgram/mL) may be added to above staining solution and incubated for 30 minutes on ice. The cells may then be washed twice with binding buffer and resuspended in DPBS. The antibody binding to cell surface c-Met may be analyzed by FACS analysis with 20,000 events acquired for each sample.
In FACS experiments performed essentially as described in this Example 3, 98.68% of MKN45 cells are stained both by C8-H241 (CAS #1365287-97-3) and Antibody I. 98.64% of MKN45 cells are stained both by C8-H241 and Antibody II. These results indicate that Antibody I and Antibody II may be used to detect c-Met levels in patient samples while treatment with C8-H241 is on-going, without requiring a wash-out period.
EXAMPLE 4
Antibodies I and II Simultaneously Bind ECD of Human c-Met with MetMAb
To determine if an antibody, or antigen-binding fragment thereof, of the present invention can bind the ECD of human c-Met at the same time as MetMAb, a binding experiment may be performed using a surface plasmon resonance biosensor such as a BIAcore® 2000, BIAcore® 3000, or a BIAcore® T100 (GE Health Care, Piscataway, N.J.) according to methods known in the art. Except as noted, all reagents and materials may be purchased from BIAcore®. The c-Met-ECD with Fc and Flis tag (c-Met-ECD-Fc-Flis) can be expressed from CHO cells and purified for this analysis. All measurements may be performed at 25° C. HBS-EP+ buffer (10 mM HEPES pH 7.4, 150 mM NaCl, 3 mM EDTA, 0.05% surfactant P20; #BR-1006-69) can be used as the running buffer and sample buffer. Mouse IgG1 anti-polyhistidine antibody (R&D systems, Mab050) may be immobilized on flow cells 1 to 4 of a CMS sensor chip at a level of 6500 response units (Rus) using an amine coupling kit to capture human c-Met-ECD-Fc-Flis. Human c-Met-ECD-Fc-Flis may be first injected to flow cell 2. An antibody, or antigen-binding fragment thereof, of the present invention may be initially injected at 500 nM to fully saturate the c-Met-ECD-Fc-Flis on the chip surface. MetMAb may then be injected immediately. Binding response units may be used to calculate binding stoichiometry. To show that simultaneous binding is independent of the addition order of the two antibodies, binding order may be reversed or alternated several times in the course of the experiment.
In experiments performed essentially as described in this Example 4, each c-Met-ECD-Fc-Flis binds 1.5 of Antibody I and 1.3 of MetMAb, expressed in HEK 293 EBNA cells. For Antibody II, each c-Met-ECD-Fc-Flis binds 1.3 of Antibody II and 1.4 of MetMAb. All combinations of order addition show that Antibodies I and II can bind to cMet-ECD-Fc-Flis in the presence of MetMAb. These data show that Antibodies I, II, or MetMAb can simultaneously bind human c-Met-ECD-Fc-Flis. Furthermore, the data indicates that the epitopes of these anti-c-Met antibodies differ.
EXAMPLE 5
Diagnostic Assay for Circulating Tumor Cells in Blood Samples
The binding of antibodies, or antigen-binding fragments thereof, of the present invention to circulating tumor cells (CTCs) may be determined with use of the CellTracks® AutoPrep® System, and CellTracks Analyzer II® or CellSpotter® Analyzer. The detection of c-Met receptor expression in CTCs may use the open-channel (4th channel) of the analyzer. The open channel allows the use of fluorescent dye with excitation/emission wavelengths similar to either FITC (fluorescein) or PE (phycoerythrin). All reagents, unless otherwise specified, may be purchased from Veridex LLC (Raritan, N.J.).
R-phycoerithrin (R-PE) fluorescent dye and a thio conjugation chemistry kit (Dojindo, #LK26) may be used for conjugation with the antibodies, or antigen-binding fragments thereof, of the present invention. The R-PE conjugated antibody may be further purified using a Protein G affinity column for IgG prior to use for staining of c-Met in CTCs. R-PE-conjugated antibodies, or antigen-binding fragments thereof, of the present invention may be evaluated in the CTC assay for optimal concentration and PE channel acquisition time.
CTCs may be defined as cells that are positive for EpCAM (epithelial cell adhesion molecule), cytokeratin 8, 18, 19 and with nuclei (DAPI staining) and negative for CD45 (marker for leukocytes). CTCs may be enriched from a 7.5 ml patient blood sample by the addition of anti-EpCAM antibody-immuno-magnetic beads. After washing of these enriched CTCs, these cells may be immunofluorescently stained with antibodies against cytokeratin, nucleus and CD45. The R-PE-conjugated antibodies, or antigen-binding fragments thereof, of the present invention may be added to the assay procedure as part of the cell staining step. The antibody may be added to the Tumor Phenotyping Reagent Cup included in the Veridex CellSearchTM CXC kit, and then the CellTracks® AutoPrep® System may be used to analyze a patient sample. Alternatively, using the Veridex Mouse/Rat CellCaptureTM CTC kit, the user may add the antibody concurrently with the DAPI and FITC stains manually. The CTCs contained in the sample cartridge within the MagNest® device may be visualized with the CellTracks Analyzer II® and images of the cells may be captured onto a computer, using software provided with this system.
In order to demonstrate the sensitivity of the CTC assay against different levels of c-Met expression, SKBR3, H441, SKOV3, MNK45, and SNUS cell lines may be chosen. SKBR3 cells (breast cancer cell line) do not express detectable levels of c-Met receptor. H441 cells (lung cancer cell line) express moderate levels of c-Met receptor. SKOV3 cells (ovarian cancer cell line) express low levels of c-Met receptor. MNK45 and SNUS, both gastric cancer cell lines, express high levels of c-Met receptor.
In experiments performed essentially as described in this Example 5, the optimal concentration of anti-c-Met antibody is found to be 0.1 microgram per test, and the optimal PE acquisition time was 0.005 to 0.007 seconds. Antibodies I and II are able to detect c-Met expression in cell lines expressing moderate and high levels of c-Met, while showing no staining in a cell line negative for c-Met.
Simultaneous Binding with C8-H241 and MetMAb
If a CTC assay is to be used in patients who are treated with c-Met targeted therapy, it is important to determine whether the therapeutic agent interferes with the diagnostic c-Met antibody. The interference of anti-c-Met therapeutic antibodies MetMAb or C8-H241 with the performance of the diagnostic test may be assessed by adding the therapeutic agent to cultured cells spiked into the test sample, and then staining for c-Met using R-PE-conjugated antibodies, or antigen-binding fragments thereof, of the present invention using the CTC assay as essentially described in this Example 5. MetMAb or C8-H241 antibodies may be added (0, 10, 30, and 90 μg/mL) to cultured cells diluted in Veridex Dilution Buffer containing 10% CellSave preservative. Test samples may be assayed for CTCs using the Veridex Mouse/Rat CellCaptureTM CTC kit, following the instructions provided in the kit or procedures otherwise known in the art. Briefly, samples may be enriched for EpCam-positive cells, and then stained with FITC-anti-cytokeratins 8, 18, and 19, DAPI, and 0.1 μg R-PE-Antibody I or II. The stained cells may be placed in a sample cartridge placed within a MagNest® device, and the cartridge may be scanned on the CellTracks Analyzer IT®. Cell images may be captured, and cells identified as CTCs are assessed for c-Met staining in the PE channel.
C8-H241 (CAS #1365287-97-3) does not interfere with Antibody I or II (Tables 3 and 4). MetMAb, expressed in HEK 293 EBNA cells, may interfere slightly with Antibody I in cells with moderate c-Met expression, but not in cells with high levels of human c-Met. There is a slight reduction in % c-Met-positive H441 cells staining with PE-conjugated Antibody I, correlating with increasing dose of MetMAb (Table 5). This is not seen in the high MET expressing cell line, MKN45. MetMAb does not interfere with Antibody II (see, for example, Table 6). Visually, the image quality in the PE channel remained consistent with or without MetMAb, and a high percentage of H441 cells remained positive for c-Met at the highest MetMAb dose.
The results support the use of an antibody, or antigen-binding fragment thereof, of the present invention in a CTC assay as a patient selection and as a diagnostic antibody for therapeutic response in MetMAb or C8-H241 treated patients in clinical studies.







TABLE 3







Percentage of positively stained cells with R-PE-Antibody I in


the CellTracks Analyzer II ® PE channel after 


incubation of cells with C8-H241













C8-H241 concentration
CTC
% cells c-Met



Cell line
(microgram/mL)
count
positive
















H441
0
363
90.4




10
342
93.0




30
384
94.5




90
347
94.5



MKN45
0
151
98.7




10
142
97.9




30
160
96.3




90
119
99.2



SKBR3
0
379
1.6




90
330
2.1

















TABLE 4







Percentage of positively stained cells with R-PE-Antibody 


II in the CellTracks Analyzer II ® PE channel after 


incubation of cells with C8-H241













C8-H241 concentration
CTC
% cells c-Met



Cell line
(microgram/mL)
count
positive
















H441
0
335
93.4




10
357
96.9




30
398
97.0




90
323
94.4



MKN45
0
133
98.5




10
147
99.3




30
115
100




90
153
100



SKBR3
0
277
3.3




90
377
0.8

















TABLE 5







Percentage of positively stained cells with R-PE-Antibody 


I in the CellTracks Analyzer II ® PE channel after 


incubation of cells with MetMAb












Cell line
MetMAb 
CTC
% cells 



(microgram/mL)
concentration count
positive
c-Met
















H441
0
319
82.8




10
383
82.5




30
382
78.3




90
366
70.0



MKN45
0
327
98.5




10
351
98.6




30
293
97.6




90
310
97.1



SKBR3
0
376
1.1




90
345
0.3

















TABLE 6







Percentage of positively stained cells with R-PE-Antibody 


II in the CellTracks Analyzer II ® PE channel after 


incubation of cells with MetMAb












Cell line
MetMAb 
CTC
% cells 



(microgram/mL)
concentration count
positive
c-Met
















H441
0
308
95.5




10
321
95.0




30
370
94.6




90
319
93.7



MKN45
0
231
99.6




10
242
99.2




30
238
98.7




90
263
99.6



SKBR3
0
350
2.3




90
305
0.3










EXAMPLE 6
Immunohistochemical (IHC) Assay for Human c-Met
An antibody, or antigen-binding fragment thereof, of the present invention may be used to detect human c-Met in normal or neoplastic human tissue that is formalin-fixed paraffin-embedded.
Briefly described, slides of human tissue or cancer cells may be prepared by baking at 60° C. for at least an hour or up to 16 hours, and then rehydrating and deparaffinizing in a series of xylene, ethanol, and water treatments on a linear stainer (Autostainer XL ST5010, Leica Microsystems). The extra-cellular domain epitope of Antibody II may be retrieved in the cells or tissues using Diva citrate antigen retrieval buffer (DV2004G1, Biocare Medical) in a high pressure decloaking chamber reaching 125° C. for 30 seconds.
The c-Met signal may be detected using the Leica Bond Refine Polymer kit (DS9800, Leica Microsystems) on the Leica Bond III automated slide stainer. Briefly, slides may be treated with Peroxide Block (3-4% hydrogen peroxide, component of DS9800, Leica Microsystems) for 5 minutes, PowerVision Super Block (PV6122, Leica Microsystems) for 10 minutes, Antibody II for 15 minutes, Post-Primary (rabbit anti-mouse IgG, component of DS9800, Leica Microsystems) for 8 minutes, Polymer (anti-rabbit poly-HRP-IgG, component of DS9800, Leica Microsystems) for 8 minutes, DAB Chromogen (from components of DS9800, Leica Microsystems) for 10 minutes, and hematoxylin counterstain (component of DS9800, Lecia Microsystems) for 5 minutes. Antibody II may be used at a concentration of 2 microgram/mL during the IHC protocol. Slides may be dehydrated from water to ethanol to xylene on a linear stainer (Autostainer XL ST5010, Leica Microsystems), and then coverslipped following routine procedures.
To determine if an antibody, or antigen-binding fragment thereof, of the present invention is selective for the ECD of human c-Met over the ECD of human RON, a pre-absorption/blocking experiment may be performed. The antibody, or antigen-binding fragment thereof, of the present invention at 2 microgram/mL may be incubated overnight with either c-Met-ECD-Fc-Flis (SEQ ID NO: 23) or the ECD of human RON (R&D Systems, #1947-MS-050) at 200× molar excess on a rotator at 4° C. After overnight incubation, the antibody, or antigen-binding fragment thereof, of the present invention may be tested against slides of human tissue or cancer cell lines as described above in Example 6.
In experiments performed essentially as described in this Example 6, the ECD of human c-MET blocks the immunoreactivity of Antibody II, while the ECD of human RON does not block the immunoreactivity of Antibody II staining. These findings support the selectivity of Antibody II to human c-MET over human RON.
For staining human tumor cell lines, 60 million cells may be harvested, formalin-fixed, and processed into histogel. The histogel cell pellets may be embedded into paraffin blocks, cored, and designed into a cell microarray that may be re-embedded in a paraffin block and then microtomed onto slides. These slides may be immunohistochemically stained and counterstained using the IHC assay protocol as described above in Example 6. MKN45 cells (human gastric carcinoma) and H441 cells (human lung adenocarcinoma) may be used as high c-MET expressers; U87MG cells (human glioblastoma-astrocytoma), H1299 (human non-small cell lung carcinoma), and Colo205 cells (human colon adenocarcinoma) may be used as intermediate expressers of c-MET; and SKBR3 (human breast carcinoma) and c-MET-transfected NIH 3T3 cells (mouse embryonic fibroblast cells transfected with human c-MET recombinant protein) may be used as low expressers of c-MET. RON-transfected NIH 3T3 cells and mock NIH 3T3 cells (mouse embryonic fibroblasts) are used as non-c-MET expressing negative controls.
In experiments performed essentially as described in this Example 6, Antibody II exhibits differential levels of immunostaining in various cell lines: strong cytoplasmic and membrane staining of 100% of the MKN45 and H441 cells with mostly negative nuclei; moderate to strong cytoplasmic and membrane staining of 100% of the U87MG, H1299, and Colo205 cells with mostly negative nuclei; and low to moderate cytoplasmic and membrane staining in 50% of the SKBR3 and in 90% of the c-MET-transfected NIH 3T3 cells with mostly negative nuclei. The mock and RON-transfected NIH 3T3 cells show only some faint cytoplasmic blush for c-Met staining and are considered negative.
For staining of human tumor tissues and normal human tissue, sections from tissue microarrays may be mounted on charged glass slides and stained with the IHC protocol as described above in Example 6. The results of the immunostaining by Antibody II may be scored by a pathologist. In experiments performed essentially as described in this Example 6, Antibody II was tested against non-small cell carcinomas of the lung (n=300), gastric carcinomas (n=61), cholangiocarcinomas (n=58), ovarian carcinomas (n=15), prostate carcinomas (n=256), and renal cell carcinomas of the kidney (n=140). A variety of immunohistochemical staining patterns (diffuse, focal, and variable) from one tumor type to another and also in different areas of the same tumor tissues are seen. Overall, Antibody II stains tumor cell membranes admixed with a variable component of cytoplasmic staining. The tumor cell nuclei are consistently stained negative, while taking up the hematoxylin counterstain. Similar to neoplastic tissues, the overall pattern of c-MET in normal human tissue (colon, kidney, uterus, liver, and lung) after testing with Antibody II is immunoreactivity that is cytoplasmic and membranous, while nuclei are consistently negative.
EXAMPLE 7
Second Immunohistochemical (IHC) Assay for Human c-Met
An antibody, or antigen-binding fragment thereof, of the present invention may be used to detect human c-Met in both commercially acquired formalin-fixed, paraffin embedded (FFPE) human biospecimen material in tissue microarray (TMA) format and whole sections of FFPE human biospecimen material.
Briefly described, slides of human tissue or cancer cells may be prepared by baking at 60° C. for at least 30 minutes or up to 2 hours to completely remove any residual water. Deparaffinization and extra-cellular domain epitope of Antibody II may be retrieved in the cells or tissues using EnVisionTM FLEX Target Retrieval Solution, Low pH (K8005, Dako) in a Dako PT Link unit reaching 97° C. for 20 minutes.
The c-Met signal may be detected using the Dako EnVisionTM FLEX+ Mouse (K8002, Dako) visualization system on the Dako Autostainer Link 48 automated slide stainer. Briefly, slides may be treated with the Peroxidase-Blocking Reagent (component of K8002, Dako) for 5 minutes, Antibody II for 15 minutes, Mouse (LINKER) reagent (signal amplifier, component of K8002, Dako) for 15 minutes, HRP polymer reagent (component of K8002, Dako) for 20 minutes, DAB chromogen/substrate working solution (from components of K8002, Dako) for 10 minutes, and hematoxylin counterstain (K8008, Dako) for 5 minutes. Antibody II may be used at a concentration of 2 μg/mL during the IHC protocol. Slides may be dehydrated from water, 95% ethanol, 100% ethanol, xylene, and then coverslipped following routine procedures.
For staining human tumor cell lines, 60 million cells may be harvested, formalin-fixed, and processed into histogel. The histogel cell pellets may be embedded into paraffin blocks, cored, and designed into a cell microarray that may be re-embedded in a paraffin block and then microtomed onto slides. These slides may be immunohistochemically stained and counterstained using the IHC assay protocol as described above in Example 7. RON-transfected NIH 3T3 cells and mock NIH 3T3 cells (mouse embryonic fibroblasts) are used as non-c-MET expressing negative controls.
In experiments performed essentially as described in this Example 7, Antibody II demonstrates selectivity over RON. In qualitative analysis by microscope, the mock and RON-transfected NIH 3T3 cells both show absent staining for RON with Antibody II and are considered negative, and quantitatively by digital image analysis, Antibody II is selective against RON as the pixel counts are compared for mock and RON-transfected NIH 3T3 cells (Table 7 and Table 8).







TABLE 7







Manual interpretation using brightfield microscope










EP1132Y antibody (Anti-
Antibody II (Anti-


NIH3T3 Cell Line
RON)
cMET)





RON transfected
Staining intense
Staining absent


Mock (vector) transfected
Staining weak
Staining absent
















TABLE 8







Digital image analysis using Aperio Positive Pixel Count algorithm









NIH3T3 Cell Line










RON transfected
Mock (vector) transfected












EP1132Y

EP1132Y



Positive Pixel
antibody
Antibody II
antibody
Antibody II


Count Category
(Anti-RON)
(Anti-cMET)
(Anti-RON)
(Anti-cMET)














Number of
10247577
70901
986755
75739


weak positive


(Nwp)


Number of
10490504
5485
198671
12261


positive (NP)


Number of
66915702
889
2055
4132


strong positive


(Nsp)


Total number
104754041
45098790
36341444
49071840


(NTotal)


Relative
221.45
0.19
3.83
0.23


Positive Pixel


Intensity Score









In experiments performed essentially as described in this Example 7, Antibody II stains tumor cell membranes admixed with a variable component of cytoplasmic staining. The tumor cell nuclei are consistently stained negative, while taking up the hematoxylin counterstain. Similar to neoplastic tissues, the overall pattern of c-MET immunoreactivity in normal human tissue after testing with Antibody II is cytoplasmic and membranous, while nuclei are consistently negative. Archived, non-neoplastic human FFPE biospecimens, that can be stained when Antibody II include, but are not limited to, Type II pneumocytes (subset), vascular endothelium, basal cells of the prostatic and uterine glands, germinal center B-cells (centroblasts), cells of the stratum basle, cells of the collecting tubules (focally), hepatocytes, and focal glandular epithelium of the: endometerium, gastrointestinal tract, respiratory tract, and ovary. Archived, non-neoplastic FFPE human biospecimens not stained by Antibody II includes, but is not limited to, neuropil, resting T-cells, the superficial most layers of the stratum spinosum, luminal cells of the prostatic epithelium, and the molecular layer of the cerebellar cortex.

## Claims

1. An antibody, or antigen-binding fragment thereof, that specifically binds to the extracellular domain (ECD) of human c-Met (SEQ ID NO: 24), comprising a light chain variable region (LCVR) and a heavy chain variable region (HCVR), wherein the LCVR comprises the complementarity determining regions (CDRs) LCDR1, LCDR2, and LCDR3, and the HCVR comprises the CDRs HCDR1, HCDR2, and HCDR3, wherein the LCDR1 is the polypeptide of RASENIYSYLA (SEQ ID NO: 1), the LCDR2 is the polypeptide of VYNAKPLAE (SEQ ID NO: 2), the LCDR3 is the polypeptide of CQHHYGTPFT (SEQ ID NO: 3), the HCDR1 is the polypeptide of KASGYSFTSYWMY (SEQ ID NO: 4), the HCDR2 is the polypeptide of GFHPGNSGTNYNQKFKG (SEQ ID NO: 5) or GFHPRNSGTNYNQKFKG (SEQ ID NO: 6), and the HCDR3 is the polypeptide of TRGYYYDGSFTY (SEQ ID NO: 7).

2. The antibody, or antigen-binding fragment thereof, of claim 1, wherein the HCDR2 is the polypeptide of GFHPGNSGTNYNQKFKG (SEQ ID NO: 5).

3. The antibody, or antigen-binding fragment thereof, of claim 1, wherein the HCDR2 is the polypeptide of GFHPRNSGTNYNQKFKG (SEQ ID NO: 6).

4. The antibody, or antigen-binding fragment thereof, of claim 1, comprising an LCVR and an HCVR, wherein the LCVR is the polypeptide of SEQ ID NO: 8, and the HCVR is the polypeptide of SEQ ID NO: 9 or SEQ ID NO: 10.

5. The antibody, or antigen-binding fragment thereof, of claim 4, wherein the LCVR is the polypeptide of SEQ ID NO: 8, and the HCVR is the polypeptide of SEQ ID NO: 9.

6. The antibody, or antigen-binding fragment thereof, of claim 4, wherein the LCVR is the polypeptide of SEQ ID NO: 8, and the HCVR is the polypeptide of SEQ ID NO: 10.

7. The antibody, or antigen-binding fragment thereof, of claim 5, comprising a light chain (LC) and a heavy chain (HC), wherein the LC is the polypeptide of SEQ ID NO: 11, and the HC is the polypeptide of SEQ ID NO: 12.

8. The antibody, or antigen-binding fragment thereof, of claim 6, comprising a light chain (LC) and a heavy chain (HC), wherein the LC is the polypeptide of SEQ ID NO: 11, and the HC is the polypeptide of SEQ ID NO: 13.

9. The antibody of claim 7, comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 12.

10. The antibody of claim 8, comprising two light chains and two heavy chains, wherein each light chain is the polypeptide of SEQ ID NO: 11, and each heavy chain is the polypeptide of SEQ ID NO: 13.

11. A composition comprising an antibody, or antigen-binding fragment thereof, of claim 6, and an acceptable carrier, diluent, or excipient.

12. A kit comprising an antibody, or antigen-binding fragment thereof, of claim 6.

13. A method of detecting human c-Met expressed or overexpressed by a human cell, comprising:
(a) contacting the cell in vitro with an antibody, or antigen-binding fragment thereof, of claim 6;
(b) removing any unbound or non-specifically bound antibody, or antigen-binding fragment thereof; and
(c) detecting and, optionally, quantifying the amount of antibody, or antigen-binding fragment thereof, which is specifically bound to the ECD of human c-Met (SEQ ID NO: 24).

14. The method of claim 13, wherein the human cell is formalin-fixed and paraffin-embedded.

15. The method of claim 13, wherein the detecting is performed by direct or indirect immunohistochemistry.

16. The method of claim 14, wherein the detecting is performed by direct or indirect immunohistochemistry.

17. A method of selecting a patient, having a tumor in which human c-Met is expressed or overexpressed, for treatment with an anti-c-Met therapeutic antibody or small molecule c-Met therapeutic compound, comprising:
(a) contacting a sample of the tumor with an antibody, or antigen-binding fragment thereof, of claim 6;
(b) removing any unbound or non-specifically bound antibody, or antigen-binding fragment thereof; and
(c) detecting and, optionally, quantifying the amount of antibody, or antigen-binding fragment thereof, which is specifically bound to the ECD of human c-Met, wherein the presence of the antibody, or antigen-binding fragment thereof, specifically bound to the ECD of human c-Met identifies the patient as being appropriate for treatment with the anti-c-Met therapeutic antibody or small molecule c-Met therapeutic compound;

and wherein the anti-c-Met therapeutic agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22; or wherein the anti-c-Met agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine.

18. The method of claim 17, wherein the human cell is formalin-fixed and paraffin-embedded.

19. The method of claim 17, wherein the detecting is performed by direct or indirect immunohistochemistry.

20. The method of claim 18, wherein the detecting is performed by direct or indirect immunohistochemistry.

21. A method of treating cancer, comprising:
(a) selecting a patient in need of treatment thereof, wherein the patient has a tumor in which human c-Met is expressed or overexpressed as determined by detecting human c-Met with an antibody, or antigen-binding fragment thereof, of claim 6; and
(b) treating the patient with an anti-c-Met therapeutic agent, wherein the anti-c-Met therapeutic agent is an antibody comprising two light chains and two heavy chains, wherein each of the light chains consists of the polypeptide of SEQ ID NO: 20 and each of the heavy chains consists of the polypeptide of SEQ ID NO: 22, or wherein the anti-c-Met agent is N-(3-Fluoro-4-(1-methyl-6-(1H-pyrazol-4-yl)-1H-indazol-5-yloxy)phenyl)-1-(4-fluorophenyl)-6-methyl-2-oxo-1,2-dihydropyridine-3-carboxamide or 6-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methyl-2H-indazol-5-ylthio)-[1,2,4]triazolo[4,3-b]pyridazine.

22. The method of claim 21, wherein the human cell is formalin-fixed and paraffin-embedded.

23. The method of claim 21, wherein the detecting is performed by direct or indirect immunohistochemistry.

24. The method of claim 22, wherein the detecting is performed by direct or indirect immunohistochemistry.