# Patent

## Title
PDGF as a biomarker for predicting resistance or effect of c-Met targeting drugs

## Abstract

Provided is a method for evaluating efficacy of, or resistance to, a c-Met targeting agent including measuring a level of a PDGF protein and/or a PDGF coding gene.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of Korean Patent Application No. 10-2014-0111704 on Aug. 26, 2014 with the Korean Intellectual Property Office, the entire disclosure of which is hereby incorporated by reference.
INCORPORATION-BY-REFERENCE OF MATERIAL ELECTRONICALLY SUBMITTED
Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted herewith and identified as follows: One 131,119 byte ASCII (Text) file named “719715_ST25-Revised.TXT,” created Aug. 8, 2016.
BACKGROUND
1. Field
Provided are a biomarker PDGF (platelet-derived growth factor) for evaluating efficacy of, or resistance to, a c-Met targeting agent and a method for evaluating efficacy of, or resistance to, a c-Met targeting agent including measuring a level of a PDGF protein and/or a PDGF coding gene.
2. Description of the Related Art
A biomarker generally refers to a measured characteristic which may be used as an indicator of some change caused in an organism by an external factor. Recent studies have been made to apply biomarkers to the diagnosis of various diseases and the prediction or monitoring of therapeutic effects of some agents. Among biomarkers relevant to drug development are pharmacodynamic markers (PD markers) for indicating whether drugs are functionally effective in vivo, and predictive markers for indicating the most likely response to particular drugs before administration. The use of such markers is helpful in establishing the clinical strategy of drugs. For example, a predictive marker, designed to indicate sensitivity or resistance to drug action, may be applied to the selection of patients to allow for more effective drug therapy while the action mode of a drug in individual patients can be monitored with a PD marker, which together can lead to the establishment of effective therapeutic strategies. Further, even in the absence of a predictive marker, a PD marker permits the early monitoring of responses to a drug, thus discriminating a drug-effective group from a drug-ineffective group in an early stage. Consequentially, more effective and successful drug therapies can be materialized. In addition, when applied to the monitoring of responses to a drug as a function of concentrations, a PD marker can be an index for calculating suitable doses of the drug.
Meanwhile, a cancer is one of the leading causes of death. Although the development of medical techniques has brought about a remarkable progress in cancer therapy, the five-year survival rate has only improved by ten percent over the past two decades. This is because cancer characteristics, such as rapid growth, metastasis, etc., make it difficult to diagnose and treat within a suitable time. The introduction of suitable biomarkers to cancer therapy would identify the characteristics of cancer to increase the opportunity of applying a suitable therapeutic at an optimal time, whereby cancer treatment could reach high success rates. For example, patients with lung cancer may differ from each other in cancer classification, genotype, and protein secretion, and thus must be treated with different, proper therapeutics. For chemotherapy using a specific drug, a corresponding biomarker, if present, would reduce the number of erroneous trials and increase possibility of success. In this regard, it is very important to explore biomarkers for predicting or monitoring the effect of anti-cancer therapeutics. A proper biomarker, if successfully exploited, can make a great contribution to the utility and value of anti-cancer drugs and the success rate of treatment with them.
c-Met is a hepatocyte growth factor (HGF) receptor. HGF acts as a multi-functional cytokine which binds to the extracellular domain of the c-Met receptor to regulate cell division, cell motility, and morphogenesis in various normal and tumor cells. The c-Met receptor is a membrane receptor that possesses tyrosine kinase activity. c-Met is a proto-oncogene, per se, that encodes the representative receptor tyrosine kinase. Occasionally, it takes part in a variety of mechanisms responsible for the development of cancer, such as oncogenesis, cancer metastasis, the migration and invasion of cancer cells, angiogenesis, etc., irrespectively of the ligand HGF, and thus has attracted intensive attention as a target for anti-cancer therapy. Targeted therapies, such as antibodies against c-Met, have been and are currently being developed.
In order to increase the effect of therapies using the developed c-Met targeting drugs, it is important to develop biomarkers for predicting the effect of the c-Met targeting drugs to select a subject who is suitable for application of the c-Met targeting drugs, and/or for monitoring the responsiveness of a patient who has been treated with the c-Met targeting drugs to establish more effective treatment strategies using the c-Met targeting drugs.
SUMMARY
Provided is a method for evaluating efficacy of a c-Met targeting agent on a patient with cancer, or the patient's resistance to the c-Met targeting agent. The method comprises measuring PDGF protein level, mRNA expression level of a gene encoding PDGF, or both, in a sample obtained from a patient with cancer before administration of a c-Met targeting agent to the patient, and in a sample obtained from the patient after administration of a c-Met targeting agent to the patient; comparing the PDGF protein level of the samples, mRNA expression level of gene encoding PDGF, or both, of the samples obtained before administration of the c-Met targeting agent to that of the samples obtained after administration of the c-Met targeting agent, and evaluating whether the c-Met targeting agent is effective in treating the cancer based on a change in PDGF protein level, mRNA expression level of a gene encoding PDGF, or both. An increase in the PDGF protein level or the mRNA expression level of gene encoding PDGF in the sample from the patient after administration of the c-Met targeting agent, compared to the PDGF protein level or the mRNA expression level in the sample before administration of the c-Met targeting agent, indicates that the c-Met targeting agent is not efficacious in treating the cancer or the patient has resistance to the c-Met targeting agent.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the expression of various human growth factors in EBC1 and EBC1-SR#6 cell lines with acquired resistance to an anti-c-Met antibody.
FIG. 2 is a graph showing % of cell viability according to PDGF Receptor (PDGFR) inhibitor Ponatinib concentration, when EBC1 cell lines and EBC1-SR#6 cell lines were treated with Ponatinib and then cultured 72 hours.
FIG. 3 is a graph showing % of cell viability according to FGFR inhibitor PD173074 concentration, when EBC1 and EBC1-SR#6 cell lines were treated with PD173074 and then cultured 72 hours.



DETAILED DESCRIPTION
It is observed that the level of PDGF in a cell with acquired resistance to a c-Met targeting agent by repeatedly treating the cell with the c-Met targeting agent, is significantly increased compared to that of a cell with no resistance. In addition, when a resistance to a c-Met targeting agent was induced, administrating an agent inhibiting PDGF signal transduction pathway leads to an increase of chemosensitivity of cancer cells. Therefore, efficacy of the c-Met targeting agent may be evaluated by measuring increase or decrease of PDGF level thereby predicting whether an innate resistance to a c-Met targeting agent (e.g., an anti-c-Met antibody) is present or an acquired resistance to a c-Met targeting agent (e.g., an anti-c-Met antibody) is induced by repeated treatment with the c-Met targeting agent.
In addition, the measurement of the expression level of PDGF in a biological sample can provide information for predicting an efficacy of, or resistance to, a c-Met targeting agent on the biological sample or a patient from whom the biological sample is isolated. This information may be used for selecting a subject who is suitable for applying the c-Met targeting agent, or determining whether or not a c-Met targeting agent can achieve a desired anticancer effect. Based thereon, uses of PDGF as a biomarker for predicting and/or evaluating an efficacy or a resistance of a c-Met targeting agent are provided.
In this disclosure, the efficacy of a c-Met targeting agent may refer to an effect of preventing, improving, alleviating, and/or treating c-Met-associated diseases, such as a cancer. For example, the effect of preventing, improving, alleviating, and/or treating a cancer may refer to a decrease in cancer cells or cancer tissues, a death of cancer cells or cancer tissues, an inhibition of cancer cell migration and/or invasion associated with cancer metastasis, and the like.
PDGF (platelet-derived growth factor) is one of the numerous growth factors, or proteins that regulate cell growth and division. In particular, it plays a significant role in blood vessel formation (angiogenesis), the growth of blood vessels from already-existing blood vessel tissue. PDGF may be from any mammal, for example, from a primate such as human, a monkey, and the like, a rodent such as a rat, a mouse, and the like, but not be limited thereto. For example, PDGF may be at least one selected from the group consisting of human PDGF (e.g., NCBI Accession No. NP_002598.4, NP_002599.1, NP_057289.1, NP_079484.1, etc.), mouse PDGF (e.g., NCBI Accession No. NP_032834.1, NP_035187.2, NP_064355.1, NP_082200.1, etc.), rat PDGF (e.g., NCBI Accession No. NP_036933.1, NP_113712.1, NP_112607.1, NP_076452.1, etc.), and the like, but not be limited thereto. PDGF coding gene or mRNA may be at least one selected from the group consisting of human PDGF gene (e.g., NCBI Accession No. NM_002607.5, NM_002608.2, NM_016205.2, NM_025208.4, etc.), mouse PDGF gene (e.g., NCBI Accession No. NM_008808.3, NM_011057.3, NM_019971.2, NM_027924.2, etc.), rat PDGF gene (e.g., NCBI Accession No. NM_012801.1, NM_031524.1, NM_031317.1, NM_023962.2, etc.), and the like, but not be limited thereto.
An embodiment provides a biomarker for predicting an efficacy or a resistance of a c-Met targeting agent, comprising a PDGF protein or a gene encoding PDGF.
Another embodiment provides a composition and a kit for predicting an efficacy or a resistance of a c-Met targeting agent, comprising an agent for measuring the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF, or a combination thereof.
Another embodiment provides a method for evaluating efficacy of a c-Met targeting agent on a patient with cancer or the patient's resistance to the c-Met targeting agent, comprising the steps of:
measuring the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF in a sample obtained from a patient with cancer before administration of a c-Met targeting agent to the patient, and in a sample obtained from the patient after administration of a c-Met targeting agent to the patient,
comparing the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF of the samples obtained before and after administration of the c-Met targeting agent, and
evaluating whether the c-Met targeting agent is effective in treating the cancer based on a change in the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF, wherein a significant increase in the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF in the sample from the patient after administration of the c-Met targeting agent, compared to the expression level in the sample before administration of the c-Met targeting agent, indicates that the c-Met targeting agent is not efficacious in treating the cancer or the patient has resistance to the c-Met targeting agent.
In an exemplary embodiment, the method for evaluating efficacy of a c-Met targeting agent on a patient with cancer or the patient's resistance to the c-Met targeting agent, may further comprise the step of administering the c-Met targeting agent to the subject determined to be efficacious for treatment.
Another embodiment provides a method for inhibiting c-Met or treating cancer in a subject, comprising administering a c-Met targeting agent to a subject who has a significant decrease in the PDGF protein level or the mRNA expression level of gene encoding PDGF in the sample from the subject after administration of the c-Met targeting agent, compared to the PDGF protein level or the mRNA expression level in the sample before administration of the c-Met targeting agent.
The method for inhibiting c-Met or treating cancer in a subject may further comprise a step of identifying a subject for application of a c-Met targeting agent, prior to the step of administration. The step of identifying may be carried out by performing the steps described in the method for evaluating efficacy of a c-Met targeting agent on a patient with cancer or the patient's resistance to the c-Met targeting agent.
As described above, when the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF is higher in the biological sample, it can be predicted that a resistance to the c-Met targeting agent is present on the biological sample or a patient from who the biological sample is isolated, or the c-Met targeting agent is not efficacious in treating the cancer. Based thereon, it can be determined that the biological sample or a patient from who the biological sample is isolated is not suitable for applying the c-Met targeting agent
The term “an agent for measuring the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF” refers to a molecule that may be used to detect the marker by examining the expression level of the PDGF marker which is increased when the patient has resistance to the c-Met targeting agent, for example, marker-specific oligonucleotides, primers, probes, antibodies, aptamers or the like.
As used herein, the term “measurement of mRNA expression level” means a process of examining the presence and expression level of mRNA of the PDGF gene in a biological sample through quantification of mRNA. Analysis method thereof includes polymerase chain reaction (PCR; e.g., reverse transcriptase polymerase chain reaction (RT-PCR), competitive RT-PCR, Real-time RT-PCR, etc.), hybridization methods (Northern blotting, Microarray, etc.), Taq-based techniques (SAGE, RNA-seq, etc.), DNA chips or the like, but is not limited thereto.
As used herein, the term “measurement of protein expression level” means a process of examining the presence and expression level of PDGF protein in a biological sample, and the protein is quantified by using an antibody that specifically binds to the protein of the gene. Analysis methods thereof include immunochromatography, immunohistochemistry, enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), enzyme immunoassay (EIA), fluorescence immunoassay (FIA), luminescence immunoassay (LIA), Western blot, FACS, protein chips and the like, but are not limited thereto.
The agent measuring the mRNA level of the gene may be an oligonucleotide, a pair of primers, or a probe. Since the nucleotide sequence of the gene encoding PDGF is known, those who are skilled in the art may design primers or probes useful for specifically amplifying target regions of the gene on the basis of the nucleotide sequence.
In an exemplary embodiment, the oligonucleotide may include an oligonucleotide having a nucleic acid sequence complementary to 10 to 100, specifically 10 to 50, specifically 10 to 30 consecutive nucleic acid sequence of the gene encoding PDGF. The oligonucleotide having the complementary nucleic acid sequence refers to an oligonucleotide having a sequence hybridizable with the marker gene, and may be an oligonucleotide including a sequence having 80% or more, specifically 90% or more, more specifically 95%, for example, 99% or more, or 100% identity to the nucleic acid sequence of the marker gene.
As used herein, the term “primer” means a short nucleic acid sequence having a free 3′ hydroxyl group, which is able to form base-pairing interaction with a complementary template and serves as a starting point for replication of the template strand. A primer is able to initiate DNA synthesis in the presence of a reagent for polymerization (i.e., DNA polymerase or reverse transcriptase) and four different nucleoside triphosphates at suitable buffers and temperature. PCR amplification may be performed using sense and antisense primers of polynucleotide encoding PDGF, and the presence of the targeted product may be examined to evaluate efficacy of, or resistance to, a c-Met targeting agent. PCR conditions and the length of sense and antisense primers may be modified on the basis of the methods known in the art.
As used herein, the term “probe” refers to a nucleic acid fragment of RNA or DNA capable of specifically binding to mRNA, ranging in length from several to hundreds of bases. The probe may be labeled so as to detect the presence or absence of a specific mRNA. The probe may be prepared in the form of oligonucleotide probe, single stranded DNA probe, double stranded DNA probe, RNA probe or the like. Hybridization may be performed using a probe complementary to the polynucleotide encoding PDGF, and efficacy or resistance of a c-Met targeting agent may be evaluated by the hybridization result. Selection of suitable probe and hybridization conditions may be modified on the basis of the methods known in the art.
The primer or probe may be chemically synthesized using a phosphoramidite solid support method or other widely known methods. These nucleic acid sequences may also be modified using many means known in the art. Non-limiting examples of such modifications include methylation, capsulation, replacement of one or more native nucleotides with analogues thereof, and inter-nucleotide modifications, for example, modifications to uncharged conjugates (e.g., methyl phosphonate, phosphotriester, phosphoroamidate, carbamate, etc.) or charged conjugates (e.g., phosphorothioate, phosphorodithioate, etc.).
The agent measuring the protein level may be an antibody or an aptamer.
As used herein, the term “antibody” refers to a specific protein molecule that indicates an antigenic region. The antibody may refer to an antibody that specifically binds to the marker protein, and includes a monoclonal antibody, a polyclonal antibody, a chimeric antibody, a human antibody, a humanized antibody or an antigen-binding fragment thereof. These antibodies may prepared by a hybridoma method, a phage antibody library method, a genetic recombination method or the like, which is typically used in the art. The term “antigen-binding fragment” refers to a functional fragment of an antibody molecule that retains at least an antigen-binding function, and it may be exemplified by scFv, (scFv)2, Fab, Fab′ or F(ab′)2, but is not limited thereto.
On the other hand, PDGF or mRNA of a gene encoding PDGF may be used as a biomarker to evaluate efficacy or resistance of a c-Met targeting agent in treating the cancer
In an exemplary embodiment, cancer diseases include all cancers on which a c-Met targeting agent exhibits its efficacy. The cancer may be a solid cancer or a blood cancer. For example, the cancer may be at least one selected from the group consisting of squamous cell carcinoma, lung cancer such as small-cell lung cancer, non-small-cell lung cancer, adenocarcinoma of the lung, and squamous cell carcinoma of the lung, peritoneal carcinoma, skin cancer, melanoma in the skin or eyeball, rectal cancer, cancer near the anus, esophagus cancer, small intestinal tumor, endocrine gland cancer, parathyroid cancer, adrenal cancer, soft-tissue sarcoma, urethral cancer, chronic or acute leukemia, lymphocytic lymphoma, hepatoma, gastrointestinal cancer, gastric cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatocellular adenoma, breast cancer, colon cancer, large intestine cancer, endometrial carcinoma or uterine carcinoma, salivary gland tumor, kidney cancer, prostate cancer, vulvar cancer, thyroid cancer, head and neck cancers, osteosarcoma, and brain cancer, but is not limited thereto. The cancer may be a primary cancer or a metastatic cancer. In a particular embodiment, the cancer may be a cancer having a resistance to a c-Met targeting agent, for example, an anti-c-Met antibody. The cancer may be a solid cancer such as gastric cancer, lung cancer, kidney cancer, and the like, which has a resistance to a c-Met targeting agent.
“c-Met” or “c-Met protein” refers to a receptor tyrosine kinase (RTK) which binds hepatocyte growth factor (HGF). c-Met may be derived (obtained) from any species, particularly a mammal, for instance, primates such as human c-Met (e.g., GenBank Accession No. NP_000236), monkey c-Met (e.g., Macaca mulatta, GenBank Accession No. NP_001162100), or rodents such as mouse c-Met (e.g., GenBank Accession No. NP_032617.2), rat c-Met (e.g., GenBank Accession No. NP_113705.1), and the like. The c-Met protein may include a polypeptide encoded by the nucleotide sequence identified as GenBank Accession No. NM_000245, a polypeptide having the amino acid sequence identified as GenBank Accession No. NP_000236 or extracellular domains thereof. The receptor tyrosine kinase c-Met participates in various mechanisms, such as cancer incidence, metastasis, migration of cancer cells, invasion of cancer cells, angiogenesis, and the like.
As used herein, the term “c-Met targeting agent” may refer to any agent capable of recognizing and/or binding to c-Met, degrading c-Met, inhibiting the expression of c-Met, or inhibiting the function of c-Met. For example, the c-Met targeting agent may be an anti-c-Met antibody that recognizes and/or binds to c-Met or an antigen-binding fragment thereof. The anti-c-Met antibody or an antigen-binding fragment thereof may bind to c-Met to induce the degradation thereof.
c-Met, a receptor for hepatocyte growth factor (HGF), may be divided into three portions: extracellular, transmembrane, and intracellular. The extracellular portion is composed of an α-subunit and a β-subunit which are linked to each other through a disulfide bond, and includes a SEMA domain responsible for binding HGF, a PSI domain (plexin-semaphorins-integrin identity/homology domain) and an IPT domain (immunoglobulin-like fold shared by plexins and transcriptional factors domain). The SEMA domain of c-Met protein may have the amino acid sequence of SEQ ID NO: 79, and is an extracellular domain that functions to bind HGF. A specific region of the SEMA domain, that is, a region having the amino acid sequence of SEQ ID NO: 71, which corresponds to a range from amino acid residues 106 to 124 of the amino acid sequence of the SEMA domain (SEQ ID NO: 79), is a loop region between the second and the third propellers within the epitopes of the SEMA domain. This region acts as an epitope for the anti-c-Met antibody.
The term “epitope,” as used herein, refers to an antigenic determinant, a part of an antigen recognized by an antibody. In one embodiment, the epitope may be a region including 5 or more contiguous (consecutive on primary, secondary (two-dimensional), or tertiary (three-dimensional) structure) amino acid residues within the SEMA domain (SEQ ID NO: 79) of c-Met protein, for instance, 5 to 19 contiguous amino acid residues within the amino acid sequence of SEQ ID NO: 71. For example, the epitope may be a polypeptide having 5 to 19 contiguous amino acids selected from among partial combinations of the amino acid sequence of SEQ ID NO: 71, wherein the polypeptide includes at least the amino sequence of SEQ ID NO: 73 (EEPSQ) which serves as an essential element for the epitope. For example, the epitope may be a polypeptide including, consisting essentially of, or consisting of the amino acid sequence of SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73.
The epitope having the amino acid sequence of SEQ ID NO: 72 corresponds to the outermost part of the loop between the second and third propellers within the SEMA domain of a c-Met protein. The epitope having the amino acid sequence of SEQ ID NO: 73 is a site to which the antibody or antigen-binding fragment according to one embodiment most specifically binds.
Thus, the dual-targeting agent to c-Met and EGFR may specifically bind to an epitope which has 5 to 19 contiguous amino acids selected from the amino acid sequence of SEQ ID NO: 71, including SEQ ID NO: 73 (EEPSQ) as an essential element. For example, the dual-targeting agent to c-Met and EGFR may specifically bind to an epitope including the amino acid sequence of SEQ ID NO: 71, SEQ ID NO: 72, or SEQ ID NO: 73.
In one embodiment, the dual-targeting agent to c-Met and EGFR or an antigen-binding fragment thereof may comprise or consist essentially of:
at least one heavy chain complementarity determining region (CDR) selected from the group consisting of (a) a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 4; (b) a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 5, SEQ ID NO: 2, or an amino acid sequence comprising 8-19 consecutive amino acids within SEQ ID NO: 2 including amino acid residues from the 3rd to 10th positions of SEQ ID NO: 2; and (c) a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 6, SEQ ID NO: 85, or an amino acid sequence comprising 6-13 consecutive amino acids within SEQ ID NO: 85 including amino acid residues from the 1st to 6th positions of SEQ ID NO: 85, or a heavy chain variable region comprising the at least one heavy chain complementarity determining region;
at least one light chain complementarity determining region (CDR) selected from the group consisting of (a) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 7, (b) a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 8, and (c) a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 9, SEQ ID NO: 15, SEQ ID NO: 86, or an amino acid sequence comprising 9-17 consecutive amino acids within SEQ ID NO: 89 including amino acid residues from the 1st to 9th positions of SEQ ID NO: 89, or a light chain variable region comprising the at least one light chain complementarity determining region;
a combination of the at least one heavy chain complementarity determining region and at least one light chain complementarity determining region; or
a combination of the heavy chain variable region and the light chain variable region.
Herein, the amino acid sequences of SEQ ID NOS: 4 to 9 are respectively represented by following Formulas I to VI, below:









Formula I



(SEQ ID NO: 4)



Xaa1-Xaa2-Tyr-Tyr-Met-Ser,






wherein Xaa1 is absent or Pro or Ser, and Xaa2 is Glu or Asp,









Formula II



(SEQ ID NO: 5)



Arg-Asn-Xaa3-Xaa4-Asn-Gly-Xaa5-Thr,






wherein Xaa3 is Asn or Lys, Xaa4 is Ala or Val, and Xaa5 is Asn or Thr,









Formula III



(SEQ ID NO: 6)



Asp-Asn-Trp-Leu-Xaa6-Tyr,






wherein Xaa6 is Ser or Thr,









Formula IV



(SEQ ID NO: 7)



Lys-Ser-Ser-Xaa7-Ser-Leu-Leu-Ala-Xaa8-Gly-Asn-



 



Xaa9-Xaa10-Asn-Tyr-Leu-Ala






wherein Xaa7 is His, Arg, Gln, or Lys, Xaa8 is Ser or Trp, Xaa9 is His or Gln, and Xaa10 is Lys or Asn,









Formula V



(SEQ ID NO: 8)



Trp-Xaa11-Ser-Xaa12-Arg-Val-Xaa13






wherein Xaa11 is Ala or Gly, Xaa12 is Thr or Lys, and Xaa13 is Ser or Pro, and









Formula VI



(SEQ ID NO: 9)



Xaa14-Gln-Ser-Tyr-Ser-Xaa15-Pro-Xaa16-Thr






wherein Xaa14 is Gly, Ala, or Gln, Xaa15 is Arg, His, Ser, Ala, Gly, or Lys, and Xaa16 is Leu, Tyr, Phe, or Met.
In one embodiment, the CDR-H1 may comprise or consist essentially of an amino acid sequence selected from the group consisting of SEQ ID NOS: 1, 22, 23, and 24. The CDR-H2 may comprise or consist essentially of an amino acid sequence selected from the group consisting of SEQ ID NOS: 2, 25, and 26. The CDR-H3 may comprise or consist essentially of an amino acid sequence selected from the group consisting of SEQ ID NOS: 3, 27, 28, and 85.
The CDR-L1 may comprise or consist essentially of an amino acid sequence selected from the group consisting of SEQ ID NOS: 10, 29, 30, 31, 32, 33, and 106. The CDR-L2 may comprise or consist essentially of an amino acid sequence selected from the group consisting of SEQ ID NOS: 11, 34, 35, and 36. The CDR-L3 may comprise or consist essentially of an amino acid sequence selected from the group consisting of SEQ ID NOS: 12, 13, 14, 15, 16, 37, 86, and 89.
In another embodiment, the antibody or antigen-binding fragment may include a heavy chain variable region comprising a polypeptide (CDR-H1) including an amino acid sequence selected from the group consisting of SEQ ID NOS: 1, 22, 23, and 24, a polypeptide (CDR-H2) including an amino acid sequence selected from the group consisting of SEQ ID NOS: 2, 25, and 26, and a polypeptide (CDR-H3) including an amino acid sequence selected from the group consisting of SEQ ID NOS: 3, 27, 28, and 85; and a light chain variable region comprising a polypeptide (CDR-L1) including an amino acid sequence selected from the group consisting of SEQ ID NOS: 10, 29, 30, 31, 32, 33 and 106, a polypeptide (CDR-L2) including an amino acid sequence selected from the group consisting of SEQ ID NOS: 11, 34, 35, and 36, and a polypeptide (CDR-L3) including an amino acid sequence selected from the group consisting of SEQ ID NOS 12, 13, 14, 15, 16, 37, 86, and 89.
In one embodiment of the dual-targeting agent to c-Met and EGFR or antigen-binding fragment, the variable region of the heavy chain includes the amino acid sequence of SEQ ID NO: 17, 74, 87, 90, 91, 92, 93, or 94 and the variable region of the light chain includes the amino acid sequence of SEQ ID NO: 18, 19, 20, 21, 75, 88, 95, 96, 97, 98, 99, or 107.
Animal-derived antibodies produced by immunizing non-immune animals with a desired antigen generally invoke immunogenicity when injected to humans for the purpose of medical treatment, and thus chimeric antibodies have been developed to inhibit such immunogenicity. Chimeric antibodies are prepared by replacing constant regions of animal-derived antibodies that cause an anti-isotype response with constant regions of human antibodies by genetic engineering. Chimeric antibodies are considerably improved in terms of anti-isotype response compared to animal-derived antibodies, but animal-derived amino acids still have variable regions, so that chimeric antibodies have side effects with respect to a potential anti-idiotype response. Humanized antibodies have been developed to reduce such side effects. Humanized antibodies are produced by grafting complementarity determining regions (CDR) which serve an important role in antigen binding in variable regions of chimeric antibodies into a human antibody framework.
In using CDR grafting to produce humanized antibodies, choosing which optimized human antibodies to use for accepting CDRs of animal-derived antibodies is critical. Antibody databases, analysis of a crystal structure, and technology for molecule modeling are used. However, even when the CDRs of animal-derived antibodies are grafted to the most optimized human antibody framework, amino acids positioned in a framework of the animal-derived CDRs affecting antigen binding are present. Therefore, in many cases, antigen binding affinity is not maintained, and thus application of additional antibody engineering technology for recovering the antigen binding affinity is necessary.
The anti c-Met antibodies may be, but are not limited to, animal antibodies (e.g., mouse-derived antibodies), chimeric antibodies (e.g., mouse-human chimeric antibodies), humanized antibodies, or human antibodies. The antibodies or antigen-binding fragments thereof may be isolated from a living body or non-naturally occurring. The antibodies or antigen-binding fragments thereof may be synthetic or recombinant. The antibody may be monoclonal.
An intact antibody includes two full-length light chains and two full-length heavy chains, in which each light chain is linked to a heavy chain by disulfide bonds. The antibody has a heavy chain constant region and a light chain constant region. The heavy chain constant region is of a gamma (γ), mu (μ), alpha (α), delta (δ), or epsilon (ε) type, which may be further categorized as gamma 1 (γ1), gamma 2 (γ2), gamma 3 (γ3), gamma 4 (γ4), alpha 1 (α1), or alpha 2 (α2). The light chain constant region is of either a kappa (κ) or lambda (λ) type.
As used herein, the term “heavy chain” refers to full-length heavy chain, and fragments thereof, including a variable region VH that includes amino acid sequences sufficient to provide specificity to antigens, and three constant regions, CH1, CH2, and CH3, and a hinge. The term “light chain” refers to a full-length light chain and fragments thereof, including a variable region VL that includes amino acid sequences sufficient to provide specificity to antigens, and a constant region CL.
The term “complementarity determining region” (“CDR”) refers to an amino acid sequence found in a hyper variable region of a heavy chain or a light chain of immunoglobulin. The heavy and light chains may respectively include three CDRs (CDRH1, CDRH2, and CDRH3; and CDRL1, CDRL2, and CDRL3). The CDR may provide contact residues that play an important role in the binding of antibodies to antigens or epitopes. The terms “specifically binding” and “specifically recognized” are well known to one of ordinary skill in the art, and indicate that an antibody and an antigen specifically interact with each other to lead to an immunological activity.
The term “antigen-binding fragment” used herein refers to fragments of an intact immunoglobulin including portions of a polypeptide including antigen-binding regions having the ability to specifically bind to the antigen. In a particular embodiment, the antigen-binding fragment may be scFv, (scFv)2, scFvFc, Fab, Fab′, or F(ab′)2, but is not limited thereto.
Among the antigen-binding fragments, Fab that includes light chain and heavy chain variable regions, a light chain constant region, and a first heavy chain constant region CH1, has one antigen-binding site.
The Fab′ fragment is different from the Fab fragment, in that Fab′ includes a hinge region with at least one cysteine residue at the C-terminal of CH1.
The F(ab′)2 antibody is formed through disulfide bridging of the cysteine residues in the hinge region of the Fab′ fragment.
Fv is the smallest antibody fragment with only a heavy chain variable region and a light chain variable region. Recombination techniques of generating the Fv fragment are widely known in the art.
Two-chain Fv includes a heavy chain variable region and a light chain region which are linked by a non-covalent bond. Single-chain Fv generally includes a heavy chain variable region and a light chain variable region which are linked by a covalent bond via a peptide linker or linked at the C-terminals to have a dimer structure like the two-chain Fv. The peptide linker may be the same as described above, including, but not limited to, those having an amino acid length of 1 to 100, or 2 to 50, and any kinds of amino acids may be included without any restrictions.
The antigen-binding fragments may be obtained using protease (for example, the Fab fragment may be obtained by restricted cleavage of a whole antibody with papain, and the F(ab′)2 fragment may be obtained by cleavage with pepsin), or may be prepared by using a genetic recombination technique.
The term “hinge region,” as used herein, refers to a region between CH1 and CH2 domains within the heavy chain of an antibody which functions to provide flexibility for the antigen-binding site.
When an animal antibody undergoes a chimerization process, the IgG1 hinge of animal origin is replaced with a human IgG1 hinge or IgG2 hinge while the disulfide bridges between two heavy chains are reduced from three to two in number. In addition, an animal-derived IgG1 hinge is shorter than a human IgG1 hinge. Accordingly, the rigidity of the hinge is changed. Thus, a modification of the hinge region may bring about an improvement in the antigen binding efficiency of the humanized antibody. The modification of the hinge region through amino acid deletion, addition, or substitution is well-known to those skilled in the art.
In one embodiment, the dual-targeting agent to c-Met and EGFR or an antigen-binding fragment thereof may be modified by any combination of deletion, insertion, addition, or substitution of at least one amino acid residue on the amino acid sequence of the hinge region so that it exhibit enhanced antigen-binding efficiency. For example, the antibody may include a hinge region including the amino acid sequence of SEQ ID NO: 100(U7-HC6), 101(U6-HC7), 102(U3-HC9), 103(U6-HC8), or 104(U8-HC5), or a hinge region including the amino acid sequence of SEQ ID NO: 105 (non-modified human hinge). In particular, the hinge region has the amino acid sequence of SEQ ID NO: 100 or 101.
In one embodiment, the dual-targeting agent to c-Met and EGFR may be a monoclonal antibody. The monoclonal antibody may be produced by the hybridoma cell line deposited with Accession No. KCLRF-BP-00220, which binds specifically to the extracellular region of c-Met protein (refer to Korean Patent Publication No. 2011-0047698, the entire disclosure of which is hereby incorporated by reference). The dual-targeting agent to c-Met and EGFR may include all the antibodies defined in Korean Patent Publication No. 2011-0047698.
In the c-Met antibody or an antigen-binding fragment thereof, the rest portion of the light chain and the heavy chain portion except the CDRs, the light chain variable region, and the heavy chain variable region as defined above, for example, the light chain constant region and the heavy chain constant region, may be from any subtype of immunoglobulin (e.g., IgA, IgD, IgE, IgG (IgG1, IgG2, IgG3, IgG4), IgM, and the like).
By way of further example, the dual-targeting agent to c-Met and EGFR or the antibody fragment may comprise or consist essentially of:
a heavy chain including the amino acid sequence selected from the group consisting of the amino acid sequence of SEQ ID NO: 62 (wherein the amino acid sequence from amino acid residues from the 1st to 17th positions is a signal peptide), or the amino acid sequence from the 18th to 462nd positions of SEQ ID NO: 62, the amino acid sequence of SEQ ID NO: 64 (wherein the amino acid sequence from the 1st to 17th positions is a signal peptide), the amino acid sequence from the 18th to 461st positions of SEQ ID NO: 64, the amino acid sequence of SEQ ID NO: 66 (wherein the amino acid sequence from the 1st to 17th positions is a signal peptide), and the amino acid sequence from the 18th to 460th positions of SEQ ID NO: 66; and
a light chain including the amino acid sequence selected from the group consisting of the amino acid sequence of SEQ ID NO: 68 (wherein the amino acid sequence from the 1st to 20th positions is a signal peptide), the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 68, the amino acid sequence of SEQ ID NO: 70 (wherein the amino acid sequence from the 1st to 20th positions is a signal peptide), the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 70, and the amino acid sequence of SEQ ID NO: 108.
For example, the dual-targeting agent to c-Met and EGFR may be selected from the group consisting of:
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 62 or the amino acid sequence from the 18th to 462nd positions of SEQ ID NO: 62 and a light chain including the amino acid sequence of SEQ ID NO: 68 or the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 68;
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 64 or the amino acid sequence from the 18th to 461st positions of SEQ ID NO: 64 and a light chain including the amino acid sequence of SEQ ID NO: 68 or the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 68;
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 66 or the amino acid sequence from the 18th to 460th positions of SEQ ID NO: 66 and a light chain including the amino acid sequence of SEQ ID NO: 68 or the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 68;
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 62 or the amino acid sequence from the 18th to 462nd positions of SEQ ID NO: 62 and a light chain including the amino acid sequence of SEQ ID NO: 70 or the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 70;
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 64 or the amino acid sequence from the 18th to 461st positions of SEQ ID NO: 64 and a light chain including the amino acid sequence of SEQ ID NO: 70 or the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 70;
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 66 or the amino acid sequence from the 18th to 460th positions of SEQ ID NO: 66 and a light chain including the amino acid sequence of SEQ ID NO: 70 or the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 70;
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 62 or the amino acid sequence from the 18th to 462nd positions of SEQ ID NO: 62 and a light chain including the amino acid sequence of SEQ ID NO: 108;
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 64 or the amino acid sequence from the 18th to 461st positions of SEQ ID NO: 64 and a light chain including the amino acid sequence of SEQ ID NO: 108; and
an antibody including a heavy chain including the amino acid sequence of SEQ ID NO: 66 or the amino acid sequence from the 18th to 460th positions of SEQ ID NO: 66 and a light chain including the amino acid sequence of SEQ ID NO: 108.
The polypeptide of SEQ ID NO: 70 is a light chain including human kappa (κ) constant region, and the polypeptide with the amino acid sequence of SEQ ID NO: 68 is a polypeptide obtained by replacing histidine at position 62 (corresponding to position 36 of SEQ ID NO: 68 according to kabat numbering) of the polypeptide with the amino acid sequence of SEQ ID NO: 70 with tyrosine. The production yield of the antibodies may be increased by the replacement. The polypeptide with the amino acid sequence of SEQ ID NO: 108 is a polypeptide obtained by replacing serine at position 32 (position 27e according to kabat numbering in the amino acid sequence from amino acid residues 21 to 240 of SEQ ID NO: 68; positioned within CDR-L1) with tryptophan. By such replacement, antibodies and antibody fragments including such sequences exhibits increased activities, such as c-Met biding affinity, c-Met degradation activity, and Akt phosphorylation inhibition.
In another embodiment, the dual-targeting agent to c-Met and EGFR may include a light chain complementarity determining region including the amino acid sequence of SEQ ID NO: 106, a light chain variable region including the amino acid sequence of SEQ ID NO: 107, or a light chain including the amino acid sequence of SEQ ID NO: 108.
As used herein, “patient” refers to an animal including a monkey, cow, horse, sheep, pig, chicken, turkey, quail, cat, dog, mouse, rat, rabbit or guinea pig as well as human, but is not limited thereto. In one embodiment, it may refer to a mammal, and in another embodiment, it may refer to a human.
As used herein, “kit” may include other elements essential for measuring the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF, in addition to the agent for measuring the expression level of PDGF protein or the mRNA expression level of gene encoding PDGF.
In one embodiment, the kit may be a kit including essential elements required for performing PCR, and to this end, the kit may include test tubes or other suitable containers, reaction buffers (varying in pH and magnesium concentrations), deoxynucleotides (dNTPs), enzymes such as Taq-polymerase and reverse transcriptase, DNase, RNase inhibitor, DEPC water, and sterile water, in addition to a pair of primers specific to the marker gene encoding PDGF that are designed by those skilled in the art.
In another embodiment, the kit may be a kit including essential elements required for performing a DNA chip, and to this end, the kit may include a base plate, onto which cDNAs corresponding to genes or fragments thereof are attached, and the base plate may include cDNA corresponding to a quantification control gene or a fragment thereof.
In still another embodiment, the kit may be a kit for measuring the PDGF protein expression level, and may include a matrix, a suitable buffer solution, a coloring enzyme, or a secondary antibody labeled with a fluorescent substance, a coloring substrate or the like for the immunological detection of antibody. As for the matrix, a nitrocellulose membrane, a 96-well plate made of polyvinyl resin, a 96-well plate made of polystyrene resin, and a slide glass may be used. As for the coloring enzyme, peroxidase and alkaline phosphatase may be used. As for the fluorescent substance, FITC, RITC or the like may be used, and as for the coloring substrate solution, ABTS (2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid)), OPD (o-phenylenediamine), or TMB (tetramethyl benzidine) or the like may be used. However, they are not limited thereto.
Analysis methods for measuring mRNA levels include RT-PCR, competitive RT-PCR, real-time RT-PCR, RNase protection assay, Northern blotting and DNA chip assay, but are not limited thereto. With the detection methods, the mRNA expression levels may be compared in the samples of the patient before and after administration of an c-Met targeting agent, and efficacy or resistance to a c-Met targeting agent may be evaluated by determining whether mRNA expression levels of the gene encoding PDGF have significantly decreased or increased.
The mRNA expression levels may be measured by a variety of polymerase chain reaction techniques, hybridization methods or DNA chip assays using primers being specific to the gene encoding PDGF.
In one embodiment, the resulting products of RT-PCR may be electrophoresed, and patterns and thicknesses of bands may be analyzed to determine the expression and levels of mRNA from the gene encoding PDGF while comparing the mRNA expression and levels with those of a control group, thereby evaluating efficacy or resistance to a c-Met targeting agent.
In another embodiment, the DNA chip may be used, in which the gene encoding PDGF or a nucleic acid corresponding to a fragment thereof is anchored at high density to a glass-like base plate. mRNA may be isolated from the sample, and a cDNA probe labeled with a fluorescent substance at its end or internal region may be prepared, followed by hybridization with the DNA chip, thereby evaluating efficacy or resistance to a c-Met targeting agent.
Analysis methods for measuring protein levels include immunochromatography, immunohistochemistry, ELISA, radioimmunoassay, enzyme immunoassay, fluorescence immunoassay, luminescence immunoassay, Western blot, FACS, protein chips or the like, but are not limited thereto. With the analysis methods, the amount of formed antigen-antibody complexes may be compared in the samples of the patient before and after administration of c-Met targeting agent, and efficacy of, or resistance to, a c-Met targeting agent may be evaluated by determining whether protein expression levels of the marker gene have significantly decreased or increased.
As used herein, the term “antigen-antibody complexes” refers to binding products of the PDGF to an antibody specific thereto. The amount of formed antigen-antibody complexes may be quantitatively determined by measuring the signal intensity of a detection label.
In one embodiment, the protein expression levels may be measured by ELISA. ELISA includes a variety of ELISA methods such as direct ELISA using a labeled antibody recognizing an antigen immobilized on a solid support, indirect ELISA using a labeled antibody recognizing a capture antibody forming complexes with an antigen immobilized on a solid support, direct sandwich ELISA using another labeled antibody recognizing an antigen in an antigen-antibody complex immobilized on a solid support, and indirect sandwich ELISA, in which another labeled antibody recognizing an antigen in an antigen-antibody complex immobilized on a solid support is reacted, and then a secondary labeled antibody recognizing the another labeled antibody may be used. More particularly, the protein expression levels may be detected by sandwich ELISA, where a sample is reacted with an antibody immobilized on a solid support, and the resulting antigen-antibody complexes are detected by adding a labeled antibody recognizing the antigen of antigen-antibody complex, followed by enzymatic color development, or by adding a secondary labeled antibody specific to the antibody which recognizes the antigen of the antigen-antibody complex, followed by enzymatic development. The efficacy of, or resistance to, a c-Met targeting agent may be evaluated by measuring the degree of complex formation of PDGF protein and antibody.
In another embodiment, the protein expression levels may be measured by Western blotting using one or more antibodies against PDGF. In this method, total proteins may be isolated from a sample, electrophoresed to be separated according to size, transferred onto a nitrocellulose membrane, and reacted with an antibody. The amount of produced antigen-antibody complexes may be measured using a labeled antibody to evaluate efficacy of, or resistance to, a c-Met targeting agent.
In still another embodiment, the protein expression levels may be measured by immunohistostaining using one or more antibodies against PDGF. In this method, cancer tissues are collected and fixed before and after administration of the c-Met targeting agent, and then paraffin-embedded blocks are prepared according to a widely known method. The blocks may cut into sections being several μm in thickness, and attach to glass slides to be reacted with one or more selected PDGF antibodies according to the known method. Subsequently, the unreacted antibodies may be washed, and the reacted antibodies labeled with one selected from the above mentioned detection labels, and then the labeled antibodies may be observed under a microscope.
In still another embodiment, the protein expression levels may be measured using a protein chip in which one or more antibodies against PDGF are arranged and fixed at a high density at predetermined positions on a substrate. In this method of sample analysis using the protein chip, proteins may be separated from a sample, and the separated proteins may be hybridized with the protein chip to form an antigen-antibody complex, which is then read to examine the presence or expression level of the protein, thereby evaluating efficacy or resistance to a c-Met targeting agent.
EXAMPLES
Hereafter, the present invention will be described in detail by examples.
The following examples are intended merely to illustrate the invention and are not construed to restrict the invention.
1.1. Production of “AbF46”, a Mouse Antibody to c-Met
1.1.1. Immunization of Mouse
To obtain immunized mice necessary for the development of a hybridoma cell line, each of five BALB/c mice (Japan SLC, Inc.), 4 to 6 weeks old, was intraperitoneally injected with a mixture of 100 μg of human c-Met/Fc fusion protein (R&D Systems) and one volume of complete Freund's adjuvant. Two weeks after the injection, a second intraperitoneal injection was conducted on the same mice with a mixture of 50 μg of human c-Met/Fc protein and one volume of incomplete Freund's adjuvant. One week after the second immunization, the immune response was finally boosted. Three days later, blood was taken from the tails of the mice and the sera were 1/1000 diluted in PBS and used to examine a titer of antibody to c-Met by ELISA. Mice found to have a sufficient antibody titer were selected for use in the cell fusion process.
1.1.2. Cell Fusion and Production of Hybridoma
Three days before cell fusion, BALB/c mice (Japan SLC, Inc.) were immunized with an intraperitoneal injection of a mixture of 50 μg of human c-Met/Fc fusion protein and one volume of PBS. The immunized mice were anesthetized before excising the spleen from the left half of the body. The spleen was meshed to separate splenocytes which were then suspended in a culture medium (DMEM, GIBCO, Invitrogen). The cell suspension was centrifuged to recover the cell layer. The splenocytes thus obtained (1×108 cells) were mixed with myeloma cells (Sp2/0) (1×108 cells), followed by spinning to give a cell pellet. The cell pellet was slowly suspended, treated with 45% polyethylene glycol (PEG) (1 mL) in DMEM for 1 min at 37° C., and supplemented with 1 mL of DMEM. To the cells was added 10 mL of DMEM over 10 min, after which incubation was conducted in a water bath at 37° C. for 5 min. Then the cell volume was adjusted to 50 mL before centrifugation. The cell pellet thus formed was resuspended at a density of 1 ̃2×105 cells/mL in a selection medium (HAT medium) and 0.1 mL of the cell suspension was allocated to each well of 96-well plates which were then incubated at 37° C. in a CO2 incubator to establish a hybridoma cell population.
1.1.3. Selection of Hybridoma Cells Producing Monoclonal Antibodies to c-Met Protein
From the hybridoma cell population established in Reference Example 1.1.2, hybridoma cells which showed a specific response to c-Met protein were screened by ELISA using human c-Met/Fc fusion protein and human Fc protein as antigens.
Human c-Met/Fc fusion protein was seeded in an amount of 50 μL (2 μg/mL)/well to microtiter plates and allowed to adhere to the surface of each well. The antibody that remained unbound was removed by washing. For use in selecting the antibodies that do not bind c-Met but recognize Fc, human Fc protein was attached to the plate surface in the same manner.
The hybridoma cell culture obtained in Reference Example 1.1.2 was added in an amount of 50 μL to each well of the plates and incubated for 1 hour. The cells remaining unreacted were washed out with a sufficient amount of Tris-buffered saline and Tween 20 (TBST). Goat anti-mouse IgG-horseradish peroxidase (HRP) was added to the plates and incubated for 1 hour at room temperature. The plates were washed with a sufficient amount of TBST, followed by reacting the peroxidase with a substrate (OPD). Absorbance at 450 nm was measured on an ELISA reader.
Hybridoma cell lines which secrete antibodies that specifically and strongly bind to human c-Met but not human Fc were selected repeatedly. From the hybridoma cell lines obtained by repeated selection, a single clone producing a monoclonal antibody was finally separated by limiting dilution. The single clone of the hybridoma cell line producing the monoclonal antibody was deposited with the Korean Cell Line Research Foundation, an international depository authority located at Yungun-Dong, Jongno-Gu, Seoul, Korea, on Oct. 6, 2009, with Accession No. KCLRF-BP-00220 according to the Budapest Treaty (refer to Korean Patent Laid-Open Publication No. 2011-0047698).
1.1.4. Production and Purification of Monoclonal Antibody
The hybridoma cell line obtained in Reference Example 1.1.3 was cultured in a serum-free medium, and the monoclonal antibody (AbF46) was produced and purified from the cell culture.
First, the hybridoma cells cultured in 50 mL of a medium (DMEM) supplemented with 10% (v/v) FBS were centrifuged and the cell pellet was washed twice or more with 20 mL of PBS to remove the FBS therefrom. Then, the cells were resuspended in 50 mL of DMEM and incubated for 3 days at 37° C. in a CO2 incubator.
After the cells were removed by centrifugation, the supernatant was stored at 4° C. before use or immediately used for the separation and purification of the antibody. An AKTA system (GE Healthcare) equipped with an affinity column (Protein G agarose column; Pharmacia, USA) was used to purify the antibody from 50 to 300 mL of the supernatant, followed by concentration with an filter (Amicon). The antibody in PBS was stored before use in the following examples.
1.2. Construction of chAbF46, a Chimeric Antibody to c-Met
A mouse antibody is apt to elicit immunogenicity in humans. To solve this problem, chAbF46, a chimeric antibody, was constructed from the mouse antibody AbF46 produced in Experimental Example 1.1.4 by replacing the constant region, but not the variable region responsible for antibody specificity, with an amino sequence of the human IgG1 antibody.
In this regard, a gene was designed to include the nucleotide sequence of “EcoRI-signal sequence-VH-NheI-CH-TGA-XhoI” (SEQ ID NO: 38) for a heavy chain and the nucleotide sequence of “EcoRI-signal sequence-VL-BsiWI-CL-TGA-XhoI” (SEQ ID NO: 39) for a light chain and synthesized. Then, a DNA fragment having the heavy chain nucleotide sequence (SEQ ID NO: 38) and a DNA fragment having the light chain nucleotide sequence (SEQ ID NO: 39) were digested with EcoRI (NEB, R0101S) and XhoI (NEB, R0146S) before cloning into a pOptiVECTM-TOPO TA Cloning Kit enclosed in an OptiCHOTM Antibody Express Kit (Cat no. 12762-019, Invitrogen), and a pcDNATM3.3-TOPO TA Cloning Kit (Cat no. 8300-01), respectively.
Each of the constructed vectors was amplified using Qiagen Maxiprep kit (Cat no. 12662), and a transient expression was performed using FreestyleTM MAX 293 Expression System (invitrogen). 293 F cells were used for the expression and cultured in FreeStyleTM 293 Expression Medium in a suspension culture manner. One day prior to the transient expression, the cells were provided in the concentration of 5×105 cells/ml, and after 24 hours, when the cell number reached to 1×106 cells/ml, the transient expression was performed. A transfection was performed by a liposomal reagent method using FreestyleTM MAX reagent (Invitrogen), wherein in a 15 ml tube, the DNA was provided in the mixture ratio of 1:1 (heavy chain DNA:light chain DNA) and mixed with 2 ml of OptiProTM SFM (Invitrogen) (A), and in another 15 ml tube, 100 ul (microliter) of FreestyleTM MAX reagent and 2 ml of OptiProTM SFM were mixed (B), followed by mixing (A) and (B) and incubating for 15 minutes. The obtained mixture was slowly mixed with the cells provided one day before the transient expression. After completing the transfection, the cells were incubated in 130 rpm incubator for 5 days under the conditions of 37° C., 80% humidity, and 8% CO2.
Afterwards, the cells were incubated in DMEM supplemented with 10% (v/v) FBS for 5 hours at 37° C. under a 5% CO2 condition and then in FBS-free DMEM for 48 hours at 37° C. under a 5% CO2 condition.
After centrifugation, the supernatant was applied to AKTA prime (GE Healthcare) to purify the antibody. In this regard, 100 mL of the supernatant was loaded at a flow rate of 5 mL/min to AKTA Prime equipped with a Protein A column (GE healthcare, 17-0405-03), followed by elution with an IgG elution buffer (Thermo Scientific, 21004). The buffer was exchanged with PBS to purify a chimeric antibody AbF46 (hereinafter referred to as “chAbF46”).
1.3. Construction of Humanized Antibody huAbF46 from Chimeric Antibody chAbF46
1.3.1. Heavy Chain Humanization
To design two domains H1-heavy and H3-heavy, human germline genes which share the highest identity/homology with the VH gene of the mouse antibody AbF46 purified in Reference Example 1.2 were analyzed. An Ig BLAST (program available online, operated by the National Center for Biotechnology Information (NCBI), Bethesda, Md.) result revealed that VH3-71 has an identity/identity/homology of 83% at the amino acid level. CDR-H1, CDR-H2, and CDR-H3 of the mouse antibody AbF46 were defined according to Kabat numbering. A design was made to introduce the CDR of the mouse antibody AbF46 into the framework of VH3-71. Back mutations to the amino acid sequence of the mouse AbF46 were conducted at positions 30 (S→T), 48 (V→L), 73 (D→N), and 78 (T→L). Then, H1 was further mutated at positions 83 (R→K) and 84 (A→T) to finally establish H1-heavy (SEQ ID NO: 40) and H3-heavy (SEQ ID NO: 41).
For use in designing H4-heavy, human antibody frameworks were analyzed by a BLAST search. The result revealed that the VH3 subtype, known to be most stable, is very similar in framework and sequence to the mouse antibody AbF46. CDR-H1, CDR-H2, and CDR-H3 of the mouse antibody AbF46 were defined according to Kabat numbering and introduced into the VH3 subtype to construct H4-heavy (SEQ ID NO: 42).
1.3.2. Light Chain Humanization
To design two domains H1-light (SEQ ID NO: 43) and H2-light (SEQ ID NO: 44), human germline genes which share the highest identity/homology with the VH gene of the mouse antibody AbF46 were analyzed. An Ig BLAST search result revealed that VK4-1 has an identity/homology of 75% at the amino acid level. CDR-L1, CDR-L2, and CDR-L3 of the mouse antibody AbF46 were defined according to Kabat numbering. A design was made to introduce the CDR of the mouse antibody AbF46 into the framework of VK4-1. Back mutations to the amino acid sequence of the mouse AbF46 were conducted at positions 36 (Y→H), 46 (L→M), and 49 (Y→I). Only one back mutation was conducted at position 49 (Y→I) on H2-light.
To design H3-light (SEQ ID NO: 45), human germline genes which share the highest identity/homology with the VL gene of the mouse antibody AbF46 were analyzed by a search for BLAST. As a result, VK2-40 was selected. VL and VK2-40 of the mouse antibody AbF46 were found to have a identity/homology of 61% at an amino acid level. CDR-L1, CDR-L2, and CDR-L3 of the mouse antibody were defined according to Kabat numbering and introduced into the framework of VK4-1. Back mutations were conducted at positions 36 (Y→H), 46 (L→M), and 49 (Y→I) on H3-light.
For use in designing H4-light (SEQ ID NO: 46), human antibody frameworks were analyzed. A Blast search revealed that the Vk1 subtype, known to be the most stable, is very similar in framework and sequence to the mouse antibody AbF46. CDR-L1, CDR-L2, and CDR-L3 of the mouse antibody AbF46 were defined according to Kabat numbering and introduced into the Vk1 subtype. Back mutations were conducted at positions 36 (Y→H), 46 (L→M), and 49 (Y→I) on H4-light.
Thereafter, DNA fragments having the heavy chain nucleotide sequences (H1-heavy: SEQ ID NO: 47, H3-heavy: SEQ ID NO: 48, H4-heavy: SEQ ID NO: 49) and DNA fragments having the light chain nucleotide sequences (H1-light: SEQ ID NO: 50, H2-light: SEQ ID NO: 51, H3-light: SEQ ID NO: 52, H4-light: SEQ ID NO: 53) were digested with EcoRI (NEB, R0101S) and XhoI (NEB, R0146S) before cloning into a pOptiVECTM-TOPO TA Cloning Kit enclosed in an OptiCHOTM Antibody Express Kit (Cat no. 12762-019, Invitrogen) and a pcDNATM3.3-TOPO TA Cloning Kit (Cat no. 8300-01), respectively, so as to construct recombinant vectors for expressing a humanized antibody.
Each of the constructed vectors was amplified using Qiagen Maxiprep kit (Cat no. 12662), and a transient expression was performed using FreestyleTM MAX 293 Expression System (invitrogen). 293 F cells were used for the expression and cultured in FreeStyleTM 293 Expression Medium in a suspension culture manner. At one day before the transient expression, the cells were provided in the concentration of 5×105 cells/ml, and after 24 hours, when the cell number reached to 1×106 cells/ml, the transient expression was performed. A transfection was performed by a liposomal reagent method using FreestyleTM MAX reagent (Invitrogen), wherein in a 15 ml tube, the DNA was provided in the mixture ratio of 1:1 (heavy chain DNA:light chain DNA) and mixed with 2 ml of OptiProTM SFM (Invitrogen) (A), and in another 15 ml tube, 100 ul (microliter) of FreestyleTM MAX reagent and 2 ml of OptiProTM SFM were mixed (B), followed by mixing (A) and (B) and incubating for 15 minutes. The obtained mixture was slowly mixed with the cells provided one day before the transient expression. After completing the transfection, the cells were incubated in 130 rpm incubator for 5 days under the conditions of 37° C., 80% humidity, and 8% CO2.
After centrifugation, the supernatant was applied to AKTA prime (GE Healthcare) to purify the antibody. In this regard, 100 mL of the supernatant was loaded at a flow rate of 5 mL/min to AKTA Prime equipped with a Protein A column (GE healthcare, 17-0405-03), followed by elution with an IgG elution buffer (Thermo Scientific, 21004). The buffer was exchanged with PBS to purify a humanized antibody AbF46 (hereinafter referred to as “huAbF46”). The humanized antibody huAbF46 used in the following examples included a combination of H4-heavy (SEQ ID NO: 42) and H4-light (SEQ ID NO: 46).
1.4. Construction of scFv Library of huAbF46 Antibody
For use in constructing an scFv of the huAbF46 antibody from the heavy and light chain variable regions of the huAbF46 antibody, a gene was designed to have the structure of “VH-linker-VL” for each of the heavy and the light chain variable region, with the linker including the amino acid sequence “GLGGLGGGGSGGGGSGGSSGVGS” (SEQ ID NO: 54). A polynucleotide sequence (SEQ ID NO: 55) encoding the designed scFv of huAbF46 was synthesized in Bioneer and an expression vector for the polynucleotide had the nucleotide sequence of SEQ ID NO: 56.
After expression, the product was found to exhibit specificity to c-Met.
1.5. Construction of Library Genes for Affinity Maturation
1.5.1. Selection of Target CDRs and Synthesis of Primers
The affinity maturation of huAbF46 was achieved. First, six complementary determining regions (CDRs) were defined according to Kabat numbering. The CDRs are given in Table 2, below.










TABLE 2







CDR
Amino Acid Sequence









CDR-H1
DYYMS




(SEQ ID NO: 1)



 



CDR-H2
FIRNKANGYTTEYSASVKG




(SEQ ID NO: 2)



 



CDR-H3
DNWFAY




(SEQ ID NO: 3)



 



CDR-L1
KSSQSLLASGNQNNYLA




(SEQ ID NO: 10)



 



CDR-L2
WASTRVS




(SEQ ID NO: 11)



 



CDR-L3
QQSYSAPLT




(SEQ ID NO: 12)










For use in the introduction of random sequences into the CDRs of the antibody, primers were designed as follows. Conventionally, N codons were utilized to introduce bases at the same ratio (25% A, 25% G, 25% C, 25% T) into desired sites of mutation. In this experiment, the introduction of random bases into the CDRs of huAbF46 was conducted in such a manner that, of the three nucleotides per codon in the wild-type polynucleotide encoding each CDR, the first and second nucleotides conserved over 85% of the entire sequence while the other three nucleotides were introduced at the same percentage (each 5%) and that the same possibility was imparted to the third nucleotide (33% G, 33% C, 33% T).
1.5.2. Construction of a Library of huAbF46 Antibodies and Affinity for c-Met
The construction of antibody gene libraries through the introduction of random sequences was carried out using the primers synthesized in the same manner as in Reference Example 1.5.1. Two PCR products were obtained using a polynucleotide covering the scFV of huAbF46 as a template, and were subjected to overlap extension PCR to give scFv library genes for huAbF46 antibodies in which only desired CDRs were mutated. Libraries targeting each of the six CDRs prepared from the scFV library genes were constructed.
The affinity for c-Met of each library was compared to that of the wildtype. Most libraries were lower in affinity for c-Met, compared to the wild-type. The affinity for c-Met was retained in some mutants.
1.6. Selection of Antibody with Improved Affinity from Libraries
After maturation of the affinity of the constructed libraries for c-Met, the nucleotide sequence of scFv from each clone was analyzed. The nucleotide sequences thus obtained are summarized in Table 3 and were converted into IgG forms. Four antibodies which were respectively produced from clones L3-1, L3-2, L3-3, and L3-5 were used in the subsequent experiments.











TABLE 3








Library




Clone
constructed
CDR Sequence









H11-4
CDR-H1
PEYYMS





(SEQ ID NO: 22)



 



YC151
CDR-H1
PDYYMS





(SEQ ID NO: 23)



 



YC193
CDR-H1
SDYYMS





(SEQ ID NO: 24)



 



YC244
CDR-H2
RNNANGNT





(SEQ ID NO: 25)



 



YC321
CDR-H2
RNKVNGYT





(SEQ ID NO: 26)



 



YC354
CDR-H3
DNWLSY





(SEQ ID NO: 27)



 



YC374
CDR-H3
DNWLTY





(SEQ ID NO: 28)



 



L1-1
CDR-L1
KSSHSLLASGNQNNYLA





(SEQ ID NO: 29)



 



L1-3
CDR-L1
KSSRSLLSSGNHKNYLA





(SEQ ID NO: 30)



 



L1-4
CDR-L1
KSSKSLLASGNQNNYLA





(SEQ ID NO: 31)



 



L1-12
CDR-L1
KSSRSLLASGNQNNYLA





(SEQ ID NO: 32)



 



L1-22
CDR-L1
KSSHSLLASGNQNNYLA





(SEQ ID NO: 33)



 



L2-9
CDR-L2
WASKRVS





(SEQ ID NO: 34)



 



L2-12
CDR-L2
WGSTRVS





(SEQ ID NO: 35)



 



L2-16
CDR-L2
WGSTRVP





(SEQ ID NO: 36)



 



L3-1
CDR-L3
QQSYSRPYT





(SEQ ID NO: 13)



 



L3-2
CDR-L3
GQSYSRPLT





(SEQ ID NO: 14)



 



L3-3
CDR-L3
AQSYSHPFS





(SEQ ID NO: 15)



 



L3-5
CDR-L3
QQSYSRPFT





(SEQ ID NO: 16)



 



L3-32
CDR-L3
QQSYSKPFT





(SEQ ID NO: 37)










1.7. Conversion of Selected Antibodies into IgG
Respective polynucleotides encoding heavy chains of the four selected antibodies were designed to have the structure of “EcoRI-signal sequence-VH-NheI-CH-XhoI” (SEQ ID NO: 38). The heavy chains of huAbF46 antibodies were used as they were because their amino acids were not changed during affinity maturation. In the case of the hinge region, however, the U6-HC7 hinge (SEQ ID NO: 57) was employed instead of the hinge of human IgG1. Genes were also designed to have the structure of “EcoRI-signal sequence-VL-BsiWI-CL-XhoI” for the light chain. Polypeptides encoding light chain variable regions of the four antibodies which were selected after the affinity maturation were synthesized in Bioneer. Then, a DNA fragment having the heavy chain nucleotide sequence (SEQ ID NO: 38) and DNA fragments having the light chain nucleotide sequences (DNA fragment including L3-1-derived CDR-L3: SEQ ID NO: 58, DNA fragment including L3-2-derived CDR-L3: SEQ ID NO: 59, DNA fragment including L3-3-derived CDR-L3: SEQ ID NO: 60, and DNA fragment including L3-5-derived CDR-L3: SEQ ID NO: 61) were digested with EcoRI (NEB, R0101S) and XhoI (NEB, R0146S) before cloning into a pOptiVECTM-TOPO TA Cloning Kit enclosed in an OptiCHOTM Antibody Express Kit (Cat no. 12762-019, Invitrogen) and a pcDNATM3.3-TOPO TA Cloning Kit (Cat no. 8300-01), respectively, so as to construct recombinant vectors for expressing affinity-matured antibodies.
Each of the constructed vectors was amplified using Qiagen Maxiprep kit (Cat no. 12662), and a transient expression was performed using FreestyleTM MAX 293 Expression System (invitrogen). 293 F cells were used for the expression and cultured in FreeStyleTM 293 Expression Medium in a suspension culture manner. One day prior to the transient expression, the cells were provided in the concentration of 5×105 cells/ml, and after 24 hours, when the cell number reached to 1×106 cells/ml, the transient expression was performed. A transfection was performed by a liposomal reagent method using FreestyleTM MAX reagent (Invitrogen), wherein in a 15 ml tube, the DNA was provided in the mixture ratio of 1:1 (heavy chain DNA:light chain DNA) and mixed with 2 ml of OptiProTM SFM (Invitrogen) (A), and in another 15 ml tube, 100 ul (microliter) of FreestyleTM MAX reagent and 2 ml of OptiProTM SFM were mixed (B), followed by mixing (A) and (B) and incubating for 15 minutes. The obtained mixture was slowly mixed with the cells provided one day before the transient expression. After completing the transfection, the cells were incubated in 130 rpm incubator for 5 days under the conditions of 37° C., 80% humidity, and 8% CO2.
After centrifugation, the supernatant was applied to AKTA prime (GE Healthcare) to purify the antibody. In this regard, 100 mL of the supernatant was loaded at a flow rate of 5 mL/min to AKTA Prime equipped with a Protein A column (GE healthcare, 17-0405-03), followed by elution with an IgG elution buffer (Thermo Scientific, 21004). The buffer was exchanged with PBS to purify four affinity-matured antibodies (hereinafter referred to as “huAbF46-H4-A1 (L3-1 origin), huAbF46-H4-A2 (L3-2 origin), huAbF46-H4-A3 (L3-3 origin), and huAbF46-H4-A5 (L3-5 origin),” respectively).
1.8. Construction of Constant Region- and/or Hinge Region-Substituted huAbF46-H4-A1
Among the four antibodies selected in Reference Example 1.7, huAbF46-H4-A1 was found to be the highest in affinity for c-Met and the lowest in Akt phosphorylation and c-Met degradation degree. In the antibody, the hinge region, or the constant region and the hinge region, were substituted.
The antibody huAbF46-H4-A1 (U6-HC7) was composed of a heavy chain including the heavy chain variable region of huAbF46-H4-A1, U6-HC7 hinge, and the constant region of human IgG1 constant region, and a light chain including the light chain variable region of huAbF46-H4-A1 and human kappa constant region. The antibody huAbF46-H4-A1 (IgG2 hinge) was composed of a heavy chain including a heavy chain variable region, a human IgG2 hinge region, and a human IgG1 constant region, and a light chain including the light chain variable region of huAbF46-H4-A1 and a human kappa constant region. The antibody huAbF46-H4-A1 (IgG2 Fc) was composed of the heavy chain variable region of huAbF46-H4-A1, a human IgG2 hinge region, and a human IgG2 constant region, and a light chain including the light variable region of huAbF46-H4-A1 and a human kappa constant region. The histidine residue at position 36 on the human kappa constant region of the light chain was changed to tyrosine in all of the three antibodies to increase antibody production.
For use in constructing the three antibodies, a polynucleotide (SEQ ID NO: 63) encoding a polypeptide (SEQ ID NO: 62) composed of the heavy chain variable region of huAbF46-H4-A1, a U6-HC7 hinge region, and a human IgG1 constant region, a polynucleotide (SEQ ID NO: 65) encoding a polypeptide (SEQ ID NO: 64) composed of the heavy chain variable region of huAbF46-H4-A1, a human IgG2 hinge region, and a human IgG1 region, a polynucleotide (SEQ ID NO: 67) encoding a polypeptide (SEQ ID NO: 66) composed of the heavy chain variable region of huAbF46-H4-A1, a human IgG2 region, and a human IgG2 constant region, and a polynucleotide (SEQ ID NO: 69) encoding a polypeptide (SEQ ID NO: 68) composed of the light chain variable region of huAbF46-H4-A1, with a tyrosine residue instead of histidine at position 36, and a human kappa constant region were synthesized in Bioneer. Then, the DNA fragments having heavy chain nucleotide sequences were inserted into a pOptiVECTM-TOPO TA Cloning Kit enclosed in an OptiCHOTM Antibody Express Kit (Cat no. 12762-019, Invitrogen) while DNA fragments having light chain nucleotide sequences were inserted into a pcDNATM3.3-TOPO TA Cloning Kit (Cat no. 8300-01) so as to construct vectors for expressing the antibodies.
Each of the constructed vectors was amplified using Qiagen Maxiprep kit (Cat no. 12662), and a transient expression was performed using FreestyleTM MAX 293 Expression System (invitrogen). 293 F cells were used for the expression and cultured in FreeStyleTM 293 Expression Medium in a suspension culture manner. One day prior to the transient expression, the cells were provided in the concentration of 5×105 cells/ml, and after 24 hours, when the cell number reached to 1×106 cells/ml, the transient expression was performed. A transfection was performed by a liposomal reagent method using FreestyleTM MAX reagent (Invitrogen), wherein in a 15 ml tube, the DNA was provided in the mixture ratio of 1:1 (heavy chain DNA:light chain DNA) and mixed with 2 ml of OptiProTM SFM (Invitrogen) (A), and in another 15 ml tube, 100 ul (microliter) of FreestyleTM MAX reagent and 2 ml of OptiProTM SFM were mixed (B), followed by mixing (A) and (B) and incubating for 15 minutes. The obtained mixture was slowly mixed with the cells provided one day before the transient expression. After completing the transfection, the cells were incubated in 130 rpm incubator for 5 days under the conditions of 37° C., 80% humidity, and 8% CO2.
After centrifugation, the supernatant was applied to AKTA prime (GE Healthcare) to purify the antibody. In this regard, 100 mL of the supernatant was loaded at a flow rate of 5 mL/min to AKTA Prime equipped with a Protein A column (GE healthcare, 17-0405-03), followed by elution with IgG elution buffer (Thermo Scientific, 21004). The buffer was exchanged with PBS to finally purify three antibodies (huAbF46-H4-A1 (U6-HC7), huAbF46-H4-A1 (IgG2 hinge), and huAbF46-H4-A1 (IgG2 Fc)). Among the three antibodies, huAbF46-H4-A1 (IgG2 Fc) was selected for the following examples, and name as L3-1Y/IgG2 (or SAIT301).
Example 1. Measurement of the Level of PDGF in Anti-c-Met Antibody Resistance Acquired Cell Line
To examine the quantitative change of PDGF when a resistance to an anti-c-Met antibody is induced, SAIT301 resistance acquired EBC1-SR#6 cell lines were prepared by repeatedly treating EBC1 (JCRB 0820) cells with SAIT301. EBC1 parent cells were all responsive to SAIT301, before inducing SAIT301 resistance. The SAIT301 resistance acquired EBC1-SR#6 cell lines were prepared as follows:
EBC1 (JCRB 0820) cell lines was treated with SAIT301 for at least 2 months, with increasing the concentration of treated antibody. The concentration of SAIT301 was increased from 1 ug/ml to 10 ug/ml until a resistance is induced. To confirm the acquisition of a resistance to SAIT301, the prepared clones were treated with SAIT301 at the concentration of 0 ug/ml, 0.016 ug/ml, 0.08 ug/ml, 0.4 ug/ml, or 2 ug/ml, and 72 hours after the antibody treatment, the number of the living cells was counted by CellTiter Glo assay (Promega, G7573). Clones where SAIT301 exhibited no effect were identified.
The obtained SAIT301 resistance acquired cell lines were named EBC1-SR#6.
The ligand assay was performed using Human Growth Factor Antibody Array (RayBiotech Inc.) to compare the expression of various human growth factors in EBC1 cell lines and EBC1-SR#6 cell lines with acquired resistance to an anti-c-Met antibody. In particular, 1×106 of EBC1 and EBC1-SR#6 cells were stabilized for 24 h in 100 mm dish respectively, followed by incubation in a serum-free medium without FBS for 24 h, then the medium were collected. One ml of the collected cell medium was added to a membrane which was protected with buffer, followed by incubation at 4° C. for 24 hr and washed. Then 1 ml of biotin-conjugated primary antibody was added, followed by incubation at 4° C. for 24 hr and washed again. Two ml of Horseradish peroxidase labeled streptavidin was added, followed by incubation at RT for 1 hr, and exposed on X-ray film developed to detect signal strength.
The measured amount of the protein in resistance acquired cell lines EBC1-SR#6 was compared to a parent cell EBC1 which is a cell before acquisition of resistance, and the results are shown in FIG. 1. As shown in FIG. 1, the PDGF level was significantly increased in EBC1-SR#6 cell lines after acquisition of resistance, compared to that before acquisition of resistance, whereas the expression level of human growth factors such as GM-CSF (granulocyte macrophage colony-stimulating factor), IGFBP6 (insulin-like growth factor binding protein 6) and VEGF (Vascular endothelial growth factor) was not different regardless of whether or not a resistance to anti-cMet antibody was acquired.
Example 2. Identification of Whether an Increase of the Expression Level of PDGF Contributes to Obtaining Resistance to Anti-cMet Antibody
To examine whether the quantitative increase of PDGF protein contributes to obtaining resistance in anti-c-Met antibody resistance acquired cell line, EBC1 and EBC1-SR#6 cell lines were treated with PDGFR (PDGF Receptor) TKI (tyrosine kinase inhibitor), then the changes of cell growth inhibition were measured using EZ-Cytox Cell viability assay kit (DaeiLab Service, Seoul, Korea).
For this, each of EBC1 cells and EBC1-SR#6 cells were seeded on 96-well plate at the amount of 5000 (5×103) cells. Twenty four hours after, the cells were solely treated with each of SAIT301, PDGFR inhibitor Ponatinib (Selleckchem USA), or FGFR (fibroblast growth factor receptor) inhibitor PD173074 (Selleckchem USA) as Negative control. Seventy two hours after the treatment, the number of the cells was measured by EZ-Cytox Cell viability assay kit.
As shown in FIG. 2, chemosensitivity of EBC1-SR#6 cell line (i.e. resistance acquired cell line) was increased (i.e. IC50 was decreased) than that of EBC1 (i.e. parental cell line), when EBC1 and EBC1-SR#6 cell lines were treated with PDGFR inhibitor Ponatinib. In contrast, as shown in FIG. 3, chemosensitivity of EBC1-SR#6 cell line was not changed markedly, when EBC1 cell lines and EBC1-SR#6 cell lines were treated with FGFR inhibitor PD173074 as Negative control. These finding suggest that increased expression level of PDGF after the acquisition of the resistance to an anti-c-Met antibody plays an important role in cell growth and proliferation of EBC1-SR#6 cell lines.
It should be understood that the exemplary embodiments described herein should be considered in a descriptive sense only and not for purposes of limitation. Descriptions of features or aspects within each embodiment should typically be considered as available for other similar features or aspects in other embodiments.
All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.
The use of the terms “a” and “an” and “the” and “at least one” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The use of the term “at least one” followed by a list of one or more items (for example, “at least one of A and B”) is to be construed to mean one item selected from the listed items (A or B) or any combination of two or more of the listed items (A and B), unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
Preferred embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred embodiments may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

## Claims

1. A method for evaluating efficacy of a c-Met targeting agent in a patient with lung cancer, the method comprising:
measuring PDGF protein level in a test sample comprising lung cancer cells obtained from a patient with lung cancer and in a reference sample comprising lung cancer cells resistant to the c-Met targeting agent,
comparing the PDGF protein level of the test sample and the reference sample,
evaluating whether the c-Met targeting agent is effective in treating the lung cancer based on a change in PDGF protein level, wherein a lower PDGF protein level in the test sample compared to the PDGF protein level in the reference sample indicates that the c-Met targeting agent is efficacious in treating the lung cancer, and
administering the c-Met targeting agent to the patient if the c-Met targeting agent is indicated to be effective in treating the lung cancer,
wherein the c-Met targeting agent comprises an anti-c-Met antibody or an antigen-binding fragment thereof.

2. The method according to claim 1, wherein measuring the PDGF protein level comprises contacting the test sample and the reference sample with an antibody, an antibody fragment or an aptamer that specifically binds to PDGF protein.

3. The method according to claim 1, wherein the anti-c-Met antibody or the antigen-binding fragment thereof recognizes or binds to a polypeptide comprising 5 to 19 contiguous amino acid residues of SEQ ID NO: 79, and wherein the polypeptide comprises at least the amino sequence of SEQ ID NO: 73.

4. The method according to claim 1, wherein the anti-c-Met antibody or the antigen-binding fragment thereof comprises:
(i) a heavy chain complementarity determining region (CDR) comprising (a) a CDR-H1 comprising SEQ ID NO: 4; (b) a CDR-H2 comprising SEQ ID NO: 5, SEQ ID NO: 2, or an amino acid sequence comprising 8-19 consecutive amino acids within SEQ ID NO: 2 comprising amino acid residues from the 3rd to 10th positions of SEQ ID NO: 2; and (c) a CDR-H3 comprising SEQ ID NO: 6, SEQ ID NO: 85, or an amino acid sequence comprising 6-13 consecutive amino acids within SEQ ID NO: 85 comprising amino acid residues from the 1st to 6th positions of SEQ ID NO: 85; and
(ii) a light chain complementarity determining region (CDR) comprising (a) a CDR-L1 comprising SEQ ID NO: 7, (b) a CDR-L2 comprising SEQ ID NO: 8, and (c) a CDR-L3 comprising SEQ ID NO: 9, SEQ ID NO: 15, SEQ ID NO: 86, or an amino acid sequence comprising 9-17 consecutive amino acids SEQ ID NO: 89 comprising amino acid residues from the 1st to 9th positions of SEQ ID NO: 89.

5. The method according to claim 1, wherein the anti-c-Met antibody or the antigen-binding fragment thereof comprises:
a heavy chain variable region comprising a polypeptide (CDR-H1) comprising SEQ ID NO: 1, 22, 23, or 24, a polypeptide (CDR-H2) comprising SEQ ID NO: 2, 25, or 26, and a polypeptide (CDR-H3) comprising SEQ ID NO: 3, 27, 28, or 85; and
a light chain variable region comprising a polypeptide (CDR-L1) comprising SEQ ID NO: 10, 29, 30, 31, 32, 33 or 106, a polypeptide (CDR-L2) comprising SEQ ID NO: 11, 34, 35, or 36, and a polypeptide (CDR-L3) comprising SEQ ID NO: 12, 13, 14, 15, 16, 37, 86, or 89.

6. The method according to claim 1, wherein the anti-c-Met antibody or the antigen-binding fragment thereof comprises:
a heavy chain variable region comprising SEQ ID NO: 17, 74, 87, 90, 91, 92, 93, or 94, and a light chain variable region comprising SEQ ID NO: 109, 18, 19, 20, 21, 75, 88, 95, 96, 97, 98, 99, or 107.

7. The method according to claim 1, wherein the anti-c-Met antibody or the antigen-binding fragment thereof comprises:
a heavy chain comprising SEQ ID NO: 62, the amino acid sequence from the 18th to 462nd positions of SEQ ID NO: 62, SEQ ID NO: 64, the amino acid sequence from the 18th to 461st positions of SEQ ID NO: 64, SEQ ID NO: 66, or the amino acid sequence from the 18th to 460th positions of SEQ ID NO: 66; and
a light chain comprising SEQ ID NO: 68, the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 68, SEQ ID NO: 70, the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 70, or SEQ ID NO: 108.

8. The method according to claim 1, wherein the anti-c-Met antibody or the antigen-binding fragment thereof comprises a heavy chain consisting of the amino acid sequence from the 18th to 460th positions of SEQ ID NO: 66, and a light chain consisting of the amino acid sequence from the 21st to 240th positions of SEQ ID NO: 68.