# Patent

## Title
Monitoring and modulating HGF/HGFR activity

## Abstract

Provided are methods and compositions for the modulation of hepatocyte growth factor activity to regulate lymphatic vessel development and function. Methods and composition for the monitoring and treatment of skin disorders, lymphedema, and metastatic cancers are disclosed. Also described are methods of identifying inhibitors of hepatocyte growth factor dependent lymphangiogenesis.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 12/784,272, filed on May 20, 2010, which is a continuation of U.S. application Ser. No. 11/394,422, filed on Mar. 31, 2006, which claims priority to U.S. Application Ser. No. 60/667,463, filed on Mar. 31, 2005. The contents of the foregoing applications are hereby incorporated by reference in their entirety.


GOVERNMENT SUPPORT
This invention was made with Government support under Grant No. CA069184 awarded by the National Institutes of Health. The Government has certain rights in this invention.


BACKGROUND
Hepatocyte growth factor (HGF) is a growth factor that can be found in human serum. The HGF receptor (HGFR) has been identified as the product of the c-Met proto-oncogene. See, e.g., Bottaro et al., Science, 251:802-804 (1991); Naldini et al., Oncogene, 6:501-504 (1991); WO 92/13097; and WO 93/15754.
SUMMARY
In one aspect, the disclosure features a method of treating a subject having an unwanted skin condition, e.g., a condition that impairs skin structure. The method includes administering, to the subject, a therapeutically effective amount of an HGF/HGFR modulator. In one aspect, the disclosure features the use of a therapeutically effective amount of an HGF/HGFR modulator (e.g., an agonist or antagonist) in the preparation of a medicament.
In one embodiment the modulator is an HGF/HGFR agonist. An HGF/HGFR agonist is an agent that directly or indirectly increases HGF/HGFR activity in the subject.
The agonist can be used to treat a condition or in the preparation of a medicament for the treatment of a condition in which increased lymphatic vessel formation is desired. Such conditions included lymphedema, e.g., acquired lymphedema. Examples of acquired lymphedema include lymphedema acquired after surgery or radiation therapy or lymphedema caused at least in part by an infection, e.g., by a pathogen, e.g., an infection such as filariasis. Other conditions in which increased lymphatic vessel formation is desired include aged skin or damaged skin, e.g., UVB-damaged skin. Still other conditions include those caused in part by a genetic or environmental factor, e.g., ultraviolet radiation. For example, the condition is epidermolysis, e.g., epidermolysis caused by aging or excessive exposure to ultra-violet light.
Many HGF/HGFR agonists increase HGFR signalling activity. Examples of HGF/HGFR agonists include a protein that includes a hepatocyte growth factor polypeptide (e.g., as modified into its mature heterodimeric form) or a biologically active fragment or analog thereof, a nucleic acid encoding a hepatocyte growth factor or a biologically active fragment or analog thereof. Other proteins and molecules, e.g., antibodies and small molecules, can also be used increase HGFR activity. For example, antibodies that bind, and optionally crosslink (e.g., dimerize) HGFR can be used to HGFR activity.
For example, the unwanted condition is an inflammatory or autoimmune skin disorder (e.g., psoriasis), or rosacea dermatosis. A therapeutically effective amount of an HGF/HGFR agonist can be used in the preparation of a medicament for the treatment of such an inflammatory or autoimmune skin disorder or rosacea dermatosis.
In one embodiment, the modulator is an HGF/HGFR antagonist. An HGF/HGFR antagonist is an agent that directly or indirectly decreases HGF/HGFR activity in a cell or in the subject. Antagonists include nucleic acids and proteins, e.g., antibodies or soluble HGF receptor fragments. For example, the antagonist can be a protein that interacts with HGF and, e.g., reduces HGF binding affinity to cell surface HGFR. For example, the protein can be (i) an antibody that recognizes HGF or HGFR, or (ii) a protein that includes a extracellular region of the HGFR, e.g., a soluble HGF receptor (e.g., fused to an Fc domain). Examples of antagonists include: a nucleic acid molecule that can bind or otherwise inhibit HGF mRNA, e.g., mRNA production, processing, or translation. Still other antagonists include: a dominant negative HGF protein or fragment thereof and an agent which decreases HGF nucleic acid expression (e.g., an artificial transcription factor or nucleic acid encoding an artificial transcription factor).
In some implementations, the modulator decreases the endogenous level of HGF or HGFR.
In one aspect, the disclosure features a method of treating a subject who has or is at risk for a neoplastic disorder, e.g., a metastatic cancer, particularly one that includes cell metastasis within lymph vessels or a cancer that has the potential to metastasize to lymph nodes. The method includes administering, to the subject, a therapeutically effective amount of an HGF/HGFR antagonist that decreases HGF/HGFR activity in the subject. A therapeutically effective amount of an HGF/HGFR antagonist can be used in the preparation of a medicament for the treatment of a subject who has or is at risk for a neoplastic disorder, e.g., a metastatic cancer.
Antagonists include nucleic acids and proteins, e.g., antibodies or soluble HGF receptor fragments. For example, the antagonist can be a protein or other agent that interacts with HGF and, e.g., reduces HGF binding affinity to cell surface HGFR. For example, the protein can be an antibody HGF or a extracellular region of the HGFR, e.g., a soluble HGF receptor. Examples of antagonists include: a nucleic acid molecule that can bind or otherwise inhibit HGF mRNA, e.g., mRNA production, processing, or translation. Still other antagonists include: a dominant negative HGF protein or fragment thereof and an agent which decreases HGF nucleic acid expression (e.g., an artificial transcription factor or nucleic acid encoding an artificial transcription factor).
In another aspect, the disclosure features a method of treating a subject who has or is at risk for a neoplastic disorder, e.g., a metastatic cancer, particularly one that includes cell metastasis within lymph vessels or a cancer that has the potential to metastasize to lymph nodes. The method includes administering, to the subject, a therapeutically effective amount of an α9 integrin antagonist that decreases α9 integrin activity in the subject. For example, the antagonist is a protein or other agent that interacts with α9 integrin or a counterpart integrin beta subunit and, e.g., reduces integrin binding affinity to cells. For example, the protein can be an antibody to α9 integrin or a counterpart integrin beta subunit or a extracellular region of an α9 integrin receptor. A therapeutically effective amount of an α9 integrin antagonist can be used in the preparation of a medicament for the treatment of a subject who has or is at risk for a neoplastic disorder, e.g., a metastatic cancer.
Examples of antagonists include: a nucleic acid molecule that can bind or otherwise inhibit α9 integrin mRNA, e.g., mRNA production, processing, or translation. Still other antagonists include: a dominant negative α9 integrin protein or fragment thereof and an agent which decreases α9 integrin nucleic acid expression (e.g., an artificial transcription factor or nucleic acid encoding an artificial transcription factor).
In still another aspect, the disclosure features a method of evaluating a cell or a subject (e.g., using cells obtained from the subject). The method includes evaluating integrin α9 and stanniocalcin 1 mRNA or protein expression in the cell or in cells from the subject. The method can be used to evaluate HGF activity in the subject. For example, the cell or cells obtained from the subject include endothelial cells, e.g., lymph endothelial cells (LEC). The cell or subject can be treated, e.g., before, during, or after the evaluating, with an agent described herein, e.g., an agonist or antagonist of HGF/HGFR. The method can be used to monitor a subject who has or is at risk for a disorder described herein and who may be treated with an agent described herein.
In another aspect, the disclosure features a method of identifying a compound that modulates lymphatic endothelial cell activity, e.g., proliferation or migration. The method includes: providing a cell or organism in which HGF/HGFR activity can be monitored; contacting the cell or organism with a test compound; and evaluating HGF/HGFR activity in the cell or organism. For example, the cell includes a reporter of HGF/HGFR activity or an organism that comprises such a cell. HGF/HGFR activity can be evaluated by assaying, e.g., protein or mRNA expression or reporter activity. A change in reporter activity or other relevant parameter, for example, indicates a change in HGF/HGFR activity. The method can further include evaluating the effect of the test compound on cell proliferation or cell migration, e.g., lymphatic endothelial cell proliferation or migration.
In one embodiment, the reporter is a gene that comprises a sequence encoding a detectable protein and an operably linked promoter that includes a region of the promoter of the HGF or HGF-R gene, e.g. region from the transcription start site to a position at least 100, 200, 300, 500, 800, 1000, 2000, or 5000 bases upstream, from the initiator MET codon to a position at least 100, 200, 300, 500, 800, 1000, 2000, or 5000 bases upstream, or from the TATA box to a position at least 100, 200, 300, 500, 800, 1000, 2000, or 5000 bases upstream.
The cell or organism is generally mammalian, e.g., human or non-human, e.g., mouse, rat, hamster, guinea pig, monkey and so forth.
In another aspect, the disclosure features a method of identifying a compound that modulates endothelial cell activity, for example, a compound that inhibits hepatocyte growth factor-dependent lymphatic endothelial cell proliferation or migration. The method includes: providing an endothelial cell (e.g., a lymphatic endothelial cell) expressing a hepatocyte growth factor receptor; contacting the endothelial cell with hepatocyte growth factor and a test compound; and evaluating the cell, e.g., for a property, e.g., a property regulated by HGF/HGFR, such as proliferation or migration. For example, the method can include determining whether proliferation or migration of the lymphatic endothelial cell is altered in the presence of the test compound. A decrease in proliferation or migration can indicate that the test compound inhibits hepatocyte growth factor-dependent lymphatic endothelial cell proliferation.
The endothelial cell can be a mammalian cell, e.g., a mouse, rat, rabbit, hamster, or human cell. The cell can be cultured or isolated; for example, the cell is from a cell line or a primary cell. In one embodiment, the cell expresses Prox 1 and the hyaluronan receptor LYVE-1.
The method can include evaluating the test compound in the presence of another HGF/HGFR pathway modulator, e.g., in the presence of a protein that includes soluble HGF, a protein that includes a soluble extracellular domain of HGFR, or antibody to HGF or HGFR.
The method can include evaluating tyrosine phosphorylation of the hepatocyte growth factor receptor, e.g., to determine if the test compound causes a decrease. In one embodiment, the lymphatic endothelial cell expresses a recombinant hepatocyte growth factor receptor or a mutant thereof.
The method can further include administering the test compound to an organism, e.g., a human or non-human mammal. The method can further include formulating a test compound or a modified test compound that retains the biological activity of the test compound as a pharmaceutical composition, e.g., by combining the compound with a pharmaceutically acceptable carrier.
In still another aspect, the disclosure features a method for evaluating a test compound, e.g., a compound that is topically applied to a test organism, e.g., a transgenic organism that includes a reporter of HGF/HGFR pathway activity. The method includes contacting a test compound to the test organism and evaluating HGF/HGFR pathway activity. For example, the evaluating can include evaluating protein or mRNA expression of HGF, HGFR, or a gene or gene product that is regulated by HGFR, e.g., α9 integrin or stanniocalcin 1. The method can also include evaluating the test compound in the presence of another HGF/HGFR pathway modulator, e.g., in the presence of a protein that includes soluble HGF, a protein that includes a soluble extracellular domain of HGFR, or antibody to HGF or HGFR.
In one embodiment, the reporter is a gene that includes a sequence encoding a detectable protein and an operably linked promoter that includes a region of the promoter of the HGF, HGFR, α9 integrin or stanniocalcin 1 gene, e.g. region from the transcription start site to a position at least 100, 200, 300, 500, 800, 1000, 2000, or 5000 bases upstream, from the initiator MET codon to a position at least 100, 200, 300, 500, 800, 1000, 2000, or 5000 bases upstream, or from the TATA box to a position at least 100, 200, 300, 500, 800, 1000, 2000, or 5000 bases upstream. The method can also include evaluating two or more such reporters.
The method can include selecting a test compound (e.g., from a library of test compounds), if it increases or decreases HGF/HGFR pathway activity. A selected test compound can formulated, e.g., a pharmaceutical composition, e.g., suitable for topical administration or other route of administration. The method can further include administering the pharmaceutical composition to a subject, e.g., a subject having or at risk for a disorder described herein.
The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims. All cited patents, applications, and references are incorporated herein by reference.



DESCRIPTION OF DRAWINGS
FIG. 1 shows quantitative RT-PCR data for lymphatic cell lineage marker mRNA levels (A-C), quantitative RT-PCR for HGFR mRNA (D), and immunoblot assays for HGFR protein (E and F).
FIG. 2A-L show dual immunofluorescence staining for the lymphatic marker LYVE-1 (green) and for HGFR (red), in lymphatic vessels.
FIG. 3A-I show dual immunofluorescence for the lymphatic marker LYVE-1 (green) and HGFR (red) in endothelial cells of lymph sacs during mouse embryonic development.
FIG. 4 shows data for lymphatic endothelial cell (LEC) proliferation (A and B) and migration assay (C) for LEC cells treated with HGF.
FIG. 5A D show data for LEC tube formation in vitro, in response to HGF and lymphatic vessel formation in vivo.
FIG. 6A-E show dual immunofluorescence staining of lymphatic vessels for LYVE-1 (green) and CD31 (red) after experimental skin inflammation.
FIG. 7A and B show QPCR data for integrin α9 and stanniocalcin 1 mRNA levels in LEC after treatment with HGF.
FIG. 8 shows representative histologic images (H&E stain and immunofluorescence to detect podoplanin) of the ileum in HGF transgenic (FIGS. 8 B,D,F,H) and wild-type mice (FIGS. 8 A,C,E,G). Scale bars: 100 μm.
FIG. 9 shows double immunofluorescence analyses of mouse ear sections for LYVE-1 (green) and CD31 (red). Induction of LYVE-1-positive lymphatic vessel formation was observed at 14 days after implantation of HGF-containing slow-release pellets (9B and C; arrowheads) but not of control pellets (9A). Systemic treatment with a blocking anti-VEGFR-3 antibody (9C) did not inhibit HGF-induced lymphatic vessel formation, as compared with control IgG treatment (9B). Newly formed blood vessels were observed in all samples. P: Pellet. Scale bars: 100 μm.



DETAILED DESCRIPTION
We have found that, among other things, the hepatocyte growth factor receptor (HGFR) is highly expressed in lymphatic endothelial cells (LEC) of the lymphatic system. Treatment of LEC with HGF promotes proliferation, migration, and organization of LECs into vessels. In addition, administration of HGF to mice potently promoted new lymphatic vessel formation. Furthermore, induction of LEC migration was largely mediated via α9 integrin.
Accordingly, it is possible to treat pathologies affected by the lymphatic system by modulating HGF/HGFR activity. A subject can also be diagnosed by evaluating a parameter that assesses HGF/HGFR activity. Agents that modulate HGF/HGFR activity can be identified, e.g., using the assay and screening methods described herein.
I. HGF and HGFR
The mature form of human HGF (hHGF), corresponding to the major form purified from human serum, is a disulfide linked heterodimer derived by proteolytic cleavage of the human pro-hormone between amino acids R494 and V495. This cleavage process generates a molecule composed of an α subunit of 440 amino acids (M.W. 69 kDa) and a β subunit of 234 amino acids (M.W. 34 kDa). The α and the β chains are produced from a single open reading frame coding for a pre-pro precursor protein. In the predicted primary structure of an exemplary mature hHGF, an interchain S—S bridge is formed between Cys 487 of the α chain and Cys 604 in the β chain (see, e.g., Nakamura et al., Nature 342:440-443, (1989)). The N-terminus of the α chain is preceded by 54 amino acids, starting with a methionine group. This segment includes a characteristic hydrophobic leader (signal) sequence of 31 residues and the prosequence. The α chain starts at amino acid (aa) 55, and contains four Kringle domains. The Kringle 1 domain extends from about aa 128 to about aa 206, the Kringle 2 domain is between about aa 211 and about aa 288, the Kringle 3 domain is defined as extending from about aa 303 to about aa 383, and the Kringle 4 domain extends from about aa 391 to about aa 464 of the α chain. An exemplary HGF contains four putative glycosylation sites, which are located at positions 294 and 402 of the α-chain and at positions 566 and 653 of the β-chain.
The HGF receptor (HGFR) has been identified as the product of the c-Met proto-oncogene, Bottaro et al., Science, 251:802-804 (1991); Naldini et al., Oncogene, 6:501-504 (1991); WO 92/13097 published Aug. 6, 1992; WO 93/15754 published Aug. 19, 1993. The receptor (AKA c-Met) typically comprises, in its native form, a 190-kDa heterodimeric (a disulfide-linked 50-kDa α-chain and a 145-kDa β-chain) membrane-spanning tyrosine kinase protein (Park et al., Proc. Natl. Acad. Sci. USA, 84:6379-6383 (1987)).
The binding activity of HGF to its receptor is believed to be conveyed by a functional domain located in the N-terminal portion of the HGF molecule, including the first two Kringle domains (Matsumoto et al., Biochem. Biophys. Res. Commun., 181:691-699 (1991); Hartmann et al. Proc. Natl. Acad. Sci., 89:11574-11578 (1992); Lokker et al., EMBO J., 11:2503-2510 (1992); Lokker and Godowski, J. Biol. Chem., 268:17145-17150 (1991)). Upon HGF binding, the c-Met protein becomes phosphorylated on tyrosine residues of the 145-kDa β-subunit.
With respect to the methods disclosed herein, HGF can be produced as a purified polypeptide, for which the amino acid sequence can be at least 80% identical (i.e., 85%, 87%, 89%, 90%, 92%, 94%, 96%, 98%, 99%, or 100% identical) to any of SEQ ID NOs:1-4 listed below or other naturally occurring variants of HGF. The receptor for HGF (HGFR) can be produced as a purified polypeptide, for which the amino acid sequence can be at least 80% identical (i.e., 85%, 87%, 89%, 90%, 92%, 94%, 96%, 98%, 99%, or 100% identical) to any of SEQ ID NOs:5-8 listed below or other naturally occurring variants of HGFR.








Human HGF



(SEQ ID NO: 1)



   1 MWVTKLLPAL LLQHVLLHLL LLPIAIPYAE GQRKRRNTIH EFKKSAKTTL



 


  51 IKIDPALKIK TKKVNTADQC ANRCTRNKGL PFTCKAFVFD KARKQCLWFP


 


 101 FNSMSSGVKK EFGHEFDLYE NKDYIRNCII GKGRSYKGTV SITKSGIKCQ


 


 151 PWSSMIPHEH SFLPSSYRGK DLQENYCRNP RGEEGGPWCF TSNPEVRYEV


 


 201 CDIPQCSEVE CMTCNGESYR GLMDHTESGK ICQRWDHQTP HRHKFLPERY


 


 251 PDKGFDDNYC RNPDGQPRPW CYTLDPHTRW EYCAIKTCAD NTMNDTDVPL


 


 301 ETTECIQGQG EGYRGTVNTI WNGIPCQRWD SQYPHEHDMT PENFKCKDLR


 


 351 ENYCRNPDGS ESPWCFTTDP NIRVGYCSQI PNCDMSHGQD CYRGNGKNYM


 


 401 GNLSQTRSGL TCSMWDKNME DLHRHIFWEP DASKLNENYC RNPDDDAHGP


 


 451 WCYTGNPLIP WDYCPISRCE GDTTPTIVNL DHPVISCAKT KQLRVVNGIP


 


 501 TRTNIGWMVS LRYRNKHICG GSLIKESWVL TARQCFPSRD LKDYEAWLGI


 


 551 HDVHGRGDEK CKQVLNVSQL VYGPEGSDLV LMKLARPAVL DDFVSTIDLP


 


 601 NYGCTIPEKT SCSVYGWGYT GLINYDGLLR VAHLYIMGNE KCSQHHRGKV


 


 651 TLNESEICAG AEKIGSGPCE GDYGGPLVCE QHKMRMVLGV IVPGRGCAIP


 


 701 NRPGIFVRVA YYAKWIHKII LTYKVPQS


 


Chimpanzee HGF


(SEQ ID NO: 2)



   1 MWVTKLLPAL LLQHVLLHLL LLPIAIPYAE GQRKRRNTIH EFKKSAKTTL



 


  51 IKIDPALKIK TKKVNTADQC ANRCTRNKGL PFTCKAFVFD KARKQCLWFP


 


 101 FNSMSSGVKK EFGHEFDLYE NKGHETFGRF LPSSYRGKDL QENYCRNPRG


 


 151 EEGGPWCFTS NPEVRYEVCD IPQCSEVECM TCNGESYRGL MDHTESGKIC


 


 201 QRWDHQTPHR HKFLPERYPD KGFDDNYCRN PDGQPRPWCY TLDPHTRWEY


 


 251 CAIKTCADNT MNDTDVPLET TECIQGQGEG YRGTVNTIWN GIPCQRWDSQ


 


 301 YPHEHDMTPE NFKCKDLREN YCRNPDGSES PWCFTTDPNI RVGYCSQIPN


 


 351 CDMSHGQDCY RGNGKNYMGN LSQTRSGLTC SMWDKNMEDL HRHIFWEPDA


 


 401 SKLNENYCRN PDDDAHGPWC YTGNPLIPWD YCPISRCEGD TTPTIVNLDH


 


 451 PVISCAKTKQ LRVVNGIPTR TNVGWMVSLR YRNKHICGGS LIKESWVLTA


 


 501 RQCFPSRDLK DYEAWLGIHD VHGRGDEKCK QVLNVSQLVY GPEGSDLVLM


 


 551 KLARPAVLDD FVSTIDLPNY GCTIPEKTSC SVYGWGYTGL INYDGLLRVA


 


 601 HLYIMGNEKC SQHHRGKVTL NESEICAGAE KIGSGPCEGD YGGPLVCEQH


 


 651 KMRMVLGVIV PGRGCAIPNR PGIFVRVAYY AKWIHKIILT YKVPQS


 


Mouse HGF


(SEQ ID NO: 3)



   1 MMWGTKLLPV LLLQHVLLHL LLLHVAIPYA EGQKKRRNTL HEFKKSAKTT



 


  51 LTKEDPLLKI KTKKVNSADE CANRCIRNRG FTFTCKAFVF DKSRKRCYWY


 


 101 PFNSMSSGVK KGFGHEFDLY ENKDYIRNCI IGKGGSYKGT VSITKSGIKC


 


 151 QPWNSMIPHE HSFLPSSYRG KDLQENYCRN PRGEEGGPWC FTSNPEVRYE


 


 201 VCDIPQCSEV ECMTCNGESY RGPMDHTESG KTCQRWDQQT PHRHKFLPER


 


 251 YPDKGFDDNY CRNPDGKPRP WCYTLDPDTP WEYCAIKTCA HSAVNETDVP


 


 301 METTECIQGQ GEGYRGTSNT IWNGIPCQRW DSQYPHKHDI TPENFKCKDL


 


 351 RENYCRNPDG AESPWCFTTD PNIRVGYCSQ IPKCDVSSGQ DCYRGNGKNY


 


 401 MGNLSKTRSG LTCSMWDKNM EDLHRHIFWE PDASKLNKNY CRNPDDDAHG


 


 451 PWCYTGNPLI PWDYCPISRC EGDTTPTIVN LDHPVISCAK TKQLRVVNGI


 


 501 PTQTTVGWMV SLKYRNKHIC GGSLIKESWV LTARQCFPAR NKDLKDYEAW


 


 551 LGIHDVHERG EEKRKQILNI SQLVYGPEGS DLVLLKLARP AILDNFVSTI


 


 601 DLPSYGCTIP EKTTCSIYGW GYTGLINADG LLRVAHLYIM GNEKCSQHHQ


 


 651 GKVTLNESEL CAGAEKIGSG PCEGDYGGPL ICEQHKMRMV LGVIVPGRGC


 


 701 AIPNRPGIFV RVAYYAKWIH KVILTYKL


 


Rat HGF


(SEQ ID NO: 4)



   1 MWVTKLLPAL LLQHVLLHLL LLPIAIPYAE GHKKRRNTIH EFKKSAKTTL



 


  51 IKIDPALKIK TKKVNTADQC ANRCTRNNGL PFTCKAFVFD KARKQCLWFP


 


 101 FNSMSSGVKK EFGHEFDLYE NKDYIRNCII GKGRSYKGTV SITKSGIKCQ


 


 151 PWSSMIPHEH SFLPSSYRGK DLQENYCRNP RGEEGGPWCF TSNPEVRYEV


 


 201 CDIPQCSEVE CMTCNGESYR GLMDHTESGK ICQRWDHQTP HRHKFLPERY


 


 251 PDKGFDDNYC RNPDGQPRPW CYTLDPHTRW EYCAIKTCAD NTVNDTDVPM


 


 301 ETTECIQGQG EGYRGTANTI WNGIPCQRWD SQYPHKHDMT PENFKCKDLR


 


 351 ENYCRNPDGS ESPWCFTTDP NIRVGYCSQI PNCDMSNGQD CYRGNGKNYM


 


 401 GNLSQTRSGL TCSMWNKNME DLHRHIFWEP DASKLNENYC RNPDDDAHGP


 


 451 WCYTGNPLIP WDYCPISRCE GDTTPTIVNL DHPVISCAKT KQLRVVNGIP


 


 501 TRTNVGWMIS LRYRNKHICG GSLIKESWVL TARQCFPSRD LKDYEAWLGI


 


 551 HDVHGRGEEK RKQVLNVSQL VYGPEGSDLV LMKLARPAVL DDFVNTIDLP


 


 601 NYGCTIPEKT SCSVYGWGYT GLINYDGLLR VAHLYIMGNE KCSQHHRGKV


 


 651 TLNESEICAG AEKIGSGPCE GDYGGPLVCE QHKMRMVLGV IVPGRGCAIP


 


 701 NRPGIFVRVA YYAKWIHKII LTYKVPES


 


Human HGFR


(SEQ ID NO: 5)



   1 MKAPAVLAPG ILVLLFTLVQ RSNGECKEAL AKSEMNVNMK YQLPNFTAET



 


  51 PIQNVILHEH HIFLGATNYI YVLNEEDLQK VAEYKTGPVL EHPDCFPCQD


 


 101 CSSKANLSGG VWKDNINMAL VVDTYYDDQL ISCGSVNRGT CQRHVFPHNH


 


 151 TADIQSEVHC IFSPQIEEPS QCPDCVVSAL GAKVLSSVKD RFINFFVGNT


 


 201 INSSYFPDHP LHSISVRRLK ETKDGFMFLT DQSYIDVLPE FRDSYPIKYV


 


 251 HAFESNNFIY FLTVQRETLD AQTFHTRIIR FCSINSGLHS YMEMPLECIL


 


 301 TEKRKKRSTK KEVFNILQAA YVSKPGAQLA RQIGASLNDD ILFGVFAQSK


 


 351 PDSAEPMDRS AMCAFPIKYV NDFFNKIVNK NNVRCLQHFY GPNHEHCFNR


 


 401 TLLRNSSGCE ARRDEYRTEF TTALQRVDLF MGQFSEVLLT SISTFIKGDL


 


 451 TIANLGTSEG RFMQVVVSRS GPSTPHVNFL LDSHPVSPEV IVEHTLNQNG


 


 501 YTLVITGKKI TKIPLNGLGC RHFQSCSQCL SAPPFVQCGW CHDKCVRSEE


 


 551 CLSGTWTQQI CLPAIYKVFP NSAPLEGGTR LTICGWDFGF RRNNKFDLKK


 


 601 TRVLLGNESC TLTLSESTMN TLKCTVGPAM NKHFNMSIII SNGHGTTQYS


 


 651 TFSYVDPVIT SISPKYGPMA GGTLLTLTGN YLNSGNSRHI SIGGKTCTLK


 


 701 SVSNSILECY TPAQTISTEF AVKLKIDLAN RETSIFSYRE DPIVYEIHPT


 


 751 KSFISGGSTI TGVGKNLNSV SVPRMVINVH EAGRNFTVAC QHRSNSEIIC


 


 801 CTTPSLQQLN LQLPLKTKAF FMLDGILSKY FDLIYVHNPV FKPFEKPVMI


 


 851 SMGNENVLEI KGNDIDPEAV KGEVLKVGNK SCENIHLHSE AVLCTVPNDL


 


 901 LKLNSELNIE WKQAISSTVL GKVIVQPDQN FTGLIAGVVS ISTALLLLLG


 


 951 FFLWLKKRKQ IKDLGSELVR YDARVHTPHL DRLVSARSVS PTTEMVSNES


 


1001 VDYRATFPED QFPNSSQNGS CRQVQYPLTD MSPILTSGDS DISSPLLQNT


 


1051 VHIDLSALNP ELVQAVQHVV IGPSSLIVHF NEVIGRGHFG CVYHGTLLDN


 


1101 DGKKIHCAVK SLNRITDIGE VSQFLTEGII MKDFSHPNVL SLLGICLRSE


 


1151 GSPLVVLPYM KHGDLRNFIR NETHNPTVKD LIGFGLQVAK GMKYLASKKF


 


1201 VHRDLAARNC MLDEKFTVKV ADFGLARDMY DKEYYSVHNK TGAKLPVKWM


 


1251 ALESLQTQKF TTKSDVWSFG VLLWELMTRG APPYPDVNTF DITVYLLQGR


 


1301 RLLQPEYCPD PLYEVMLKCW HPKAEMRPSF SELVSRISAI FSTFIGEHYV


 


1351 HVNATYVNVK CVAPYPSLLS SEDNADDEVD TRPASFWETS


 


Chimpanzee HGFR


(SEQ ID NO: 6)



   1 MKAPAVLAPG ILVLLFTLVQ RSNGECKEAL AKSEMNVNMK YQLPNFTAET



 


  51 PIQNVILHEH HIFLGATNYI YVLNEEDLQK VAEYKTGPVL EHPDCFPCQD


 


 101 CSSKANLSGG VWKDNINMAL VVDTYYDDQL ISCGSVNRGT CQRHVFPHNH


 


 151 TADIQSEVHC IFSPQIEEPS QCPDCVVSAL GAKVLSSVKD RFINFFVGNT


 


 201 INSSYFPDHP LHSISVRRLK ETKDGFMFLT DQSYIDVLPE FRDSYPIKYV


 


 251 HAFESNNFIY FLTVQRETLD AQTFHTRIIR FCSINSGLHS YMEMPLECIL


 


 301 TEKRKKRSTK KEVFNILQAA YVSKPGAQLA RQIGASLNDD ILFGVFAQSK


 


 351 PDSAEPMDRS AMCAFPIKYV NDFFNKIVNK NNVRCLQHFY GPNHEHCFNR


 


 401 TLLRNSSSCE ARRDEYRTEF TTALQRVDLF MGQFSEVLLT SISTFIKGDL


 


 451 TIANLGTSEG RFMQVVVSRS GPSTPHVNFL LDSHPVSPEV IVEHTLNQNG


 


 501 YTLVVTGKKI TKIPLNGLGC RHFQSCSQCL SAPPFVQCGW CHDKCVRSEE


 


 551 CLSGTWTQQI CLPAIYKVFP NSAPLEGGTR LTICGWDFGF RRNNKFDLKK


 


 601 TRVLLGNESC TLTLSESTMN TLKCTVGPAM NKHFNMSIII SNGHGTTQYS


 


 651 TFSYVDPVIT SISPKYGPMA GGTLLTLTGN YLNSGNSRHI SIGGKTCTLK


 


 701 SVSNSILECY TPAQTISTEF AVKLKIDLAN RETSIFSYRE DPIVYEIHPT


 


 751 KSFISTWWKE PLNIVSFLFC FASGGSTITG VGKNLNSVSV PRMVINVHEA


 


 801 GRNFTVACQH RSNSEIICCT TPSLQQLNLQ LPLKTKAFFM LDGILSKYFD


 


 851 LIYVHNPVFK PFEKPVMISM GNENVLEIKG NDIDPEAVKG EVLKVGNKSC


 


 901 ENIHLHSEAV LCTVPNDLLK LNSELNIEWK QAISSTVLGK VIVQPDQNFT


 


 951 GLIAGVVSIS IALLLLLGFF LWLKKRKQIK DLGSELVRYD ARVHTPHLDR


 


1001 LVSARSVSPT TEMVSNESVD YRATFPEDQF PNSSQNGSCR QVQYPLTDMS


 


1051 PILTSGDSDI SSPLLQNTVH IDLSALNPEL VQAVQHVVIG PSSLIVHFNE


 


1101 VIGRGHFGCV YHGTLLDNDG KKIHCAVKSL NRITDIGEVS QFLTEGIIMK


 


1151 DFSHPNVLSL LGICLRSEGS PLVVLPYMKH GDLRNFIRNE THNPTVKDLI


 


1201 GFGLQVAKGM KYLASKKFVH RDLAARNCML DEKFTVKVAD FGLARDMYDK


 


1251 EYYSVHNKTG AKLPVKWMAL ESLQTQKFTT KSDVWSFGVL LWELMTRGAP


 


1301 PYPDVNTFDI TVYLLQGRRL LQPEYCPDPL YEVMLKCWHP KAEMRPSFSE


 


1351 LVSRISAIFS TFIGEHYVHV NATYVNVKCV APYPSLLSSE DNADDEVDTR


 


1401 PASFWETS


 


Mouse HGFR


(SEQ ID NO: 7)



   1 MKAPTVLAPG ILVLLLSLVQ RSHGECKEAL VKSEMNVNMK YQLPNFTAET



 


  51 PIQNVVLHGH HIYLGATNYI YVLNDKDLQK VSEFKTGPVL EHPDCLPCRD


 


 101 CSSKANSSGG VWKDNINMAL LVDTYYDDQL ISCGSVNRGT CQRHVLPPDN


 


 151 SADIQSEVHC MFSPEEESGQ CPDCVVSALG AKVLLSEKDR FINFFVGNTI


 


 201 NSSYPPGYSL HSISVRRLKE TQDGFKFLTD QSYIDVLPEF LDSYPIKYIH


 


 251 AFESNHFIYF LTVQKETLDA QTFHTRIIRF CSVDSGLHSY MEMPLECILT


 


 301 EKRRKRSTRE EVFNILQAAY VSKPGANLAK QIGASPSDDI LFGVFAQSKP


 


 351 DSAEPVNRSA VCAFPIKYVN DFFNKIVNKN NVRCLQHFYG PNHEHCFNRT


 


 401 LLRNSSGCEA RSDEYRTEFT TALQRVDLFM GRLNQVLLTS ISTFIKGDLT


 


 451 IANLGTSEGR FMQVVLSRTA HLTPHVNFLL DSHPVSPEVI VEHPSNQNGY


 


 501 TLVVTGKKIT KIPLNGLGCG HFQSCSQCLS APYFIQCGWC HNQCVRFDEC


 


 551 PSGTWTQEIC LPAVYKVFPT SAPLEGGTVL TICGWDFGFR KNNKFDLRKT


 


 601 KVLLGNESCT LTLSESTTNT LKCTVGPAMS EHFNVSVIIS NSRETTQYSA


 


 651 FSYVDPVITS ISPRYGPQAG GTLLTLTGKY LNSGNSRHIS IGGKTCTLKS


 


 701 VSDSILECYT PAQTTSDEFP VKLKIDLANR ETSSFSYRED PVVYEIHPTK


 


 751 SFISGGSTIT GIGKTLNSVS LPKLVIDVHE VGVNYTVACQ HRSNSEIICC


 


 801 TTPSLKQLGL QLPLKTKAFF LLDGILSKHF DLTYVHNPVF EPFEKPVMIS


 


 851 MGNENVVEIK GNNIDPEAVK GEVLKVGNQS CESLHWHSGA VLCTVPSDLL


 


 901 KLNSELNIEW KQAVSSTVLG KVIVQPDQNF AGLIIGAVSI SVVVLLLSGL


 


 951 FLWMRKRKHK DLGSELVRYD ARVHTPHLDR LVSARSVSPT TEMVSNESVD


 


1001 YRATFPEDQF PNSSQNGACR QVQYPLTDLS PILTSGDSDI SSPLLQNTVH


 


1051 IDLSALNPEL VQAVQHVVIG PSSLIVHFNE VIGRGHFGCV YHGTLLDNDG


 


1101 KKIHCAVKSL NRITDIEEVS QFLTEGIIMK DFSHPNVLSL LGICLRSEGS


 


1151 PLVVLPYMKH GDLRNFIRNE THNPTVKDLI GFGLQVAKGM KYLASKKFVH


 


1201 RDLAARNCML DEKFTVKVAD FGLARDMYDK EYYSVHNKTG AKLPVKWMAL


 


1251 ESLQTQKFTT KSDVWSFGVL LWELMTRGAP PYPDVNTFDI TIYLLQGRRL


 


1301 LQPEYCPDAL YEVMLKCWHP KAEMRPSFSE LVSRISSIFS TFIGEHYVHV


 


1351 NATYVNVKCV APYPSLLPSQ DNIDGEGNT


 


Rat HGFR


(SEQ ID NO: 8)



   1 MKAPTALAPG ILLLLLTLAQ RSHGECKEAL VKSEMNVNMK YQLPNFTAET



 


  51 PIQNVVLHGH HIYLGATNYI YVLNDKDLQK VSEFKTGPVV EHPDCFPCQD


 


 101 CSSKANVSGG VWKDNVNMAL LVDTYYDDQL ISCGSVNRGT CQRHVLPPDN


 


 151 AADIQSEVHC MFSPLAEEES GQCPDCVVSA LGAKVLLSEK DRFINFFVGN


 


 201 TINSSYPPDY SLHSISVRRL KETQDGFKFL TDQSYIDVLG EFRDSYPIKY


 


 251 IHAFESNHFI YFLTVQKETL DAQTFHTRII RFCSVDSGLH SYMEMPLECI


 


 301 LTEKRRKRST REEVFNILQA AYVSKPGANL AKQIGASPYD DILYGVFAQS


 


 351 KPDSAEPMNR SAVCAFPIKY VNDFFNKIVN KNNVRCLQHF YGPNHEHCFN


 


 401 RTLLRNSSGC EVRSDEYRTE FTTALQAVDL FMGRLNHVLL TSISTFIKGD


 


 451 LTIANLGTSE GRFMQVVLSR TAHFTPHVNF LLDSHPVSPE VIVEHPSNQN


 


 501 GYTLVVTGKK ITKIPLNGLG CGHFQSCSQC LSAPYFIQCG WCHNRCVHSN


 


 551 ECPSGTWTQE ICLPAVYKVF PTSAPLEGGT MLTICGWDFG FKKNNKFDLR


 


 601 KTKVLLGNES CTLTLSESTT NTLKCTVGPA MSEHFNVSVI VSNSRETTQY


 


 651 SAFSYVDPVI TSISPRYGPH AGGTLLTLTG KYLNSGNSRH ISIGGKTCTL


 


 701 KSVSDSILEC YTPGHTVSAE FPVKLKIDLA DRVTSSFSYG EDPFVSEIHP


 


 751 TKSFISGGST ITGIGKNLNS VSTPKLVIEV HDVGVNYTVA CQHRSSSEII


 


 801 CCTTPSLQQL DLQLPLKTKA FFLLDGILSK HFDLTYVHDP MFKPFEKPVM


 


 851 ISMGNENVVE IKGDDIDPEA VKGEVLKVGN KSCENLHWHS EALLCTVPSD


 


 901 LLKLNGGELN IEWKQAVSST VLGKVIVQPD QNFAGLIIGA VSISVVVLLV


 


 951 SGLFLWLRKR KHKDLGSELV RYDARVHTPH LDRLVSARSV SPTTEMVSNE


 


1001 SVDYRATFPE DQFPNSSQNG ACRQVQYPLT DLSPILTSGD SDISSPLLQN


 


1051 TVHIDLSALN PELVQAVQHV VIGPSSLIVH FNEVIGRGHF GCVYHGTLLD


 


1101 SDGKKIHCAV KSLNRITDIE EVSQFLTEGI IMKDFSHPNV LSLLGICLRS


 


1151 EGSPLVVLPY MKHGDLRNFI RNETHNPTVK DLIGFGLQVA KGMKYLASKK


 


1201 FVHRDLAARN CMLDEKFTVK VADFGLARDM YDKEYYSVHN KTGAKLPVKW


 


1251 MALESLQTQK FTTKSDVWSF GVLLWELMTR GAPPYPDVNT FDITIYLLQG


 


1301 RRLLQPEYCP DALYEVMLKC WHPKAEMRPS FSELVSRISS IFSTFIGEHY


 


1351 VHVNATYVNV KCVAPYPSLL PSQDNIDGEA NT






Exemplary regions of HGFR include:
















Region
52..487









/region_name=“semaphorin domain”



/note=“Sema”



/db_xref=“CDD:25341”










Region
519..561









/region_name=“domain found in Plexins, Semaphorins


and




Integrins”



/note=“PSI”



/db_xref=“CDD:25325”










Region
563..656









/region_name=“First repeat of the IPT domain of


Plexins




and Cell Surface Receptors (PCSR)”



/note=“IPT_plexin_repeat1”



/db_xref=“CDD:27712”










Region
657..740









/region_name=“Second repeat of the IPT domain of


Plexins




and Cell Surface Receptors (PCSR)”



/note=“IPT_plexin_repeat2”



/db_xref=“CDD:27711”










Region
742..837









/region_name=“Third repeat of the IPT domain of


Plexins




and Cell Surface Receptors (PCSR)”



/note=“IPT_plexin_repeat3”



/db_xref=“CDD:27713”










Region
839..932









/region_name=“IPT domain of Plexins and Cell


Surface




Receptors (PCSR) and related proteins”



/note=“IPT_PCSR”



/db_xref=“CDD:27705”









In some embodiments, HGF, and biologically active fragments thereof are provided as purified polypeptides. Purified polypeptides include polypeptides that are generated in vitro (e.g., by in vitro translation or by use of an automated polypeptide synthesizer) and polypeptides that are initially expressed in a cell (e.g., a prokaryotic cell, a eukaryotic cell, an insect cell, a yeast cell, a mammalian cell, a plant cell) and subsequently purified. Cells that express a purified polypeptide can include cells that encode an endogenous gene, cells transduced with an expression vector encoding a polypeptide, and cells that are experimentally manipulated to induce expression of an endogenous gene that is not typically expressed in that cell type (e.g., gene activation technology). In some embodiments, polypeptides are fusion proteins (e.g., an HGFR-glutathione-S-transferase fusion) that may include a protease cleavage site to allow cleavage and separation of the fusion protein into separate polypeptides. In some embodiments, a polypeptide can include an amino acid sequence that facilitates purification of the polypeptide (e.g., a multiple histidine tag, a FLAG tag, etc). Methods for isolating proteins from cells or polypeptides that are expressed by cells, include affinity purification, size exclusion chromatography, high performance liquid chromatography, and other chromatographic purification methods. The polypeptides can be post-translationally modified, e.g., glycosylated.
Purified HGF (e.g., purified human HGF) can be obtained from a mammalian cell line stably transfected with a cDNA encoding the human HGF polypeptide listed herein as SEQ ID NO:2 and secreting mature HGF as described, e.g., in U.S. Pat. No. 5,686,292 to Schwall, or Naka et al., Journal of Biol. Chem., 267(28):20114-20119, (1992). In some embodiments, HGF can be a single chain variant that lacks mitogenic activity but retains high affinity receptor binding, as described in Lokker et al, EMBO J., 11(7):2503-2510, (1992).
II. HGF and HGFR HGF/HGFR Modulators
A variety of agents can be used as a HGF/HGFR modulator to treat pathologies related to the lymphatic system, e.g., induced lymphedema, lymphangiomas, tumor lymphangiogenesis, or tumor metastasis. The agent may be any type of compound that can be administered to a subject (e.g., antibodies, proteins, peptides, glycoproteins, glycopeptides, glycolipids, polysaccharides, oligosaccharides, nucleic acids, bioorganic molecules, peptidomimetics, pharmacological agents and their metabolites, transcriptional and translation control sequences, and the like). In one embodiment, the HGF/HGFR modulator is a biologic, e.g., a protein having a molecular weight of between 5-300 kDa.
For example, a HGF/HGFR modulator may inhibit binding of HGF to an HGFR or may prevent HGF-mediated NF-κB activation. A typical HGF/HGFR modulator can bind to HGFR, e.g., a single chain variant of HGF that lacks mitogenic activity but retains high affinity receptor binding (see, e.g., Lokker et al, EMBO J., 11(7):2503-2510, (1992)). A HGF/HGFR modulator that binds to HGF may alter the conformation of HGF, hinder binding of HGF to HGFR, or otherwise decrease the affinity of HGF for a HGFR or prevent the interaction between HGF and a HGFR.
A HGF/HGFR modulator (e.g., an antibody) may bind to HGF or to a HGFR with a Kd of less than 10−6, 10−7, 10−8, 10−9, or 10−10 M. In one embodiment, the HGF/HGFR modulator binds to HGF with an affinity at least 5, 10, 20, 50, 100, 200, 500, or 1000 better than its affinity for hepatocyte growth factor-like/macrophage stimulating protein (HGF1/MSP). In one embodiment, the HGF/HGFR modulator binds to HGF or HGFR with an affinity at least 5, 10, 20, 50, 100, 200, 500, or 1000-fold better than its affinity for the macrophage stimulating 1 receptor (RON) (e.g., NP—002438). A preferred HGF/HGFR modulator specifically binds HGF or HGFR, such as a HGF or HGFR specific antibody.
Exemplary HGF protein molecules include human HGF (e.g., NP—001010932, shown as SEQ ID NO:1)), Chimpanzee HGF (e.g., XP—519174, shown as SEQ ID NO:2), mouse HGF (e.g., CAA51054, shown as SEQ ID NO:3), and Rat HGF (e.g., 1602237A, shown as SEQ ID NO:4). Also included are proteins that include an amino acid sequence at least 90, 92, 95, 97, 98, 99% identical and completely identical to the mature processed region of the aforementioned HGF proteins (e.g., an amino acid sequence at least 90, 92, 95, 97, 98, 99% identical or completely identical to amino acids 25-1390 of SEQ ID NO:1 and proteins encoded by a nucleic acid that hybridizes under high stringency conditions to a human, chimp, mouse, or rat gene encoding a naturally occurring HGF protein. Preferably, a HGF protein, in its processed mature form, is capable of providing at least one HGF activity, e.g., binding to HGFR.
Calculations of “homology” or “sequence identity” between two sequences (the terms are used interchangeably herein) are performed as follows. The sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The optimal alignment is determined as the best score using the GAP program in the GCG software package with a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences.
As used herein, the term “hybridizes under high stringency conditions” describes conditions for hybridization and washing. Guidance for performing hybridization reactions can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6, which is incorporated by reference. Aqueous and nonaqueous methods are described in that reference and either can be used. High stringency hybridization conditions include hybridization in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 65° C., or substantially similar conditions.
Exemplary HGF/HGFR modulators include antibodies that bind to HGF or HGFR and soluble forms of the HGFR that compete with cell surface HGFR for binding to HGF. An example of a soluble form of the HGFR is an Fc fusion protein that includes at least a portion of the extracellular domain of HGFR (e.g., a soluble HGF-binding fragment of HGFR), referred to as HGFR-Fc (see e.g., Mark et al., Journal of Biol. Chem., 267(36):26166-26171, (1992)). Other soluble forms of HGFR, e.g., forms that do not include an Fc domain, can also be used. Antibody HGF/HGFR modulators are further discussed below. Other types of HGF/HGFR modulators, e.g., small molecules, nucleic acid or nucleic acid-based aptamers, and peptides, can be isolated by screening, e.g., as described in Jhaveri et al. Nat. Biotechnol. 18:1293 and U.S. Pat. No. 5,223,409. Exemplary assays for determining if an agent binds to HGF or HGFR and for determining if an agent modulates a HGF/HGFR interaction are described, e.g., in U.S. Pat. No. 6,468,529 to Schwall et al.
An exemplary soluble form of the HGFR protein includes a region of the HGFR protein that binds to HGF, e.g., an extracellular domain, e.g., domain of in the extracellular region. This region can be physically associated, e.g., fused to another amino acid sequence, e.g., an Fc domain, at its N- or C-terminus. The region from HGFR can be spaced by a linker from the heterologous amino acid sequence. Michieli et al. (2005), Cancer Cell, 6:61-73, describes an exemplary HGFR fusion protein.
A. Antibodies
Exemplary HGF/HGFR modulators include antibodies that bind to HGF and/or HGFR. In one embodiment, the antibody inhibits the interaction between HGF and a HGFR, e.g., by physically blocking the interaction, decreasing the affinity of HGF and/or HGFR for its counterpart, disrupting or destabilizing HGF complexes, sequestering HGF or a HGFR, or targeting HGF or HGFR for degradation. In one embodiment, the antibody can bind to HGF or HGFR at an epitope that includes one or more amino acid residues that participate in the HGF/HGFR binding interface. Such amino acid residues can be identified, e.g., by alanine scanning. In another embodiment, the antibody can bind to residues that do not participate in the HGF/HGFR binding. For example, the antibody can alter a conformation of HGF or HGFR and thereby reduce binding affinity, or the antibody may sterically hinder HGF/HGFR binding. The antibody may bind to the α subunit or the β subunit of HGF.
In addition to antibodies that bind to HGF and/or HGFR, other antibodies can be used. In one embodiment, the antibody can prevent activation of a HGF/HGFR mediated event or activity. For example, it is possible to use an antibody to α9 integrin, which is upregulated by HGF. For example, certain antibodies to α9 can inhibit HGF induced migration of cells.
As used herein, the term “antibody” refers to a protein that includes at least one immunoglobulin variable region, e.g., an amino acid sequence that provides an immunoglobulin variable domain or an immunoglobulin variable domain sequence. For example, an antibody can include a heavy (H) chain variable region (abbreviated herein as VH), and a light (L) chain variable region (abbreviated herein as VL). In another example, an antibody includes two heavy (H) chain variable regions and two light (L) chain variable regions. The term “antibody” encompasses antigen-binding fragments of antibodies (e.g., single chain antibodies, Fab fragments, F(ab′)2 fragments, Fd fragments, Fv fragments, and dAb fragments) as well as complete antibodies, e.g., intact and/or full length immunoglobulins of types IgA, IgG (e.g., IgG1, IgG2, IgG3, IgG4), IgE, IgD, IgM (as well as subtypes thereof). The light chains of the immunoglobulin may be of types kappa or lambda. In one embodiment, the antibody is glycosylated. An antibody can be functional for antibody-dependent cytotoxicity and/or complement-mediated cytotoxicity, or may be non-functional for one or both of these activities.
The VH and VL regions can be further subdivided into regions of hypervariability, termed “complementarity determining regions” (“CDR”), interspersed with regions that are more conserved, termed “framework regions” (FR). The extent of the FRs and CDRs has been precisely defined (see, e.g., Kabat, E. A., et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, US Department of Health and Human Services, NIH Publication No. 91-3242; and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917). Kabat definitions are used herein. Each VH and VL is typically composed of three CDRs and four FRs, arranged from amino-terminus to carboxyl-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
An “immunoglobulin domain” refers to a domain from the variable or constant domain of immunoglobulin molecules. Immunoglobulin domains typically contain two β-sheets formed of about seven β-strands, and a conserved disulfide bond (see, e.g., A. F. Williams and A. N. Barclay (1988) Ann. Rev Immunol. 6:381-405). An “immunoglobulin variable domain sequence” refers to an amino acid sequence that can form a structure sufficient to position CDR sequences in a conformation suitable for antigen binding. For example, the sequence may include all or part of the amino acid sequence of a naturally-occurring variable domain. For example, the sequence may omit one, two, or more N- or C-terminal amino acids, internal amino acids, may include one or more insertions or additional terminal amino acids, or may include other alterations. In one embodiment, a polypeptide that includes an immunoglobulin variable domain sequence can associate with another immunoglobulin variable domain sequence to form a target binding structure (or “antigen binding site”), e.g., a structure that interacts with HGF or HGFR.
The VH or VL chain of the antibody can further include all or part of a heavy or light chain constant region, to thereby form a heavy or light immunoglobulin chain, respectively. In one embodiment, the antibody is a tetramer of two heavy immunoglobulin chains and two light immunoglobulin chains. The heavy and light immunoglobulin chains can be connected by disulfide bonds. The heavy chain constant region typically includes three constant domains, CH1, CH2, and CH3. The light chain constant region typically includes a CL domain. The variable region of the heavy and light chains contains a binding domain that interacts with an antigen. The constant regions of the antibodies typically mediate the binding of the antibody to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system.
One or more regions of an antibody can be human, effectively human, or humanized. For example, one or more of the variable regions can be human or effectively human. For example, one or more of the CDRs, e.g., HC CDR1, HC CDR2, HC CDR3, LC CDR1, LC CDR2, and LC CDR3, can be human. Each of the light chain CDRs can be human. HC CDR3 can be human. One or more of the framework regions can be human, e.g., FR1, FR2, FR3, and FR4 of the HC or LC. In one embodiment, all the framework regions are human, e.g., derived from a human somatic cell, e.g., a hematopoietic cell that produces immunoglobulins or a non-hematopoietic cell. In one embodiment, the human sequences are germline sequences, e.g., encoded by a germline nucleic acid. One or more of the constant regions can be human, effectively human, or humanized. In another embodiment, at least 70, 75, 80, 85, 90, 92, 95, or 98% of the framework regions (e.g., FR1, FR2, and FR3, collectively, or FR1, FR2, FR3, and FR4, collectively) or the entire antibody can be human, effectively human, or humanized. For example, FR1, FR2, and FR3 collectively can be at least 70, 75, 80, 85, 90, 92, 95, 98, or 99% identical, or completely identical, to a human sequence encoded by a human germline segment.
An “effectively human” immunoglobulin variable region is an immunoglobulin variable region that includes a sufficient number of human framework amino acid positions such that the immunoglobulin variable region does not elicit an immunogenic response in a normal human. An “effectively human” antibody is an antibody that includes a sufficient number of human amino acid positions such that the antibody does not elicit an immunogenic response in a normal human.
A “humanized” immunoglobulin variable region is an immunoglobulin variable region that is modified such that the modified form elicits less of an immune response in a human than does the non-modified form, e.g., is modified to include a sufficient number of human framework amino acid positions such that the immunoglobulin variable region does not elicit an immunogenic response in a normal human. Descriptions of “humanized” immunoglobulins include, for example, U.S. Pat. Nos. 6,407,213 and 5,693,762. In some cases, humanized immunoglobulins can include a non-human amino acid at one or more framework amino acid positions.
Antibodies that bind to HGF or a HGFR can be generated by a variety of means, including immunization, e.g., using an animal, or in vitro methods such as phage display. All or part of HGF or HGFR can be used as an immunogen or as a target for selection. For example, HGF or a fragment thereof or HGFR or a fragment thereof, can be used as an immunogen. In one embodiment, the immunized animal contains immunoglobulin producing cells with natural, human, or partially human immunoglobulin loci. In one embodiment, the non-human animal includes at least a part of a human immunoglobulin gene. For example, it is possible to engineer mouse strains deficient in mouse antibody production with large fragments of the human Ig loci. Accordingly, by using hybridoma technology, at least partly human, antigen-specific monoclonal antibodies with the desired specificity can be produced and selected. See, e.g., XENOMOUSETM, Green et al. (1994) Nat. Gen. 7:13-21; US 2003-0070185; U.S. Pat. No. 5,789,650; and WO 96/34096.
Non-human antibodies to HGF and HGFR can also be produced, e.g., in a rodent. The non-human antibody can be humanized, e.g., as described in EP 239 400; U.S. Pat. Nos. 6,602,503; 5,693,761; and 6,407,213, deimmunized, or otherwise modified to make it effectively human.
EP 239 400 (Winter et al.) describes altering antibodies by substitution (within a given variable region) of their complementarity determining regions (CDRs) for one species with those from another. Typically, CDRs of a non-human (e.g., murine) antibody are substituted into the corresponding regions in a human antibody by using recombinant nucleic acid technology to produce sequences encoding the desired substituted antibody. Human constant region gene segments of the desired isotype (usually gamma I for CH and kappa for CL) can be added and the humanized heavy and light chain genes can be co-expressed in mammalian cells to produce soluble humanized antibody. Other methods for humanizing antibodies can also be used. For example, other methods can account for the three dimensional structure of the antibody, framework positions that are in three dimensional proximity to binding determinants, and immunogenic peptide sequences. See, e.g., WO 90/07861; U.S. Pat. Nos. 5,693,762; 5,693,761; 5,585,089; and 5,530,101; Tempest et al. (1991) Biotechnology 9:266-271 and U.S. Pat. No. 6,407,213.
Fully human monoclonal antibodies that bind to HGF and HGFR can be produced, e.g., using in vitro-primed human splenocytes, as described by Boerner et al. (1991) J. Immunol. 147:86-95. They may be prepared by repertoire cloning as described by Persson et al. (1991) Proc. Nat. Acad. Sci. USA 88:2432-2436 or by Huang and Stollar (1991) J. Immunol. Methods 141:227-236; also U.S. Pat. No. 5,798,230. Large nonimmunized human phage display libraries may also be used to isolate high affinity antibodies that can be developed as human therapeutics using standard phage technology (see, e.g., Hoogenboom et al. (1998) Immunotechnology 4:1-20; Hoogenboom et al. (2000) Immunol Today 2:371-378; and US 2003-0232333).
Antibodies and other proteins described herein can be produced in prokaryotic and eukaryotic cells. In one embodiment, the antibodies (e.g., scFv's) are expressed in a yeast cell such as Pichia (see, e.g., Powers et al. (2001) J. Immunol. Methods 251:123-35), Hanseula, or Saccharomyces. 
Antibodies, particularly full length antibodies, e.g., IgGs, can be produced in mammalian cells. Exemplary mammalian host cells for recombinant expression include Chinese Hamster Ovary (CHO cells) (including dihydrofolate reductase-negative CHO cells, described in Urlaub and Chasin (1980) Proc. Natl. Acad. Sci. USA 77:4216-4220, used with a DHFR selectable marker, e.g., as described in Kaufman and Sharp (1982) Mol. Biol. 159:601-621), lymphocytic cell lines, e.g., NS0 myeloma cells and SP2 cells, COS cells, K562, and a cell from a transgenic animal, e.g., a transgenic mammal. For example, the cell can be a mammary epithelial cell.
In addition to the nucleic acid sequence encoding the immunoglobulin domain, the recombinant expression vectors may carry additional nucleic acid sequences, such as sequences that regulate replication of the vector in host cells (e.g., origins of replication) and selectable marker genes. The selectable marker gene facilitates selection of host cells into which the vector has been introduced (see e.g., U.S. Pat. Nos. 4,399,216; 4,634,665; and 5,179,017). Exemplary selectable marker genes include the dihydrofolate reductase (DHFR) gene (for use in dhfr− host cells with methotrexate selection/amplification) and the neo gene (for G418 selection).
In an exemplary system for recombinant expression of an antibody (e.g., a full length antibody or an antigen-binding portion thereof), a recombinant expression vector encoding both the antibody heavy chain and the antibody light chain is introduced into dhfr− CHO cells by calcium phosphate-mediated transfection. Within the recombinant expression vector, the antibody heavy and light chain genes are each operatively linked to enhancer/promoter regulatory elements (e.g., derived from SV40, CMV, adenovirus and the like, such as a CMV enhancer/AdMLP promoter regulatory element or an SV40 enhancer/AdMLP promoter regulatory element) to drive high levels of transcription of the genes. The recombinant expression vector also carries a DHFR gene, which allows for selection of CHO cells that have been transfected with the vector using methotrexate selection/amplification. The selected transformant host cells are cultured to allow for expression of the antibody heavy and light chains and intact antibody is recovered from the culture medium. Standard molecular biology techniques are used to prepare the recombinant expression vector, to transfect the host cells, to select for transformants, to culture the host cells, and to recover the antibody from the culture medium. For example, some antibodies can be isolated by affinity chromatography with a Protein A or Protein G.
Antibodies (and Fc fusions) may also include modifications, e.g., modifications that alter Fc function, e.g., to decrease or remove interaction with an Fc receptor or with C1q, or both. For example, the human IgG1 constant region can be mutated at one or more residues, e.g., one or more of residues 234 and 237, e.g., according to the numbering in U.S. Pat. No. 5,648,260. Other exemplary modifications include those described in U.S. Pat. No. 5,648,260.
For some proteins that include an Fc domain, the antibody/protein production system may be designed to synthesize antibodies or other proteins in which the Fc region is glycosylated. For example, the Fc domain of IgG molecules is glycosylated at asparagine 297 in the CH2 domain. The Fc domain can also include other eukaryotic post-translational modifications. In other cases, the protein is produced in a form that is not glycosylated.
Antibodies and other proteins can also be produced by a transgenic animal. For example, U.S. Pat. No. 5,849,992 describes a method for expressing an antibody in the mammary gland of a transgenic mammal. A transgene is constructed that includes a milk-specific promoter and nucleic acid sequences encoding the antibody of interest, e.g., an antibody described herein, and a signal sequence for secretion. The milk produced by females of such transgenic mammals includes, secreted-therein, the protein of interest, e.g., an antibody or Fc fusion protein. The protein can be purified from the milk, or for some applications, used directly.
Methods described in the context of antibodies can be adapted to other proteins, e.g., Fc fusions and soluble receptor fragments.
B. Variants of HGF
In some embodiments, HGF proteins can be HGF variants that are resistant to proteolytic cleavage by enzymes that are capable of in vivo conversion of HGF into its two-chain form. The variants are preferably stabilized in single-chain form by site directed mutagenesis within a region recognized by an enzyme capable of converting HGF into its two-chain form. These HGF variants retain substantially full receptor binding affinity of the corresponding wild-type HGF, but do not activate the HGFR. In one embodiment, HGF variants can have enhanced receptor binding affinity relative to the corresponding wild-type HGF but be unable to activate the HGFR. Such compounds are competitive antagonists of the corresponding wild-type HGF and, when present in sufficient concentration, are capable of inhibiting the binding of wild-type HGF to HGFR. See, e.g., Lokker et al, EMBO J., 11(7):2503-2510, (1992) and U.S. Pat. No. 5,316,921 to Godowski et al. Accordingly they can be used as HGF/HGFR antagonists.
C. Peptides
In some embodiments, the HGF/HGFR modulator can be a peptide of 32 amino acids or less that independently binds to but does not activate a target molecule (e.g., HGFR). Some such peptides can include one or more disulfide bonds. Other peptides, so-called “linear peptides,” are devoid of cysteines. In one embodiment, the peptides are artificial, i.e., not present in Nature or not present in a protein encoded by one or more genomes of interest, e.g., the human genome. Synthetic peptides may have little or no structure in solution (e.g., unstructured), heterogeneous structures (e.g., alternative conformations or “loosely structured), or a singular native structure (e.g., cooperatively folded). Some synthetic peptides adopt a particular structure when bound to a target molecule. Some exemplary synthetic peptides are so-called “cyclic peptides” that have at least a disulfide bond and, for example, a loop of about 4 to 12 non-cysteine residues. Exemplary peptides are less than 28, 24, 20, or 18 amino acids in length.
Peptide sequences that independently bind HGFR can be identified by any of a variety of methods. For example, they can be selected from a display library or an array of peptides. After identification, such peptides can be produced synthetically or by recombinant means. The sequences can be incorporated (e.g., inserted, appended, or attached) into longer sequences.
The techniques discussed in Kay et al., Phage Display of Peptides and Proteins: A Laboratory Manual (Academic Press, Inc., San Diego 1996) and U.S. Pat. No. 5,223,409 are useful for preparing a library of potential binders corresponding to the selected parental template. Peptide display libraries can be prepared according to such techniques, and screened for peptides that bind to and inhibit HGFR.
In addition, phage libraries or selected populations from phage libraries can be counter-selected, e.g., by counter-selection with an HGFR binding domain that lacks a SEMA (semaphorin) domain or a PSI (plexin/semaphorin/integrin) domain, both of which contribute to HGF binding. Such procedures can be used to discard peptides that do not contact the HGF binding site.
Peptides can also be synthesized using alternative backbones, e.g., a peptoid backbone, e.g., to produce a compound which has increased protease resistance. In particular this method can be used to make a compound that binds to and inhibits activation of HGFR and is not cleaved, e.g., by serum proteases.
A polypeptide that inhibits HGFR activation can be associated with (e.g., conjugated to) a polymer, e.g., a substantially non-antigenic polymers, such as polyalkylene oxides or polyethylene oxides. Suitable polymers will vary substantially by weight. Polymers having molecular number average weights ranging from about 200 to about 35,000 (or about 1,000 to about 15,000, and 2,000 to about 12,500) can be used. A plurality of polymer moieties can be attached to one polypeptide, e.g., at least two, three, or four such moieties, e.g., having an average molecular weight of about 2,000 to 7,000 Daltons.
For example, the polypeptide can be conjugated to a water soluble polymer, e.g., hydrophilic polyvinyl polymers, e.g. polyvinylalcohol and polyvinylpyrrolidone. A non-limiting list of such polymers include polyalkylene oxide homopolymers such as polyethylene glycol (PEG) or polypropylene glycols, polyoxyethylenated polyols, copolymers thereof and block copolymers thereof, provided that the water solubility of the block copolymers is maintained. Additional useful polymers include polyoxyalkylenes such as polyoxyethylene, polyoxypropylene, and block copolymers of polyoxyethylene and polyoxypropylene (Pluronics); polymethacrylates; carbomers; branched or unbranched polysaccharides which comprise the saccharide monomers D-mannose, D- and L-galactose, fucose, fructose, D-xylose, L-arabinose, D-glucuronic acid, sialic acid, D-galacturonic acid, D-mannuronic acid (e.g. polymannuronic acid, or alginic acid), D-glucosamine, D-galactosamine, D-glucose and neuraminic acid including homopolysaccharides and heteropolysaccharides such as lactose, amylopectin, starch, hydroxyethyl starch, amylose, dextrane sulfate, dextran, dextrins, glycogen, or the polysaccharide subunit of acid mucopolysaccharides, e.g. hyaluronic acid; polymers of sugar alcohols such as polysorbitol and polymannitol; heparin or heparon.
Other compounds can also be attached to the same polymer, e.g., a cytotoxin, a label, or another targeting agent or an unrelated agent. Mono-activated, alkoxy-terminated polyalkylene oxides (PAO's), e.g., monomethoxy-terminated polyethylene glycols (mPEG's); C1-4 alkyl-terminated polymers; and bis-activated polyethylene oxides (glycols) can be used for crosslinking See, e.g., U.S. Pat. No. 5,951,974.
D. Nucleic Acid Antagonists
In certain implementations, nucleic acid antagonists are used to decrease expression of an endogenous gene encoding HGF, a HGFR, integrin α9, or stanniocalcin 1. In one embodiment, the nucleic acid antagonist is an siRNA that targets mRNA encoding HGF or a HGFR. Other types of antagonistic nucleic acids can also be used, e.g., a dsRNA, a ribozyme, a triple-helix former, or an antisense nucleic acid. In some embodiments, nucleic acid antagonists can be directed to downstream effector targets of HGFR activation (e.g., human α9 integrin, an exemplary sequence of which is listed under Genbank No. NM—002207).
siRNAs are small double stranded RNAs (dsRNAs) that optionally include overhangs. For example, the duplex region of an siRNA is about 18 to 25 nucleotides in length, e.g., about 19, 20, 21, 22, 23, or 24 nucleotides in length. Typically, the siRNA sequences are exactly complementary to the target mRNA. dsRNAs and siRNAs in particular can be used to silence gene expression in mammalian cells (e.g., human cells). siRNAs also include short hairpin RNAs (shRNAs) with 29-base-pair stems and 2-nucleotide 3′ overhangs. See, e.g., Clemens et al. (2000) Proc. Natl. Acad. Sci. USA 97:6499-6503; Billy et al. (2001) Proc. Natl. Sci. USA 98:14428-14433; Elbashir et al. (2001) Nature. 411:494-8; Yang et al. (2002) Proc. Natl. Acad. Sci. USA 99:9942-9947; Siolas et al. (2005), Nat. Biotechnol. 23(2):227-31; 20040086884; U.S. 20030166282; 20030143204; 20040038278; and 20030224432.
Anti-sense agents can include, for example, from about 8 to about 80 nucleobases (i.e., from about 8 to about 80 nucleotides), e.g., about 8 to about 50 nucleobases, or about 12 to about 30 nucleobases. Anti-sense compounds include ribozymes, external guide sequence (EGS) oligonucleotides (oligozymes), and other short catalytic RNAs or catalytic oligonucleotides which hybridize to the target nucleic acid and modulate its expression. Anti-sense compounds can include a stretch of at least eight consecutive nucleobases that are complementary to a sequence in the target gene. An oligonucleotide need not be 100% complementary to its target nucleic acid sequence to be specifically hybridizable. An oligonucleotide is specifically hybridizable when binding of the oligonucleotide to the target interferes with the normal function of the target molecule to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the oligonucleotide to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment or, in the case of in vitro assays, under conditions in which the assays are conducted.
Hybridization of antisense oligonucleotides with mRNA (e.g., an mRNA encoding HGF or HGFR) can interfere with one or more of the normal functions of mRNA. The functions of mRNA to be interfered with include all key functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in by the RNA. Binding of specific protein(s) to the RNA may also be interfered with by antisense oligonucleotide hybridization to the RNA.
Exemplary antisense compounds include DNA or RNA sequences that specifically hybridize to the target nucleic acid, e.g., the mRNA encoding HGF or HGFR. The complementary region can extend for between about 8 to about 80 nucleobases. The compounds can include one or more modified nucleobases. Modified nucleobases may include, e.g., 5-substituted pyrimidines such as 5-iodouracil, 5-iodocytosine, and C5-propynyl pyrimidines such as C5-propynylcytosine and C5-propynyluracil. Other suitable modified nucleobases include N4—(C1-C12) alkylaminocytosines and N4,N4—(C1-C12) dialkylaminocytosines. Modified nucleobases may also include 7-substituted-8-aza-7-deazapurines and 7-substituted-7-deazapurines such as, for example, 7-iodo-7-deazapurines, 7-cyano-7-deazapurines, 7-aminocarbonyl-7-deazapurines. Examples of these include 6-amino-7-iodo-7-deazapurines, 6-amino-7-cyano-7-deazapurines, 6-amino-7-aminocarbonyl-7-deazapurines, 2-amino-6-hydroxy-7-iodo-7-deazapurines, 2-amino-6-hydroxy-7-cyano-7-deazapurines, and 2-amino-6-hydroxy-7-aminocarbonyl-7-deazapurines. Furthermore, N6—(C1-C12) alkylaminopurines and N6,N6—(C1-C12) dialkylaminopurines, including N6-methylaminoadenine and N6,N6-dimethylaminoadenine, are also suitable modified nucleobases. Similarly, other 6-substituted purines including, for example, 6-thioguanine may constitute appropriate modified nucleobases. Other suitable nucleobases include 2-thiouracil, 8-bromoadenine, 8-bromoguanine, 2-fluoroadenine, and 2-fluoroguanine Derivatives of any of the aforementioned modified nucleobases are also appropriate. Substituents of any of the preceding compounds may include C1-C30 alkyl, C2-C30 alkenyl, C2-C30 alkynyl, aryl, aralkyl, heteroaryl, halo, amino, amido, nitro, thio, sulfonyl, carboxyl, alkoxy, alkylcarbonyl, alkoxycarbonyl, and the like.
Descriptions of other types of nucleic acid agents are also available. See, e.g., U.S. Pat. Nos. 4,987,071; 5,116,742; and 5,093,246; Woolf et al. (1992) Proc Natl Acad Sci USA; Antisense RNA and DNA, D. A. Melton, Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1988); 89:7305-9; Haselhoff and Gerlach (1988) Nature 334:585-59; Helene, C. (1991) Anticancer Drug Des. 6:569-84; Helene (1992) Ann. N.Y. Acad. Sci. 660:27-36; and Maher (1992) Bioassays 14:807-15.
E. Artificial Transcription Factors
Artificial transcription factors can also be used to regulate expression of HGF, a HGFR, integrin α9, or stanniocalcin 1. The artificial transcription factor can be designed or selected from a library, e.g., for ability to bind to a sequence in an endogenous gene encoding HGF or HGFR, e.g., in a regulatory region, e.g., the promoter. For example, the artificial transcription factor can be prepared by selection in vitro (e.g., using phage display, U.S. Pat. No. 6,534,261) or in vivo, or by design based on a recognition code (see, e.g., WO 00/42219 and U.S. Pat. No. 6,511,808). See, e.g., Rebar et al. (1996) Methods Enzymol 267:129; Greisman and Pabo (1997) Science 275:657; Isalan et al. (2001) Nat. Biotechnol 19:656; and Wu et al. (1995) Proc. Natl. Acad. Sci. USA 92:344 for, among other things, methods for creating libraries of varied zinc finger domains.
Optionally, an artificial transcription factor can be fused to a transcriptional regulatory domain, e.g., an activation domain to activate transcription or a repression domain to repress transcription. In particular, repression domains can be used to decrease expression of endogenous genes encoding HGF or HGFR. The artificial transcription factor can itself be encoded by a heterologous nucleic acid that is delivered to a cell or the protein itself can be delivered to a cell (see, e.g., U.S. Pat. No. 6,534,261). The heterologous nucleic acid that includes a sequence encoding the artificial transcription factor can be operably linked to an inducible promoter, e.g., to enable fine control of the level of the artificial transcription factor in the cell, e.g., an endothelial cell.
F. Pharmaceutical Compositions
A HGF/HGFR modulator (e.g., an antibody or soluble HGFR protein, e.g., a HGFR extracellular region fused to a Fc) can be formulated as a pharmaceutical composition, e.g., for administration to a subject to a pathology related to the lymphatic system (e.g., a disorder described herein, such as lymphedema, lymphatic filariasis, lymphangiomas, tumor lymphangiogenesis, or tumor metastasis). Typically, a pharmaceutical composition includes a pharmaceutically acceptable carrier. As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. The composition can include a pharmaceutically acceptable salt, e.g., an acid addition salt or a base addition salt (see, e.g., Berge, S. M., et al. (1977) J. Pharm. Sci. 66:1-19).
The HGF/HGFR modulator can be formulated according to standard methods. Pharmaceutical formulation is a well-established art, and is further described, e.g., in Gennaro (ed.), Remington: The Science and Practice of Pharmacy, 20th ed., Lippincott, Williams & Wilkins (2000) (ISBN: 0683306472); Ansel et al., Pharmaceutical Dosage Forms and Drug Delivery Systems, 7th Ed., Lippincott Williams & Wilkins Publishers (1999) (ISBN: 0683305727); and Kibbe (ed.), Handbook of Pharmaceutical Excipients American Pharmaceutical Association, 3rd ed. (2000) (ISBN: 091733096X).
In one embodiment, the HGF/HGFR modulator (e.g., an antibody or HGFR-Fc) can be formulated with excipient materials, such as sodium chloride, sodium dibasic phosphate heptahydrate, sodium monobasic phosphate, and a stabilizer. It can be provided, for example, in a buffered solution at a suitable concentration and can be stored at 2-8° C.
The pharmaceutical compositions may be in a variety of forms. These include, for example, liquid, semi-solid and solid dosage forms, such as liquid solutions (e.g., injectable and infusible solutions), dispersions or suspensions, tablets, pills, powders, liposomes and suppositories. The preferred form can depend on the intended mode of administration and therapeutic application. Typically compositions for the agents described herein are in the form of injectable or infusible solutions.
Such compositions can be administered by a parenteral mode (e.g., intravenous, subcutaneous, intraperitoneal, or intramuscular injection). The phrases “parenteral administration” and “administered parenterally” as used herein mean modes of administration other than enteral and topical administration, usually by injection, and include, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal, epidural and intrasternal injection and infusion.
The composition can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable for stable storage at high concentration. Sterile injectable solutions can be prepared by incorporating an agent described herein in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating an agent described herein into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying that yields a powder of an agent described herein plus any additional desired ingredient from a previously sterile-filtered solution thereof. The proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prolonged absorption of injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, monostearate salts and gelatin.
In certain embodiments, the HGF/HGFR modulator may be prepared with a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants, and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are patented or generally known. See, e.g., Sustained and Controlled Release Drug Delivery Systems, J. R. Robinson, ed., Marcel Dekker, Inc., New York, 1978.
A HGF/HGFR modulator (e.g., an antibody or soluble HGFR protein) can be modified, e.g., with a moiety that improves its stabilization and/or retention in circulation, e.g., in blood, serum, or other tissues, e.g., by at least 1.5, 2, 5, 10, or 50 fold.
For example, the HGF/HGFR modulator (e.g., an antibody or soluble HGFR protein) can be associated with a polymer, e.g., a substantially non-antigenic polymer, such as a polyalkylene oxide or a polyethylene oxide. Suitable polymers will vary substantially by weight. Polymers having molecular number average weights ranging from about 200 to about 35,000 Daltons (or about 1,000 to about 15,000, and 2,000 to about 12,500) can be used.
For example, a HGF/HGFR modulator can be conjugated to a water soluble polymer, e.g., a hydrophilic polyvinyl polymer, e.g., polyvinylalcohol or polyvinylpyrrolidone. A non-limiting list of such polymers include polyalkylene oxide homopolymers such as polyethylene glycol (PEG) or polypropylene glycols, polyoxyethylenated polyols, copolymers thereof and block copolymers thereof, provided that the water solubility of the block copolymers is maintained. Additional useful polymers include polyoxyalkylenes such as polyoxyethylene, polyoxypropylene, and block copolymers of polyoxyethylene and polyoxypropylene (Pluronics); polymethacrylates; carbomers; and branched or unbranched polysaccharides.
When the HGF/HGFR modulator (e.g., an antibody or soluble HGFR protein) is used in combination with a second agent, the two agents can be formulated separately or together. For example, the respective pharmaceutical compositions can be mixed, e.g., just prior to administration, and administered together or can be administered separately, e.g., at the same or different times.
The lymphatic vascular system plays a pivotal role in tissue fluid homeostasis, which affects and is affected by a number of pathologies including, e.g., cancer cell metastasis; acquired lymphedema, e.g., induced by surgery, radiation therapy, or infection; skin conditions, e.g., epidermolysis caused by aging or excessive exposure to ultra-violet light. In addition, tumor metastasis occurs primarily through the lymphatic system, and the extent of lymph node involvement is a key prognostic factor for severity of disease. Lymphangiogenesis and the quantity of intratumoral lymphatic vessels in primary tumors have been correlated with tumor metastasis in animal experiments, for example, in breast cancer. (Skobe et al., Nature Medicine 7(2):192-198 (2001)). Intratumoral lymphatic vasculature can play an important role in the metastasis of many tumor types such as breast, colon, lung, thyroid, gastric, squamous cell cancers, mesotheliomas, osteosarcomas, and neuroblastomas.
G. Administration
The HGF/HGFR modulator (e.g., an antibody or soluble HGFR protein) or other agent can be administered to a subject, e.g., a human subject, by a variety of methods. For many applications, the route of administration is one of: intravenous injection or infusion (IV), subcutaneous injection (SC), intraperitoneally (IP), or intramuscular injection. The HGF/HGFR modulator can be administered as a fixed dose, or a dose adjusted for the subject's weight (e.g., a mg/kg dose).
The dose can also be chosen to reduce or avoid production of antibodies against the HGF/HGFR modulator.
The route and/or mode of administration of the can also be tailored for the individual case, e.g., by monitoring the subject, e.g., using tomographic imaging, lymphangiography, and standard parameters associated with the particular disease, e.g., criteria for assessing lymphatic and lymphatic system-related disorders.
Dosage regimens are adjusted to provide the desired response, e.g., a therapeutic response or a combinatorial therapeutic effect. Generally, any combination of doses (either separate or co-formulated) of the HGF/HGFR modulator (e.g., an antibody) (and optionally a second agent) can be used in order to provide a subject with the agent in bioavailable quantities. For example, doses in the range of 1 mg/kg-100 mg/kg, 0.5-20 mg/kg, or 1-10 mg/kg can be administered.
Dosage unit form or “fixed dose” as used herein refers to physically discrete units suited as unitary dosages for the subjects to be treated; each unit contains a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier and optionally in association with the other agent.
The HGF/HGFR modulator may be administered at least once between about 10 minutes to about 48 hours, more preferably between about 10 minutes and 24 hours, more preferably within 3 hours, after the onset of symptoms or manifestation of a lymphatic or lymphatic system-related disorder. For example, the agent may be administered to a patient suffering or at risk for lymphedema. Single or multiple dosages may be given. Alternatively, or in addition, the HGF/HGFR modulator agent may be administered via continuous infusion. The treatment can continue for days, weeks, months or even years so as to adequately modulate lymphangiogenesis in lymphatic or lymphatic system related disorders.
The HGF/HGFR modulator can be administered one time per week for between about 1 to 10 weeks, preferably between 2 to 8 weeks, more preferably between about 3 to 7 weeks, and even more preferably for about 4, 5, or 6 weeks. The skilled artisan will appreciate that certain factors may influence the dosage and timing required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present. Moreover, treatment of a subject with a therapeutically effective amount of a compound can include a single treatment or, preferably, can include a series of treatments.
If a subject is at risk for developing a disorder described herein (e.g., filariasis) or another lymphatic system-related disorder, the HGF/HGFR modulator can be administered before the onset of the condition as a preventative measure. The duration of such preventative treatment can be a single dosage of the HGF/HGFR modulator or the treatment may continue (e.g., multiple dosages), for example, a subject at risk for a disorder described herein may be treated with the HGF/HGFR modulator for days, weeks, months, or even years so as to prevent the injury from occurring.
A pharmaceutical composition may include a “therapeutically effective amount” of an agent described herein. Such effective amounts can be determined based on the effect of the administered agent, or the combinatorial effect of agents if more than one agent is used. A therapeutically effective amount of an agent may also vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the compound to elicit a desired response in the individual, e.g., amelioration of at least one disorder parameter or amelioration of at least one symptom of the disorder. A therapeutically effective amount is also one in which any toxic or detrimental effects of the composition is outweighed by the therapeutically beneficial effects.
An antagonist of HGF/HGFR can be used to treat cancer. Examples of cancerous disorders include, but are not limited to, solid tumors, soft tissue tumors, and metastatic lesions. Examples of solid tumors include malignancies, e.g., sarcomas, adenocarcinomas, and carcinomas, of the various organ systems, such as those affecting lung, breast, lymphoid, gastrointestinal (e.g., colon), and genitourinary tract (e.g., renal, urothelial cells), pharynx, prostate, ovary as well as adenocarcinomas which include malignancies such as most colon cancers, rectal cancer, renal-cell carcinoma, liver cancer, non-small cell carcinoma of the lung, cancer of the small intestine and so forth. Metastatic lesions of the aforementioned cancers, and particularly metastatic forms of these cancers, can also be treated or prevented using the methods and compositions described herein.
The method can be used to treat malignancies of the various organ systems, such as those affecting lung, breast, lymphoid, gastrointestinal (e.g., colon), and genitourinary tract, prostate, ovary, pharynx, as well as adenocarcinomas which include malignancies such as most colon cancers, renal-cell carcinoma, prostate cancer and/or testicular tumors, non-small cell carcinoma of the lung, cancer of the small intestine and cancer of the esophagus. Exemplary solid tumors that can be treated include: fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, non-small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, and retinoblastoma.
The term “carcinoma” is recognized by those skilled in the art and refers to malignancies of epithelial or endocrine tissues including respiratory system carcinomas, gastrointestinal system carcinomas, genitourinary system carcinomas, testicular carcinomas, breast carcinomas, prostatic carcinomas, endocrine system carcinomas, and melanomas. Exemplary carcinomas include those forming from tissue of the cervix, lung, prostate, breast, head and neck, colon and ovary. The term also includes carcinosarcomas, e.g., which include malignant tumors composed of carcinomatous and sarcomatous tissues. An “adenocarcinoma” refers to a carcinoma derived from glandular tissue or in which the tumor cells form recognizable glandular structures. The term “sarcoma” is recognized by those skilled in the art and refers to malignant tumors of mesenchymal derivation.
H. Devices and Kits
Pharmaceutical compositions that include the HGF/HGFR modulator (e.g., an antibody or soluble HGFR) can be administered with a medical device. The device can designed with features such as portability, room temperature storage, and ease of use so that it can be used in emergency situations, e.g., by an untrained subject or by emergency personnel in the field, removed to medical facilities and other medical equipment. The device can include, e.g., one or more housings for storing pharmaceutical preparations that include HGF/HGFR modulator, and can be configured to deliver one or more unit doses of the HGF/HGFR modulator.
For example, the pharmaceutical composition can be administered with a needleless hypodermic injection device, such as the devices disclosed in U.S. Pat. Nos. 5,399,163; 5,383,851; 5,312,335; 5,064,413; 4,941,880; 4,790,824; or 4,596,556. Examples of well-known implants and modules include: U.S. Pat. No. 4,487,603, which discloses an implantable micro-infusion pump for dispensing medication at a controlled rate; U.S. Pat. No. 4,486,194, which discloses a therapeutic device for administering medicaments through the skin; U.S. Pat. No. 4,447,233, which discloses a medication infusion pump for delivering medication at a precise infusion rate; U.S. Pat. No. 4,447,224, which discloses a variable flow implantable infusion apparatus for continuous drug delivery; U.S. Pat. No. 4,439,196, which discloses an osmotic drug delivery system having multi-chamber compartments; and U.S. Pat. No. 4,475,196, which discloses an osmotic drug delivery system. Many other devices, implants, delivery systems, and modules are also known.
A HGF/HGFR modulator (e.g., an antibody or soluble HGFR protein) can be provided in a kit. In one embodiment, the kit includes (a) a container that contains a composition that includes a HGF/HGFR modulator, and optionally (b) informational material. The informational material can be descriptive, instructional, marketing or other material that relates to the methods described herein and/or the use of the agents for therapeutic benefit. In one embodiment, the kit also includes a second agent for treating lymphatic and lymphatic system-related disorders. For example, the kit includes a first container that contains a composition that includes the HGF/HGFR modulator, and a second container that includes the second agent.
The informational material of the kits is not limited in its form. In one embodiment, the informational material can include information about production of the compound, molecular weight of the compound, concentration, date of expiration, batch or production site information, and so forth. In one embodiment, the informational material relates to methods of administering the HGF/HGFR modulator (e.g., an antibody or soluble HGFR protein), e.g., in a suitable dose, dosage form, or mode of administration (e.g., a dose, dosage form, or mode of administration described herein), to treat a subject who has had or who is at risk for a lymphatic or lymphatic system-related disorder. The information can be provided in a variety of formats, include printed text, computer readable material, video recording, or audio recording, or as information that provides a link or address to substantive material.
In addition to the HGF/HGFR modulator, the composition in the kit can include other ingredients, such as a solvent or buffer, a stabilizer, or a preservative. The HGF/HGFR modulator can be provided in any form, e.g., liquid, dried or lyophilized form, preferably substantially pure and/or sterile. When the agents are provided in a liquid solution, the liquid solution preferably is an aqueous solution. When the agents are provided in a dried form, reconstitution generally is achieved by the addition of a suitable solvent. The solvent, e.g., sterile water or buffer, can optionally be provided in the kit.
The kit can include one or more containers for the composition or compositions containing the agents. In some embodiments, the kit contains separate containers, dividers or compartments for the composition and informational material. For example, the composition can be contained in a bottle, vial, or syringe, and the informational material can be contained in a plastic sleeve or packet. In other embodiments, the separate elements of the kit are contained within a single, undivided container. For example, the composition is contained in a bottle, vial or syringe that has attached thereto the informational material in the form of a label. In some embodiments, the kit includes a plurality (e.g., a pack) of individual containers, each containing one or more unit dosage forms (e.g., a dosage form described herein) of the agents. The containers can include a combination unit dosage, e.g., a unit that includes both the HGF/HGFR modulator and the second agent, e.g., in a desired ratio. For example, the kit includes a plurality of syringes, ampules, foil packets, blister packs, or medical devices, e.g., each containing a single combination unit dose. The containers of the kits can be air tight, waterproof (e.g., impermeable to changes in moisture or evaporation), and/or light-tight.
The kit optionally includes a device suitable for administration of the composition, e.g., a syringe or other suitable delivery device. The device can be provided pre-loaded with one or both of the agents or can be empty, but suitable for loading.
III. Methods of Screening for Modulators of HGF/HGFR Pathway Activity
Screening of putative modulators of expression of HGF/HGFR pathway (e.g., HGF, HGFR, integrin α9 and stanniocalcin 1) can be carried out by determining the effect of the modulators on HGF or HGFR promoter activity in vitro or in vivo. For example, a nucleic acid that includes a HGFR promoter (e.g., of the human, monkey or mouse HGFR gene) or regulatory region thereof, e.g., Gambarotta et al. (1994), J. Biol. Chem., 269(17):12852-12857 or e.g., a HGF promoter (e.g., of the human, monkey or mouse HGF gene) or regulatory region thereof, e.g., Bell et al. (1998), J. Biol. Chem., 273(12):6900-6908 can be operably linked to a nucleic acid that encodes a reporter polypeptide, e.g., one of the reporter polypeptides described below (e.g., enhanced green fluorescent protein). Other promoters that can be used include those of other genes modulated by HGF/HGFR pathway activity, e.g., integrin α9 and stanniocalcin 1. The nucleic acid including the target promoter operably linked to the reporter nucleic acid can be introduced into cells in culture and/or be used to generate a transgenic animal, allowing evaluation of promoter activity in vivo. In some embodiments, a transgenic animal can also be evaluated for other phenotypes (e.g., induction or repression of gene expression in skin) affected by administration of an HGF/HGFR modulator.
A. Evaluating Effects of Putative HGF/HGFR Modulators on Skin
Methods disclosed herein allow evaluating a compound for its effect on the expression of HGF or HGFR or other target gene in an experimental subject. In some embodiments, the effect of a compound on skin (e.g., a therapeutic compound for a skin condition) can be evaluated in the same experimental subject in which expression is determined. The effect on skin is usually determined as an effect on the expression of a gene under the control of a skin-metabolism-related promoter. Such promoters include those which control the expression and/or synthesis of: a product which is a component of the skin, e.g., the dermis or epidermis; a product which affects hydration or nutrition of the skin; a product which promotes the synthesis, or degradation, of components of the skin; a product which affects the vasculature of the skin; a product which affects hair follicle metabolism; a product which affects skin glandular structures; a product which affects subcutaneous musculature; a product which affects adipose tissue; or a product which affects cutaneous nerves.
Methods of the invention are useful for evaluating a compound for an effect on a parameter related to the appearance or health of the skin, for example, the elasticity of the skin, the propensity of the skin to wrinkle, the ability of the skin to retain fluids, e.g., water or an oil, the ability of the skin to resist or repair damage, e.g., light or UV induced damage, the metabolism of hair follicles including growth cycling or pigment deposition, or subcutaneous muscle tone and function. Generally, effects on these parameters will be evaluated indirectly, e.g., by the effect on the expression of a reporter gene under the control of a promoter which is normally coupled to a gene which encodes a product which affects any of the these parameters.
Transgenic Animals
Transgenic animals which can be used in the methods of the invention include non-human mammals, such as pigs, e.g., mini-pigs; or rodents, e.g., mice, rats, or guinea pigs, e.g., hairless mice (described in, for example, Begona M. et al. (1994) Proc. Natl. Acad. Sci. 91:7717-7721), nude mice, senescence accelerated mice (described in, for example, Takeda et al. (1991) L. Am. Geriatr. Soc. 39:911-19), or transgenic mutant mice which exhibit a phenotype of accelerated aging. One or more, and preferably essentially all, of the cells of the animal include a transgene. The transgenic animals can be homozygous or heterozygous for the transgene. Mice are a preferred subject animal.
Many methods of making transgenic animals, e.g., mice, are known in the art. One exemplary approach is described below.
Procedures for embryo manipulation and microinjection are described in, for example, Manipulating the Mouse Embryo (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986, the contents of which are incorporated herein by reference). Mouse zygotes can be collected from six week old females that have been super ovulated with pregnant mares serum (PMS) followed 48 hours later with human chorionic gonadotropin. Primed females are placed with males and checked for vaginal plugs on the following morning. Pseudo pregnant females are selected for estrus, placed with proved sterile vasectomized males and used as recipients. Zygotes are collected and cumulus cells removed. Furthermore, blastocysts can be harvested. Pronuclear embryos are recovered from female mice mated to males. Females are treated with pregnant mare serum, PMS, to induce follicular growth and human chorionic gonadotropin, hCG, to induce ovulation. Embryos are recovered in a Dulbecco's modified phosphate buffered saline (DPBS) and maintained in Dulbecco's modified essential medium (DMEM) supplemented with 10% fetal bovine serum.
Microinjection of a transgenic construct can be performed using standard micro manipulators attached to a microscope. For instance, embryos are typically held in 100 microliter drops of DPBS under oil while being microinjected. DNA solution is microinjected into the male pronucleus. Successful injection is monitored by swelling of the pronucleus. Recombinant ES cells can be injected into blastocysts, using similar techniques. Immediately after injection embryos are transferred to recipient females, e.g. mature mice mated to vasectomized male mice. In a general protocol, recipient females are anesthetized, paralumbar incisions are made to expose the oviducts, and the embryos are transformed into the ampullary region of the oviducts. The body wall is sutured and the skin closed with wound clips.
Screening for the Presence of the Targeting Construct
Transgenic animals can be identified after birth by standard protocols. DNA from tail tissue can be screened for the presence of the targeting construct using southern blots and/or PCR. Offspring that appear to be mosaics are then crossed to each other if they are believed to carry the targeting construct in their germ line to generate homozygous transgenic animals. If it is unclear whether the offspring will have germ line transmission, they can be crossed with a parental or other strain and the offspring screened for heterozygosity. The heterozygotes are identified by southern blots and/or PCR amplification of the DNA.
The heterozygotes can then be crossed with each other to generate homozygous transgenic offspring. Homozygotes may be identified by southern blotting of equivalent amounts of genomic DNA from mice that are the product of this cross, as well as mice that are known heterozygotes and wild type mice. Probes to screen the southern blots can be designed as set forth above.
Other means of identifying and characterizing the transgenic offspring are known in the art. For example, northern blots can be used to probe the mRNA for the presence or absence of transcripts encoding the reporter gene. In addition, western blots can be used to assess the level of expression of the transgene in various tissues of these offspring by probing the western blot with an antibody against the protein encoded by the transgene, or an antibody against the marker gene product, where this gene is expressed. Finally, in situ analysis (such as fixing the cells and labeling with antibody) and/or FACS (fluorescence activated cell sorting) analysis of various cells from the offspring can be performed using suitable antibodies to look for the presence or absence of the transgene product. Transgenic animals can be generated that have two separate transgenes with distinct promoters operably linked to detectably distinct reporters, e.g., by interbreeding mice transgenic for the individual promoter-reporter transgenes.
Other transgenic animals can be used in methods of the invention. Methods for the preparation of a variety of animals are known in the art. A protocol for the production of a transgenic pig can be found in White and Yannoutsos, Current Topics in Complement Research: 64th Forum in Immunology, pp. 88-94; U.S. Pat. No. 5,523,226; U.S. Pat. No. 5,573,933; PCT Application WO93/25071; and PCT Application WO95/04744. A protocol for the production of a transgenic rat can be found in Bader and Ganten, Clinical and Experimental Pharmacology and Physiology, Supp. 3:S81-S87, 1996. A protocol for the production of a transgenic cow can be found in Transgenic Animal Technology, A Handbook, 1994, ed., Carl A. Pinkert, Academic Press, Inc. A protocol for the production of a transgenic sheep can be found in Transgenic Animal Technology, A Handbook, 1994, ed., Carl A. Pinkert, Academic Press, Inc.
Reporter Genes
Promoter activity can be assayed by coupling a reporter gene to a promoter of interest (e.g., the HGF, HGFR, integrin α9 or stanniocalcin 1 promoter). The reporter gene can be any gene which encodes a detectable product, preferably one which can be detected with relative ease, e.g., a gene product which is fluorescent, or which catalyzes a reaction which can be determined by formation of a colored, fluorescent, or luminescent product. For example, the reporter gene can encode an enzyme, e.g., an enzyme which produces a detectable product, e.g., a colored, fluorescent, luminescent product. Reporter genes are known in the art and include a β-galactosidase gene, a luciferase gene, a green fluorescent protein gene, a cyan fluorescent protein, a yellow fluorescent protein, a red fluorescent protein, an alkaline phosphatase gene, a horseradish peroxidase gene, a β-lactamase gene, or a chloramphenicol acetyl transferase gene. Reporter genes are described in, for example, Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.
IV. Diagnostic Assays
A. Nucleic Acid and Protein Detection
Arrays are useful molecular tools for characterizing a sample, e.g., a sample from a subject. For example, an array having capture probes for multiple genes, including probes for HGF, HGFR, integrin α9 and stanniocalcin 1 nucleic acids, or for multiple proteins. Arrays can have many addresses, e.g., locatable sites, on a substrate. The featured arrays can be configured in a variety of formats, non-limiting examples of which are described below.
The substrate can be opaque, translucent, or transparent. The addresses can be distributed, on the substrate in one dimension, e.g., a linear array; in two dimensions, e.g., a planar array; or in three dimensions, e.g., a three dimensional array. The solid substrate may be of any convenient shape or form, e.g., square, rectangular, ovoid, or circular.
Arrays can be fabricated by a variety of methods, e.g., photolithographic methods (see, e.g., U.S. Pat. Nos. 5,143,854; 5,510,270; and 5,527,681), mechanical methods (e.g., directed-flow methods as described in U.S. Pat. No. 5,384,261), pin based methods (e.g., as described in U.S. Pat. No. 5,288,514), and bead based techniques (e.g., as described in PCT US/93/04145).
The capture probe can be a single-stranded nucleic acid, a double-stranded nucleic acid (e.g., which is denatured prior to or during hybridization), or a nucleic acid having a single-stranded region and a double-stranded region. Preferably, the capture probe is single-stranded. The capture probe can be selected by a variety of criteria, and preferably is designed by a computer program with optimization parameters. The capture probe can be selected to hybridize to a sequence rich (e.g., non-homopolymeric) region of the gene. The Tm of the capture probe can be optimized by prudent selection of the complementarity region and length. Ideally, the Tm of all capture probes on the array is similar, e.g., within 20, 10, 5, 3, or 2° C. of one another.
The isolated nucleic acid is preferably mRNA that can be isolated by routine methods, e.g., including DNase treatment to remove genomic DNA and hybridization to an oligo-dT coupled solid substrate (e.g., as described in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y). The substrate is washed, and the mRNA is eluted.
The isolated mRNA can be reversed transcribed and optionally amplified, e.g., by reverse transcription polymerase chain reaction (RT-PCR), e.g., as described in (U.S. Pat. No. 4,683,202). The nucleic acid can be an amplification product, e.g., from PCR (U.S. Pat. Nos. 4,683,196 and 4,683,202); rolling circle amplification (“RCA,” U.S. Pat. No. 5,714,320), isothermal RNA amplification or NASBA (U.S. Pat. Nos. 5,130,238; 5,409,818; and 5,554,517), and strand displacement amplification (U.S. Pat. No. 5,455,166). The nucleic acid can be labeled during amplification, e.g., by the incorporation of a labeled nucleotide. Examples of preferred labels include fluorescent labels, e.g., red-fluorescent dye Cy5TM (Amersham) or green-fluorescent dye Cy3TM (Amersham), and chemiluminescent labels, e.g., as described in U.S. Pat. No. 4,277,437. Alternatively, the nucleic acid can be labeled with biotin, and detected after hybridization with labeled streptavidin, e.g., streptavidin-phycoerythrin (Molecular Probes).
The labeled nucleic acid can be contacted to the array. In addition, a control nucleic acid or a reference nucleic acid can be contacted to the same array. The control nucleic acid or reference nucleic acid can be labeled with a label other than the sample nucleic acid, e.g., one with a different emission maximum. Labeled nucleic acids can be contacted to an array under hybridization conditions. The array can be washed, and then imaged to detect fluorescence at each address of the array.
The expression level of a HGF or HGFR protein can be determined using an antibody specific for the polypeptide (e.g., using a western blot or an ELISA assay). Moreover, the expression levels of multiple proteins, including HGF and HGFR, can be rapidly determined in parallel using a polypeptide array having antibody capture probes for each of the polypeptides. Antibodies specific for a polypeptide can be generated by a method described herein (see “Antibody Generation”).
A low-density (96 well format) protein array has been developed in which proteins are spotted onto a nitrocellulose membrane (Ge (2000) Nucleic Acids Res. 28, e3, I-VII). A high-density protein array (e.g., 100,000 samples within 222×222 mm) used for antibody screening can be produced by spotting proteins onto polyvinylidene difluoride (PVDF) (Lueking et al. (1999) Anal. Biochem. 270:103-111). See also, e.g., Mendoza et al. (1999). Biotechniques 27:778-788; MacBeath and Schreiber (2000) Science 289:1760-1763; and De Wildt et al. (2000). Nature Biotech. 18:989-994. These art-known methods and others can be used to generate an array of antibodies for detecting the abundance of polypeptides in a sample. The sample can be labeled, e.g., biotinylated, for subsequent detection with streptavidin coupled to a fluorescent label. The array can then be scanned to measure binding at each address.
The nucleic acid and polypeptide arrays of the invention can be used in wide variety of applications. For example, the arrays can be used to analyze a patient sample. The sample is compared to data obtained previously, e.g., known clinical specimens or other patient samples. Further, the arrays can be used to characterize a cell culture sample, e.g., to determine a cellular state after varying a parameter, e.g., exposing the cell culture to an antigen, a transgene, or a test compound.
The expression data can be stored in a database, e.g., a relational database such as a SQL database (e.g., Oracle or Sybase database environments). The database can have multiple tables. For example, raw expression data can be stored in one table, wherein each column corresponds to a gene being assayed, e.g., an address or an array, and each row corresponds to a sample. A separate table can store identifiers and sample information, e.g., the batch number of the array used, date, and other quality control information.
Expression profiles obtained from gene expression analysis on an array can be used to compare samples and/or cells in a variety of states as described in Golub et al. ((1999) Science 286:531). In one embodiment, expression (e.g., mRNA expression or protein expression) information for a gene encoding HGF and/or a gene encoding HGFR are evaluated, e.g., by comparison a reference value, e.g., a reference value. Reference values can be obtained from a control, a reference subject. Reference values can also be obtained from statistical analysis, e.g., to provide a reference value for a cohort of subject, e.g., age and gender matched subject, e.g., normal subjects or subject who have or at risk for a lymphatic or lymphatic system-related disorder. Statistical similarity to a particular reference (e.g., to a reference for a risk-associated cohort) or a normal cohort can be used to provide an assessment (e.g., an indication of risk a lymphatic disorder) to a subject, e.g., a subject who has not a prior lymphatic disorder, a subject who has a risk for a lymphatic disorder (e.g., a genetic predisposition), or a subject who has had a lymphatic disorder.
Subjects suitable for treatment can also be evaluated for expression and/or activity of HGF/HGFR pathway activity, e.g., HGF expression, HGFR expression, integrin α9 expression and stanniocalcin 1 expression, as well as modification states or other parameters associated with these factors. In some embodiments, subjects can be identified as suitable for treatment if the expression and/or activity for HGF and/or HGFR is altered (e.g., elevated) relative to a reference, e.g., reference value, e.g., a reference value associated with normal.
Subjects who are being administered an agent described herein or other treatment for a lymphatic or lymphatic system-related disorder can be evaluated as described for expression and/or activity of HGF and/or HGFR. The subject can be evaluated at multiple times. e.g., at multiple times during a course of therapy, e.g., during a therapeutic regimen. Treatment of the subject can be modified depending on how the subject is responding to the therapy. For example, a reduction in HGF and/or HGFR expression or activity can be indicative of responsiveness if the agent being administered is an antagonist.
Particular effects mediated by an agent may show a difference (e.g., relative to an untreated subject, control subject, or other reference) that is statistically significant (e.g., P value<0.05 or 0.02). Statistical significance can be determined by any art known method. Exemplary statistical tests include: the Students T-test, Mann Whitney U non-parametric test, and Wilcoxon non-parametric statistical test. Some statistically significant relationships have a P value of less than 0.05 or 0.02.
B. Methods of Evaluating Genetic Material
There are numerous methods for evaluating genetic material to provide genetic information. These methods can be used to evaluate a genetic locus that includes a gene encoding HGF or a gene encoding HGFR, as well as other loci. The methods can be used to evaluate one or more nucleotides, e.g., a coding or non-coding region of the gene, e.g., in a regulatory region (e.g., a promoter, a region encoding an untranslated region or intron, and so forth).
Nucleic acid samples can analyzed using biophysical techniques (e.g., hybridization, electrophoresis, and so forth), sequencing, enzyme-based techniques, and combinations-thereof. For example, hybridization of sample nucleic acids to nucleic acid microarrays can be used to evaluate sequences in an mRNA population and to evaluate genetic polymorphisms. Other hybridization based techniques include sequence specific primer binding (e.g., PCR or LCR); Southern analysis of DNA, e.g., genomic DNA; Northern analysis of RNA, e.g., mRNA; fluorescent probe based techniques (see, e.g., Beaudet et al. (2001) Genome Res. 11(4):600-8); and allele specific amplification. Enzymatic techniques include restriction enzyme digestion; sequencing; and single base extension (SBE). These and other techniques are well known to those skilled in the art.
Electrophoretic techniques include capillary electrophoresis and Single-Strand Conformation Polymorphism (SSCP) detection (see, e.g., Myers et al. (1985) Nature 313:495-8 and Ganguly (2002) Hum Mutat. 19(4):334-42). Other biophysical methods include denaturing high pressure liquid chromatography (DHPLC).
In one embodiment, allele specific amplification technology that depends on selective PCR amplification may be used to obtain genetic information. Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al. (1989) Nucl. Acids Res. 17:2437-2448) or at the extreme 3′ end of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (Prossner (1993) Tibtech 11:238). In addition, it is possible to introduce a restriction site in the region of the mutation to create cleavage-based detection (Gasparini et al. (1992) Mol. Cell. Probes 6:1). In another embodiment, amplification can be performed using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad. Sci. USA 88:189). In such cases, ligation will occur only if there is a perfect match at the 3′ end of the 5′ sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification.
Enzymatic methods for detecting sequences include amplification based-methods such as the polymerase chain reaction (PCR; Saiki, et al. (1985) Science 230:1350-1354) and ligase chain reaction (LCR; Wu. et al. (1989) Genomics 4:560-569; Barringer et al. (1990), Gene 1989:117-122; F. Barany (1991) Proc. Natl. Acad. Sci. USA 1988:189-193); transcription-based methods utilize RNA synthesis by RNA polymerases to amplify nucleic acid (U.S. Pat. Nos. 6,066,457; 6,132,997; and 5,716,785; Sarkar et al., (1989) Science 244:331-34; Stofler et al., (1988) Science 239:491); NASBA (U.S. Pat. Nos. 5,130,238; 5,409,818; and 5,554,517); rolling circle amplification (RCA; U.S. Pat. Nos. 5,854,033 and 6,143,495) and strand displacement amplification (SDA; U.S. Pat. Nos. 5,455,166 and 5,624,825). Amplification methods can be used in combination with other techniques.
Other enzymatic techniques include sequencing using polymerases, e.g., DNA polymerases and variations thereof such as single base extension technology. See, e.g., U.S. Pat. Nos. 6,294,336; 6,013,431; and 5,952,174.
Fluorescence based detection can also be used to detect nucleic acid polymorphisms. For example, different terminator ddNTPs can be labeled with different fluorescent dyes. A primer can be annealed near or immediately adjacent to a polymorphism, and the nucleotide at the polymorphic site can be detected by the type (e.g., “color”) of the fluorescent dye that is incorporated.
Hybridization to microarrays can also be used to detect polymorphisms, including SNPs. For example, a set of different oligonucleotides, with the polymorphic nucleotide at varying positions with the oligonucleotides can be positioned on a nucleic acid array. The extent of hybridization as a function of position and hybridization to oligonucleotides specific for the other allele can be used to determine whether a particular polymorphism is present. See, e.g., U.S. Pat. No. 6,066,454.
In one implementation, hybridization probes can include one or more additional mismatches to destabilize duplex formation and sensitize the assay. The mismatch may be directly adjacent to the query position, or within 10, 7, 5, 4, 3, or 2 nucleotides of the query position. Hybridization probes can also be selected to have a particular Tm, e.g., between 45-60° C., 55-65° C., or 60-75° C. In a multiplex assay, Tms can be selected to be within 5, 3, or 2° C. of each other.
It is also possible to directly sequence the nucleic acid for a particular genetic locus, e.g., by amplification and sequencing, or amplification, cloning and sequence. High throughput automated (e.g., capillary or microchip based) sequencing apparati can be used. In still other embodiments, the sequence of a protein of interest is analyzed to infer its genetic sequence. Methods of analyzing a protein sequence include protein sequencing, mass spectroscopy, sequence/epitope specific immunoglobulins, and protease digestion.
Any combination of the above methods can also be used. The above methods can be used to evaluate any genetic locus, e.g., in a method for analyzing genetic information from particular groups of individuals or in a method for analyzing a polymorphism associated with a lymphatic or lymphatic system-related disorder, e.g., in a gene encoding HGF, HGFR, integrin α9 or stanniocalcin 1.
C. In Vivo Imaging
HGFR HGF/HGFR binding agents (e.g., antibodies) can be used detecting the presence of HGF and/or HGFR in vivo (e.g., in vivo imaging in a subject), respectively. The method can be used to evaluate (e.g., diagnose, localize, or stage) a condition described herein, e.g., a lymphatic disorder or risk for such a disorder. The method includes: (i) administering to a subject (and optionally a control subject) a HGF/HGFR binding agent (e.g., an antibody that binds to HGF or HGFR), under conditions that allow interaction of the binding agent and HGF or HGFR to occur; and (ii) detecting the binding agent, for example, to locate or otherwise identify HGF or HGFR expressing cells. A statistically significant increase in the amount of the complex in the subject relative to the reference, e.g., the control subject or subject's baseline, can be a factor that may lead to a diagnosis of a lymphatic or lymphatic system-related disorder or risk for such a disorder.
Preferably, the HGF/HGFR binding agent used in the in vivo (and also in vitro) diagnostic methods is directly or indirectly labeled with a detectable substance to facilitate detection of the bound or unbound binding agent. Suitable detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials and radioactive materials. In one embodiment, the HGF or HGFR binding protein is coupled to a radioactive ion, e.g., indium (111In), iodine (131I or 125I), yttrium (90Y), actinium (225Ac), bismuth (212Bi or 213Bi), sulfur (35S), carbon (14C), tritium (3H), rhodium (188Rh), or phosphorous (32P). In another embodiment, the HGF/HGFR binding protein is labeled with an NMR contrast agent.
In one aspect, the invention features a method of imaging vasculature (e.g., lymphatic vasculature) in a patient who is at risk for a lymphatic or lymphatic system-related disorder, or has such a disorder which is progressing. The method includes: providing an agent that binds to HGF or HGFR, e.g., an agent described herein, wherein the protein is physically associated to an imaging agent; administering the agent to a patient, e.g., with a risk for a lymphatic or lymphatic system-related disorder; and locating the agent within the patient, e.g., by imaging the patient, e.g., to detect HGF or HGFR expressing cells.
EXAMPLES
Example 1
HGFR is Expressed at a Higher Level in Lymphatic Endothelial Cells than in Blood Vascular Endothelial Cells and is Functional
Quantitative real-time RT-PCR (QPCR) confirmed that three independently established lines of primary LEC expressed high levels of mRNA of the major lymphatic lineage markers Prox1 and LYVE-1 but expressed low levels of the blood vascular lineage marker Flt-1, relative to blood vascular endothelial cells (BVEC) (FIG. 1A-C). HGFR mRNA levels in LEC were measured by QPCR and found to be at more than 2-fold higher than levels in BVEC (FIG. 1D). In addition, immunoprecipitation and western blot analyses demonstrated that HGFR protein expression was higher in LEC than in BVEC (FIG. 1E). Since treatment of LEC with 30 ng/ml HGF resulted in increased phosphorylation of HGFR (FIG. 1F), HGFR is functional in LEC. In sum, HGFR is expressed at a higher level in LEC than in BVEC and is activated when LEC are treated with HGF.
Example 2
HGFR Expression is Expressed in Lymphatic Vessels During Inflammation and Tissue Repair In Vivo
Differential immunofluorescence analyses of normal mouse skin were performed, using antibodies against HGFR and against the lymphatic-specific hyaluronan receptor LYVE-1. Little or no expression of HGFR was detected in quiescent lymphatic vessels in normal skin. In order to determine whether HGFR might be upregulated by lymphatic endothelium during pathological processes, we immunostained samples of chronically inflamed murine skin obtained from experimentally induced delayed-type hypersensitivity reactions in VEGF-A transgenic (VEGF-TG) mice that are characterized by lymphatic vessel enlargement and proliferation, Kunstfeld et al. (2004), Blood, 104(4):1048-1057. Seven days after induction of skin inflammation, enlarged LYVE-1-positive lymphatic vessels were detected in VEGF-TG mice but not in wild-type mice (FIG. 2A, D). LYVE-1-positive lymphatic vessels strongly expressed HGFR, whereas little or no HGFR expression was detected in the normal lymphatic vessels of wild-type mice (FIG. 2A-F).
Two to three weeks after experimentally-induced full-thickness skin wounds in mice, pronounced lymphangiogenesis is found within the granulation tissue. Double immunofluorescence analyses of wound tissue at day 21 after wounding revealed several LYVE-1-positive lymphatic vessels that also expressed HGFR (FIG. 2G-L).
To further characterize the possible role of HGFR during embryonic lymphatic vessel formation, mouse embryonic tissues were examined at embryonic days (E) 10.5 to 14.5 when active budding and proliferation of lymphatic vessel progenitors occurs. At E11.5, LYVE-1 expression was detected on endothelial cells of the anterior cardinal vein. These cells expressed little or no HGFR, whereas HGFR expression was already detected within the pharyngeal region of the foregut and in mesenchymal cells (FIG. 3A-C). However, at E12.5, HGFR expression was clearly detectable on LYVE-1-positive endothelial cells of the anterior cardinal vein (FIG. 3F: arrowheads), whereas only occasional HGFR expression was found on endothelial cells lining the primitive lymph sacs, overlapping with LYVE-1 reactivity (FIG. 3D-F). By E14.5, strong HGFR expression was detected on the vast majority of LYVE-1-positive lymphatic endothelial cells (FIG. 3G-I). At this stage, HGFR was still weakly expressed by endothelial cells lining the jugular vein and artery, which were LYVE-1-negative.
Example 3
HGF Directly Promotes LEC Proliferation and Migration
HGF is the only known ligand of HGFR and has been shown to induce proliferation and migration of human vascular endothelial cells (HVEC), e.g., Bussolino et al. (1992), J. Cell Biol., 119:629-641. To investigate whether the differential expression levels of HGFR by LEC versus BVEC might result in their differential response toward HGF stimulation, we next investigated the effects of HGF on LEC versus BVEC proliferation in vitro. HGF potently induced LEC proliferation with a minimal effective concentration of 1 ng/ml (p<0.01), as compared with untreated control cultures. Although HGF also induced BVEC proliferation at this concentration, the extent of growth stimulation was higher in LEC than in BVEC (FIG. 4A). Thus far, VEGF-C and VEGF-D are the only known growth factors that directly promote LEC proliferation via activation of the VEGF receptor-3 (VEGFR-3), e.g., Jussila and Alitalo (2002), Physiol Rev, 82:673-700, and effects of FGF-2 on lymphangiogenesis have been proposed to be the result of upregulation of VEGFR-3 ligands because they could be inhibited by blockade of the VEGFR-3 pathway, e.g., Chang et al. (2004), PNAS, 101:11658-11663; Kubo et al. (2002), PNAS, 99:8868-8873. To investigate whether HGF directly or indirectly stimulates LEC proliferation, we next treated LEC with HGF, in the presence or absence of blocking antibodies against VEGFR-3 or HGFR. Incubation of LEC with a HGFR blocking antibody potently blocked the stimulation of LEC proliferation by HGF (p<0.001), whereas incubation with a VEGFR-3 blocking antibody—at a dose that efficiently blocked growth stimulation by VEGF-C (data not shown)—or with control IgG did not affect HGF-induced proliferation (FIG. 4B). These results indicate that HGF-induced LEC proliferation occurs independently from activation of the VEGF-R3 pathway and is dependent upon efficient binding of HGF to its receptor.
HGF treatment also dose-dependently promoted migration of LEC and BVEC, with a minimal effective concentration of 3 ng/ml (FIG. 4C). To investigate whether HGF stimulation might also promote the formation of lymphatic tubes in vitro, confluent LEC cultures were overlaid with type I collagen as previously described Hirakawa et al. (2003), Am. J. Pathol., 162:575-586. HGF potently induced cord formation by LEC with a minimal effective dose of 3 ng/ml (p<0.001), as compared with untreated control cultures (FIG. 5A, B).
Example 4
HGF Promotes Lymphatic Vessel Formation In Vivo
To investigate whether HGF might also induce lymphangiogenesis in vivo, we implanted matrigels with or without HGF subcutaneously into FVB mice as described in Hirakawa et al. (2003), Am. J. Pathol., 162:575-586. Immunostaining for the lymphatic-specific glycoprotein podoplanin, e.g., Schacht et al. (2003), EMBO J., 22:3546-3556, revealed pronounced formation of new lymphatic vessels within HGF-containing matrigels at day 7 after implantation, whereas no lymphatic vessels were observed within control matrigels (FIG. 5C,D).
Example 5
Systemic Blockade of HGFR Inhibits Lymphatic Vessel Enlargement During Experimental Skin Inflammation
Because we found that HGFR was strongly expressed by the enlarged lymphatic vessels during experimental skin inflammation in mice, we next investigated whether HGF might directly contribute to lymphatic vessel enlargement in vivo. Delayed-type hypersensitivity reactions were induced by topical application to mouse ears as described Kunstfeld et al. (2004), Blood, 104(4):1048-1057. One day prior to induction of experimental inflammation, 100 μg of a blocking antibody against HGFR or an equal amount of control immunoglobulin G were injected intraperitoneally. Immunofluorescence analyses at 24 hours after induction of inflammation revealed a greatly reduced size of lymphatic vessels in mice that had received treatment with the HGF-R blocking antibody, as compared with mice that had received control IgG (FIG. 6A, B). Computer-assisted morphometric analyses of sections stained for LYVE-1 and CD31 demonstrated that the average size of lymphatic vessels, and the percentage of tissue area covered by lymphatic vessels, were significantly decreased after injection of the HGF-R blocking antibody (P<0.01), as compared with control IgG-treated mice (FIG. 6C, D). The density of lymphatic vessels was not significantly different between the two treatment groups (FIG. 6E).
Example 6
HGF Promotes LEC Migration Via Integrin α9
To define possible molecular mechanisms that might mediate the effects of HGF on LEC, two independent lines of LEC were incubated with or without 30 ng/ml HGF for 6 hours, followed by microarray analyses using the Affymetrix HU133v2TM arrays. We found that stanniocalcin 1 was one of the most highly up-regulated genes after HGF treatment. Moreover, the expression of the integrin alpha 9 was also significantly upregulated after HGF treatment. These results were confirmed by QPCR analysis (FIG. 7A).
Co-incubation of LEC with HGF in the presence or absence of a specific integrin alpha 9 blocking antibody revealed that blockade of the integrin alpha 9 partially blocked HGF-induced migration (p=0.0143), whereas incubation with a HGF-R blocking antibody completely inhibited the effect of HGF on LEC migration (p=0.0074) (FIG. 7B).
Example 7
HGF Promotes Lymphatic Vessel Formation In Vivo Independently of VEGF
To determine the effect of HGF overexpression in vivo, the lymphatic vasculature was investigated in previously established metallothionein I promoter-driven HGF transgenic mice (Takayama et al. (1996) Proc. Natl. Acad. Sci. USA, 93:5866-5871). The analysis focused on the skin and the small intestine where lymphatic vessels are most abundant and where abnormalities of the lymphatic system are most easily detected in genetic mouse models. Vascular enlargement was detected in the mucosa and submucosa of the ileum in HGF transgenic mice (FIG. 8B), as compared with wild-type mice (FIG. 8A). Immunofluorescence stains for the lymphatic-specific marker podoplanin revealed pronounced dilation of central lacteals and enlargement of lymphatic vessels in the submucosa of the ileum in HGF transgenic mice (FIG. 8C, D). Podoplanin stains also revealed an increased number and an enlargement of lymphatic vessels in the skin of HGF transgenic mice (FIG. 8G, H), whereas no major histological abnormalities were observed (FIG. 8E, F). Enhanced lymphatic vessel formation and enlargement were also observed in the duodenum and liver of HGF transgenic mice.
To examine whether HGF promotes the formation of new lymphatic vessels directly or indirectly via the VEGFR-3 pathway, slow-release pellets (with or without HGF) were implanted subcutaneously into mouse ears, and mice were treated systemically with a blocking antibody against mouse VEGFR-3 or with control IgG. After 14 days, immunofluorescence stains for CD31 and LYVE-1 revealed pronounced lymphatic vessel formation surrounding HGF-containing pellets, but not surrounding control pellets (FIG. 9A-C). However, treatment with an anti-VEGFR-3 blocking antibody did not prevent lymphatic vessel formation induced by HGF (FIG. 9B, C). Mice implanted with HGF-containing pellets showed moderately enhanced formation of blood vessels.
The results shown in these examples indicate that HGF is a protein target for controlling lymphangiogenesis.
OTHER EMBODIMENTS
A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. For example, combinations of nucleic acid and antibody modulators of HGF and HGFR activity are contemplated. Accordingly, other embodiments are within the scope of the following claims.

## Claims

1. A method of treating a subject diagnosed as having lymphedema, the method comprising:
selecting a subject diagnosed as having lymphedema;
administering to the subject a pharmaceutical composition comprising a purified nucleic acid molecule comprising a sequence that encodes a wildtype hepatocyte growth factor (HGF) protein in an amount sufficient to promote lymph vessel formation in the subject.

2. The method of claim 1, wherein the wildtype HGF protein is a wildtype human HGF protein.

3. The method of claim 1, wherein the pharmaceutical composition is administered by intravenous injection, subcutaneous injection, intramuscular injection, or intraperitoneal injection.

4. The method of claim 1, wherein the pharmaceutical composition is administered in a single dose.

5. The method of claim 1, wherein the pharmaceutical composition is administered in multiple doses.

6. The method of claim 1, wherein the pharmaceutical composition includes a pharmaceutically acceptable carrier.

7. A method of treating a subject diagnosed as having lymphedema, the method comprising:
selecting a subject diagnosed as having lymphedema;
administering to the subject a pharmaceutical composition comprising a purified nucleic acid molecule comprising a sequence that encodes a hepatocyte growth factor (HGF) protein comprising a sequence at least 90% identical to amino acids 55 to 728 of SEQ ID NO: 1 and having lymphangiogenic activity, in an amount sufficient to promote lymph vessel formation in the subject.

8. The method of claim 7, wherein the HGF protein comprises a sequence at least 92% identical to amino acids 55 to 728 of SEQ ID NO: 1.

9. The method of claim 8, wherein the HGF protein comprises a sequence at least 95% identical to amino acids 55 to 728 of SEQ ID NO: 1.

10. The method of claim 9, wherein the HGF protein comprises a sequence at least 97% identical to amino acids 55 to 728 of SEQ ID NO: 1.

11. The method of claim 10, wherein the HGF protein comprises a sequence at least 99% identical to amino acids 55 to 728 of SEQ ID NO: 1.

12. The method of claim 11, wherein the HGF protein comprises amino acids 55 to 728 of SEQ ID NO: 1.

13. The method of claim 7, wherein the pharmaceutical composition is administered by intravenous injection, subcutaneous injection, intramuscular injection, or intraperitoneal injection.

14. The method of claim 7, wherein the pharmaceutical composition is administered in a single dose.

15. The method of claim 7, wherein the pharmaceutical composition is administered in multiple doses.

16. The method of claim 7, wherein the pharmaceutical composition includes a pharmaceutically acceptable carrier.