Methods of detection of cancer using peptide profiles

Abstract

The disclosed methods address the identification and monitoring of cancer in a subject using serum peptide profiles. Such profiles allow the detection of the differential presence of certain serum peptide markers in comparison with controls. The profiles can be determined employing mass spectrometry.

1 . A method of identifying cancer of the prostate in a subject comprising detecting an increase in a complement C3f peptide or a fragment thereof, a ITIH4, clusterin, complement C4-alpha, kininogen or factor XIII peptide fragment, or any combination thereof in a biological sample obtained from the subject, thereby identifying cancer of the prostate in the subject. 
     
     
         2 . The method of  claim 1 , further comprising detecting a decrease in fibrinopeptideA peptide or a fragment thereof, or a fibrinogen-alpha peptide fragment, or any combination thereof in a biological sample obtained from the subject. 
     
     
         3 . A method of identifying cancer of the bladder in a subject comprising detecting an increase in a complement C3f peptide or a fragment thereof, a ITIH4, clusterin, complement C4-alpha, fibrinogen-alpha, APO A-I, APO A-IV, APO E or kininogen peptide fragment, or any combination thereof in a biological sample obtained from the subject, thereby identifying cancer of the bladder in the subject. 
     
     
         4 . The method of  claim 3 , further comprising detecting a decrease in a fibrinopeptideA peptide, bradykinin peptide, or a fragment thereof, a C4-alpha, ITIH4, or fibrinogen-alpha peptide fragment, or any combination thereof in a biological sample obtained from the subject. 
     
     
         5 . A method of identifying cancer of the breast in a subject comprising detecting an increase in a fibrinopeptideA peptide, bradykinin peptide, or a fragment thereof, a ITIH4, complement C4-alpha, fibrinogen-alpha, APO A-IV, factorXIII or transthyretin peptide fragment, or any combination thereof in a biological sample obtained from the subject, thereby identifying cancer of the breast in the subject. 
     
     
         6 . The method of  claim 5 , further comprising detecting a decrease in a fibrinopeptideA peptide, complement C3f peptide, or a fragment thereof, or any combination thereof in a biological sample obtained from the subject. 
     
     
         7 . A method of identifying cancer of the prostate in a subject comprising detecting a decrease in a fibrinopeptideA or a fragment thereof and a fibrinogen-alpha peptide fragment and an increase in a complement C3f peptide or a fragment thereof, a ITIH4, clusterin, complement C4-alpha, kininogen and factor XIII peptide fragment in a biological sample obtained from the subject, thereby identifying cancer of the prostate in the subject. 
     
     
         8 . A method of identifying cancer of the bladder in a subject comprising detecting a decrease in a fibrinopeptideA peptide, bradykinin peptide, or a fragment thereof, a C4-alpha, ITIH4, and fibrinogen-alpha peptide fragment and an increase in a complement C3f peptide or a fragment thereof, a ITIH4, clusterin, complement C4-alpha, fibrinogen-alpha, APO A-I, APO A-IV, APO E and kininogen peptide fragment in a biological sample obtained from the subject, thereby identifying cancer of the bladder in the subject. 
     
     
         9 . A method of identifying cancer of the breast in a subject comprising detecting a decrease in a fibrinopeptideA peptide and complement C3f peptide, or a fragment thereof, and an increase in a fibrinopeptideA peptide, bradykinin peptide, or a fragment thereof, a ITIH4, complement C4-alpha, fibrinogen-alpha, APO A-IV, factor XIII and transthyretin peptide fragment in a biological sample obtained from the subject, thereby identifying cancer of the breast in the subject. 
     
     
         10 . The method of  claim 7 , wherein the fibrinopeptideA peptide fragment is selected from the group consisting of DSGEGDFLAEGGGVR (SEQ ID NO. 1), SGEGDFLAEGGGVR (SEQ ID NO. 2), GEGDFLAEGGGVR (SEQ ID NO. 3), EGDFLAEGGGVR (SEQ ID NO. 4), GDFLAEGGGVR (SEQ ID NO. 5), DFLAEGGGVR (SEQ ID NO. 6) and LAEGGGVR (SEQ ID NO. 25). 
     
     
         11 . The method of  claim 8 , wherein the fibrinopeptideA peptide fragment is selected from the group consisting of DSGEGDFLAEGGGVR (SEQ ID NO. 1), SGEGDFLAEGGGVR (SEQ ID NO. 2), GEGDFLAEGGGVR (SEQ ID NO. 3), EGDFLAEGGGVR (SEQ ID NO. 4), GDFLAEGGGVR (SEQ ID NO. 5), DFLAEGGGVR (SEQ ID NO. 6), FLAEGGGVR (SEQ ID NO. 24) and LAEGGGVR (SEQ ID NO. 25). 
     
     
         12 . The method of  claim 9 , wherein the fibrinopeptideA peptide fragment that is decreased is selected from the group consisting of SGEGDFLAEGGGVR (SEQ ID NO. 2) and GEGDFLAEGGGVR (SEQ ID NO. 3) and the fibrinopeptideA fragment that is increased is FLAEGGGVR (SEQ ID NO. 24). 
     
     
         13 . The method of  claim 7 , wherein the complement C3f peptide fragment is selected from the group consisting of, SSKITHRIHWESASLL (SEQ ID NO. 8), SKITHRIHWESASLL (SEQ ID NO. 9), KITHRIHWESASLL (SEQ ID NO. 10), THRIHWESASLL (SEQ ID NO. 11), and IHWESASLL (SEQ ID NO. 28). 
     
     
         14 . The method of  claim 8 , wherein the complement C3f peptide fragment is selected from the group consisting of SSKITHRIHWESASLL (SEQ ID NO. 8), SKITHRIHWESASLL (SEQ ID NO. 9), KITHRIHWESASLL (SEQ ID NO. 10), THRIHWESASLL (SEQ ID NO. 11), HWESASLL (SEQ ID NO. 12), RIHWESASLL (SEQ ID NO. 27), IHWESASLL (SEQ ID NO. 28) and SSKITHRIHWESASL (SEQ ID NO. 29). 
     
     
         15 . The method of  claim 9 , wherein the complement C3f peptide fragment is selected from the group consisting of SSKITHRIHWESASLL (SEQ ID NO. 8), HWESASLL (SEQ ID NO. 12), and ITHRIHWESASLL (SEQ ID NO. 26). 
     
     
         16 . The method of  claim 7 , wherein the ITIH4 peptide fragment is selected from the group consisting of PGVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 13), SRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 15), HAAYHPFR (SEQ ID NO. 34), QLGLPGPPDVPDHAAYHPFR (SEQ ID NO. 35), HAAYHPF (SEQ ID NO. 39) NVHSGSTFFKYYLQGAKIPKPEASFSPR (SEQ ID NO. 40) and NVHSAGAAGSRMNFRPGVLSS (SEQ ID NO. 41). 
     
     
         17 . The method of  claim 8 , wherein the ITIH4 peptide fragment that is increased is selected from the group consisting of PGVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 13), SRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 15), HAAYHPFR (SEQ ID NO. 34), QAGAAGSRMNFRPGVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 36), MNFRPGVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 37), NVHSGSTFFKYYLQGAKIPKPEASFSPR (SEQ ID NO. 40) and NVHSAGAAGSRMNFRPGVLSS (SEQ ID NO. 41), and the ITIH4 peptide fragment that is decreased is selected from the group consisting of GVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 14) and HAAYHPF (SEQ ID NO. 39). 
     
     
         18 . The method of  claim 9 , wherein the ITIH4 peptide fragment is selected from the group consisting of GLPGPPDVPDHAAYHPF (SEQ ID NO. 16), HAAYHPFR (SEQ ID NO. 34), QLGLPGPPDVPDHAAYHPFR (SEQ ID NO. 35), SSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 38) and NVHSAGAAGSRMNFRPGVLSS (SEQ ID NO. 41). 
     
     
         19 . The method of  claim 7 , wherein the clusterin peptide fragment is HFFFPKSRIV (SEQ ID NO. 17). 
     
     
         20 . The method of  claim 8 , wherein the clusterin peptide fragment is selected from the group consisting of HFFFPKSRIV (SEQ ID NO. 17) and HFFFPK (SEQ ID NO. 18). 
     
     
         21 . The method of  claim 8 , wherein the bradykinin peptide fragment is selected from the group consisting of RPPGFSPFR (SEQ ID NO. 19) and RPPGFSPF (SEQ ID NO. 20). 
     
     
         22 . The method of  claim 7 , wherein the complement C4-alpha peptide fragment is GLEEELQFSLGSKINVKVGGNS (SEQ ID NO. 23). 
     
     
         23 . The method of  claim 8 , wherein the complement C4-alpha peptide fragment that is increased is selected from the group consisting of RNGFKSHALQLNNRQI (SEQ ID NO. 21), GLEEELQFSLGSKINVKVGGNS (SEQ ID NO. 23), NGFKSHALQLNNR (SEQ ID NO. 31), and the complement C4-alpha peptide fragment that is decreased is GLEEELQFSLGSKINV (SEQ ID NO. 33). 
     
     
         24 . The method of  claim 9 , wherein the complement C4-alpha peptide fragment is selected from the group consisting of RNGFKSHALQLNNRQI (SEQ ID NO. 21), NGFKSHALQLNNRQI (SEQ ID NO. 22), GLEEELQFSLGSKINVKVGGNS (SEQ ID NO. 23), NGFKSHALQLNNRQ (SEQ ID NO. 30), GLEEELQFSLGSKINVKVGGNSKGTL (SEQ ID NO. 32) and GLEEELQFSLGSKINV (SEQ ID NO. 33). 
     
     
         25 . The method of  claim 7 , wherein the fibrinogen-alpha peptide fragment is selected from the group consisting of SSSYSKQFTSSTSYNRGDSTFESKSYKMA (SEQ ID NO. 55) and SSSYSKQFTSSTSYNRGDSTFESKSYKM (SEQ ID NO. 56). 
     
     
         26 . The method of  claim 8 , wherein the fibrinogen-alpha peptide fragment that is increased is selected from the group consisting of SSSYSKQFTSSTSYNRGDSTFESKSYKMA (SEQ ID NO. 55), SSSYSKQFTSSTSYNRGDSTFESKSYKM (SEQ ID NO. 56), SSSYSKQFTSSTSYNRGDSTFESKSY (SEQ ID NO. 57), SSSYSKQFTSSTSYNRGDSTFESKS (SEQ ID NO. 58), and SSYSKQFTSSTSYNRGDSTFE (SEQ ID NO. 60), and the fibrinogen-alpha peptide fragment that is decreased is GSESGIFTNTKESSSHHPGIAEFPSRG (SEQ ID NO. 61). 
     
     
         27 . The method of  claim 9 , wherein the fibrinogen-alpha peptide fragment is selected from the group consisting of SSYSKQFTSSTSYNRGDSTFE (SEQ ID NO. 60) and DEAGSEADHEGTHSTKRGHAKSRPV (SEQ ID NO. 62). 
     
     
         28 . The method of  claim 7 , wherein the kininogen peptide fragment is NLGHGHKHERDQGHGHQ (SEQ ID NO. 52). 
     
     
         29 . The method of  claim 8 , wherein the kininogen peptide fragment is selected from the group consisting of KHNLGHGHKHERDQGHGHQ (SEQ ID NO. 51) or NLGHGHKHERDQGHGHQ (SEQ ID NO. 52). 
     
     
         30 . The method of  claim 8 , wherein the APO A-I peptide fragment is selected from the group consisting of QGLLPVLESFKVSFLSALEEYTKKLNTQ (SEQ ID NO. 42), VSFLSALEEYTKKLNTQ (SEQ ID NO. 43) and ATEHLSTLSEKAKPALEDL (SEQ ID NO. 44). 
     
     
         31 . The method of  claim 8 , wherein the APO A-IV peptide fragment is selected from the group consisting of GNTEGLQKSLAELGGHLDQQVEEFR (SEQ ID NO. 46), SLAELGGHLDQQVEEFR (SEQ ID NO. 47) and SLAELGGHLDQQVEEF (SEQ ID NO. 48). 
     
     
         32 . The method of  claim 9 , wherein the APO A-IV peptide fragment is ISASAEELRQRLAPLAEDVRGNL (SEQ ID NO. 45). 
     
     
         33 . The method of  claim 8 , wherein the APO E peptide fragment is selected from the group consisting of AATVGSLAGQPLQERAQAWGERLR (SEQ ID NO. 49) and AATVGSLAGQPLQERAQAWGERL (SEQ ID NO. 50). 
     
     
         34 . The method of  claim 7 , wherein the factor XIII peptide fragment is AVPPNNSNAAEDDLPTVELQGVVPR (SEQ ID NO. 53). 
     
     
         35 . The method of  claim 9 , wherein the factor XIII peptide fragment is AVPPNNSNAAEDDLPTVELQGVVPR (SEQ ID NO. 53). 
     
     
         36 . The method of  claim 9 , wherein the transthyretin peptide fragment is ALGISPFHEHAEVVFTANDSGPR (SEQ ID NO. 54). 
     
     
         37 . The method of  claim 1 , wherein the biological sample comprises plasma or serum or a preparation thereof. 
     
     
         38 . The method of  claim 1 , wherein the detecting comprises analyzing the biological sample, or a preparation thereof using mass spectrometry. 
     
     
         39 . The method of  claim 38 , wherein the mass spectrometry is MALDI TOF mass spectrometry. 
     
     
         40 . The method of  claim 38 , wherein the mass spectrometry is Fourier-transform ion cyclotron resonance mass spectrometry. 
     
     
         41 . The method of  claim 38 , wherein the mass spectrometry is electrospray ionization mass spectrometry. 
     
     
         42 . The method of  claim 1 , wherein the detecting comprises analyzing the biological sample or a preparation thereof on a solid support, wherein peptides in the sample bind to the solid support. 
     
     
         43 . An isolated or identified peptide profile indicating cancer of the prostate comprising an increased amount of peptides or peptide fragments selected from the group consisting of SSKITHRIHWESASLL (SEQ ID NO. 8), SKITHRIHWESASLL (SEQ ID NO. 9), KITHRIHWESASLL (SEQ ID NO. 10), THRIHWESASLL (SEQ ID NO. 11), PGVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 13), SRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 15), HFFFPKSRIV (SEQ ID NO. 17), and GLEEELQFSLGSKINVKVGGNS (SEQ ID NO. 23), IHWESASLL (SEQ ID NO. 28), HAAYHPFR (SEQ ID NO. 34), QLGLPGPPDVPDHAAYHPFR (SEQ ID NO. 35), HAAYHPF (SEQ ID NO. 39) NVHSGSTFFKYYLQGAKIPKPEASFSPR (SEQ ID NO. 40) NVHSAGAAGSRMNFRPGVLSS (SEQ ID NO. 41), NLGHGHKHERDQGHGHQ (SEQ ID NO. 52), AVPPNNSNAAEDDLPTVELQGWPR (SEQ ID NO. 53) and combinations thereof. 
     
     
         44 . (canceled) 
     
     
         45 . An isolated or identified peptide profile indicating cancer of the bladder comprising an increased amount of peptides or peptide fragments selected from the group consisting of SSKITHRIHWESASLL (SEQ ID NO. 8), SKITHRIHWESASLL (SEQ ID NO. 9), KITHRIHWESASLL (SEQ ID NO. 10), THRIHWESASLL (SEQ ID NO. 11), HWESASLL (SEQ ID NO. 12), PGVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 13), SRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 15), HFFFPKSRIV (SEQ ID NO. 17), HFFFPK (SEQ ID NO. 18), RNGFKSHALQLNNRQI (SEQ ID NO. 21), GLEEELQFSLGSKINVKVGGNS (SEQ ID NO. 23), (SEQ ID NO. 27), IHWESASLL (SEQ ID NO. 28), SSKITHRIHWESASL (SEQ ID NO. 29), NGFKSHALQLNNR (SEQ ID NO. 31), HAAYHPFR (SEQ ID NO. 34), QAGAAGSRMNFRPGVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 36), MNFRPGVLSSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 37), NVHSGSTFFKYYLQGAKIPKPEASFSPR (SEQ ID NO. 40), NVHSAGAAGSRMNFRPGVLSS (SEQ ID NO. 41), QGLLPVLESFKVSFLSALEEYTKKLNTQ (SEQ ID NO. 42), VSFLSALEEYTKKLNTQ (SEQ ID NO. 43), ATEHLSTLSEKAKPALEDL (SEQ ID NO. 44), GNTEGLQKSLAELGGHLDQQVEEFR (SEQ ID NO. 46), SLAELGGHLDQQVEEFR (SEQ ID NO. 47), SLAELGGHLDQQVEEF (SEQ ID NO. 48), AATVGSLAGQPLQERAQAWGERLR (SEQ ID NO. 49), AATVGSLAGQPLQERAQAWGERL (SEQ ID NO. 50), KHNLGHGHKHERDQGHGHQ (SEQ ID NO. 51), NLGHGHKHERDQGHGHQ (SEQ ID NO. 52), GSESGIFTNTKESSSHHPGIAEFPSRG (SEQ ID NO. 61) and combinations thereof. 
     
     
         46 . (canceled) 
     
     
         47 . An isolated or identified peptide profile indicating cancer of the breast comprising an increased amount of peptides or peptide fragments selected from the group consisting of GLPGPPDVPDHAAYHPF (SEQ ID NO. 16), RPPGFSPFR (SEQ ID NO. 19), RPPGFSPF (SEQ ID NO. 20), RNGFKSHALQLNNRQI (SEQ ID NO. 21), NGFKSHALQLNNRQI (SEQ ID NO. 22) GLEEELQFSLGSKINVKVGGNS (SEQ ID NO. 23), FLAEGGGVR (SEQ ID NO. 24), NGFKSHALQLNNRQ (SEQ ID NO. 30), GLEEELQFSLGSKINVKVGGNSKGTL (SEQ ID NO. 32), GLEEELQFSLGSKINV (SEQ ID NO. 33), HAAYHPFR (SEQ ID NO. 34), QLGLPGPPDVPDHAAYHPFR (SEQ ID NO. 35), SSRQLGLPGPPDVPDHAAYHPF (SEQ ID NO. 38), NVHSAGAAGSRMNFRPGVLSS (SEQ ID NO. 41), ISASAEELRQRLAPLAEDVRGNL (SEQ ID NO. 45), AVPPNNSNAAEDDLPTVELQGVVPR (SEQ ID NO. 53), ALGISPFHEHAEVVFTANDSGPR (SEQ ID NO. 54), SSYSKQFTSSTSYNRGDSTFE (SEQ ID NO. 60) DEAGSEADHEGTHSTKRGHAKSRPV (SEQ ID NO. 62) and combinations thereof. 
     
     
         48 - 50 . (canceled) 
     
     
         51 . A method of generating a peptide profile of a subject having, or at risk of having, cancer of the prostate, comprising the steps of:
 i) combining an exogenous peptide selected from the group consisting of a complement C3f, ITIH4, clusterin, complement C4-alpha, fibrinopeptide A kininogen, factor XIII, fibrinogenA peptide and combinations thereof with a biological sample from the subject; and   ii) proteolytically digesting a peptide of step i),   thereby generating a peptide profile of the subject.   
     
     
         52 - 71 . (canceled) 
     
     
         72 . A kit for generating a peptide profile of a subject having, or at risk of having, cancer of the bladder, breast, prostate or thyroid comprising an exogenous peptide or peptide fragment selected form the group consisting of complement C3f peptide, ITIH4 peptide, clusterin peptide, complement C4-alpha peptide, fibrinopeptideA peptide, bradykinin peptide, APO A-I peptide, APOA-IV peptide, APO E peptide, kininogen peptide, factor XIII peptide, transthyretin peptide and fibrinogenA peptide and instructions for use. 
     
     
         73 - 76 . (canceled) 
     
     
         77 . An isolated peptide fragment selected from the group consisting of a complement C3f, ITIH4, clusterin, complement C4-alpha, fibrinopeptideA, bradykinin, APO A-I, APOA-IV, APO E, kininogen, factor XIII, transthyretin and fibrinogenA peptide fragment. 
     
     
         78 . A method of identifying cancer of the thyroid in a subject comprising detecting an increase in a complement C3f peptide or a fragment thereof, thereby identifying cancer of the thyroid in the subject. 
     
     
         79 . The method of  claim 78 , further comprising detecting a decrease in fibrinopeptideA peptide or a fragment thereof, or a fibrinogen-alpha peptide fragment, or any combination thereof in a biological sample obtained from the subject. 
     
     
         80 . The method  claim 78 , wherein the step of detecting comprises an optical detection method. 
     
     
         81 . The method of  claim 80 , wherein the optical detection method comprises a fluorescence method. 
     
     
         82 . The method of  claim 81 , wherein the fluorescence method comprises a sandwich immunoassay.