Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1844, Issue 5, 2014, Pages 866-873

  Omenn, Gilbert S ^a,b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

Biomarker; Human Plasma Peptide Atlas; Human Proteome Peptide Atlas; Human Proteome Project; Splice variant protein; Splice variant transcript

Indexed keywords

ISOPROTEIN; PEPTIDE; PLASMA PROTEIN; PROTEIN; PROTEIN VARIANT; PROTEOME; SPLICE VARIANT PROTEIN; UNCLASSIFIED DRUG;

ALTERNATIVE RNA SPLICING; ARTICLE; ATLAS; GENE; GENE EXPRESSION; GENOME; HUMAN; MASS SPECTROMETRY; NEOPLASM; PLASMA; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; RNA SEQUENCE;

BIOMARKER; HUMAN PLASMA PEPTIDE ATLAS; HUMAN PROTEOME PEPTIDE ATLAS; HUMAN PROTEOME PROJECT; SPLICE VARIANT PROTEIN; SPLICE VARIANT TRANSCRIPT;

ALTERNATIVE SPLICING; BLOOD PROTEINS; CHROMOSOMES, HUMAN; HUMAN GENOME PROJECT; HUMANS; NEOPLASMS; PROTEIN ISOFORMS; PROTEOME; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 84898599862     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.10.016     Document Type: Article

References (40)

1. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J.P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N. Stange-Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J.C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R.H. Waterston, R.K. Wilson, L.W. Hillier, J.D. McPherson, M.A. Marra, E.R. Mardis, L.A. Fulton, A.T. Chinwalla, K.H. Pepin, W.R. Gish, S.L. Chissoe, M.C. Wendl, K.D. Delehaunty, T.L. Miner, A. Delehaunty, J.B. Kramer, L.L. Cook, R.S. Fulton, D.L. Johnson, P.J. Minx, S.W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J.F. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, M. Frazier, R.A. Gibbs, D.M. Muzny, S.E. Scherer, J.B. Bouck, E.J. Sodergren, K.C. Worley, C.M. Rives, J.H. Gorrell, M.L. Metzker, S.L. Naylor, R.S. Kucherlapati, D.L. Nelson, G.M. Weinstock, Y. Sakaki, A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh, C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor, J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert, P. Wincker, D.R. Smith, L. Doucette-Stamm, M. Rubenfield, K. Weinstock, H.M. Lee, J. Dubois, A. Rosenthal, M. Platzer, G. Nyakatura, S. Taudien, A. Rump, H. Yang, J. Yu, J. Wang, G. Huang, J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin, R.W. Davis, N.A. Federspiel, A.P. Abola, M.J. Proctor, R.M. Myers, J. Schmutz, M. Dickson, J. Grimwood, D.R. Cox, M.V. Olson, R. Kaul, N. Shimizu, K. Kawasaki, S. Minoshima, G.A. Evans, M. Athanasiou, R. Schultz, B.A. Roe, F. Chen, H. Pan, J. Ramser, H. Lehrach, R. Reinhardt, W.R. McCombie, M. de la Bastide, N. Dedhia, H. Blocker, K. Hornischer, G. Nordsiek, R. Agarwala, L. Aravind, J.A. Bailey, A. Bateman, S. Batzoglou, E. Birney, P. Bork, D.G. Brown, C.B. Burge, L. Cerutti, H.C. Chen, D. Church, M. Clamp, R.R. Copley, T. Doerks, S.R. Eddy, E.E. Eichler, T.S. Furey, J. Galagan, J.G. Gilbert, C. Harmon, Y. Hayashizaki, D. Haussler, H. Hermjakob, K. Hokamp, W. Jang, L.S. Johnson, T.A. Jones, S. Kasif, A. Kaspryzk, S. Kennedy, W.J. Kent, P. Kitts, E.V. Koonin, I. Korf, D. Kulp, D. Lancet, T.M. Lowe, A. McLysaght, T. Mikkelsen, J.V. Moran, N. Mulder, V.J. Pollara, C.P. Ponting, G. Schuler, J. Schultz, G. Slater, A.F. Smit, E. Stupka, J. Szustakowski, D. Thierry-Mieg, J. Thierry-Mieg, L. Wagner, J. Wallis, R. Wheeler, A. Williams, Y.I. Wolf, K.H. Wolfe, S.P. Yang, R.F. Yeh, F. Collins, M.S. Guyer, J. Peterson, A. Felsenfeld, K.A. Wetterstrand, A. Patrinos, M.J. Morgan, P. de Jong, J.J. Catanese, K. Osoegawa, H. Shizuya, S. Choi, and Y.J. Chen Initial sequencing and analysis of the human genome Nature 409 2001 860 921 (Pubitemid 32165345)
2. J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, R.A. Holt, J.D. Gocayne, P. Amanatides, R.M. Ballew, D.H. Huson, J.R. Wortman, Q. Zhang, C.D. Kodira, X.H. Zheng, L. Chen, M. Skupski, G. Subramanian, P.D. Thomas, J. Zhang, G.L. Gabor Miklos, C. Nelson, S. Broder, A.G. Clark, J. Nadeau, V.A. McKusick, N. Zinder, A.J. Levine, R.J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, V. Di Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A.E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T.J. Heiman, M.E. Higgins, R.R. Ji, Z. Ke, K.A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G.V. Merkulov, N. Milshina, H.M. Moore, A.K. Naik, V.A. Narayan, B. Neelam, D. Nusskern, D.B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z. Wang, A. Wang, X. Wang, J. Wang, M. Wei, R. Wides, C. Xiao, C. Yan, A. Yao, J. Ye, M. Zhan, W. Zhang, H. Zhang, Q. Zhao, L. Zheng, F. Zhong, W. Zhong, S. Zhu, S. Zhao, D. Gilbert, S. Baumhueter, G. Spier, C. Carter, A. Cravchik, T. Woodage, F. Ali, H. An, A. Awe, D. Baldwin, H. Baden, M. Barnstead, I. Barrow, K. Beeson, D. Busam, A. Carver, A. Center, M.L. Cheng, L. Curry, S. Danaher, L. Davenport, R. Desilets, S. Dietz, K. Dodson, L. Doup, S. Ferriera, N. Garg, A. Gluecksmann, B. Hart, J. Haynes, C. Haynes, C. Heiner, S. Hladun, D. Hostin, J. Houck, T. Howland, C. Ibegwam, J. Johnson, F. Kalush, L. Kline, S. Koduru, A. Love, F. Mann, D. May, S. McCawley, T. McIntosh, I. McMullen, M. Moy, L. Moy, B. Murphy, K. Nelson, C. Pfannkoch, E. Pratts, V. Puri, H. Qureshi, M. Reardon, R. Rodriguez, Y.H. Rogers, D. Romblad, B. Ruhfel, R. Scott, C. Sitter, M. Smallwood, E. Stewart, R. Strong, E. Suh, R. Thomas, N.N. Tint, S. Tse, C. Vech, G. Wang, J. Wetter, S. Williams, M. Williams, S. Windsor, E. Winn-Deen, K. Wolfe, J. Zaveri, K. Zaveri, J.F. Abril, R. Guigo, M.J. Campbell, K.V. Sjolander, B. Karlak, A. Kejariwal, H. Mi, B. Lazareva, T. Hatton, A. Narechania, K. Diemer, A. Muruganujan, N. Guo, S. Sato, V. Bafna, S. Istrail, R. Lippert, R. Schwartz, B. Walenz, S. Yooseph, D. Allen, A. Basu, J. Baxendale, L. Blick, M. Caminha, J. Carnes-Stine, P. Caulk, Y.H. Chiang, M. Coyne, C. Dahlke, A. Mays, M. Dombroski, M. Donnelly, D. Ely, S. Esparham, C. Fosler, H. Gire, S. Glanowski, K. Glasser, A. Glodek, M. Gorokhov, K. Graham, B. Gropman, M. Harris, J. Heil, S. Henderson, J. Hoover, D. Jennings, C. Jordan, J. Jordan, J. Kasha, L. Kagan, C. Kraft, A. Levitsky, M. Lewis, X. Liu, J. Lopez, D. Ma, W. Majoros, J. McDaniel, S. Murphy, M. Newman, T. Nguyen, N. Nguyen, M. Nodell, S. Pan, J. Peck, M. Peterson, W. Rowe, R. Sanders, J. Scott, M. Simpson, T. Smith, A. Sprague, T. Stockwell, R. Turner, E. Venter, M. Wang, M. Wen, D. Wu, M. Wu, A. Xia, A. Zandieh, and X. Zhu The sequence of the human genome Science 291 2001 1304 1351 (Pubitemid 32173090)
3. L.E. Hood, G.S. Omenn, R.L. Moritz, R. Aebersold, K.R. Yamamoto, M. Amos, J. Hunter-Cevera, and L. Locascio New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences Proteomics 12 2012 2773 2783
4. P. Legrain, R. Aebersold, A. Archakov, A. Bairoch, K. Bala, L. Beretta, J. Bergeron, C.H. Borchers, G.L. Corthals, C.E. Costello, E.W. Deutsch, B. Domon, W. Hancock, F. He, D. Hochstrasser, G. Marko-Varga, G.H. Salekdeh, S. Sechi, M. Snyder, S. Srivastava, M. Uhlen, C.H. Wu, T. Yamamoto, Y.K. Paik, and G.S. Omenn The human proteome project: current state and future direction Mol. Cell. Proteomics 10 2011 (M111 009993)
5. G.S. Omenn, D.J. States, M. Adamski, T.W. Blackwell, R. Menon, H. Hermjakob, R. Apweiler, B.B. Haab, R.J. Simpson, J.S. Eddes, E.A. Kapp, R.L. Moritz, D.W. Chan, A.J. Rai, A. Admon, R. Aebersold, J. Eng, W.S. Hancock, S.A. Hefta, H. Meyer, Y.K. Paik, J.S. Yoo, P. Ping, J. Pounds, J. Adkins, X. Qian, R. Wang, V. Wasinger, C.Y. Wu, X. Zhao, R. Zeng, A. Archakov, A. Tsugita, I. Beer, A. Pandey, M. Pisano, P. Andrews, H. Tammen, D.W. Speicher, and S.M. Hanash Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database Proteomics 5 2005 3226 3245 (Pubitemid 41192032)
6. D.J. States, G.S. Omenn, T.W. Blackwell, D. Fermin, J. Eng, D.W. Speicher, and S.M. Hanash Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study Nat. Biotechnol. 24 2006 333 338 (Pubitemid 43372157)
7. A. Keller, J. Eng, N. Zhang, X.J. Li, and R. Aebersold A uniform proteomics MS/MS analysis platform utilizing open XML file formats Mol. Syst. Biol. 1 2005 2005 0017
8. T. Farrah, E.W. Deutsch, G.S. Omenn, D.S. Campbell, Z. Sun, J.A. Bletz, P. Mallick, J.E. Katz, J. Malmstrom, R. Ossola, J.D. Watts, B. Lin, H. Zhang, R.L. Moritz, and R. Aebersold A high-confidence human plasma proteome reference set with estimated concentrations in Peptide Atlas Mol. Cell. Proteomics 10 2011 (M110 006353)
9. L. Reiter, M. Claassen, S.P. Schrimpf, M. Jovanovic, A. Schmidt, J.M. Buhmann, M.O. Hengartner, and R. Aebersold Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry Mol. Cell. Proteomics 8 2009 2405 2417
10. T. Farrah, E.W. Deutsch, M.R. Hoopmann, J.L. Hallows, Z. Sun, C.Y. Huang, and R.L. Moritz The state of the human proteome in 2012 as viewed through Peptide Atlas J. Proteome Res. 12 2013 162 171
11. Z. Cao, S. Yende, J.A. Kellum, and R.A. Robinson Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow Int. J. Proteomics 2013 654356
12. R. Aebersold, G.D. Bader, A.M. Edwards, J.E. van Eyk, M. Kussmann, J. Qin, and G.S. Omenn The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community J. Proteome Res. 12 2013 23 27
13. G. Marko-Varga, G.S. Omenn, Y.K. Paik, and W.S. Hancock A first step toward completion of a genome-wide characterization of the human proteome J. Proteome Res. 12 2013 1 5
14. L. Fagerberg, P. Oksvold, M. Skogs, C. Algenas, E. Lundberg, F. Ponten, A. Sivertsson, J. Odeberg, D. Klevebring, C. Kampf, A. Asplund, E. Sjostedt, C. Al-Khalili Szigyarto, P.H. Edqvist, I. Olsson, U. Rydberg, P. Hudson, J. Ottosson Takanen, H. Berling, L. Bjorling, H. Tegel, J. Rockberg, P. Nilsson, S. Navani, K. Jirstrom, J. Mulder, J.M. Schwenk, M. Zwahlen, S. Hober, M. Forsberg, K. von Feilitzen, and M. Uhlen Contribution of antibody-based protein profiling to the Human Chromosome-Centric Proteome Project (C-HPP) J. Proteome Res. 12 2013 2439 2448
15. M. Beck, A. Schmidt, J. Malmstroem, M. Claassen, A. Ori, A. Szymborska, F. Herzog, O. Rinner, J. Ellenberg, and R. Aebersold The quantitative proteome of a human cell line Mol. Syst. Biol. 7 2011 549
16. N. Nagaraj, J.R. Wisniewski, T. Geiger, J. Cox, M. Kircher, J. Kelso, S. Paabo, and M. Mann Deep proteome and transcriptome mapping of a human cancer cell line Mol. Syst. Biol. 7 2011 548
17. T. Geiger, A. Wehner, C. Schaab, J. Cox, and M. Mann Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins Mol. Cell. Proteomics 11 2012 (M111 014050)
18. H.J. Lee, S.K. Jeong, K. Na, M.J. Lee, S.H. Lee, J.S. Lim, H.J. Cha, J.Y. Cho, J.Y. Kwon, H. Kim, S.Y. Song, J.S. Yoo, Y.M. Park, W.S. Hancock, and Y.K. Paik Comprehensive genome-wide proteomic analysis of human placental tissue for the chromosome-centric human proteome project J. Proteome Res. 12 2013 2458 2466
19. J. Munoz, T.Y. Low, Y.J. Kok, A. Chin, C.K. Frese, V. Ding, A. Choo, and A.J. Heck The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells Mol. Syst. Biol. 7 2011 550
20. C.A. Gelfand, and G.S. Omenn Preanalytical variables for plasma and serum proteome analyses A.R. Ivanov, A.V. Lazarev, Sample Preparation in Biological Mass Spectrometry 2011 Springer New York 269 289
21. M. Uhlen, P. Oksvold, L. Fagerberg, E. Lundberg, K. Jonasson, M. Forsberg, M. Zwahlen, C. Kampf, K. Wester, S. Hober, H. Wernerus, L. Bjorling, and F. Ponten Towards a knowledge-based Human Protein Atlas Nat. Biotechnol. 28 2010 1248 1250
22. A.M. Edwards, R. Isserlin, G.D. Bader, S.V. Frye, T.M. Willson, and F.H. Yu Too many roads not taken Nature 470 2011 163 165
23. P. Rajan, D.J. Elliott, C.N. Robson, and H.Y. Leung Alternative splicing and biological heterogeneity in prostate cancer Nat. Rev. Urol. 6 2009 454 460
24. B. Alberts Molecular Biology of the Cell 5th ed. 2008 Garland Science New York
25. B.R. Graveley Alternative splicing: increasing diversity in the proteomic world Trends Genet. 17 2001 100 107 (Pubitemid 32140790)
26. A.I. Nesvizhskii, F.F. Roos, J. Grossmann, M. Vogelzang, J.S. Eddes, W. Gruissem, S. Baginsky, and R. Aebersold Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides Mol. Cell. Proteomics 5 2006 652 670
27. K. Ning, and A.I. Nesvizhskii The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment BMC Bioinf. 11 Suppl. 11 2010 S14
28. R.J. Weatheritt, N.E. Davey, and T.J. Gibson Linear motifs confer functional diversity onto splice variants Nucleic Acids Res. 40 2012 7123 7131
29. K.F. Au, H. Jiang, L. Lin, Y. Xing, and W.H. Wong Detection of splice junctions from paired-end RNA-seq data by SpliceMap Nucleic Acids Res. 38 2010 4570 4578
30. J. Merkin, C. Russell, P. Chen, and C.B. Burge Evolutionary dynamics of gene and isoform regulation in mammalian tissues Science 338 2012 1593 1599
31. G.S. Omenn, R. Menon, and Y. Zhang Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology J. Proteomics 90 2013 28 37
32. R. Menon, Q. Zhang, Y. Zhang, D. Fermin, N. Bardeesy, R.A. DePinho, C. Lu, S.M. Hanash, G.S. Omenn, and D.J. States Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer Cancer Res. 69 2009 300 309
33. R. Menon, and G.S. Omenn Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers Cancer Res. 70 2010 3440 3449
34. S. Liu, H. Im, A. Bairoch, M. Cristofanilli, R. Chen, S. Dalton, E.W. Deutsch, S. Fanayan, C. Gates, P. Gaudet, M. Hincapie, S. Hanash, H. Kim, S.K. Jeong, E. Lundberg, G. Mias, R. Menon, Z. Mu, E. Nice, Y.K. Paik, M. Uhlén, L. Wells, S.L. Wu, F. Yan, F. Zhang, Y. Zhang, M. Snyder, G.S. Omenn, R. Beavis, and W.S. Hancock A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17 J. Proteome Res. 12 2013 45 57
35. J. Gao, A.S. Ade, V.G. Tarcea, T.E. Weymouth, B.R. Mirel, H.V. Jagadish, and D.J. States Integrating and annotating the interactome using the MiMI plugin for Cytoscape Bioinformatics 25 2009 137 138
36. R. Menon, A. Roy, S. Mukherjee, S. Belkin, Y. Zhang, and G.S. Omenn Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers J. Proteome Res. 10 2011 5503 5511
37. Y. Guan, C.L. Ackert-Bicknell, B. Kell, O.G. Troyanskaya, and M.A. Hibbs Functional genomics complements quantitative genetics in identifying disease-gene associations PLoS Comput. Biol. 6 2010 e1000991
38. E.Y. Zhang, M. Cristofanilli, F. Robertson, J.M. Reuben, Z. Mu, R.C. Beavis, H. Im, M. Snyder, M. Hofree, T. Ideker, G.S. Omenn, S. Fanayan, S.K. Jeong, Y.K. Paik, A.F. Zhang, S.L. Wu, and W.S. Hancock Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer J. Proteome Res. 12 2013 2805 2817
39. V. Visconte, H. Makishima, J.P. Maciejewski, and R.V. Tiu Emerging roles of the spliceosomal machinery in myelodysplastic syndromes and other hematological disorders Leukemia 26 2012 2447 2454
40. M. Vidal, D.W. Chan, M. Gerstein, M. Mann, G.S. Omenn, D. Tagle, and S. Sechi The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare Clin. Proteomics 9 2012 6