Alternative splice variants, a new class of protein cancer biomarker candidates: Findings in pancreatic cancer and breast cancer with systems biology implications

Disease Markers

Volumn 28, Issue 4, 2010, Pages 241-251

  Omenn, Gilbert S ^a   Yocum, Anastasia K ^a,b   Menon, Rajasree ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN HEALTH SYSTEM   (United States)

Author keywords

Alternative splicing; breast cancer; mouse models; pancreatic cancer; protein interaction networks; protein isoforms; proteomics; splice variants; systems biology

Indexed keywords

BETA CAROTENE; BIOLOGICAL MARKER; EPIDERMAL GROWTH FACTOR RECEPTOR 2; PROTEIN; RETINOL;

ALTERNATIVE RNA SPLICING; BREAST CANCER; CANCER CELL CULTURE; CANCER TISSUE; CLINICAL TRIAL; DATA BASE; GENE; HUMAN; LUNG CANCER; NONHUMAN; PANCREAS ADENOCARCINOMA; PANCREATIC DUCTAL ADENOCARCINOMA; PLASMA; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; REVIEW; SYSTEMS BIOLOGY;

EID: 77954131742     PISSN: 02780240     EISSN: None     Source Type: Journal    
DOI: 10.1155/2010/705847     Document Type: Review

References (38)

1. A.J. Aguirre, N. Bardeesy, M. Sinha et al., Activated Kras and Ink4a/Arf deficiency cooperate to produce metastatic pancreatic ductal adenocarcinoma, Genes & Development 17 (2003), 3112-3126.
2. P. Argani, C. Rosty, R.E. Reiter et al., Discovery of new markers of cancer through serial analysis of gene expression: prostate stem cell antigen is overexpressed in pancreatic adenocarcinoma, Cancer Res 61 (2001), 4320-4324.
3. N. Bardeesy, A.J. Aguirre, G.C. Chu et al., Both p16Ink4a and the p19Arf-p53 pathway constrain progression of pancreatic adenocarcinoma in the mouse, Proc Natl Acad Sci USA 103 (2006), 5947-5952.
4. T. Barrett, D.B. Troup, S.E. Wilhite et al., NCBI GEO: mining tens of millions of expression profiles-database and tools update, Nucl Acids Res 35 (2007), D760-D765.
5. M.B. Boxer, J.-k. Jiang, M.G. Vander Heiden et al., Evaluation of substituted N,N'-diarylsulfonamides as activators of the tumor cell specific M2 isoform of pyruvate kinase, Journal of Medicinal Chemistry 53 (2009), 1048-1055.
6. L. Bracco and J. Kearsey, The relevance of alternative RNA splicing to pharmacogenomics, Trends in Biotechnology 21 (2003), 346-353.
7. R. Chen, T.A. Brentnall, S. Pan et al., Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer, Mol Cell Proteomics 6 (2007), 1331-1342.
8. H.R. Christofk, M.G. Vander Heiden, M.H. Harris et al., The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth, Nature 452 (2008), 230-233.
9. H.R. Christofk, M.G. Vander Heiden, N. Wu et al., Pyruvate kinase M2 is a phosphotyrosine-binding protein, Nature 452 (2008), 181-186.
10. R. Craig and R.C. Beavis, TANDEM: matching proteins with tandem mass spectra, Bioinformatics 20 (2004), 1466-1467.
11. E.W. Deutsch, The PeptideAtlas Project, in: Proteome Bioinformatics, S. Hubbard and A.R. Jones, eds, Methods in Molecular Biology (Totowa, NJ: Humana Press, 2010).
12. J. Earl, L. Yan, L.J. Vitone et al., Evaluation of the 4q32-34 locus in European familial pancreatic cancer, Cancer Epidemiology Biomarkers & Prevention 15 (2006), 1948-1955.
13. V.M. Faca, K.S. Song, H. Wang et al., A mouse to human search for plasma proteome changes associated with pancreatic tumor development, PLoS Med 5 (2008), e123.
14. J. Gao, A.S. Ade, V.G. Tarcea et al., Integrating and annotating the interactome using the MiMI plugin for cytoscape, Bioinformatics 25 (2009), 137-138.
15. L. Gilboa, R. Ben-Levy, Y. Yarden et al., Roles for a cytoplasmic tyrosine and tyrosine kinase activity in the interactions of neu receptors with coated pits, Journal of Biological Chemistry 270 (1995), 7061-7067.
16. H.C. Harsha, K. Kandasamy, P. Ranganathan et al., A compendium of potential biomarkers of pancreatic cancer, PLoS Med 6 (2009), e1000046.
17. Y. He, B. Vogelstein, V.E. Velculescu et al., The antisense transcriptomes of human cells, Science 322 (2008), 1855-1857.
18. T. Hitosugi, S. Kang, M.G. Vander Heiden et al., Tyrosine phosphorylation inhibits PKM2 to promote theWarburg effect and tumor growth, Sci Signal 2 (2009), ra73-.
19. A. Jemal, R. Siegel, E.Ward et al., Cancer statistics, 2009, CA Cancer J Clin 59 (2009), 225-249.
20. N. Kim, S. Shin, and S. Lee, ECgene: Genome-based EST clustering and gene modeling for alternative splicing, Genome Research 15 (2005), 566-576.
21. P. Kim, N. Kim, Y. Lee et al., ECgene: genome annotation for alternative splicing, Nucl Acids Res 33 (2005), D75-D79.
22. Y.M. Kumar, K.M. Gurusamy, V.M. Pamecha et al., Tumor M2-pyruvate kinase as tumor marker in exocrine pancreatic cancer: a meta-analysis, Pancreas 35 (2007), 114-119.
23. T.P. Larsson, C.G. Murray, T. Hill et al., Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery, FEBS Letters 579 (2005), 690-698.
24. K. Lee, M. Hyun, and J.-R. Kim, Growth factor-dependent activation of the MAPK pathway in human pancreatic cancer: MEK/ERK and p38 MAP kinase interaction in uPA synthesis, Clinical and Experimental Metastasis 20 (2003), 499-505.
25. C. Marks, Mouse Models of Human Cancers Consortium (MMHCC) from the NCI, Disease Models & Mechanisms 2 (2009), 111-111
26. R. Menon and G.S. Omenn, Identification of Alternatively Spliced Transcripts using a Proteomic Informatics Approach, in: Data Mining in Proteomics, M. Hamacher, C. Stephan and M. Eisenacher, eds, Totowa, New Jersey: Humana Press, 2010.
27. R. Menon and G.S. Omenn, Proteomic characterization of novel alternative splice variant proteins in HER2/neu-induced breast cancers, Cancer Res 70 (2010), 3440-3449.
28. R. Menon, Q. Zhang, Y. Zhang et al., Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer, Cancer Res 69 (2009), 300-309.
29. G.S. Omenn, G.E. Goodman, M.D. Thornquist et al., Effects of a combination of beta-carotene and vitamin A on lung cancer and cardiovascular disease, N Engl J Med 334 (1996), 1150-1155.
30. H. Parkinson, M. Kapushesky, M. Shojatalab et al., ArrayExpress - a public database of microarray experiments and gene expression profiles, Nucl Acids Res 35 (2007), D747-D750.
31. E. Quevillon, V. Silventoinen, S. Pillai et al., InterProScan: protein domains identifier, Nucl Acids Res 33 (2005), W116-W120.
32. D.R. Rhodes, J. Yu, K. Shanker et al., ONCOMINE: a cancer microarray database and integrated data-mining platform, Neoplasia 6 (2004), 1-6.
33. D.M. Simeone, B. Ji, M. Banerjee et al., CEACAM1, a novel serum biomarker for pancreatic cancer, Pancreas 34 (2007), 436-443.
34. K. Thorsen, K.D. Sorensen, A.S. Brems-Eskildsen et al., Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis, Mol Cell Proteomics 7 (2008), 1214-1224.
35. M. Ventrucci, A. Cipolla, C. Racchini et al., Tumor M2- pyruvate kinase, a newmetabolic marker for pancreatic cancer, Digestive Diseases and Sciences 49 (2004), 1149-1155.
36. H. Wang, S.G. Clouthier, V. Galchev et al., Intact-proteinbased high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids, Mol Cell Proteomics 4 (2005), 618-625.
37. O.Warburg, On the origin of cancer cells, Science 123 (1956), 309-314.
38. J.R. Whiteaker, H. Zhang, L. Zhao et al., Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer, J Proteome Res 6 (2007), 3962-3975.