Creation of a human secretome: A novel composite library of human secreted proteins: Validation using ovarian cancer gene expression data and a virtual secretome array

Clinical Cancer Research

Volumn 21, Issue 21, 2015, Pages 4960-4969

  Vathipadiekal, Vinod ^a,b   Wang, Victoria ^b,c   Wei, Wei ^a,b   Waldron, Levi ^b,c,d,g   Drapkin, Ronny ^e   Gillette, Michael ^a,f   Skates, Steven ^a,b   Birrer, Michael ^a,b  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d CITY UNIVERSITY OF NEW YORK   (United States)

^e BRIGHAM AND WOMEN S HOSPITAL   (United States)

^f BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^g CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CA 125 ANTIGEN; FIBROBLAST GROWTH FACTOR 18; G PROTEIN COUPLED RECEPTOR; MEMBRANE PROTEIN; MESSENGER RNA; PROTEIN GPR172A; PROTEIN HE4; TUMOR MARKER; UNCLASSIFIED DRUG; PROTEOME; TRANSCRIPTOME;

ARTICLE; BIOINFORMATICS; CANCER DIAGNOSIS; COMPARATIVE STUDY; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE MAPPING; GENETIC ASSOCIATION; GENETIC DATABASE; GENOMICS; HUMAN; MICROARRAY ANALYSIS; MOLECULAR LIBRARY; OVARY CANCER; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN SECRETION; TRANSCRIPTOMICS; VALIDATION PROCESS; VIRTUAL SECRETOME ARRAY; BIOLOGY; CLUSTER ANALYSIS; GENE LIBRARY; GENETICS; METABOLISM; OVARY TUMOR; PROCEDURES; PROTEOMICS; REPRODUCIBILITY; SECRETION (PROCESS); SIGNAL TRANSDUCTION;

BIOMARKERS, TUMOR; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE LIBRARY; HUMANS; OVARIAN NEOPLASMS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; TRANSCRIPTOME;

EID: 84947261071     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-14-3173     Document Type: Article

References (35)

1. Siegel R, Naishadham D, Jemal A. Cancer statistics, 2012. CA Cancer J Clin 2012;62:10-29.
2. Siegel R, DeSantis C, Virgo K, Stein K, Mariotto A, Smith T, et al. Cancer treatment and survivorship statistics, 2012. CA Cancer J Clin 2012;62:220-41.
3. Jacobs I, Bast RC Jr. The CA 125 tumour-associated antigen: a review of the literature. Hum Reprod 1989;4:1-12.
4. Sjovall K, Nilsson B, Einhorn N. The significance of serum CA 125 elevation in malignant and nonmalignant diseases. Gynecol Oncol 2002;85:175-8.
5. Chudecka-Glaz A, Rzepka-Gorska I, Wojciechowska I. Human epididymal protein 4 (HE4) is a novel biomarker and a promising prognostic factor in ovarian cancer patients. Eur J Gynaecol Oncol 2012;33:382-90.
6. Hertlein L, Stieber P, Kirschenhofer A, Furst S, Mayr D, Hofmann K, et al. Human epididymis protein 4 (HE4) in benign and malignant diseases. Clin Chem Lab Med 2012;50:2181-8.
7. Barlund M, Forozan F, Kononen J, Bubendorf L, Chen Y, Bittner ML, et al. Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis. J Natl Cancer Inst 2000;92:1252-9.
8. Wang T, Hopkins D, Schmidt C, Silva S, Houghton R, Takita H, et al. Identification of genes differentially over-expressed in lung squamous cell carcinoma using combination of cDNA subtraction and microarray analysis. Oncogene 2000;19:1519-28.
9. Xu J, Stolk JA, Zhang X, Silva SJ, Houghton RL, Matsumura M, et al. Identification of differentially expressed genes in human prostate cancer using subtraction and microarray. Cancer Res 2000;60:1677-82.
10. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer [see comments]. Nat Genet 1996;14:457-60.
11. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997;278:680-6.
12. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999;286:531-7.
13. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503-11.
14. Mok SC, Bonome T, Vathipadiekal V, Bell A, Johnson ME, Wong KK, et al. A gene signature predictive for outcome in advanced ovarian cancer identifies a survival factor: microfibril-associated glycoprotein 2. Cancer Cell 2009;16:521-32.
15. Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, et al. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest 2013;123:517-25.
16. McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res 2011;39:D1011-5.
17. Bonome T, Levine DA, Shih J, Randonovich M, Pise-Masison CA, Bogomolniy F, et al. A gene signature predicting for survival in suboptimally debulked patients with ovarian cancer. Cancer Res 2008;68:5478-86.
18. Skates SJ, Horick NK, Moy JM, Minihan AM, Seiden MV, Marks JR, et al. Pooling of case specimens to create standard serum sets for screening cancer biomarkers. Cancer Epidemiol Biomarkers Prev 2007;16:334-41.
19. Clark HF, Gurney AL, Abaya E, Baker K, Baldwin D, Brush J, et al. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Genome Res 2003;13:2265-70.
20. Diehn M, Bhattacharya R, Botstein D, Brown PO. Genome-scale identification of membrane-associated human mRNAs. PLoS Genet 2006;2:e11.
21. Melkonyan HS, Chang WC, Shapiro JP, Mahadevappa M, Fitzpatrick PA, Kiefer MC, et al. SARPs: a family of secreted apoptosis-related proteins. Proc Natl Acad Sci U S A 1997;94:13636-41.
22. Kolodkin AL, Matthes DJ, Goodman CS. The semaphorin genes encode a family of transmembrane and secreted growth cone guidance molecules. Cell 1993;75:1389-99.
23. Maglione D, Guerriero V, Viglietto G, Ferraro MG, Aprelikova O, Alitalo K, et al. Two alternative mRNAs coding for the angiogenic factor, placenta growth factor (PlGF), are transcribed from a single gene of chromosome 14. Oncogene 1993;8:925-31.
24. Levanon K, Crum C, Drapkin R. New insights into the pathogenesis of serous ovarian cancer and its clinical impact. J Clin Oncol 2008;26:5284-93.
25. Karst AM, Drapkin R. Ovarian cancer pathogenesis: a model in evolution. J Oncol 2010;2010:932371.
26. Hellstrom I, Raycraft J, Hayden-Ledbetter M, Ledbetter JA, Schummer M, McIntosh M, et al. The HE4 (WFDC2) protein is a biomarker for ovarian carcinoma. Cancer Res 2003;63:3695-700.
27. Mok SC, Chao J, Skates S, Wong K, Yiu GK, Muto MG, et al. Prostasin, a potential serum marker for ovarian cancer: identification through microarray technology. J Natl Cancer Inst 2001;93:1458-64.
28. Kim JH, Skates SJ, Uede T, Wong KK, Schorge JO, Feltmate CM, et al. Osteopontin as a potential diagnostic biomarker for ovarian cancer. JAMA 2002;287:1671-9.
29. Oehler MK, Caffier H. Diagnostic value of serum VEGF in women with ovarian tumors. Anticancer Res 1999;19:2519-22.
30. Flyvbjerg A, Mogensen O, Mogensen B, Nielsen OS. Elevated serum insulin-like growth factor-binding protein 2 (IGFBP-2) and decreased IGFBP-3 in epithelial ovarian cancer: correlation with cancer antigen 125 and tumor-associated trypsin inhibitor. J Clin Endocrinol Metab 1997;82:2308-13.
31. Pavlou MP, Diamandis EP. The cancer cell secretome: a good source for discovering biomarkers? J Proteomics 2010;73:1896-906.
32. Farrah T, Deutsch EW, Aebersold R. Using the Human Plasma PeptideAtlas to study human plasma proteins. Methods Mol Biol 2011;728:349-74.
33. Kindelberger DW, Lee Y, Miron A, Hirsch MS, Feltmate C, Medeiros F, et al. Intraepithelial carcinoma of the fimbria and pelvic serous carcinoma: evidence for a causal relationship. Am J Surg Pathol 2007;31:161-9.
34. Wei W, Mok SC, Oliva E, Kim SH, Mohapatra G, Birrer MJ. FGF18 as a prognostic and therapeutic biomarker in ovarian cancer. J Clin Invest 2013;123:4435-48.
35. Turner N, Grose R. Fibroblast growth factor signalling: from development to cancer. Nat Rev Cancer 2010;10:116-29.