Expression profile of COL2A1 and the pseudogene SLC6A10P predicts tumor recurrence in high-grade serous ovarian cancer

International Journal of Cancer

Volumn 138, Issue 3, 2016, Pages 679-688

  Ganapathi, Mahrukh K ^a   Jones, Wendell D ^b   Sehouli, Jalid ^c   Michener, Chad M ^d   Braicu, Ioana E ^c   Norris, Eric J ^a   Biscotti, Charles V ^d   Vaziri, Susan A J ^e   Ganapathi, Ram N ^a  

^a LEVINE CANCER INSTITUTE   (United States)

^b IQVIA   (United States)

^c CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^d LERNER RESEARCH INSTITUTE   (United States)

^e TAUSSIG CANCER INSTITUTE   (United States)

Author keywords

COL2A1; high grade serous ovarian cancer; pseudogene; RNA Seq; SLC6A10P; tumor recurrence

Indexed keywords

CARBOPLATIN; PACLITAXEL; PLATINUM COMPLEX; CARRIER PROTEIN; COL2A1 PROTEIN, HUMAN; COLLAGEN TYPE 2; CREATINE TRANSPORTER;

ADULT; AGED; ARTICLE; CANCER GRADING; CANCER RECURRENCE; CANCER SURVIVAL; COL2A1 GENE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE OVEREXPRESSION; GENETIC ASSOCIATION; HUMAN; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; NEXT GENERATION SEQUENCING; ONCOGENE; OVARY CANCER; PREDICTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PSEUDOGENE; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SLC6A10P GENE; CYSTADENOCARCINOMA; GENETICS; METABOLISM; MIDDLE AGED; OVARY TUMOR; PATHOLOGY; TUMOR RECURRENCE;

ADULT; AGED; COLLAGEN TYPE II; CYSTADENOCARCINOMA, SEROUS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MEMBRANE TRANSPORT PROTEINS; MIDDLE AGED; NEOPLASM GRADING; NEOPLASM RECURRENCE, LOCAL; OVARIAN NEOPLASMS; PSEUDOGENES; SEQUENCE ANALYSIS, RNA;

EID: 84955626599     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.29815     Document Type: Article

References (40)

1. Cannistra SA., Cancer of the ovary. N Engl J Med 2004; 351: 2519-29.
2. Berchuck A, Iversen ES, Luo J, et al., Microarray analysis of early stage serous ovarian cancers shows profiles predictive of favorable outcome. Clin Cancer Res 2009; 15: 2448-55.
3. Bonome T, Lee JY, Park DC, et al., Expression profiling of serous low malignant potential, low-grade, and high-grade tumors of the ovary. Cancer Res 2005; 65: 10602-12.
4. Cooke SL, Ng CK, Melnyk N, et al., Genomic analysis of genetic heterogeneity and evolution in high-grade serous ovarian carcinoma. Oncogene 2010; 29: 4905-13.
5. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609-15.
6. Shih Ie M, Nakayama K, Wu G, et al., Amplification of the ch19p13.2 NACC1 locus in ovarian high-grade serous carcinoma. Mod Pathol 2011; 24: 638-45.
7. Tothill RW, Tinker AV, George J, et al., Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome. Clin Cancer Res 2008; 14: 5198-208.
8. Spentzos D, Levine DA, Ramoni MF, et al., Gene expression signature with independent prognostic significance in epithelial ovarian cancer. J Clin Oncol 2004; 22: 4700-10.
9. Spentzos D, Levine DA, Kolia S, et al., Unique gene expression profile based on pathologic response in epithelial ovarian cancer. J Clin Oncol 2005; 23: 7911-18.
10. Hartmann LC, Lu KH, Linette GP, et al., Gene expression profiles predict early relapse in ovarian cancer after platinum-paclitaxel chemotherapy. Clin Cancer Res 2005; 11: 2149-55.
11. Jazaeri AA, Awtrey CS, Chandramouli GV, et al., Gene expression profiles associated with response to chemotherapy in epithelial ovarian cancers. Clin Cancer Res 2005; 11: 6300-10.
12. Etemadmoghadam D, deFazio A, Beroukhim R, et al., Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas. Clin Cancer Res 2009; 15: 1417-27.
13. Yoshihara K, Tajima A, Yahata T, et al., Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets. PLoS One 2010; 5: e9615.
14. Pils D, Hager G, Tong D, et al., Validating the impact of a molecular subtype in ovarian cancer on outcomes: a study of the OVCAD Consortium. Cancer Sci 2012; 103: 1334-41.
15. Gillet JP, Calcagno AM, Varma S, et al., Multidrug resistance-linked gene signature predicts overall survival of patients with primary ovarian serous carcinoma. Clin Cancer Res 2012; 18: 3197-206.
16. Barlin JN, Jelinic P, Olvera N, et al., Validated gene targets associated with curatively treated advanced serous ovarian carcinoma. Gynecol Oncol 2013; 128: 512-17.
17. Verhaak RG, Tamayo P, Yang JY, et al., Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest 2013; 123: 517-25.
18. Yoshihara K, Tsunoda T, Shigemizu D, et al., High-risk ovarian cancer based on 126-gene expression signature is uniquely characterized by downregulation of antigen presentation pathway. Clin Cancer Res 2012; 18: 1374-85.
19. Zang RY, Harter P, Chi DS, et al., Predictors of survival in patients with recurrent ovarian cancer undergoing secondary cytoreductive surgery based on the pooled analysis of an international collaborative cohort. Br J Cancer 2011; 105: 890-6.
20. Hu J, Khanna V, Jones MW, et al., Comparative study of primary and recurrent ovarian serous carcinomas: comparative genomic hybridization analysis with a potential application for prognosis. Gynecol Oncol 2003; 89: 369-75.
21. Ross JS, Ali SM, Wang K, et al., Comprehensive genomic profiling of epithelial ovarian cancer by next generation sequencing-based diagnostic assay reveals new routes to targeted therapies. Gynecol Oncol 2013; 130: 554-9.
22. Pennington KP, Walsh T, Harrell MI, et al., Germline and somatic mutations in homologous recombination genes predict platinum response and survival in ovarian, fallopian tube, and peritoneal carcinomas. Clin Cancer Res 2014; 20: 764-75.
23. Ozsolak F, Milos P., RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 2011; 12: 87-98.
24. Wang Z, Gerstein M, Snyder M., RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009; 10: 57-63.
25. Bullard JH, Purdom E, Hansen KD, et al., Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010; 11: 94.
26. Vandesompele J, De Preter K, Pattyn F, et al., Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002; 3: RESEARCH0034.
27. Li B, Dewey CN., RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011; 12: 323.
28. Kaplan EL, Meier P., Nonparametric estimation from incomplete observations. J Am Stat Assoc 1958; 53: 457-81.
29. Cox DR, Oakes D., Analysis of survival data. London: Chapman & Hall, 1984.
30. Benjamini Y, Hochberg Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995; 57: 289-300.
31. Wu YH, Chang TH, Huang YF, et al., COL11A1 promotes tumor progression and predicts poor clinical outcome in ovarian cancer. Oncogene 2013; 33: 3432-40.
32. Cheon DJ, Tong Y, Sim MS, et al., A collagen-remodeling gene signature regulated by TGF-beta signaling is associated with metastasis and poor survival in serous ovarian cancer. Clin Cancer Res 2014; 20: 711-23.
33. Shi W, Gerster K, Alajez NM, et al., MicroRNA-301 mediates proliferation and invasion in human breast cancer. Cancer Res 2011; 71: 2926-37.
34. Vincourt JB, Etienne S, Cottet J, et al., Cpropeptides of procollagens I alpha 1 and II that differentially accumulate in enchondromas versus chondrosarcomas regulate tumor cell survival and migration. Cancer Res 2010; 70: 4739-48.
35. O'Reilly MS, Boehm T, Shing Y, et al., Endostatin: an endogenous inhibitor of angiogenesis and tumor growth. Cell 1997; 88: 277-85.
36. Mundel TM, Kalluri R., Type IV collagen-derived angiogenesis inhibitors. Microvasc Res 2007; 74: 85-9.
37. Palmieri D, Poggi S, Ulivi V, et al., Pro-collagen I COOH-terminal trimer induces directional migration and metalloproteinases in breast cancer cells. J Biol Chem 2003; 278: 3639-47.
38. Visigalli D, Palmieri D, Strangio A, et al., The carboxyl terminal trimer of procollagen I induces pro-metastatic changes and vascularization in breast cancer cells xenografts. BMC Cancer 2009; 9: 59.
39. Ndika JD, Lusink V, Beaubrun C, et al., Cloning and characterization of the promoter regions from the parent and paralogous creatine transporter genes. Gene 2014; 533: 488-93.
40. TCGA. Available at: http://www.cbioportal.org/public-portal, accessed on January 15, 2014.