Meta-analysis of transcriptome reveals let-7b as an unfavorable prognostic biomarker and predicts molecular and clinical subclasses in high-grade serous ovarian carcinoma

International Journal of Cancer

Volumn 134, Issue 2, 2014, Pages 306-318

  Tang, Zhiqun ^a   Ow, Ghim Siong ^a   Thiery, Jean Paul ^a,b,c   Ivshina, Anna V ^a   Kuznetsov, Vladimir A ^a,b,c,d  

^a BIOINFORMATICS INSTITUTE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

cancer biomarker; high grade serous ovarian carcinoma; microRNA let 7; survival prognosis; tumor classification

Indexed keywords

BIOLOGICAL MARKER; LETHAL 7B PROTEIN; MICRORNA; ONCOPROTEIN; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; CANCER PROGNOSIS; CANCER RESISTANCE; CANCER STAGING; CANCER SURVIVAL; FEMALE; GENETIC ASSOCIATION; GENETIC CODE; GENETIC TRANSCRIPTION; HUMAN; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; OVARY CARCINOMA; OVERALL SURVIVAL; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; REPRODUCIBILITY; SURVIVAL RATE; TREATMENT RESPONSE;

CANCER BIOMARKER; HIGH-GRADE SEROUS OVARIAN CARCINOMA; MICRORNA LET-7; SURVIVAL PROGNOSIS; TUMOR CLASSIFICATION;

AGED; CYSTADENOCARCINOMA, SEROUS; FEMALE; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; MIDDLE AGED; NEOPLASM GRADING; NEOPLASM INVASIVENESS; NEOPLASM STAGING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARIAN NEOPLASMS; PROGNOSIS; SURVIVAL RATE; TUMOR MARKERS, BIOLOGICAL;

EID: 84887492120     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.28371     Document Type: Article

References (50)

1. Siegel R, Naishadham D, Jemal A,. Cancer statistics, 2012. CA Cancer J Clin 2012; 62: 10-29.
2. Cho KR, Shih Ie M., Ovarian cancer. Annu Rev Pathol 2009; 4: 287-313.
3. Karst AM, Levanon K, Drapkin R,. Modeling high-grade serous ovarian carcinogenesis from the fallopian tube. Proc Natl Acad Sci USA 2011; 108: 7547-52.
4. Kim J, Coffey DM, Creighton CJ, et al. High-grade serous ovarian cancer arises from fallopian tube in a mouse model. Proc Natl Acad Sci USA 2012; 109: 3921-6.
5. 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.
6. Shih KK, Qin LX, Tanner EJ, et al. A microRNA survival signature (MiSS) for advanced ovarian cancer. Gynecol Oncol 2011; 121: 444-50.
7. Nam EJ, Yoon H, Kim SW, et al. MicroRNA expression profiles in serous ovarian carcinoma. Clin Cancer Res 2008; 14: 2690-5.
8. Dahiya N, Sherman-Baust CA, Wang TL, et al. MicroRNA expression and identification of putative miRNA targets in ovarian cancer. PLoS One 2008; 3: e2436.
9. Zhang L, Volinia S, Bonome T, et al. Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer. Proc Natl Acad Sci USA 2008; 105: 7004-9. (Pubitemid 351754520)
10. Wang Y, Hu X, Greshock J, et al. Genomic DNA copy-number alterations of the let-7 family in human cancers. PLoS One 2012; 7: e44399.
11. Vaughan S, Coward JI, Bast RC, Jr, et al. Rethinking ovarian cancer: recommendations for improving outcomes. Nat Rev Cancer 2011; 11: 719-25.
12. Tuma RS,. Origin of ovarian cancer may have implications for screening. J Natl Cancer Inst 2010; 102: 11-13.
13. TCGA. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609-15.
14. Wang V, Li C, Lin M, et al. Ovarian cancer is a heterogeneous disease. Cancer Genet Cytogenet 2005; 161: 170-3. (Pubitemid 41133485)
15. Helland A, Anglesio MS, George J, et al. Deregulation of MYCN, LIN28B and LET7 in a molecular subtype of aggressive high-grade serous ovarian cancers. PLoS One 2011; 6: e18064.
16. Calin GA, Croce CM,. MicroRNA signatures in human cancers. Nat Rev Cancer 2006; 6: 857-66. (Pubitemid 44629897)
17. Chan XH, Nama S, Gopal F, et al. Targeting Glioma stem cells by functional inhibition of a prosurvival OncomiR-138 in malignant gliomas. Cell Rep 2012; 2: 591-602.
18. Lagos-Quintana M, Rauhut R, Lendeckel W, et al. Identification of novel genes coding for small expressed RNAs. Science 2001; 294: 853-8. (Pubitemid 33032103)
19. Valastyan S, Weinberg RA,. Roles for microRNAs in the regulation of cell adhesion molecules. J Cell Sci 2011; 124: 999-1006.
20. Reinhart BJ, Slack FJ, Basson M, et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000; 403: 901-6. (Pubitemid 30130993)
21. Koh W, Sheng CT, Tan B, et al. Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of hepatic nuclear factor 4 alpha. BMC Genomics 2010; 11 (Suppl 1): S6.
22. The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609-15.
23. 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.
24. Bonome T, Levine DA, Shih J, et al. A gene signature predicting for survival in suboptimally debulked patients with ovarian cancer. Cancer Res 2008; 68: 5478-86.
25. Crijns AP, Fehrmann RS, de Jong S, et al. Survival-related profile, pathways, and transcription factors in ovarian cancer. PLoS Med 2009; 6: e24.
26. Hernandez E, Bhagavan BS, Parmley TH, et al. Interobserver variability in the interpretation of epithelial ovarian cancer. Gynecol Oncol 1984; 17: 117-23. (Pubitemid 14176297)
27. Johnson WE, Li C, Rabinovic A,. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8: 118-27. (Pubitemid 44906106)
28. Kerr MK, Churchill GA,. Statistical design and the analysis of gene expression microarray data. Genet Res 2001; 77: 123-8. (Pubitemid 32390329)
29. Motakis E, Ivshina AV, Kuznetsov VA,. Data-driven approach to predict survival of cancer patients: estimation of microarray genes' prediction significance by Cox proportional hazard regression model. IEEE Eng Med Biol Mag 2009; 28: 58-66.
30. Kuznetsov VA, Senko OV, Miller LD, et al. Statistically weighted voting analysis of microarrays for molecular pattern selection and discovery cancer genotypes. Int J Comput Sci Netw Secur 2006; 6: 73-83.
31. McShane LM, Altman DG, Sauerbrei W, et al. REporting recommendations for tumour MARKer prognostic studies (REMARK). Br J Cancer 2005; 93: 387-91. (Pubitemid 43080010)
32. Antonov AV, Knight RA, Melino G, et al. MIRUMIR: an online tool to test microRNAs as biomarkers to predict survival in cancer using multiple clinical data sets. Cell Death Differ 2013; 20: 367.
33. Yang H, Kong W, He L, et al. MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res 2008; 68: 425-33. (Pubitemid 351380068)
34. Xu CX, Xu M, Tan L, et al. MicroRNA miR-214 regulates ovarian cancer cell stemness by targeting p53/Nanog. J Biol Chem 2012; 287: 34970-8.
35. Xu D, Takeshita F, Hino Y, et al. miR-22 represses cancer progression by inducing cellular senescence. J Cell Biol 2011; 193: 409-24.
36. Ahmed N, Abubaker K, Findlay J, et al. Epithelial mesenchymal transition and cancer stem cell-like phenotypes facilitate chemoresistance in recurrent ovarian cancer. Curr Cancer Drug Targets 2010; 10: 268-78.
37. Marchini S, Fruscio R, Clivio L, et al. Resistance to platinum-based chemotherapy is associated with epithelial to mesenchymal transition in epithelial ovarian cancer. Eur J Cancer 2013; 49: 520-30.
38. Yang D, Sun Y, Hu L, et al. Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer. Cancer Cell 2013; 23: 186-99.
39. Alvero AB, Chen R, Fu HH, et al. Molecular phenotyping of human ovarian cancer stem cells unravels the mechanisms for repair and chemoresistance. Cell Cycle 2009; 8: 158-66.
40. Yin G, Chen R, Alvero AB, et al. TWISTing stemness, inflammation and proliferation of epithelial ovarian cancer cells through MIR199A2/214. Oncogene 2010; 29: 3545-53.
41. Matei D, Emerson RE, Lai YC, et al. Autocrine activation of PDGFRalpha promotes the progression of ovarian cancer. Oncogene 2006; 25: 2060-9.
42. Huber-Keener KJ, Liu X, Wang Z, et al. Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data. PLoS One 2012; 7: e41333.
43. Flahaut M, Meier R, Coulon A, et al. The Wnt receptor FZD1 mediates chemoresistance in neuroblastoma through activation of the Wnt/beta-catenin pathway. Oncogene 2009; 28: 2245-56.
44. Zhang H, Zhang X, Wu X, Li W, et al. Interference of Frizzled 1 (FZD1) reverses multidrug resistance in breast cancer cells through the Wnt/beta-catenin pathway. Cancer Lett 2012; 323: 106-13.
45. Rosano L, Cianfrocca R, Spinella F, et al. Acquisition of chemoresistance and EMT phenotype is linked with activation of the endothelin A receptor pathway in ovarian carcinoma cells. Clin Cancer Res 2011; 17: 2350-60.
46. Zhou HY, Pon YL, Wong AS,. HGF/MET signaling in ovarian cancer. Curr Mol Med 2008; 8: 469-80.
47. Gutova M, Najbauer J, Gevorgyan A, et al. Identification of uPAR-positive chemoresistant cells in small cell lung cancer. PLoS One 2007; 2: e243.
48. Helleman J, Jansen MP, Span PN, et al. Molecular profiling of platinum resistant ovarian cancer. Int J Cancer 2006; 118: 1963-71.
49. Heise C, Ganly I, Kim YT, et al. Efficacy of a replication-selective adenovirus against ovarian carcinomatosis is dependent on tumor burden, viral replication and p53 status. Gene Ther 2000; 7: 1925-9.
50. Behrens BC, Hamilton TC, Masuda H, et al. Characterization of a cis-diamminedichloroplatinum(II)-resistant human ovarian cancer cell line and its use in evaluation of platinum analogues. Cancer Res 1987; 47: 414-18. (Pubitemid 17009602)