Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma

BMC Cancer

Volumn 15, Issue 1, 2015, Pages

  Hao, Yibin ^a   Wu, Wei ^a,b   Shi, Fachun ^c   Dalmolin, Rodrigo ^d   Yan, Ming ^a   Tian, Fu ^a   Chen, Xiaobing ^a   Chen, Guoyong ^a   Cao, Wei ^a  

^a ZHENGZHOU UNIVERSITY   (China)

^b UNIVERSITY OF CALGARY   (Canada)

^c Zheng Zhou University   (China)

^d FEDERAL UNIVERSITY OF RIO GRANDE DO NORTE   (Brazil)

Author keywords

Cancer initiatome; Co expression network; ESCC; ESCCAL 1; Esophageal cancer; lncRNA; Long noncoding RNA

Indexed keywords

LONG UNTRANSLATED RNA; SMALL INTERFERING RNA;

AGED; APOPTOSIS; ARTICLE; BIOINFORMATICS; CARCINOGENESIS; CELL INVASION; COHORT ANALYSIS; CONTROLLED STUDY; DISEASE ACTIVITY; DISEASE ASSOCIATION; ESCCAL 1 GENE; ESOPHAGEAL SQUAMOUS CELL CARCINOMA; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; HUMAN; IN VITRO STUDY; MALE; MOLECULAR DYNAMICS; MOLECULAR PATHOLOGY; ONCOGENE; POLYMERASE CHAIN REACTION; PREDICTION; QUANTITATIVE ANALYSIS; CARCINOMA, SQUAMOUS CELL; ESOPHAGEAL NEOPLASMS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; PREDICTIVE VALUE;

AGED; CARCINOMA, SQUAMOUS CELL; ESOPHAGEAL NEOPLASMS; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; MALE; PREDICTIVE VALUE OF TESTS; RNA, LONG NONCODING;

EID: 84925641949     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/s12885-015-1179-z     Document Type: Article

References (50)

1. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.
2. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22(9):1775-89.
3. Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012;482(7385):339-46.
4. Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, et al. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature. 1991;349(6304):38-44.
5. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007;129(7):1311-23.
6. Bu D, Yu K, Sun S, Xie C, Skogerbo G, Miao R, et al. NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res. 2012;40(Database issue):D210-5.
7. Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H, et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res. 2011;39(9):3864-78.
8. Guo X, Gao L, Liao Q, Xiao H, Ma X, Yang X, et al. Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. Nucleic Acids Res. 2013;41(2):e35.
9. Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, et al. Cancer incidence and mortality worldwide: Sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 2015;136(5):E359-86.
10. Dulak AM, Stojanov P, Peng S, Lawrence MS, Fox C, Stewart C, et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet. 2013;45(5):478-86.
11. Song Y, Li L, Ou Y, Gao Z, Li E, Li X, et al. Identification of genomic alterations in oesophageal squamous cell cancer. Nature. 2014;509(7498):91-5.
12. Wu W, Chan JA. Understanding the Role of Long Noncoding RNAs in the Cancer Genome. In: Wu W, Choudhry H, editors. Next Generation Sequencing in Cancer Research-Decoding Cancer Genome. Volume Vol 1. 1st ed. New York: Springer; 2013. p. 199-215.
13. Gutschner T, Diederichs S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol. 2012;9(6):703-19.
14. Ji P, Diederichs S, Wang W, Boing S, Metzger R, Schneider PM, et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene. 2003;22(39):8031-41.
15. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010;464(7291):1071-6.
16. Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, et al. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011;71(20):6320-6.
17. Kim K, Jutooru I, Chadalapaka G, Johnson G, Frank J, Burghardt R, et al. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene. 2013;32(13):1616-25.
18. Li D, Feng J, Wu T, Wang Y, Sun Y, Ren J, et al. Long intergenic noncoding RNA HOTAIR is overexpressed and regulates PTEN methylation in laryngeal squamous cell carcinoma. Am J Pathol. 2013;182(1):64-70.
19. Lv XB, Lian GY, Wang HR, Song E, Yao H, Wang MH. Long noncoding RNA HOTAIR is a prognostic marker for esophageal squamous cell carcinoma progression and survival. PLoS One. 2013;8(5):e63516.
20. Bhan A, Hussain I, Ansari KI, Kasiri S, Bashyal A, Mandal SS. Antisense transcript long noncoding RNA (lncRNA) HOTAIR is transcriptionally induced by estradiol. J Mole Biol. 2013;425(19):3707-22.
21. Fu X, Ravindranath L, Tran N, Petrovics G, Srivastava S. Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1. DNA Cell Biol. 2006;25(3):135-41.
22. Prensner JR, Chinnaiyan AM. The emergence of lncRNAs in cancer biology. Cancer Discov. 2011;1(5):391-407.
23. Wu W, Bhagat TD, Yang X, Song JH, Cheng Y, Agarwal R, et al. Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett's esophagus and esophageal adenocarcinoma. Gastroenterology. 2013;144(5):956-66. e954.
24. Li X, Wu Z, Mei Q, Li X, Guo M, Fu X, et al. Long non-coding RNA HOTAIR, a driver of malignancy, predicts negative prognosis and exhibits oncogenic activity in oesophageal squamous cell carcinoma. Br J Cancer. 2013;109(8):2266-78.
25. Ge XS, Ma HJ, Zheng XH, Ruan HL, Liao XY, Xue WQ, et al. HOTAIR, a prognostic factor in esophageal squamous cell carcinoma, inhibits WIF-1 expression and activates Wnt pathway. Cancer Sci. 2013;104(12):1675-82.
26. Chen FJ, Sun M, Li SQ, Wu QQ, Ji L, Liu ZL, et al. Upregulation of the long non-coding RNA HOTAIR promotes esophageal squamous cell carcinoma metastasis and poor prognosis. Mol Carcinog. 2013;52(11):908-15.
27. Xu Y, Wang J, Qiu M, Xu L, Li M, Jiang F, et al. Upregulation of the long noncoding RNA TUG1 promotes proliferation and migration of esophageal squamous cell carcinoma. Tumour Biol. 2014 Oct 31. [Epub ahead of print].
28. Wang CM, Wu QQ, Li SQ, Chen FJ, Tuo L, Xie HW, et al. Upregulation of the long non-coding RNA PlncRNA-1 promotes esophageal squamous carcinoma cell proliferation and correlates with advanced clinical stage. Dig Dis Sci. 2014;59(3):591-7.
29. Li W, Zheng J, Deng J, You Y, Wu H, Li N, et al. Increased levels of the long intergenic non-protein coding RNA POU3F3 promote DNA methylation in esophageal squamous cell carcinoma cells. Gastroenterology. 2014;146(7):1714-26. e1715.
30. Pan F, Yao J, Chen Y, Zhou C, Geng P, Mao H, et al. A novel long non-coding RNA FOXCUT and mRNA FOXC1 pair promote progression and predict poor prognosis in esophageal squamous cell carcinoma. Int J Clin Exp Pathol. 2014;7(6):2838-49.
31. Yang X, Song JH, Cheng Y, Wu W, Bhagat T, Yu Y, et al. Long non-coding RNA HNF1A-AS1 regulates proliferation and migration in oesophageal adenocarcinoma cells. Gut. 2014;63(6):881-90.
32. Chen D, Zhang Z, Mao C, Zhou Y, Yu L, Yin Y, et al. ANRIL inhibits p15(INK4b) through the TGFbeta1 signaling pathway in human esophageal squamous cell carcinoma. Cell Immunol. 2014;289(1-2):91-6.
33. Li J, Chen Z, Tian L, Zhou C, He MY, Gao Y, et al. LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma. Gut. 2014;63(11):1700-10.
34. Cao W, Wu W, Shi F, Chen X, Wu L, Yang K, et al. Integrated analysis of long noncoding RNA and coding RNA expression in esophageal squamous cell carcinoma. Int J Genomics. 2013;2013:480534.
35. Eichler GS, Huang S, Ingber DE. Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles. Bioinformatics. 2003;19(17):2321-2.
36. Smyth GK, Michaud J, Scott HS. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics. 2005;21(9):2067-75.
37. Castro MA, Wang X, Fletcher MN, Meyer KB, Markowetz F. RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations. Genome Biol. 2012;13(4):R29.
38. Ishibashi Y, Hanyu N, Nakada K, Suzuki Y, Yamamoto T, Yanaga K, et al. Profiling gene expression ratios of paired cancerous and normal tissue predicts relapse of esophageal squamous cell carcinoma. Cancer Res. 2003;63(16):5159-64.
39. van Baal JW, Milana F, Rygiel AM, Sondermeijer CM, Spek CA, Bergman JJ, et al. A comparative analysis by SAGE of gene expression profiles of esophageal adenocarcinoma and esophageal squamous cell carcinoma. Cell Oncol. 2008;30(1):63-75.
40. Ma S, Bao JY, Kwan PS, Chan YP, Tong CM, Fu L, et al. Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma. Gastroenterology. 2012;143(3):675-86. e671-612.
41. Guo Y, Chen Z, Zhang L, Zhou F, Shi S, Feng X, et al. Distinctive microRNA profiles relating to patient survival in esophageal squamous cell carcinoma. Cancer Res. 2008;68(1):26-33.
42. Kano M, Seki N, Kikkawa N, Fujimura L, Hoshino I, Akutsu Y, et al. miR-145, miR-133a and miR-133b: Tumor-suppressive miRNAs target FSCN1 in esophageal squamous cell carcinoma. Int J Cancer. 2010;127(12):2804-14.
43. Greenawalt DM, Duong C, Smyth GK, Ciavarella ML, Thompson NJ, Tiang T, et al. Gene expression profiling of esophageal cancer: comparative analysis of Barrett's esophagus, adenocarcinoma, and squamous cell carcinoma. Int J Cancer. 2007;120(9):1914-21.
44. Li JD, Feng QC, Li JS. Differential gene expression profiling of oesophageal squamous cell carcinoma by DNA microarray and bioinformatics analysis. J Int Med Res. 2010;38(6):1904-12.
45. Potter SS, Branford WW. Evolutionary conservation and tissue-specific processing of Hoxa 11 antisense transcripts. Mamm Genome. 1998;9(10):799-806.
46. Chau YM, Pando S, Taylor HS. HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the uterine endometrium. J Clin Endocrinol Metab. 2002;87(6):2674-80.
47. Tang S, Gao L, Bi Q, Xu G, Wang S, Zhao G, et al. SDR9C7 promotes lymph node metastases in patients with esophageal squamous cell carcinoma. PLoS One. 2013;8(1):e52184.
48. Anderegg U, Breitschwerdt K, Kohler MJ, Sticherling M, Haustein UF, Simon JC, et al. MEL4B3, a novel mRNA is induced in skin tumors and regulated by TGF-beta and pro-inflammatory cytokines. Exp Dermatol. 2005;14(9):709-18.
49. Lee HS, Kim SW, Hong JC, Jung SB, Jeon CH, Park JW, et al. Expression of MAGE A1-6 and the clinical characteristics of papillary thyroid carcinoma. Anticancer Res. 2013;33(4):1731-5.
50. Okano M, Yamamoto H, Ohkuma H, Kano Y, Kim H, Nishikawa S, et al. Significance of INHBA expression in human colorectal cancer. Oncol Rep. 2013;30(6):2903-8.