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

BMC Cancer

Yibin Hao⁵  Wei Wu³  Fachun Shi¹  Rodrigo JS Dalmolin²  Ming Yan⁴  Fu Tian⁵  Xiaobing Chen⁵  Guoyong Chen⁵  Wei Cao⁵ 

[1] Science and Education Department, Health Bureau of ZhengZhou, Zhengzhou, China

[2] Department of Biochemistry, Bioscience Center and Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil

[3] Department of Pathology and Experimental Medicine, University of Calgary, Calgary, AB, Canada

[4] Medical School, Zhengzhou University, Zhengzhou, Henan, China

[5] Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, Zhengzhou 450007, PR, China

关键词: Cancer initiatome;    ESCCAL-1;    ESCC;    Esophageal cancer;    Co-expression network;    lncRNA;    Long noncoding RNA;   

Others  :  1143783
DOI  :  10.1186/s12885-015-1179-z

 received in 2014-08-25, accepted in 2015-03-09,  发布年份 2015

【 摘 要 】

Background

Long non-coding RNAs (lncRNAs) are pervasively transcribed in the genome. They have important regulatory functions in chromatin remodeling and gene expression. Dysregulated lncRNAs have been studied in cancers, but their role in esophageal squamous cell carcinoma (ESCC) remains largely unknown. We have conducted lncRNA expression screening and a genome-wide analysis of lncRNA and coding gene expression on primary tumor and adjacent normal tissue from four ESCC patients, tend to understand the functionality of lncRNAs in carcinogenesis of esopheagus in combination with experimental and bioinformatics approach.

Methods

LncRNA array was used for coding and non-coding RNA expression. R program and Bioconductor packages (limma and RedeR) were used for differential expression and co-expression network analysis, followed by independent confirmation and functional studies of inferred onco-lncRNA ESCCAL-1 using quantitative real time polymerase chain reaction, small interfering RNA-mediatedknockdown, apoptosis and invasion assays in vitro.

Results

The global coding and lncRNA gene expression pattern is able to distinguish ESCC from adjacent normal tissue. The co-expression network from differentially expressed coding and lncRNA genes in ESCC was constructed, and the lncRNA function may be inferred from the co-expression network. LncRNA ESCCAL-1 is such an example as a predicted novel onco-lncRNA, and it is overexpressed in 65% of an independent ESCC patient cohort (n = 26). More over, knockdown of ESCCAL-1 expression increases esophageal cancer cell apoptosis and reduces the invasion in vitro.

Conclusion

Our study uncovered the landscape of ESCC-associated lncRNAs. The systematic analysis of coding and lncRNAs co-expression network increases our understanding of lncRNAs in biological network. ESCCAL-1 is a novel putative onco-lncRNA in esophageal cancer development.

【 授权许可】

   
2015 Hao et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [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 Next Generation Sequencing in Cancer Research-Decoding Cancer Genome. Volume Vol 1. 1st edition. Edited by Wu W, Choudhry H. Springer, New York; 2013:199-215.
• [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. BioMed Central Full Text
• [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.