Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer

Oncotarget

Volumn 6, Issue 28, 2015, Pages 25003-25016

  Li, Yongsheng ^a   Chen, Juan ^a   Zhang, Jinwen ^a   Wang, Zishan ^a   Shao, Tingting ^a   Jiang, Chunjie ^a   Xu, Juan ^a   Li, Xia ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

Functional synergistic network; Hallmark of cancer; Long non coding RNA; Network hub; Prognostic module

Indexed keywords

LONG UNTRANSLATED RNA; TUMOR MARKER; MESSENGER RNA;

ARTICLE; CANCER PROGNOSIS; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCATION; GENETIC ASSOCIATION; GENETIC PARAMETERS; GENETIC REGULATION; GLIOBLASTOMA; LONG NONCODING RNA FUNCTIONAL SYNERGISTIC NETWORK; OVARY CANCER; PROSTATE CANCER; PROTEIN PROTEIN INTERACTION; ALGORITHM; BIOLOGICAL MODEL; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETICS; HUMAN; MALE; NEOPLASM; OVARY TUMOR; PATHOLOGY; PROGNOSIS; PROSTATE TUMOR;

ALGORITHMS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE ONTOLOGY; GENE REGULATORY NETWORKS; GLIOBLASTOMA; HUMANS; MALE; MODELS, GENETIC; NEOPLASMS; OVARIAN NEOPLASMS; PROGNOSIS; PROSTATIC NEOPLASMS; RNA, LONG NONCODING; RNA, MESSENGER;

EID: 84944454213     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.4660     Document Type: Article

References (64)

1. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome research. 2012; 22:1775-1789.
2. Lau E. Non-coding RNA: Zooming in on lncRNA functions. Nature reviews genetics. 2014; 15:574-575.
3. Flintoft L. Non-coding RNA: Structure and function for lncRNAs. Nature reviews genetics. 2013; 14:598.
4. Xu J, Li CX, Li YS, Lv JY, Ma Y, Shao TT, Xu LD, Wang YY, Du L, Zhang YP, Jiang W, Li CQ, Xiao Y, Li X. MiRNA-miRNA synergistic network: construction via coregulating functional modules and disease miRNA topological features. Nucleic acids research. 2011; 39:825-836.
5. Xu J, Li Y, Li X, Li C, Shao T, Bai J, Chen H, Li X. Dissection of the potential characteristic of miRNA-miRNA functional synergistic regulations. Molecular bioSystems. 2013; 9:217-224.
6. Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annual review of biochemistry. 2012; 81:145-166.
7. Yang G, Lu X, Yuan L. LncRNA: a link between RNA and cancer. Biochimica et biophysica acta. 2014; 1839:1097-1109.
8. Pachnis V, Brannan CI, Tilghman SM. The structure and expression of a novel gene activated in early mouse embryogenesis. The EMBO journal. 1988; 7:673-681.
9. Shi Y, Wang Y, Luan W, Wang P, Tao T, Zhang J, Qian J, Liu N, You Y. Long non-coding RNA H1 promotes glioma cell invasion by deriving miR-675. PLoS One. 2014; 9:e86295.
10. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007; 129:1311-1323.
11. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010; 464:1071-1076.
12. Wang P, Ren Z, Sun P. Overexpression of the long non-coding RNA MEG3 impairs in vitro glioma cell proliferation. Journal of cellular biochemistry. 2012; 113:1868-1874.
13. Tseng YY, Moriarity BS, Gong W, Akiyama R, Tiwari A, Kawakami H, Ronning P, Reuland B, Guenther K, Beadnell TC, Essig J, Otto GM, O'Sullivan MG, Largaespada DA, Schwertfeger KL, Marahrens Y, et al. PVT1 dependence in cancer with MYC copy-number increase. Nature. 2014; 512:82-86.
14. Shi X, Sun M, Liu H, Yao Y, Song Y. Long non-coding RNAs: a new frontier in the study of human diseases. Cancer letters. 2013; 339:159-166.
15. Nagoshi H, Taki T, Hanamura I, Nitta M, Otsuki T, Nishida K, Okuda K, Sakamoto N, Kobayashi S, Yamamoto-Sugitani M, Tsutsumi Y, Kobayashi T, Matsumoto Y, Horiike S, Kuroda J, Taniwaki M. Frequent PVT1 rearrangement and novel chimeric genes PVT1-NBEA and PVT1-WWOX occur in multiple myeloma with 8q24 abnormality. Cancer research. 2012; 72:4954-4962.
16. Guan Y, Kuo WL, Stilwell JL, Takano H, Lapuk AV, Fridlyand J, Mao JH, Yu M, Miller MA, Santos JL, Kalloger SE, Carlson JW, Ginzinger DG, Celniker SE, Mills GB, Huntsman DG, et al. Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer. Clinical cancer research: an official journal of the American Association for Cancer Research. 2007; 13:5745-5755.
17. Wilkosz J, Brys M, Rozanski W. Urine markers and prostate cancer. Central European journal of urology. 2011; 64:9-14.
18. Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012; 482:339-346.
19. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011; 477:295-300.
20. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010; 329:689-693.
21. Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nature methods. 2015; 12:71-78.
22. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B,Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & development. 2011; 25:1915-1927.
23. Guo X, Gao L, Liao Q, Xiao H, Ma X, Yang X, Luo H, Zhao G, Bu D, Jiao F, Shao Q, Chen R, Zhao Y. Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. Nucleic acids research. 2013; 41:e35.
24. Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H, Zhao G, Luo H, Bu D, Zhao H, Skogerbo G, Wu Z, Zhao Y. Largescale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic acids research. 2011; 39:3864-3878.
25. Li J, Chen Z, Tian L, Zhou C, He MY, Gao Y, Wang S, Zhou F, Shi S, Feng X, Sun N, Liu Z, Skogerboe G, Dong J,Yao R, Zhao Y, et al. LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma. Gut. 2014; 63:1700-1710.
26. Hu Y, Chen HY, Yu CY, Xu J, Wang JL, Qian J, Zhang X, Fang JY. A long non-coding RNA signature to improve prognosis prediction of colorectal cancer. Oncotarget. 2014; 5:2230-2242.
27. Pujana MA, Ruiz A, Badenas C, Puig-Butille JA, Nadal M, Stark M, Gomez L, Valls J, Sole X, Hernandez P, Cerrato C, Madrigal I, de Cid R, Aguilar H, Capella G, Cal S, et al. Molecular characterization of a t(9, 12)(p21;q13) balanced chromosome translocation in combination with integrative genomics analysis identifies C9orf14 as a candidate tumor-suppressor. Genes, chromosomes & cancer. 2007; 46:155-162.
28. Benetatos L, Vartholomatos G, Hatzimichael E. MEG3 imprinted gene contribution in tumorigenesis. International journal of cancer Journal international du cancer. 2011; 129:773-779.
29. Zhang X, Gejman R, Mahta A, Zhong Y, Rice KA, Zhou Y, Cheunsuchon P, Louis DN, Klibanski A. Maternally expressed gene 3, an imprinted noncoding RNA gene, is associated with meningioma pathogenesis and progression. Cancer research. 2010; 70:2350-2358.
30. Sheng X, Li J, Yang L, Chen Z, Zhao Q, Tan L, Zhou Y, Li J. Promoter hypermethylation influences the suppressive role of maternally expressed 3, a long non-coding RNA, in the development of epithelial ovarian cancer. Oncology reports. 2014; 32:277-285.
31. Tani H, Onuma Y, Ito Y, Torimura M. Long non-coding RNAs as surrogate indicators for chemical stress responses in human-induced pluripotent stem cells. PLoS One. 2014; 9:e106282.
32. Tani H, Torimura M. Identification of short-lived long noncoding RNAs as surrogate indicators for chemical stress response. Biochemical and biophysical research communications. 2013; 439:547-551.
33. Hung T, Chang HY. Long noncoding RNA in genome regulation: prospects and mechanisms. RNA biology. 2010; 7:582-585.
34. Berghoff EG, Clark MF, Chen S, Cajigas I, Leib DE, Kohtz JD. Evf2 (Dlx6as) lncRNA regulates ultraconserved enhancer methylation and the differential transcriptional control of adjacent genes. Development. 2013; 140:4407-4416.
35. Zotenko E, Mestre J, O'Leary DP, Przytycka TM. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS computational biology. 2008; 4:e1000140.
36. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011; 144:646-674.
37. Day BW, Stringer BW, Al-Ejeh F, Ting MJ, Wilson J, Ensbey KS, Jamieson PR, Bruce ZC, Lim YC, Offenhauser C, Charmsaz S, Cooper LT, Ellacott JK, Harding A, Leveque L, Inglis P, et al. EphA3 maintains tumorigenicity and is a therapeutic target in glioblastoma multiforme. Cancer cell. 2013; 23:238-248.
38. Li M, Mukasa A, Inda MM, Zhang J, Chin L, Cavenee W, Furnari F. Guanylate binding protein 1 is a novel effector of EGFR-driven invasion in glioblastoma. The Journal of experimental medicine. 2011; 208:2657-2673.
39. Nieman KM, Kenny HA, Penicka CV, Ladanyi A, Buell-Gutbrod R, Zillhardt MR, Romero IL, Carey MS, Mills GB, Hotamisligil GS, Yamada SD, Peter ME, Gwin K, Lengyel E. Adipocytes promote ovarian cancer metastasis and provide energy for rapid tumor growth. Nature medicine. 2011; 17:1498-1503.
40. Tan DS, Agarwal R, Kaye SB. Mechanisms of transcoelomic metastasis in ovarian cancer. The Lancet Oncology. 2006; 7:925-934.
41. Taverna G, Pedretti E, Di Caro G, Borroni EM, Marchesi F, Grizzi F, et al. Inflammation and prostate cancer: friends or foe? Inflammation research: official journal of the European Histamine Research Society. 2015; 64:275-286.
42. Liu X, Goldstein AS. Inflammation promotes prostate differentiation. Proceedings of the National Academy of Sciences of the United States of America. 2014; 111:1666-1667.
43. De Marzo AM, Platz EA, Sutcliffe S, Xu J, Gronberg H, Drake CG, Nakai Y, Isaacs WB, Nelson WG. Inflammation in prostate carcinogenesis. Nature reviews Cancer. 2007; 7:256-269.
44. Wu G, Stein L. A network module-based method for identifying cancer prognostic signatures. Genome biology. 2012; 13:R112.
45. Yang D, Sun Y, Hu L, Zheng H, Ji P, Pecot CV, Zhao Y, Reynolds S, Cheng H, Rupaimoole R, Cogdell D, Nykter M, Broaddus R, Rodriguez-Aguayo C, Lopez-Berestein G, Liu J, et al. Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer. Cancer cell. 2013; 23:186-199.
46. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, et al. The somatic genomic landscape of glioblastoma. Cell. 2013; 155:462-477.
47. Xu D, Takeshita F, Hino Y, Fukunaga S, Kudo Y, Tamaki A, Matsunaga J, Takahashi RU, Takata T, Shimamoto A, Ochiya T, Tahara H. miR-22 represses cancer progression by inducing cellular senescence. The Journal of cell biology. 2011; 193:409-424.
48. He S, Zeng S, Zhou ZW, He ZX, Zhou SF. HsamicroRNA-181a is a regulator of a number of cancer genes and a biomarker for endometrial carcinoma in patients: a bioinformatic and clinical study and the therapeutic implication. Drug design, development and therapy. 2015; 9:1103-1175.
49. Kuhn SA, Martin M, Brodhun M, Kratzsch T, Hanisch UK, Haberl H. Overexpression of protease-activated receptor type 1 (PAR-1) in glioblastoma multiforme WHO IV cells and blood vessels revealed by NCAM-assisted glioblastoma border labeling. Neurological research. 2014; 36:709-721.
50. Amand M, Erpicum C, Bajou K, Cerignoli F, Blacher S, Martin M, Dequiedt F, Drion P, Singh P, Zurashvili T, Vandereyken M, Musumeci L, Mustelin T, Moutschen M, Gilles C, Noel A, et al. DUSP3/VHR is a pro-angiogenic atypical dual-specificity phosphatase. Molecular cancer. 2014; 13:108.
51. Noerholm M, Balaj L, Limperg T, Salehi A, Zhu LD, Hochberg FH, Breakefield XO, Carter BS, Skog J. RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls. BMC cancer. 2012; 12:22.
52. Schumann T, Adhikary T, Wortmann A, Finkernagel F, Lieber S, Schnitzer E, Legrand N, Schober Y, Nockher WA, Toth PM, Diederich WE, Nist A, Stiewe T, Wagner U, Reinartz S, Muller-Brusselbach S, et al. Deregulation of PPARbeta/delta target genes in tumor-associated macrophages by fatty acid ligands in the ovarian cancer microenvironment. Oncotarget. 2015.
53. Li JH, Liu S, Zhou H, Qu LH, Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic acids research. 2014; 42:D92-97.
54. Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, Chen Y, Liu XS. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nature structural & molecular biology. 2013; 20:908-913.
55. Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007; 8:118-127.
56. Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nature genetics. 2013; 45:1121-1126.
57. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 2005; 102:15545-15550.
58. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, et al. Human Protein Reference Database-2009 update. Nucleic acids research. 2009; 37:D767-772.
59. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science. 2002; 298:824-827.
60. Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, Zhang Q, Yan G, Cui Q. LncRNADisease: a database for long-noncoding RNA-associated diseases. Nucleic acids research. 2013; 41:D983-986.
61. Zhao T, Xu J, Liu L, Bai J, Xu C, Xiao Y, Li X, Zhang L. Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features. Molecular bioSystems. 2015; 11:126-136.
62. Plaisier CL, Pan M, Baliga NS. A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome research. 2012; 22:2302-2314.
63. Yang JH, Li JH, Jiang S, Zhou H, Qu LH. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic acids research. 2013; 41:D177-187.
64. Makinen VP, Civelek M, Meng Q, Zhang B, Zhu J, Levian C, Huan T, Segre AV, Ghosh S, Vivar J, Nikpay M, Stewart AF, Nelson CP, Willenborg C, Erdmann J, Blakenberg S, et al. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PLoS genetics. 2014; 10:e1004502.