Construction of a lncRNA-mediated feed-forward loop network reveals global topological features and prognostic motifs in human cancers

Oncotarget

Volumn 7, Issue 29, 2016, Pages 45937-45947

  Ning, Shangwei ^a   Gao, Yue ^a   Wang, Peng ^a   Li, Xiang ^b   Zhi, Hui ^a   Zhang, Yan ^a   Liu, Yue ^a   Zhang, Jizhou ^a   Guo, Maoni ^a   Han, Dong ^b   Li, Xia ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b NATIONAL CENTER FOR NANOSCIENCE AND TECHNOLOGY   (China)

Author keywords

Feed forward loop; Long non coding RNA; Network motif; Prognostic biomarker; Topological feature

Indexed keywords

BIOLOGICAL MARKER; LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA; TRANSCRIPTION FACTOR; TRANSCRIPTOME; TUMOR MARKER;

ARTICLE; CANCER PROGNOSIS; CANCER SURVIVAL; CANCER THERAPY; CARCINOGENESIS; FEED FORWARD LOOP; FUNCTIONAL NETWORK MOTIF; GENE FUNCTION; GENETIC TRANSCRIPTION; HUMAN; MOLECULAR INTERACTION; NEOPLASM; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETICS; KAPLAN MEIER METHOD; MORTALITY; PROGNOSIS;

BIOMARKERS, TUMOR; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; KAPLAN-MEIER ESTIMATE; MICRORNAS; NEOPLASMS; PROGNOSIS; RNA, LONG NONCODING; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84979879873     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.10004     Document Type: Article

References (53)

1. Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA and Ponting CP. Considerations when investigating lncRNA function in vivo. Elife. 2014; 3:e03058.
2. St Laurent G, Wahlestedt C and Kapranov P. The Landscape of long noncoding RNA classification. Trends Genet. 2015; 31:239-251.
3. Quinn JJ and Chang HY. Unique features of long noncoding RNA biogenesis and function. Nat Rev Genet. 2015; 17:47-62.
4. Zhang M, Gu H, Xu W and Zhou X. Down-regulation of lncRNA MALAT1 reduces cardiomyocyte apoptosis and improves left ventricular function in diabetic rats. Int J Cardiol. 2016; 203:214-216.
5. Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo FW, Meadows S, Montoya NR, Herrera NG, et al. DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. 2015; 528:517-522.
6. 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, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010; 464:1071-1076.
7. Salmena L, Poliseno L, Tay Y, Kats L and Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011; 146:353-358.
8. Guttman M and Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012; 482:339-346.
9. Redmond AM and Carroll JS. Defining and targeting transcription factors in cancer. Genome Biol. 2009; 10:311.
10. Shields BB, Pecot CV, Gao H, McMillan E, Potts M, Nagel C, Purinton S, Wang Y, Ivan C, Kim HS, Borkowski RJ, Khan S, Rodriguez-Aguayo C, et al. A genomescale screen reveals context-dependent ovarian cancer sensitivity to miRNA overexpression. Mol Syst Biol. 2015; 11:842.
11. Legnini I, Morlando M, Mangiavacchi A, Fatica A and Bozzoni I. A feedforward regulatory loop between HuR and the long noncoding RNA linc-MD1 controls early phases of myogenesis. Mol Cell. 2014; 53:506-514.
12. Yan Z, Shah PK, Amin SB, Samur MK, Huang N, Wang X, Misra V, Ji H, Gabuzda D and Li C. Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Res. 2012; 40:e135.
13. Li M and Izpisua Belmonte JC. Roles for noncoding RNAs in cell-fate determination and regeneration. Nat Struct Mol Biol. 2015; 22:2-4.
14. Chen CL, Tseng YW, Wu JC, Chen GY, Lin KC, Hwang SM and Hu YC. Suppression of hepatocellular carcinoma by baculovirus-mediated expression of long non-coding RNA PTENP1 and MicroRNA regulation. Biomaterials. 2015; 44:71-81.
15. Yan X, Hu Z, Feng Y, Hu X, Yuan J, Zhao SD, Zhang Y, Yang L, Shan W, He Q, Fan L, Kandalaft LE, Tanyi JL, et al. Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. Cancer Cell. 2015; 28:529-540.
16. Wang P, Ning S, Zhang Y, Li R, Ye J, Zhao Z, Zhi H, Wang T, Guo Z and Li X. Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. Nucleic Acids Res. 2015; 43:3478-3489.
17. Yang JH, Li JH, Jiang S, Zhou H and Qu LH. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2013; 41:D177-187.
18. Ning S, Zhao Z, Ye J, Wang P, Zhi H, Li R, Wang T, Wang J, Wang L and Li X. SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. PLoS One. 2014; 9:e103851.
19. Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM and Hatzigeorgiou AG. DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long noncoding RNAs. Nucleic Acids Res. 2013; 41:D239-245.
20. Li JH, Liu S, Zhou H, Qu LH and Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014; 42:D92-97.
21. Wang J, Lu M, Qiu C and Cui Q. TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res. 2010; 38:D119-122.
22. Amaral LA, Scala A, Barthelemy M and Stanley HE. Classes of small-world networks. Proc Natl Acad Sci U S A. 2000; 97:11149-11152.
23. Simos T, Georgopoulou U, Thyphronitis G, Koskinas J and Papaloukas C. Analysis of protein interaction networks for the detection of candidate hepatitis B and C biomarkers. IEEE J Biomed Health Inform. 2015; 19:181-189.
24. Xu J, Li Y, Lu J, Pan T, Ding N, Wang Z, Shao T, Zhang J, Wang L and Li X. The mRNA related ceRNA-ceRNA landscape and significance across 20 major cancer types. Nucleic Acids Res. 2015; 43:8169-8182.
25. Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, Zhang Q, Yan G and Cui Q. LncRNADisease: a database for longnon-coding RNA-associated diseases. Nucleic Acids Res. 2013; 41:D983-986.
26. Li Y, Qiu C, Tu J, Geng B, Yang J, Jiang T and Cui Q. HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 2014; 42:D1070-1074.
27. Mathsyaraja H and Eisenman RN. Parsing Myc Paralogs in Oncogenesis. Cancer Cell. 2016; 29:1-2.
28. Huang X, Yang Y, Guo Y, Cao ZL, Cui ZW, Hu TC and Gao LB. Association of a let-7 KRAS rs712 polymorphism with the risk of breast cancer. Genet Mol Res. 2015; 14:16913-16920.
29. Zhang E, Li W, Yin D, De W, Sun S and Han L. c-Mycregulated long non-coding RNA H19 indicates a poor prognosis and affects cell proliferation in non-small-cell lung cancer. Tumour Biol. 2015.
30. Tan M, Wu J and Cai Y. Suppression of Wnt signaling by the miR-29 family is mediated by demethylation of WIF-1 in non-small-cell lung cancer. Biochem Biophys Res Commun. 2013; 438:673-679.
31. Boeri M, Verri C, Conte D, Roz L, Modena P, Facchinetti F, Calabro E, Croce CM, Pastorino U and Sozzi G. MicroRNA signatures in tissues and plasma predict development and prognosis of computed tomography detected lung cancer. Proc Natl Acad Sci U S A. 2011; 108:3713-3718.
32. Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, Zhu W, Wu W, Chen R and Zhao Y. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res. 2014; 42:D98-103.
33. Salvador MA, Wicinski J, Cabaud O, Toiron Y, Finetti P, Josselin E, Lelievre H, Kraus-Berthier L, Depil S, Bertucci F, Collette Y, Birnbaum D, Charafe-Jauffret E and Ginestier C. The histone deacetylase inhibitor abexinostat induces cancer stem cells differentiation in breast cancer with low Xist expression. Clin Cancer Res. 2013; 19:6520-6531.
34. Ostrander JH, Daniel AR, Lofgren K, Kleer CG and Lange CA. Breast tumor kinase (protein tyrosine kinase 6) regulates heregulin-induced activation of ERK5 and p38 MAP kinases in breast cancer cells. Cancer Res. 2007; 67:4199-4209.
35. Gotte M, Mohr C, Koo CY, Stock C, Vaske AK, Viola M, Ibrahim SA, Peddibhotla S, Teng YH, Low JY, Ebnet K, Kiesel L and Yip GW. miR-145-dependent targeting of junctional adhesion molecule A and modulation of fascin expression are associated with reduced breast cancer cell motility and invasiveness. Oncogene. 2010; 29:6569-6580.
36. Schrauder MG, Strick R, Schulz-Wendtland R, Strissel PL, Kahmann L, Loehberg CR, Lux MP, Jud SM, Hartmann A, Hein A, Bayer CM, Bani MR, Richter S, et al. Circulating micro-RNAs as potential blood-based markers for early stage breast cancer detection. PLoS One. 2012; 7:e29770.
37. Du L, Schageman JJ, Subauste MC, Saber B, Hammond SM, Prudkin L, Wistuba, II, Ji L, Roth JA, Minna JD and Pertsemlidis A. miR-93, miR-98, and miR-197 regulate expression of tumor suppressor gene FUS1. Mol Cancer Res. 2009; 7:1234-1243.
38. Lv J, Yu YQ, Li SQ, Luo L and Wang Q. Aflatoxin B1 promotes cell growth and invasion in hepatocellular carcinoma HepG2 cells through H19 and E2F1. Asian Pac J Cancer Prev. 2014; 15:2565-2570.
39. Berteaux N, Lottin S, Monte D, Pinte S, Quatannens B, Coll J, Hondermarck H, Curgy JJ, Dugimont T and Adriaenssens E. H19 mRNA-like noncoding RNA promotes breast cancer cell proliferation through positive control by E2F1. J Biol Chem. 2005; 280:29625-29636.
40. Huang da W, Sherman BT and Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4:44-57.
41. Tarangelo A, Lo N, Teng R, Kim E, Le L, Watson D, Furth EE, Raman P, Ehmer U and Viatour P. Recruitment of Pontin/Reptin by E2f1 amplifies E2f transcriptional response during cancer progression. Nat Commun. 2015; 6:10028.
42. Guo CJ, Pan Q, Li DG, Sun H and Liu BW. miR-15b and miR-16 are implicated in activation of the rat hepatic stellate cell: An essential role for apoptosis. J Hepatol. 2009; 50:766-778.
43. Barrans S, Crouch S, Smith A, Turner K, Owen R, Patmore R, Roman E and Jack A. Rearrangement of MYC is associated with poor prognosis in patients with diffuse large B-cell lymphoma treated in the era of rituximab. J Clin Oncol. 2010; 28:3360-3365.
44. Landi MT, Zhao Y, Rotunno M, Koshiol J, Liu H, Bergen AW, Rubagotti M, Goldstein AM, Linnoila I, Marincola FM, Tucker MA, Bertazzi PA, Pesatori AC, Caporaso NE, McShane LM and Wang E. MicroRNA expression differentiates histology and predicts survival of lung cancer. Clin Cancer Res. 2010; 16:430-441.
45. Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, Macura K, Blass G, Kellis M, Werber M and Herrmann BG. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell. 2013; 24:206-214.
46. 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, 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.
47. Jiang W, Mitra R, Lin CC, Wang Q, Cheng F and Zhao Z. Systematic dissection of dysregulated transcription factormiRNA feed-forward loops across tumor types. Brief Bioinform. 2015.
48. Fang Z, Xu C, Li Y, Cai X, Ren S, Liu H, Wang Y, Wang F, Chen R, Qu M, Wang Y, Zhu Y, Zhang W, et al. A feedforward regulatory loop between androgen receptor and PlncRNA-1 promotes prostate cancer progression. Cancer Lett. 2016; 374:62-74.
49. Liu X, Xiao ZD, Han L, Zhang J, Lee SW, Wang W, Lee H, Zhuang L, Chen J, Lin HK, Wang J, Liang H and Gan B. LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress. Nat Cell Biol. 2016; 18:431-442.
50. Li J, Ma W, Zeng P, Wang J, Geng B, Yang J and Cui Q. LncTar: a tool for predicting the RNA targets of long noncoding RNAs. Brief Bioinform. 2015; 16:806-812.
51. Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kahari A, Kinsella RJ, Kulesha E, Maheswari U, et al. Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res. 2010; 38:D563-569.
52. Cancer Genome Atlas Research N. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012; 489:519-525.
53. Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P and Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006; 24:537-544.