Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer

Nature Structural and Molecular Biology

Volumn 20, Issue 7, 2013, Pages 908-913

  Du, Zhou ^a   Fei, Teng ^b,c,d   Verhaak, Roel G W ^e   Su, Zhen ^f   Zhang, Yong ^a   Brown, Myles ^b,c   Chen, Yiwen ^d   Liu, X Shirley ^b,d  

^a TONGJI UNIVERSITY   (China)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^e UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^f CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; SMALL INTERFERING RNA;

ARTICLE; CANCER CELL; CANCER GENETICS; CANCER GROWTH; CANCER PROGNOSIS; CELL GROWTH; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; OVERALL SURVIVAL; PRIORITY JOURNAL; PROGRESSION FREE SURVIVAL; PROSTATE CANCER; RNA INTERFERENCE; TUMOR PROMOTION;

ADENOCARCINOMA; AMINO ACID SEQUENCE; CELL LINE, TUMOR; CONSERVED SEQUENCE; DNA PROBES; DNA, INTERGENIC; EXONS; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, OVERLAPPING; HUMANS; INTRONS; KAPLAN-MEIER ESTIMATE; MALE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR TARGETED THERAPY; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; PROSTATIC NEOPLASMS; PROTEIN CONFORMATION; RNA, LONG UNTRANSLATED; RNA, NEOPLASM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TUMOR MARKERS, BIOLOGICAL;

EID: 84880154515     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2591     Document Type: Article

References (58)

1. Ota, T. et al. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat. Genet. 36, 40-45 (2004).
2. Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
3. Khalil, A.M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106, 11667-11672 (2009).
4. Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
5. Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
6. Prensner, J.R. & Chinnaiyan, A.M. The emergence of lncRNAs in cancer biology. Cancer Discov. 1, 391-407 (2011).
7. Wapinski, O. & Chang, H.Y. Long noncoding RNAs and human disease. Trends Cell Biol. 21, 354-361 (2011).
8. Lee, G.L., Dobi, A. & Srivastava, S. Prostate cancer: diagnostic performance of the PCA3 urine test. Nat. Rev. Urol. 8, 123-124 (2011).
9. Liao, Q. et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res. 39, 3864-3878 (2011).
10. Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F. & Mattick, J.S. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. USA 105, 716-721 (2008).
11. Michelhaugh, S.K. et al. Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. J. Neurochem. 116, 459-466 (2011).
12. Gellert, P., Ponomareva, Y., Braun, T. & Uchida, S. Noncoder: a web interface for exon array-based detection of long non-coding RNAs. Nucleic Acids Res. 41, e20 (2013).
13. Johnson, R. Long non-coding RNAs in Huntington's disease neurodegeneration. Neurobiol. Dis. 46, 245-254 (2012).
14. Zhang, X. et al. Long non-coding RNA expression profiles predict clinical phenotypes in glioma. Neurobiol. Dis. 48, 1-8 (2012).
15. Raghavachari, N. et al. A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease. BMC Med. Genomics 5, 28 (2012).
16. Xu, W. et al. Human transcriptome array for high-throughput clinical studies. Proc. Natl. Acad. Sci. USA 108, 3707-3712 (2011).
17. Levin, J.Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
18. Taylor, B.S. et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 18, 11-22 (2010).
19. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
20. Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789 (2012).
21. Kapur, K., Xing, Y., Ouyang, Z. & Wong, W.H. Exon arrays provide accurate assessments of gene expression. Genome Biol. 8, R82 (2007).
22. Prensner, J.R. et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat. Biotechnol. 29, 742-749 (2011).
23. Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63 (2009).
24. Petrovics, G. et al. Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients. Oncogene 23, 605-611 (2004).
25. Mourtada-Maarabouni, M., Pickard, M.R., Hedge, V.L., Farzaneh, F. & Williams, G.T. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene 28, 195-208 (2009).
26. Clemson, C.M. et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol. Cell 33, 717-726 (2009).
27. Kretz, M. et al. Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev. 26, 338-343 (2012).
28. Wang, K.C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120-124 (2011).
29. Szegedi, K. et al. The anti-apoptotic protein G1P3 is overexpressed in psoriasis and regulated by the non-coding RNA, PRINS. Exp. Dermatol. 19, 269-278 (2010).
30. Wagner, L.A. et al. EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression. Blood 109, 5191-5198 (2007).
31. The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
32. Hammerman, P.S. et al. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519-525 (2012).
33. Ishii, N. et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J. Hum. Genet. 51, 1087-1099 (2006).
34. Rapicavoli, N.A., Poth, E.M. & Blackshaw, S. The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev. Biol. 10, 49 (2010).
35. Chan, A.S., Thorner, P.S., Squire, J.A. & Zielenska, M. Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between rhabdomyosarcoma subtypes. Oncogene 21, 3029-3037 (2002).
36. Gupta, R.A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076 (2010).
37. Rinn, J.L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323 (2007).
38. Kogo, R. et al. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 71, 6320-6326 (2011).
39. Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899-905 (2010).
40. Garraway, L.A. et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436, 117-122 (2005).
41. Akavia, U.D. et al. An integrated approach to uncover drivers of cancer. Cell 143, 1005-1017 (2010).
42. Tran, V.G. et al. H19 antisense RNA can up-regulate Igf2 transcription by activation of a novel promoter in mouse myoblasts. PLoS ONE 7, e37923 (2012).
43. Califano, A., Butte, A.J., Friend, S., Ideker, T. & Schadt, E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat. Genet. 44, 841-847 (2012).
44. Pe'er, D. & Hacohen, N. Principles and strategies for developing network models in cancer. Cell 144, 864-873 (2011).
45. Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939-953 (2010).
46. Syvnen, A.C. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat. Rev. Genet. 2, 930-942 (2001).
47. Meyerson, M., Gabriel, S. & Getz, G. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11, 685-696 (2010).
48. Flicek, P. et al. Ensembl 2012. Nucleic Acids Res. 40, D84-D90 (2012).
49. Jiang, H. & Wong, W.H. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24, 2395-2396 (2008).
50. Kuhn, R.M., Haussler, D. & Kent, W.J. The UCSC genome browser and associated tools. Brief. Bioinform. 14, 144-161 (2013).
51. Seok, J., Xu, W., Gao, H., Davis, R.W. & Xiao, W. JETTA: junction and exon toolkits for transcriptome analysis. Bioinformatics 28, 1274-1275 (2012).
52. Johnson, W.E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118-127 (2007).
53. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
54. Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl. Acad. Sci. USA 104, 20007-20012 (2007).
55. Mermel, C.H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
56. Taylor, B.S. et al. Functional copy-number alterations in cancer. PLoS ONE 3, e3179 (2008).
57. Lin, M.F., Jungreis, I. & Kellis, M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatica 27, 275-282 (2011).
58. Lindblad-Toh, K. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476-482 (2011).