Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis
In an in silico study, Anindya Dutta and colleagues study the expression of long noncoding RNAs in brain tumors and normal brain tissue and the possible implications for disease prognosis.
Vyšlo v časopise:
Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis. PLoS Med 13(12): e32767. doi:10.1371/journal.pmed.1002192
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pmed.1002192
Souhrn
In an in silico study, Anindya Dutta and colleagues study the expression of long noncoding RNAs in brain tumors and normal brain tissue and the possible implications for disease prognosis.
Zdroje
1. Ostrom QT, Gittleman H, Liao P, Rouse C, Chen Y, Dowling J, et al. CBTRUS statistical report: primary brain and central nervous system tumors diagnosed in the United States in 2007–2011. Neuro Oncol. 2014 Oct;16(Suppl 4):iv1–63.
2. Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, Wu TD, et al. Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell. 2006;9(3):157–73. doi: 10.1016/j.ccr.2006.02.019 16530701
3. Verhaak RGW, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010;17(1):98–110. doi: 10.1016/j.ccr.2009.12.020 20129251
4. Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, et al. Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. N Engl J Med. 2015;372(26):2481–98. doi: 10.1056/NEJMoa1402121 26061751
5. Suzuki H, Aoki K, Chiba K, Sato Y, Shiozawa Y, Shiraishi Y, et al. Mutational landscape and clonal architecture in grade II and III gliomas. Nat Genet. 2015;47(5):458–68. doi: 10.1038/ng.3273 25848751
6. van den Bent MJ, Dubbink HJ, Marie Y, Brandes AA, Taphoorn MJB, Wesseling P, et al. IDH1 and IDH2 mutations are prognostic but not predictive for outcome in anaplastic oligodendroglial tumors: a report of the European Organization for Research and Treatment of Cancer Brain Tumor Group. Clin Cancer Res. 2010;16(5):1597–604. doi: 10.1158/1078-0432.CCR-09-2902 20160062
7. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447(7146):799–816. doi: 10.1038/nature05874 17571346
8. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science. 2005;309(5740):1559–63. doi: 10.1126/science.1112014 16141072
9. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, et al. Antisense transcription in the mammalian transcriptome. Science. 2005;309(5740):1564–6. doi: 10.1126/science.1112009 16141073
10. 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. doi: 10.1038/nature08975 20393566
11. Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A, et al. Genome-wide mapping and characterization of notch-regulated long noncoding RNAs in acute leukemia. Cell. 2014;158(3):593–606. doi: 10.1016/j.cell.2014.05.049 25083870
12. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 2014;21(2):198–206. doi: 10.1038/nsmb.2764 24463464
13. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature. 2012;491(7424):454–7. doi: 10.1038/nature11508 23064229
14. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013;493(7431):231–5. doi: 10.1038/nature11661 23201690
15. Yoon J-H, Abdelmohsen K, Srikantan S, Yang X, Martindale JL, De S, et al. LincRNA-p21 suppresses target mRNA translation. Mol Cell. 2012;47(4):648–55. doi: 10.1016/j.molcel.2012.06.027 22841487
16. Gomez JA, Wapinski OL, Yang YW, Bureau J-F, Gopinath S, Monack DM, et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell. 2016;152(4):743–54.
17. Mousavi K, Zare H, Dell’Orso S, Grontved L, Gutierrez-Cruz G, Derfoul A, et al. ERNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell. 2013;51(5):606–17. doi: 10.1016/j.molcel.2013.07.022 23993744
18. Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR, et al. MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis. Mol Cell Biol. 2015;35(3):498–513. doi: 10.1128/MCB.01079-14 25403490
19. Ng SY, Johnson, Stanton LW. Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J. 2012;31(3):522–33. doi: 10.1038/emboj.2011.459 22193719
20. Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz CC, et al. The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. Cell Stem Cell. 2015;16(4):439–47. doi: 10.1016/j.stem.2015.02.007 25800779
21. Rapicavoli NA, Poth EM, Blackshaw S. The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol. 2010;10(1):1–10.
22. Aprea J, Prenninger S, Dori M, Ghosh T, Monasor LS, Wessendorf E, et al. Transcriptome sequencing during mouse brain development identifies long non‐coding RNAs functionally involved in neurogenic commitment. EMBO J. 2013;32(24):3145–60. doi: 10.1038/emboj.2013.245 24240175
23. Bernard D, Prasanth K V, Tripathi V, Colasse S, Nakamura T, Xuan Z, et al. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 2010;29(18):3082–93. doi: 10.1038/emboj.2010.199 20729808
24. Kerin T, Ramanathan A, Rivas K, Grepo N, Coetzee GA, Campbell DB. A noncoding RNA antisense to moesin at 5p14.1 in autism. Sci Transl Med. 2012;4(128):128ra40. doi: 10.1126/scitranslmed.3003479 22491950
25. Zhao X, Tang Z, Zhang H, Atianjoh FE, Zhao J-Y, Liang L, et al. A long noncoding RNA contributes to neuropathic pain by silencing Kcna2 in primary afferent neurons. Nat Neurosci. 2013;16(8):1024–31. doi: 10.1038/nn.3438 23792947
26. Yuan JH, Yang F, Wang F, Ma JZ, Guo YJ, Tao QF, et al. A long noncoding RNA activated by TGF-β promotes the invasion-metastasis cascade in hepatocellular carcinoma. Cancer Cell. 2014;25(5):666–81. doi: 10.1016/j.ccr.2014.03.010 24768205
27. Sakurai K, Reon BJ, Anaya J, Dutta A. The lncRNA DRAIC/PCAT29 locus constitutes a tumor-suppressive nexus. Mol Cancer Res. 2015;13(5):828–38. doi: 10.1158/1541-7786.MCR-15-0016-T 25700553
28. Malik R, Patel L, Prensner JR, Shi Y, Iyer M, Subramaniyan S, et al. The lncRNA PCAT29 inhibits oncogenic phenotypes in prostate cancer. Mol Cancer Res. 2014;12(8):1081–7. doi: 10.1158/1541-7786.MCR-14-0257 25030374
29. Ellis BC, Molloy PL, Graham LD. CRNDE: a long non-coding RNA involved in cancer, neurobiology and development. Front Genet. 2012;3:270. doi: 10.3389/fgene.2012.00270 23226159
30. Wang Y, Wang Y, Li J, Zhang Y, Yin H, Han B. CRNDE, a long-noncoding RNA, promotes glioma cell growth and invasion through mTOR signaling. Cancer Lett. 2015;367(2):122–8. doi: 10.1016/j.canlet.2015.03.027 25813405
31. Zhang K, Sun X, Zhou X, Han L, Chen L. Long non-coding RNA HOTAIR promotes glioblastoma cell cycle progression in an EZH2 dependent manner. Oncotarget. 2014;6(1):537–46.
32. Zhang X, Kiang KM, Zhang GP, Leung GK. long non-coding RNAs dysregulation and function in glioblastoma stem cells. Noncoding RNA. 2015;1(1):69–86.
33. Gill BJ, Pisapia DJ, Malone HR, Goldstein H, Lei L, Sonabend A, et al. MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma. Proc Natl Acad Sci U S A. 2014;111(34):12550–5. doi: 10.1073/pnas.1405839111 25114226
34. Akula N, Barb J, Jiang X, Wendland JR, Choi KH, Sen SK, et al. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Mol Psychiatry. 2014;19(11):1179–85. doi: 10.1038/mp.2013.170 24393808
35. Jaffe AE, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, et al. Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nat Neurosci. 2015;18(1):154–61. doi: 10.1038/nn.3898 25501035
36. Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, et al. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Mol Syst Biol. 2014;10(12):774.
37. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36. doi: 10.1186/gb-2013-14-4-r36 23618408
38. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotech. 2013;31(1):46–53.
39. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25(18):1915–27. doi: 10.1101/gad.17446611 21890647
40. Wang L, Park HJ, Dasari S, Wang S, Kocher J-P, Li W. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013;41(6):e74. doi: 10.1093/nar/gkt006 23335781
41. Wilhelm M, Schlegl J, Hahne H, Gholami AM, Lieberenz M, Savitski MM, et al. Mass-spectrometry-based draft of the human proteome. Nature. 2014;509(7502):582–7. doi: 10.1038/nature13319 24870543
42. Massey FJ Jr. The Kolmogorov-Smirnov test for goodness of fit. J Am Stat Assoc. 1951;46(253):68–78.
43. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57(1):289–300.
44. Cox DR. Regression models and life-tables. J R Stat Soc Ser B. 1972;34(2):187–220.
45. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009;458(7235):223–7. doi: 10.1038/nature07672 19182780
46. Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 2015;47(3):199–208. doi: 10.1038/ng.3192 25599403
47. Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2013;2013(2):1–24.
48. Shi Y, Wang Y, Luan W, Wang P, Tao T, Zhang J, et al. Long non-coding RNA H19 promotes glioma cell invasion by deriving miR-675. PLoS ONE. 2014;9(1):e86295. doi: 10.1371/journal.pone.0086295 24466011
49. Wen PY, Kesari S. Malignant gliomas in adults. N Engl J Med. 2008;359(5):492–507. doi: 10.1056/NEJMra0708126 18669428
50. Lin N, Chang KY, Li Z, Gates K, Rana Z, Dang J, et al. An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell. 2014;53(6):1005–19. doi: 10.1016/j.molcel.2014.01.021 24530304
51. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell. 2011;147(7):1537–50. doi: 10.1016/j.cell.2011.11.055 22196729
52. Gerstung M, Pellagatti A, Malcovati L, Giagounidis A, Porta MG, Jädersten M, et al. Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nat Commun. 2015;6:5901. doi: 10.1038/ncomms6901 25574665
53. Stead LF, Berri S, Wood HM, Egan P, Conway C, Daly C, et al. The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma. Neoplasia. 2012;14(11):1075–86. 23226101
54. Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, et al. DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 2012;13(12):R124. doi: 10.1186/gb-2012-13-12-r124 23383675
55. Garzon R, Volinia S, Papaioannou D, Nicolet D, Kohlschmidt J, Yan PS, et al. Expression and prognostic impact of lncRNAs in acute myeloid leukemia. Proc Natl Acad Sci U S A. 2014;111(52):18679–84. doi: 10.1073/pnas.1422050112 25512507
56. Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M, et al. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Res. 2012;22(6):1006–14. doi: 10.1101/gr.140061.112 22581800
57. White N, Cabanski C, Silva-Fisher J, Dang H, Govindan R, Maher C. Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer. Genome Biol. 2014;15(8):429. doi: 10.1186/s13059-014-0429-8 25116943
58. Brennan CW, Verhaak RGW, McKenna A, Campos B, Noushmehr H, Salama SR, et al. The somatic genomic landscape of glioblastoma. Cell. 2013;155(2):462–77. doi: 10.1016/j.cell.2013.09.034 24120142
59. Zwiener I, Frisch B, Binder H. Transforming RNA-Seq data to improve the performance of prognostic gene signatures. PLoS ONE. 2014;9(1):e85150. doi: 10.1371/journal.pone.0085150 24416353
60. Yan X, Hu Z, Feng Y, Hu X, Yuan J, Zhao SD, et al. Comprehensive genomic characterization of long non-coding RNAs across human cancers. Cancer Cell. 2015;28(4):529–40. doi: 10.1016/j.ccell.2015.09.006 26461095
61. Matouk IJ, DeGroot N, Mezan S, Ayesh S, Abu-lail R, Hochberg A, et al. The H19 non-coding RNA is essential for human tumor growth. PLoS ONE. 2007;2(9):e845. doi: 10.1371/journal.pone.0000845 17786216
62. Yoshimizu T, Miroglio A, Ripoche M-A, Gabory A, Vernucci M, Riccio A, et al. The H19 locus acts in vivo as a tumor suppressor. Proc Natl Acad Sci U S A. 2008;105(34):12417–22. doi: 10.1073/pnas.0801540105 18719115
63. Ozawa T, Riester M, Cheng Y-K, Huse JT, Squatrito M, Helmy K, et al. Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma. Cancer Cell. 2014;26(2):288–300. doi: 10.1016/j.ccr.2014.06.005 25117714
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