Genome‑wide analysis reveals the emerging roles of long non‑coding RNAs in cancer (Review)
- Authors:
- Xiaoxia Ren
-
Affiliations: Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, P.R. China - Published online on: November 22, 2019 https://doi.org/10.3892/ol.2019.11141
- Pages: 588-594
This article is mentioned in:
Abstract
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Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, et al: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 420:563–573. 2002. View Article : Google Scholar : PubMed/NCBI | |
|
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al: Landscape of transcription in human cells. Nature. 489:101–108. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 458:223–227. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Jathar S, Kumar V, Srivastava J and Tripathi V: Technological developments in lncRNA biology. Adv Exp Med Biol. 1008:283–323. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Zheng GX, Do BT, Webster DE, Khavari PA and Chang HY: Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. Nat Struct Mol Biol. 21:585–590. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Zhang Z, Wang X, Cao S, Han X, Wang Z, Zhao X, Liu X, Li G, Pan X and Lei D: The long noncoding RNA TUG1 promotes laryngeal cancer proliferation and migration. Cell Physiol Biochem. 49:2511–2520. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Tseng YY, Moriarity BS, Gong W, Akiyama R, Tiwari A, Kawakami H, Ronning P, Reuland B, Guenther K, Beadnell TC, et al: PVT1 dependence in cancer with MYC copy-number increase. Nature. 512:82–86. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Sánchez Y and Huarte M: Long non-coding RNAs: Challenges for diagnosis and therapies. Nucleic Acid Ther. 23:15–20. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
Veneziano D, Di Bella S, Nigita G, Laganà A, Ferro A and Croce CM: Noncoding RNA: Current deep sequencing data analysis approaches and challenges. Hum Mutat. 37:1283–1298. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, et al: The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 47:199–208. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E and Chang HY: Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 129:1311–1323. 2007. View Article : Google Scholar : PubMed/NCBI | |
|
Botti G, Marra L, Malzone MG, Anniciello A, Botti C, Franco R and Cantile M: LncRNA HOTAIR as prognostic circulating marker and potential therapeutic target in patients with tumor diseases. Curr Drug Targets. 18:27–34. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
He Y, Luo Y, Liang B, Ye L, Lu G and He W: Potential applications of MEG3 in cancer diagnosis and prognosis. Oncotarget. 8:73282–73295. 2017.PubMed/NCBI | |
|
Peng Z, Wang J, Shan B, Yuan F, Li B, Dong Y, Peng W, Shi W, Cheng Y, Gao Y, et al: Genome-wide analyses of long noncoding RNA expression profiles in lung adenocarcinoma. Sci Rep. 7:153312017. View Article : Google Scholar : PubMed/NCBI | |
|
Wang W, Zhao Z, Yang F, Wang H, Wu F, Liang T, Yan X, Li J, Lan Q, Wang J and Zhao J: An immune-related lncRNA signature for patients with anaplastic gliomas. J Neurooncol. 136:263–271. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Evans JR, Feng FY and Chinnaiyan AM: The bright side of dark matter: lncRNAs in cancer. J Clin Invest. 126:2775–2782. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Russell MR, Penikis A, Oldridge DA, Alvarez-Dominguez JR, McDaniel L, Diamond M, Padovan O, Raman P, Li Y, Wei JS, et al: CASC15-S is a tumor suppressor lncRNA at the 6p22 neuroblastoma susceptibility locus. Cancer Res. 75:3155–3166. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, et al: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 6:pl12013. View Article : Google Scholar : PubMed/NCBI | |
|
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, et al: The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2:401–404. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Lin C, Yuan G, Hu Z, Zeng Y, Qiu X, Yu H and He S: Bioinformatics analysis of the interactions among lncRNA, miRNA and mRNA expression, genetic mutations and epigenetic modifications in hepatocellular carcinoma. Mol Med Rep. 19:1356–1364. 2019.PubMed/NCBI | |
|
Liu H, Li J, Koirala P, Ding X, Chen B, Wang Y, Wang Z, Wang C, Zhang X and Mo YY: Long non-coding RNAs as prognostic markers in human breast cancer. Oncotarget. 7:20584–20596. 2016.PubMed/NCBI | |
|
Pan W, Zhou L, Ge M, Zhang B, Yang X, Xiong X, Fu G, Zhang J, Nie X, Li H, et al: Whole exome sequencing identifies lncRNA GAS8-AS1 and LPAR4 as novel papillary thyroid carcinoma driver alternations. Hum Mol Genet. 25:1875–1884. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Liu J, Wu W and Jin J: A novel mutation in SIRT1-AS leading to a decreased risk of HCC. Oncol Rep. 34:2343–2350. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Zampetaki A, Albrecht A and Steinhofel K: Long non-coding RNA structure and function: Is there a link? Front Physiol. 9:12012018. View Article : Google Scholar : PubMed/NCBI | |
|
Yao RW, Wang Y and Chen LL: Cellular functions of long noncoding RNAs. Nat Cell Biol. 21:542–551. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Wu XS, Wang F, Li HF, Hu YP, Jiang L, Zhang F, Li ML, Wang XA, Jin YP, Zhang YJ, et al: LncRNA-PAGBC acts as a microRNA sponge and promotes gallbladder tumorigenesis. EMBO Rep. 18:1837–1853. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Signal B, Gloss BS and Dinger ME: Computational approaches for functional prediction and characterisation of long noncoding RNAs. Trends Genet. 32:620–637. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Jaksik R, Iwanaszko M, Rzeszowska-Wolny J and Kimmel M: Microarray experiments and factors which affect their reliability. Biol Direct. 10:462015. View Article : Google Scholar : PubMed/NCBI | |
|
Shi Y and Shang J: Long noncoding RNA expression profiling using arraystar LncRNA microarrays. Methods Mol Biol. 1402:43–61. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Sun Y and Ma L: New insights into long non-coding RNA MALAT1 in cancer and metastasis. Cancers (Basel). 11:2019. View Article : Google Scholar | |
|
Tee AE, Bing L, Song R, Li J, Pasquier E, Cheung BB, Jiang C, Marshall GM, Haber M, Norris MD, et al: The long noncoding RNA MALAT1 promotes tumor-driven angiogenesis by up-regulating pro-angiogenic gene expression. Oncotarget. 7:8663–8675. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Xia T, Liao Q, Jiang X, Shao Y, Xiao B, Xi Y and Guo J: Long noncoding RNA associated-competing endogenous RNAs in gastric cancer. Sci Rep. 4:60882014. View Article : Google Scholar : PubMed/NCBI | |
|
Ji J, Tang J, Deng L, Xie Y, Jiang R, Li G and Sun B: LINC00152 promotes proliferation in hepatocellular carcinoma by targeting EpCAM via the mTOR signaling pathway. Oncotarget. 6:42813–42824. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Wang Y, Li M, Dong C, Ma Y, Xiao L, Zuo S, Gong Y, Ren T and Sun B: Linc00152 knockdown inactivates the Akt/mTOR and Notch1 pathways to exert its anti-hemangioma effect. Life Sci. 223:22–28. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Zhang Y, Xiang C, Wang Y, Duan Y, Liu C, Jin Y and Zhang Y: lncRNA LINC00152 knockdown had effects to suppress biological activity of lung cancer via EGFR/PI3K/AKT pathway. Biomed Pharmacother. 94:644–651. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Xu J, Guo J, Jiang Y, Liu Y, Liao K, Fu Z and Xiong Z: Improved characterization of the relationship between long intergenic non-coding RNA Linc00152 and the occurrence and development of malignancies. Cancer Med. 8:4722–4731. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Zhu Y, Dai B, Zhang H, Shi G, Shen Y and Ye D: Long non-coding RNA LOC572558 inhibits bladder cancer cell proliferation and tumor growth by regulating the AKT-MDM2-p53 signaling axis. Cancer Lett. 380:369–374. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Podnar J, Deiderick H, Huerta G and Hunicke-Smith S: Next-generation sequencing RNA-Seq library construction. Curr Protoc Mol Biol. 106:4.21.1–19. 2014. View Article : Google Scholar | |
|
Metzker ML: Sequencing technologies-the next generation. Nat Rev Genet. 11:31–46. 2010. View Article : Google Scholar : PubMed/NCBI | |
|
Lin T, Hou PF, Meng S, Chen F, Jiang T, Li ML, Shi ML, Liu JJ, Zheng JN and Bai J: Emerging roles of p53 related lncRNAs in cancer progression: A systematic review. Int J Biol Sci. 15:1287–1298. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Sánchez Y, Segura V, Marín-Béjar O, Athie A, Marchese FP, González J, Bujanda L, Guo S, Matheu A and Huarte M: Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature. Nat Commun. 5:58122014. View Article : Google Scholar : PubMed/NCBI | |
|
Hünten S, Kaller M, Drepper F, Oeljeklaus S, Bonfert T, Erhard F, Dueck A, Eichner N, Friedel CC, Meister G, et al: p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pulsed stable isotope labeling with amino acids in cell culture (pSILAC) and next generation sequencing (NGS) analyses. Mol Cell Proteomics. 14:2609–2629. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Kaller M, Götz U and Hermeking H: Loss of p53-inducible long non-coding RNA LINC01021 increases chemosensitivity. Oncotarget. 8:102783–102800. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Yamaguchi H and Hung MC: Regulation and role of EZH2 in cancer. Cancer Res Treat. 46:209–222. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Qi Y, Ooi HS, Wu J, Chen J, Zhang X, Tan S, Yu Q, Li YY, Kang Y, Li H, et al: MALAT1 long ncRNA promotes gastric cancer metastasis by suppressing PCDH10. Oncotarget. 7:12693–12703. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Michalak EM, Burr ML, Bannister AJ and Dawson MA: The roles of DNA, RNA and histone methylation in ageing and cancer. Nat Rev Mol Cell Biol. 20:573–589. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Merry CR, Forrest ME, Sabers JN, Beard L, Gao XH, Hatzoglou M, Jackson MW, Wang Z, Markowitz SD and Khalil AM: DNMT1-associated long non-coding RNAs regulate global gene expression and DNA methylation in colon cancer. Hum Mol Genet. 24:6240–6253. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Somasundaram S, Forrest ME, Moinova H, Cohen A, Varadan V, LaFramboise T, Markowitz S and Khalil AM: The DNMT1-associated lincRNA DACOR1 reprograms genome-wide DNA methylation in colon cancer. Clin Epigenetics. 10:1272018. View Article : Google Scholar : PubMed/NCBI | |
|
Kondo A, Nonaka A, Shimamura T, Yamamoto S, Yoshida T, Kodama T, Aburatani H and Osawa T: Long noncoding RNA JHDM1D-AS1 promotes tumor growth by regulating angiogenesis in response to nutrient starvation. Mol Cell Biol. 37:2017. View Article : Google Scholar | |
|
Hu Q, Ye Y, Chan LC, Li Y, Liang K, Lin A, Egranov SD, Zhang Y, Xia W, Gong J, et al: Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nat Immunol. 20:835–851. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Schmitt AM and Chang HY: Long noncoding RNAs in cancer pathways. Cancer Cell. 29:452–463. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Matsui M and Corey DR: Non-coding RNAs as drug targets. Nat Rev Drug Discov. 16:167–179. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
de Kok JB, Verhaegh GW, Roelofs RW, Hessels D, Kiemeney LA, Aalders TW, Swinkels DW and Schalken JA: DD3(PCA3), a very sensitive and specific marker to detect prostate tumors. Cancer Res. 62:2695–2698. 2002.PubMed/NCBI | |
|
Prensner JR, Zhao S, Erho N, Schipper M, Iyer MK, Dhanasekaran SM, Magi-Galluzzi C, Mehra R, Sahu A, Siddiqui J, et al: RNA biomarkers associated with metastatic progression in prostate cancer: A multi-institutional high-throughput analysis of SChLAP1. Lancet Oncol. 15:1469–1480. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Smolle MA, Bauernhofer T, Pummer K, Calin GA and Pichler M: Current insights into long non-coding RNAs (LncRNAs) in prostate cancer. Int J Mol Sci. 18:2017. View Article : Google Scholar | |
|
Merry CR, Mcmahon S, Thompson CL, Miskimen KL, Harris LN and Khalil AM: Integrative transcriptome-wide analyses reveal critical HER2-regulated mRNAs and lincRNAs in HER2+ breast cancer. Breast Cancer Res Treat. 150:321–334. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Li W, Zhai L, Wang H, Liu C, Zhang J, Chen W and Wei Q: Downregulation of LncRNA GAS5 causes trastuzumab resistance in breast cancer. Oncotarget. 7:27778–27786. 2016.PubMed/NCBI | |
|
Fradet V, Toren P, Nguile-Makao M, Lodde M, Lévesque J, Léger C, Caron A, Bergeron A, Ben-Zvi T, Lacombe L, et al: Prognostic value of urinary prostate cancer antigen 3 (PCA3) during active surveillance of patients with low-risk prostate cancer receiving 5α-reductase inhibitors. BJU Int. 121:399–404. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Ma W, Chen X, Ding L, Ma J, Jing W, Lan T, Sattar H, Wei Y, Zhou F and Yuan Y: The prognostic value of long noncoding RNAs in prostate cancer: A systematic review and meta-analysis. Oncotarget. 8:57755–57765. 2017.PubMed/NCBI | |
|
Liu L, Meng T, Yang XH, Sayim P, Lei C, Jin B, Ge L and Wang HJ: Prognostic and predictive value of long non-coding RNA GAS5 and mircoRNA-221 in colorectal cancer and their effects on colorectal cancer cell proliferation, migration and invasion. Cancer Biomark. 22:283–299. 2018. View Article : Google Scholar : PubMed/NCBI |
