GENOME-WIDE ANALYSIS OF LONG NON-CODING RNA (LNCRNA) OF AUTOIMMUNE THYROID DISEASES USING BIOINFORMATICS APPROACHES
Keywords:
Keywords, lncRNA, autoimmune thyroid disease, GENEMANIAAbstract
Objective: Long non-coding RNA's (lncRNA's) have a crucial role in cancer biology. In this study, the genome sequence analysis of lncRNA expression in autoimmune thyroid disease is done to identify novel targets for further study of the disease.
Methods: All the data were collected from Disgenet and Ensemble genome browser. Gene ontology and network analysis were performed using the standard enrichment annotation method. Association of lncRNA and their targeted mRNA were analyzed by GENEMANIA.
Results: Of the all 334 lncRNA transcripts identified, only four had coding potential. LncRNA'stranscripts ENST00000462973, ENST00000555326 were involved in autoimmune thyroid disease pathway which corresponds to thyroid peroxidase (TPO) and thyroid-stimulating hormone receptor (TSHR), and this could provide better insights to therapeutics.
Conclusion: Our current study on the potential link between lncRNAs and autoimmune thyroid disease presents a novel area for further investigations into the target genes of such lncRNAs, leading to therapeutic strategies for the disease.
Keywords: lncRNA, Autoimmune thyroid disease, GENEMANIA
Downloads
References
Wilson BJ, Nicholls SG. The human genome project and recent advances in personalized genomics. J Risk Management Healthcare Policy 2015;8:9.
Shendure J, Mitra RD, Varma C, Church GM. Advanced sequencing technologies: methods and goals. Nat Rev Genet 2004;5:335-44.
Hernandez LM. editor. Diffusion and Use of Genomic Innovations in Health and Medicine: Workshop Summary. National Academies Press; 2008.
De Vargas AF. The human genome project and its importance in clinical medicine. Int Congr Ser 2002;1237:3-13.
National Human Genome Research Institute, USA, est; 1989. Available from: http://www.genome.gov/12011238. [Last accessed on 10 Jan 2016].
Wellcome trusts Sanger institude. The human genome project. Available from: https://www.sanger.ac.uk/about/history/ hgp/. [Last accessed on 10 Jan 2016].
Louro R, El-Jundi T, Nakaya HI, Reis EM, Verjovski-Almeida S. Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci. Genomics 2008;92:18-25.
Wong DT. Salivary extracellular noncoding RNA: emerging biomarkers for molecular diagnostics. Clin Ther 2015;37:540-51.
Koshimizu TA, Fujiwara Y, Sakai N, Shibata K, Tsuchiya H. Oxytocin stimulates expression of a noncoding RNA tumor marker in a human neuroblastoma cell line. Life Sci 2010;86:455-60.
Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J. A new frontier for molecular medicine: noncoding RNAs. Biochim Biophysica Acta (BBA)-Rev Cancer 2005;1756:65-75.
Storz G, Opdyke JA, Zhang A. Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 2004;7:140-4.
Vogel J, Wagner EG. Target identification of small noncoding RNAs in bacteria. Curr Opin Microbiol 2007;10:262-70.
Li C, Li Y, Shen L, Huang J, Sun Y, Luo Y, et al. The role of noncoding regions of classical swine fever virus C-strain in its adaptation to the rabbit. Virus Res 2014;183:117-22.
Santosh B, Varshney A, Yadava PK. Nonâ€coding RNAs: biological functions and applications. Cell Biochem Function 2015;33:14-22.
Alvarez ML, DiStefano JK. The role of non-coding RNAs in diabetic nephropathy: potential applications as biomarkers for disease development and progression. Diabetes Res Clin Pract 2013;99:1-11.
Fu M, Huang G, Zhang Z, Liu J, Huang Z, Yu B, et al. Expression profile of long noncoding RNAs in cartilage from knee osteoarthritis patients. Osteoarthritis Cartilage 2015;23:423-32.
Beltrami C, Angelini TG, Emanueli C. Noncoding RNAs in diabetes vascular complications. J Mol Cell Cardiol 2015;89:42-50.
Lv J, Liu H, Huang Z, Su J, He H, Xiu Y, et al. Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Res 2013;41:10044-61.
Sun J, Lin Y, Wu J. Long non-coding RNA expression profiling of mouse testis during postnatal development. PloS One 2013;8:750-7.
Luo X, Pan J, Wang L, Wang P, Zhang M, Liu M, et al. Epigenetic regulation of lncRNA connects ubiquitin-proteasome system with infection-inflammation in preterm births and preterm premature rupture of membranes. BMC Pregnancy Childbirth 2015;15:21.
Xin M, Wang Y, Yao Y, Song N, Hu Z, Qin D, et al. Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol 2011;11:61.
Hao Y, Wu W, Shi F, Dalmolin RJ, Yan M, Tian F, et al. Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma. BMC Cancer 2015;15:1.
Isin M, Dalay N. LncRNAs and neoplasia. Clin Chim Acta 2015;444:280-8.
Parolia A, Crea F, Xue H, Wang Y, Mo F, Ramnarine VR, et al. The long non-coding RNA PCGEM1 is regulated by androgen receptor activity in vivo. Mol Cancer 2015;14:1.
Gao W, Zhu M, Wang H, Zhao S, Zhao D, Yang Y, et al. Association of polymorphisms in long non-coding RNA H19 with coronary artery disease risk in a Chinese population. Mutat Res 2015;772:15-22.
Li Z, Zhao X, Zhou Y, Liu Y, Zhou Q, Ye H, Wang Y, et al. The long non-coding RNA HOTTIP promotes progression and gemcitabine resistance by regulating HOXA13 in pancreatic cancer. J Transl Med 2015;13:84.
Zhao W, Mu Y, Ma L, Wang C, Tang Z, Yang S, et al. Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development. Sci Rep 2015;5. Doi:10.1038/srep08957. [Article in Press]
Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Mol Cancer 2011;10:1-38.
Han D, Wang M, Ma N, Xu Y, Jiang Y, Gao X. Long noncoding RNAs: novel players in colorectal cancer. Cancer Lett 2015;361:13-21.
Haemmerle M, Gutschner T. Long non-coding RNAs in cancer and development: where do we go from here? Int J Mol Sci 2015;16:1395-405.
Villegas VE, Zaphiropoulos PG. Neighboring gene regulation by antisense long non-coding RNAs. Int J Mol Sci 2015;16:3251-66.
Kornienko AE, Guenzl PM, Barlow DP, Pauler FM. Gene regulation by the act of long non-coding RNA transcription. BMC Biol 2013;11:1.
Loewen G, Jayawickramarajah J, Zhuo Y, Shan B. Functions of lncRNA HOTAIR in lung cancer. J Hematol Oncol 2014;7:90.
Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, et al. Genome-wide screening and functional analysis identifies a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol 2014;15:512.
Xu G, Chen J, Pan Q, Huang K, Pan J, Zhang W, et al. Long noncoding RNA expression profiles of lung adenocarcinoma ascertained by microarray analysis. PloS One 2014;9:e104044. Doi:10.1371/journal.pone.0104044. [Article in Press]
Dong R, Jia D, Xue P, Cui X, Li K, Zheng S, et al. Genome-wide analysis of long noncoding RNA (lncRNA) expression in hepatoblastoma tissues. PloS One 2014;9:e85599. Doi:10.1371/journal.pone.0085599. [Article in Press]
Pearce SH, Merriman TR. Genetics of type 1 diabetes and autoimmune thyroid disease. Endocrinol Metab Clin North Am 2009;38:289-301.
Taylor JC, Gough SC, Hunt PJ, Brix TH, Chatterjee K, Connell JM, Franklyn JA, et al. A genome-wide screen in 1119 relative pairs with autoimmune thyroid disease. J Clin Endocrinol Metab 2006;91:646-53.
Ban Y, Ban Y, Ban Y. Autoimmune thyroid disease genes identified in non-caucasians. Open J Endocr Metab Dis 2012;2:107-16.
Shiva S, Ilkhchooyi F, Rezamand A. Thyroid autoimmunity at the onset of type 1 diabetes mellitus in children. Open J Immunol 2013;3:37-40.
Gesing A, Lewiński A, Karbownik-Lewińska M. The thyroid gland and the process of aging; what is new? Thyroid Res 2012;5:1-5.
Bauer-Mehren A, Bundschus M, Rautschka M, Mayer MA, Sanz F, Furlong LI. Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases. PloS One 2011;6:e20284. Doi:10.1371/journal.pone.0020284. [Article in Press]
Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, et al. GeneMANIA cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics 2010;26:2927-8.
Bionaz M. Nutrigenomics approaches to fine-tune metabolism and milk production: is this the future of ruminant nutrition? Adv Dairy Res 2014;2:e107. Doi:10.4172/2329-888X. 1000e107. [Article in Press].