Discovery of isomiRs in PBMCs of diseased vis-à-vis healthy Indian water buffaloes
Tóm tắt
MicroRNA isoforms are the variants of a canonical miRNA-sequence with alteration at the 3` or 5` termini due to addition, deletion and/or substitution of nucleotide. The present study aims at identifying the isomiRs of the expressed miRNAs in peripheral blood mononuclear cells (PBMCs) of diseased vis-à-vis healthy buffaloes, vis-à-vis exploring the molecular pathways of the predicted target genes of the isomiRs/miRNAs. Four groups of experimental animals (adult, male or female) were included in the study: a) Brucellosis (Murrah breed), b) Paratuberculosis or Johne’s disease (Murrah breed); c) Brucellosis (Nili-Ravi breed) and d) control group of healthy buffaloes of the Murrah breed. The small RNA (sRNA) samples, extracted from PBMCs of each of the four groups, pooled into four samples and then were subjected to next-generation sequencing (Ion-Torrent PGM™ platform). The NGS data were analyzed using the miRanalyzer tool and R-programming to identify the differentially expressed (up and down-regulated (fold change ratio > 2)) miRNAs (exhibiting isomiRs and uniquely expressed miRNAs having isomiRs) of each of the three disease-groups as compared to the healthy-Murrah group. The target genes of these selected differentially and uniquely expressed miRNA & isomiRs were predicted using three different online tools (TargetScan, PicTar, and miRDB). These target genes were analyzed to determine their role in systems biology. We identified 153, 125 and 139 isomiR-exhibiting miRNAs that were common in those three experimental groups (healthy vs. Brucellosis-Murrah, Johne’s disease-Murrah, and Brucellosis-Nili-Ravi, respectively). Gene ontology and pathway analyses of the target genes (Panther classification system) yielded several biological hits. Functional classification of the target genes indicated that these target genes were involved in different systems biology related functions like molecular binding, enzyme modulation, signal modulation, etc. The specificity of function was varying in the three experimental groups. We are presenting the first report on the identification of isomiRs and functional classification of the target genes in water buffaloes. The results revealed that isomiRs may be involved in the biological processes and can be used in disease diagnosis.
Tài liệu tham khảo
citation_journal_title=Nature; citation_title=The functions of animal microRNAs; citation_author=V Ambros; citation_volume=431; citation_issue=2006; citation_publication_date=2004; citation_pages=350-355; citation_doi=10.1038/nature02871; citation_id=CR1
citation_journal_title=PLoSComput Biol; citation_title=Characterization and identification of microRNA core promoters in four model species; citation_author=X Zhou, J Ruan, G Wang, W Zhang, R Wang; citation_volume=3; citation_issue=3; citation_publication_date=2007; citation_pages=e37; citation_id=CR2
citation_journal_title=World J Exp Med; citation_title=MicroRNA-regulated viral vectors for gene therapy; citation_author=A Geisler, H Fechner; citation_volume=6; citation_issue=2; citation_publication_date=2016; citation_pages=37-54; citation_doi=10.5493/wjem.v6.i2.37; citation_id=CR3
citation_journal_title=Mol Clin Oncol; citation_title=The role of microRNAs in gallbladder cancer; citation_author=G Yang, L Zhang, R Li, L Wang; citation_volume=5; citation_publication_date=2016; citation_pages=7-13; citation_doi=10.3892/mco.2016.905; citation_id=CR4
citation_journal_title=Annu Rev Biochem; citation_title=Regulation of mRNA translation and stability by microRNAs; citation_author=MR Fabian, N Sonenberg, W Filipowicz; citation_volume=79; citation_publication_date=2010; citation_pages=351-379; citation_doi=10.1146/annurev-biochem-060308-103103; citation_id=CR5
citation_journal_title=RNA; citation_title=Complexity of the microRNA repertoire revealed by next-generation sequencing; citation_author=LW Lee, S Zhang, A Etheridge, L Ma, D Martin, D Galas, K Wang; citation_volume=16; citation_issue=11; citation_publication_date=2010; citation_pages=2170-2180; citation_doi=10.1261/rna.2225110; citation_id=CR6
Guo L, Liang T, Yu J, Zou Q. A Comprehensive Analysis of miRNA/isomer Expression with Gender Difference. PLoS One. 2016;11(5):e0154955.
https://doi.org/10.1371/journal.pone.0154955
.
Singh J, Mukhopadhyay CS, Kaur S, Malhotra P, Sethi RS, Choudhary RK. Identification of the MicroRNA Repertoire in TLR-Ligand Challenged Bubaline PBMCs as a Model of Bacterial and Viral Infection. PLoS One. 2016:e0156598.
https://doi.org/10.1371/journal.pone.0156598
.
citation_journal_title=PLoS One; citation_title=Illumina Sequencing Reveals Aberrant Expression of MicroRNAs and Their Variants in Whitefish (Coregonus lavaretus) Liver after Exposure to Microcystin-LR; citation_author=P Brzuzan, M Florczyk, A Łakomiak, M Woźny; citation_volume=11; citation_issue=7; citation_publication_date=2016; citation_pages=e0158899; citation_doi=10.1371/journal.pone.0158899; citation_id=CR9
citation_journal_title=Gene; citation_title=Dysregulation of miRNA isoform level at 5′ end in Alzheimer's disease; citation_author=S Wang, Y Xu, M Li, J Tu, Z Lu; citation_volume=584; citation_issue=2; citation_publication_date=2016; citation_pages=167-172; citation_doi=10.1016/j.gene.2016.02.020; citation_id=CR10
citation_journal_title=PLoS One; citation_title=Distinctive profile of IsomiR expression and novel microRNAs in rat heart left ventricle; citation_author=MK McGahon, JM Yarham, A Daly, J Guduric-Fuchs, LJ Ferguson, DA Simpson, A Collins; citation_volume=8; citation_issue=6; citation_publication_date=2013; citation_pages=e65809; citation_doi=10.1371/journal.pone.0065809; citation_id=CR11
citation_journal_title=Malaysian J Pathol; citation_title=IsomiRs have functional importance; citation_author=TG Chin, D Nicholas; citation_volume=37; citation_issue=2; citation_publication_date=2015; citation_pages=73-81; citation_id=CR12
citation_journal_title=Sci China Life Sci; citation_title=Uridylation and adenylation of RNAs; citation_author=J Song, J Song, B Mo, XM Chen; citation_volume=58; citation_publication_date=2015; citation_pages=1057; citation_doi=10.1007/s11427-015-4954-9; citation_id=CR13
citation_journal_title=Plant BiotechnolJ; citation_title=Global microRNA modification in cotton (Gossypium hirsutum L.); citation_author=F Xie, Q Wang, B Zhang; citation_volume=13; citation_publication_date=2015; citation_pages=492-500; citation_doi=10.1111/pbi.12271; citation_id=CR14
citation_journal_title=BMC Genomics; citation_title=A highly expressed miR-101 isomiR is a functional silencing small RNA; citation_author=F Llorens, M Bañez-Coronel, L Pantano, JA Río, I Ferrer, X Estivill, E Martí; citation_volume=14; citation_publication_date=2013; citation_pages=104; citation_doi=10.1186/1471-2164-14-104; citation_id=CR15
citation_journal_title=Nucleic Acids Res; citation_title=miRanalyzer: a microRNA detection and analysis tool for next- generation sequencing experiments; citation_author=M Hackenberg, M Sturm, D Langenberger, JM Falcon-Perez, AM Aransay; citation_volume=37; citation_publication_date=2009; citation_pages=W68-W76; citation_doi=10.1093/nar/gkp347; citation_id=CR16
Singh J, Dhanoa JK, Choudhary RK, Singh A, Sethi RS, Mukhopadhyay CS. Discovery and comparative analysis of bubaline microRNAs in PBMCs of diseased vis-à-vis healthy Indian water buffalo. Computational Biology and Chemistry. In pipeline.
citation_journal_title=Nucleic Acids Res; citation_title=miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades; citation_author=MR Friedländer, SD Mackowiak, N Li, W Chen, N Rajewsky; citation_volume=40; citation_issue=1; citation_publication_date=2012; citation_pages=37-52; citation_doi=10.1093/nar/gkr688; citation_id=CR18
citation_journal_title=Genome Res; citation_title=PANTHER: a library of protein families and subfamilies indexed by function; citation_author=PD Thomas, MJ Campbell, A Kejariwal, H Mi, B Karlak, R Daverman, K Diemer, A Muruganujan, A Narechania; citation_volume=13; citation_issue=9; citation_publication_date=2003; citation_pages=2129-2141; citation_doi=10.1101/gr.772403; citation_id=CR19
citation_journal_title=Nucleic Acids Res; citation_title=PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways; citation_author=H Mi, N Guo, A Kejariwal, PD Thomas; citation_volume=35; citation_issue=Database; citation_publication_date=2007; citation_pages=D247-DD52; citation_doi=10.1093/nar/gkl869; citation_id=CR20
citation_journal_title=Nucleic Acids Res; citation_title=Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists; citation_author=DW Huang, BT Sherman, RA Lempicki; citation_volume=37; citation_issue=1; citation_publication_date=2009; citation_pages=1-13; citation_doi=10.1093/nar/gkn923; citation_id=CR21
citation_journal_title=Nature Protoc; citation_title=Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources; citation_author=DW Huang, BT Sherman, RA Lempicki; citation_volume=4; citation_issue=1; citation_publication_date=2009; citation_pages=44-57; citation_doi=10.1038/nprot.2008.211; citation_id=CR22
Myers MJ, Murtaugh MP. Cytokines in Animal Health and Disease. 1st ed: CRC Press; 1995. ISBN-10: 0824794354
citation_journal_title=PLoS One; citation_title=Differentially Expressed Genes in Resistant and Susceptible Common Bean (Phaseolus vulgaris L.) Genotypes in Response to Fusarium oxysporum f. sp. phaseoli; citation_author=R Xue, J Wu, Z Zhu, L Wang, X Wang, S Wang; citation_volume=10; citation_issue=6; citation_publication_date=2015; citation_pages=e0127698; citation_doi=10.1371/journal.pone.0127698; citation_id=CR24
citation_journal_title=J Clin Res Ped Endo; citation_title=Diagnosis of Diseases of Steroid Hormone Production, Metabolism and Action; citation_author=JW Honour; citation_volume=1; citation_issue=5; citation_publication_date=2009; citation_pages=209-226; citation_doi=10.4274/jcrpe.v1i5.209; citation_id=CR25
citation_journal_title=Cell Mol Life Sci; citation_title=The epidermal growth factor receptor family: Biology driving targeted therapeutics; citation_author=MJ Wieduwilt, MM Moasser; citation_volume=65; citation_issue=10; citation_publication_date=2008; citation_pages=1566-1584; citation_doi=10.1007/s00018-008-7440-8; citation_id=CR26
citation_journal_title=BMC Research Notes; citation_title=Computational prediction of disease microRNAs in domestic animals; citation_author=T Buza, M Arick, H Wang, DG Peterson; citation_volume=7; citation_publication_date=2014; citation_pages=403; citation_doi=10.1186/1756-0500-7-403; citation_id=CR27
citation_journal_title=Trends Genet; citation_title=IsomiRs – the overlooked repertoire in the dynamic microRNAome; citation_author=CT Neilsen, GJ Goodall, CP Bracken; citation_volume=28; citation_issue=11; citation_publication_date=2012; citation_pages=544-549; citation_doi=10.1016/j.tig.2012.07.005; citation_id=CR28
citation_journal_title=Curr Opin Genet Dev; citation_title=The evolution of animal microRNA function; citation_author=R Niwa, FJ Slack; citation_volume=17; citation_publication_date=2007; citation_pages=145-150; citation_doi=10.1016/j.gde.2007.02.004; citation_id=CR29
citation_journal_title=Genome Biol; citation_title=MicroRNAs and their isomiRs function cooperatively to target common biological pathways; citation_author=N Cloonan, S Wani, Q Xu, J Gu, K Lea, S Heater, C Barbacioru, AL Steptoe; citation_volume=12; citation_publication_date=2011; citation_pages=R126; citation_doi=10.1186/gb-2011-12-12-r126; citation_id=CR30
citation_journal_title=PLoS Genet; citation_title=Bacterial Infection Drives the Expression Dynamics of microRNAs and their isomiRs; citation_author=KJ Siddle, L Tailleux, M Deschamps, YHE Loh, C Deluen, B Gicquel; citation_volume=11; citation_issue=3; citation_publication_date=2015; citation_pages=e1005064; citation_doi=10.1371/journal.pgen.1005064; citation_id=CR31
citation_journal_title=Proc Natl Acad Sci U S A; citation_title=PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease; citation_author=J Boele, H Persson, JW Shin, Y Ishizu, IS Newie, R Søkilde, SM Hawkins, C Coarfa, K Ikeda, K-I Takayama; citation_volume=111; citation_publication_date=2014; citation_pages=11467-11472; citation_doi=10.1073/pnas.1317751111; citation_id=CR32
citation_journal_title=Genes Dev; citation_title=Selective stabilization of mammalian microRNAs by 3′ adenylation mediated by the cytoplasmic poly (A) polymerase GLD-2; citation_author=T Katoh, Y Sakaguchi, K Miyauchi, T Suzuki, S-I Kashiwabara, T Baba, T Suzuki; citation_volume=23; citation_publication_date=2009; citation_pages=433-438; citation_doi=10.1101/gad.1761509; citation_id=CR33
citation_journal_title=Nature; citation_title=CPEB and two poly (A) polymerases control miR-122 stability and p53 mRNA translation; citation_author=DM Burns, A D’Ambrogio, S Nottrott, JD Richter; citation_volume=473; citation_publication_date=2011; citation_pages=105-108; citation_doi=10.1038/nature09908; citation_id=CR34
citation_journal_title=Comput Biol Chem; citation_title=Biocomputational identification and validation of novel microRNAs predicted from bubaline whole genome shotgun sequences; citation_author=HK Manku, JK Dhanoa, S Kaur, JS Arora, CS Mukhopadhyay; citation_volume=70; citation_publication_date=2017; citation_pages=96-106; citation_doi=10.1016/j.compbiolchem.2017.08.005; citation_id=CR35
citation_journal_title=PLoS One; citation_title=Analysis of Biobanked Serum from a Mycobacterium avium subsp Johne’s disease Bovine Infection Model Confirms the Remarkable Stability of Circulating miRNA Profiles and Defines a Bovine Serum miRNA Repertoire; citation_author=RG Shaughnessy, D Farrell, K Riepema, D Bakker, SV Gordon; citation_volume=10; citation_issue=12; citation_publication_date=2015; citation_pages=e0145089; citation_doi=10.1371/journal.pone.0145089; citation_id=CR36
citation_journal_title=Bioinformatics; citation_title=isomiRID: a framework to identify microRNA isoforms; citation_author=LFV Oliveira, AP Christoff, R Margis; citation_volume=29; citation_issue=20; citation_publication_date=2013; citation_pages=2521-2523; citation_doi=10.1093/bioinformatics/btt424; citation_id=CR37
citation_journal_title=Front PlantSci; citation_title=isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology; citation_author=G Sablok, AK Srivastva, P Suprasanna, V Baev, PJ Ralph; citation_volume=6; citation_publication_date=2015; citation_pages=949; citation_doi=10.3389/fpls.2015.00949; citation_id=CR38
citation_journal_title=Nucleic Acids Res; citation_title=DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data; citation_author=Y Zhang, Q Zang, H Zhang, R Ban, Y Yang, F Iqbal, A Li, Q Shi; citation_volume=44; citation_publication_date=2016; citation_pages=W166-W175; citation_doi=10.1093/nar/gkw427; citation_id=CR39
citation_journal_title=BMC Bioinformatics; citation_title=isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation; citation_author=G Urgese, G Paciello, A Acquaviva, E Ficarra; citation_volume=17; citation_publication_date=2016; citation_pages=148; citation_doi=10.1186/s12859-016-0958-0; citation_id=CR40
citation_journal_title=Sci Rep; citation_title=mirPRo – a novel standalone program for differential expression and variation analysis of miRNAs; citation_author=J Shi, M Dong, L Li, L Liu, A Luz-Madrigal, PA Tsonis, K Rio-Tsonis, C Liang; citation_volume=5; citation_publication_date=2015; citation_pages=14617; citation_doi=10.1038/srep14617; citation_id=CR41
