Blood miRNomes and transcriptomes reveal novel longevity mechanisms in the long-lived bat, Myotis myotis
Tóm tắt
Chiroptera, the bats, are the only order of mammals capable of true self-powered flight. Bats exhibit a number of other exceptional traits such as echolocation, viral tolerance and, perhaps most puzzlingly, extreme longevity given their body size. Little is known about the molecular mechanisms driving their extended longevity particularly at the levels of gene expression and post-transcriptional regulation. To elucidate the molecular mechanisms that may underlie their unusual longevity, we have deep sequenced 246.5 million small RNA reads from whole blood of the long-lived greater mouse-eared bats, Myotis myotis, and conducted a series of genome-wide comparative analyses between bat and non-bat mammals (human, pig and cow) in both blood miRNomes and transcriptomes, for the first time. We identified 539 miRNA gene candidates from bats, of which 468 unique mature miRNA were obtained. More than half of these miRNA (65.1 %) were regarded as bat-specific, regulating genes involved in the immune, ageing and tumorigenesis pathways. We have also developed a stringent pipeline for genome-wide miRNome comparisons across species, and identified 37 orthologous miRNA groups shared with bat, human, pig and cow, 6 of which were differentially expressed. For bats, 3 out of 4 up-regulated miRNA (miR-101-3p, miR-16-5p, miR-143-3p) likely function as tumor suppressors against various kinds of cancers, while one down-regulated miRNA (miR-221-5p) acts as a tumorigenesis promoter in human breast and pancreatic cancers. Additionally, a genome-wide comparison of mRNA transcriptomes across species also revealed specific gene expression patterns in bats. 127 up-regulated genes were enriched mainly in mitotic cell cycle and DNA repair mechanisms, while 364 down-regulated genes were involved primarily in mitochondrial activity. Our comprehensive and integrative analyses revealed bat-specific and differentially expressed miRNA and mRNA that function in key longevity pathways, producing a distinct bat gene expression pattern. For the first time, we show that bats may possess unique regulatory mechanisms for resisting tumorigenesis, repairing cellular damage and preventing oxidative stresses, all of which likely contribute to the extraordinary lifespan of Myotis myotis.
Tài liệu tham khảo
Austad SN. Methusaleh's Zoo: how nature provides us with clues for extending human health span. J Comp Pathol. 2010;142 Suppl 1:S10–21.
Munshi-South J, Wilkinson GS. Bats and birds: Exceptional longevity despite high metabolic rates. Ageing Res Rev. 2010;9:12–9.
Selman C, Blount JD, Nussey DH, Speakman JR. Oxidative damage, ageing, and life-history evolution: where now? Trends Ecol Evol. 2012;27:570–7.
Podlutsky AJ, Khritankov AM, Ovodov ND, Austad SN. A new field record for bat longevity. J Gerontol A Biol Sci Med Sci. 2005;60:1366–8.
Seim I, Fang X, Xiong Z, Lobanov AV, Huang Z, Ma S, Feng Y, Turanov AA, Zhu Y, Lenz TL, et al. Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii. Nat Commun. 2013;4:2212.
Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell. 2003;115:787–98.
Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75:843–54.
Smith-Vikos T, Slack FJ. MicroRNAs and their roles in aging. J Cell Sci. 2012;125:7–17.
Li N, Muthusamy S, Liang R, Sarojini H, Wang E. Increased expression of miR-34a and miR-93 in rat liver during aging, and their impact on the expression of Mgst1 and Sirt1. Mech Ageing Dev. 2011;132:75–85.
Maes OC, An J, Sarojini H, Wang E. Murine microRNAs implicated in liver functions and aging process. Mech Ageing Dev. 2008;129:534–41.
Persengiev S, Kondova I, Otting N, Koeppen AH, Bontrop RE. Genome-wide analysis of miRNA expression reveals a potential role for miR-144 in brain aging and spinocerebellar ataxia pathogenesis. Neurobiol Aging. 2011;32:2316 e2317–2327.
Simmons NB. Order chiroptera, Mammal species of the world: a taxonomic and geographic reference, vol. 1. 2005. p. 312–529.
Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P, Stupka E, Rossiter SJ. Genome-wide signatures of convergent evolution in echolocating mammals. Nature. 2013;502:228–31.
Zhang G, Cowled C, Shi Z, Huang Z, Bishop-Lilly KA, Fang X, Wynne JW, Xiong Z, Baker ML, Zhao W, et al. Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science. 2013;339:456–60.
Shen YY, Liang L, Zhu ZH, Zhou WP, Irwin DM, Zhang YP. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci U S A. 2010;107:8666–71.
Lei M, Dong D, Mu S, Pan YH, Zhang S. Comparison of Brain Transcriptome of the Greater Horseshoe Bats (Rhinolophus ferrumequinum) in Active and Torpid Episodes. PLoS One. 2014;9:e107746.
Cowled C, Stewart CR, Likic VA, Friedlander MR, Tachedjian M, Jenkins KA, Tizard ML, Cottee P, Marsh GA, Zhou P, et al. Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing. BMC Genomics. 2014;15:682.
Glennon NB, Jabado O, Lo MK, Shaw ML. Transcriptome Profiling of the Virus-Induced Innate Immune Response in Pteropus vampyrus and Its Attenuation by Nipah Virus Interferon Antagonist Functions. J Virol. 2015;89:7550–66.
Dong D, Lei M, Liu Y, Zhang S. Comparative inner ear transcriptome analysis between the Rickett's big-footed bats (Myotis ricketti) and the greater short-nosed fruit bats (Cynopterus sphinx). BMC Genomics. 2013;14:916.
Platt 2nd RN, Vandewege MW, Kern C, Schmidt CJ, Hoffmann FG, Ray DA. Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Mol Biol Evol. 2014;31:1536–45.
Liew CC, Ma J, Tang HC, Zheng R, Dempsey AA. The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool. J Lab Clin Med. 2006;147:126–32.
Huang Z, Gallot A, Lao NT, Puechmaille SJ, Foley NM, Jebb D, Bekaert M, Teeling EC. A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals. Mol Ecol Resour. 2016;16:150–62.
Etebari K, Asgari S. Accuracy of microRNA discovery pipelines in non-model organisms using closely related species genomes. PLoS One. 2014;9:e84747.
Paczynska P, Grzemski A, Szydlowski M. Distribution of miRNA genes in the pig genome. BMC Genet. 2015;16:6.
Baskerville S, Bartel DP. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA. 2005;11:241–7.
Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 2004;14:1902–10.
Berezikov E. Evolution of microRNA diversity and regulation in animals. Nat Rev Genet. 2011;12:846–60.
Deng B, Fang J, Zhang X, Qu L, Cao Z, Wang B. Role of gelsolin in cell proliferation and invasion of human hepatocellular carcinoma cells. Gene. 2015;571:292–7.
Tari AM, Hung MC, Li K, Lopez-Berestein G. Growth inhibition of breast cancer cells by Grb2 downregulation is correlated with inactivation of mitogen-activated protein kinase in EGFR, but not in ErbB2, cells. Oncogene. 1999;18:1325–32.
Brooks R, Fuhler GM, Iyer S, Smith MJ, Park MY, Paraiso KH, Engelman RW, Kerr WG. SHIP1 inhibition increases immunoregulatory capacity and triggers apoptosis of hematopoietic cancer cells. J Immunol. 2010;184:3582–9.
Bos JL, Rehmann H, Wittinghofer A. GEFs and GAPs: critical elements in the control of small G proteins. Cell. 2007;129:865–77.
Ksionda O, Limnander A, Roose JP. RasGRP Ras guanine nucleotide exchange factors in cancer. Front Biol (Beijing). 2013;8:508–32.
Sharma A, Fonseca LL, Rajani C, Yanagida JK, Endo Y, Cline JM, Stone JC, Ji J, Ramos JW, Lorenzo PS. Targeted deletion of RasGRP1 impairs skin tumorigenesis. Carcinogenesis. 2014;35:1084–91.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–8.
Wang L, Li L, Guo R, Li X, Lu Y, Guan X, Gitau SC, Wang L, Xu C, Yang B, Shan H. miR-101 promotes breast cancer cell apoptosis by targeting Janus kinase 2. Cell Physiol Biochem. 2014;34:413–22.
Liu L, Yu X, Guo X, Tian Z, Su M, Long Y, Huang C, Zhou F, Liu M, Wu X. miR-143 is downregulated in cervical cancer and promotes apoptosis and inhibits tumor formation by targeting Bcl-2. Mol Med Rep. 2012;5:753–60.
Faraoni I, Antonetti FR, Cardone J, Bonmassar E. miR-155 gene: a typical multifunctional microRNA. Biochim Biophys Acta. 2009;1792:497–505.
Dhakshinamoorthy S, Jain AK, Bloom DA, Jaiswal AK. Bach1 competes with Nrf2 leading to negative regulation of the antioxidant response element (ARE)-mediated NAD(P)H:quinone oxidoreductase 1 gene expression and induction in response to antioxidants. J Biol Chem. 2005;280:16891–900.
Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature. 2011;479:223–7.
Lenaz G. The mitochondrial production of reactive oxygen species: mechanisms and implications in human pathology. IUBMB Life. 2001;52:159–64.
Crawford DR, Wang Y, Schools GP, Kochheiser J, Davies KJA. Down-regulation of mammalian mitochondrial RNAs during oxidative stress. Free Radic Biol Med. 1997;22:551–9.
Brunet-Rossinni AK. Reduced free-radical production and extreme longevity in the little brown bat (Myotis lucifugus) versus two non-flying mammals. Mech Ageing Dev. 2004;125:11–20.
Zhao Z, Oh S, Li D, Ni D, Pirooz SD, Lee J-H, Yang S, Lee J-Y, Ghozalli I, Costanzo V. A dual role for UVRAG in maintaining chromosomal stability independent of autophagy. Dev Cell. 2012;22:1001–16.
Gudmundsdottir K, Ashworth A. The roles of BRCA1 and BRCA2 and associated proteins in the maintenance of genomic stability. Oncogene. 2006;25:5864–74.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2.
Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7:e30619.
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol. 2008;26:407–15.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.
Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42:D68–73.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2004;5:R1.
Conesa A, Gotz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008;2008:619832.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45.
Bao H, Kommadath A, Sun X, Meng Y, Arantes AS, Plastow GS, Guan LL, Stothard P. Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species. BMC Genomics. 2013;14:609.
Leidinger P, Backes C, Deutscher S, Schmitt K, Mueller SC, Frese K, Haas J, Ruprecht K, Paul F, Stahler C, et al. A blood based 12-miRNA signature of Alzheimer disease patients. Genome Biol. 2013;14:R78.
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
Memczak S, Papavasileiou P, Peters O, Rajewsky N. Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood. PLoS One. 2015;10:e0141214.
Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007;23:1061–7.
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database. 2011;2011:bar030.
Patro R, Mount SM, Kingsford C. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nat Biotechnol. 2014;32:462–4.
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.