{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T22:12:22Z","timestamp":1783548742971,"version":"3.55.0"},"reference-count":77,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T00:00:00Z","timestamp":1611792000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Interleukin-27 (IL-27) is a pleiotropic cytokine that influences the innate and adaptive immune systems. It inhibits viral infection and regulates the expression of microRNAs (miRNAs). We recently reported that macrophages differentiated from human primary monocytes in the presence of IL-27 and human AB serum resisted human immunodeficiency virus (HIV) infection and showed significant autophagy induction. In the current study, the miRNA profiles in these cells were investigated, especially focusing on the identification of novel miRNAs regulated by IL-27-treatment. The miRNA sequencing analysis detected 38 novel miRNAs. Real-time reverse transcription polymerase chain reaction (RT-PCR) analysis confirmed that IL-27 differentially regulated the expression of 16 of the 38 miRNAs. Overexpression of the synthesized miRNA mimics by transfection revealed that miRAB40 had potent HIV-inhibiting and autophagy-inducing properties. B18R, an interferon (IFN)-neutralization protein, partially suppressed both activities, indicating that the two functions were induced via IFN-dependent and -independent pathways. Although the target mRNA(s) of miRAB40 involving in the induction of both functions was unable to identify in this study, the discovery of miRAB40, a potential HIV-inhibiting and autophagy inducing miRNA, may provide novel insights into the miRNA (small none-coding RNA)-mediated regulation of HIV inhibition and autophagy induction as an innate immune response.<\/jats:p>","DOI":"10.3390\/ijms22031290","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T09:03:45Z","timestamp":1611824625000},"page":"1290","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["MicroRNA Profiles in Monocyte-Derived Macrophages Generated by Interleukin-27 and Human Serum: Identification of a Novel HIV-Inhibiting and Autophagy-Inducing MicroRNA"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1474-1796","authenticated-orcid":false,"given":"Tomozumi","family":"Imamichi","sequence":"first","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suranjana","family":"Goswami","sequence":"additional","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojun","family":"Hu","sequence":"additional","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvain","family":"Laverdure","sequence":"additional","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Yang","sequence":"additional","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ju","family":"Qiu","sequence":"additional","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Chen","sequence":"additional","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brad T.","family":"Sherman","sequence":"additional","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1413-2763","authenticated-orcid":false,"given":"Weizhong","family":"Chang","sequence":"additional","affiliation":[{"name":"Laboratory of Human Retrovirology and Immunoinformatics, Applied and Development Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,1,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"D155","DOI":"10.1093\/nar\/gky1141","article-title":"miRBase: From microRNA sequences to function","volume":"47","author":"Kozomara","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41580-018-0045-7","article-title":"Regulation of microRNA function in animals","volume":"20","author":"Gebert","year":"2019","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.molcel.2016.09.004","article-title":"Pairing beyond the Seed Supports MicroRNA Targeting Specificity","volume":"64","author":"Broughton","year":"2016","journal-title":"Mol. Cell"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1002\/wrna.121","article-title":"Posttranscriptional upregulation by microRNAs","volume":"3","author":"Vasudevan","year":"2012","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.semcdb.2014.05.015","article-title":"Functional interactions among microRNAs and long noncoding RNAs","volume":"34","author":"Yoon","year":"2014","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nrg.2016.20","article-title":"Endogenous microRNA sponges: Evidence and controversy","volume":"17","author":"Thomson","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2007","DOI":"10.1002\/jcp.25854","article-title":"Interplay between miRNAs and human diseases","volume":"233","author":"Paul","year":"2018","journal-title":"J. Cell. Physiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/nrd.2016.246","article-title":"MicroRNA therapeutics: Towards a new era for the management of cancer and other diseases","volume":"16","author":"Rupaimoole","year":"2017","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1093\/cvr\/cvw174","article-title":"Identifying circulating microRNAs as biomarkers of cardiovascular disease: A systematic review","volume":"111","author":"Navickas","year":"2016","journal-title":"Cardiovasc. Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"402","DOI":"10.3389\/fendo.2018.00402","article-title":"Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation","volume":"9","author":"Hayder","year":"2018","journal-title":"Front. Endocrinol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"7321","DOI":"10.1038\/ncomms8321","article-title":"Exosome-delivered microRNAs modulate the inflammatory response to endotoxin","volume":"6","author":"Alexander","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.3389\/fimmu.2020.01167","article-title":"Exosomal MicroRNAs as Mediators of Cellular Interactions Between Cancer Cells and Macrophages","volume":"11","author":"Kwon","year":"2020","journal-title":"Front. Immunol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1002\/1878-0261.12144","article-title":"Cell-to-cell communication: MicroRNAs as hormones","volume":"11","author":"Bayraktar","year":"2017","journal-title":"Mol. Oncol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"119","DOI":"10.3389\/fgene.2013.00119","article-title":"Circulating miRNAs: Cell-cell communication function?","volume":"4","author":"Turchinovich","year":"2013","journal-title":"Front. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1038\/nature06205","article-title":"Interferon modulation of cellular microRNAs as an antiviral mechanism","volume":"449","author":"Pedersen","year":"2007","journal-title":"Nature"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"167","DOI":"10.4103\/1735-5362.253364","article-title":"Inhibition of herpes simplex virus type 1 replication by novel hsa-miR-7704 in vitro","volume":"14","author":"Shabani","year":"2019","journal-title":"Res. Pharm. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/ni.2366","article-title":"IL-12 family cytokines: Immunological playmakers","volume":"13","author":"Vignali","year":"2012","journal-title":"Nat. Immunol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1146\/annurev-immunol-032414-112134","article-title":"The immunobiology of interleukin-27","volume":"33","author":"Yoshida","year":"2015","journal-title":"Annu. Rev. Immunol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.imlet.2008.01.011","article-title":"Advances in understanding the anti-inflammatory properties of IL-27","volume":"117","author":"Stumhofer","year":"2008","journal-title":"Immunol. Lett."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.cytogfr.2015.07.008","article-title":"The biology of interleukin-27 reveals unique pro- and anti-inflammatory functions in immunity","volume":"26","author":"Garbers","year":"2015","journal-title":"Cytokine Growth Factor Rev."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5377","DOI":"10.4049\/jimmunol.177.8.5377","article-title":"Two-Sided Roles of IL-27: Induction of Th1 Differentiation on Naive CD4+ T Cells versus Suppression of Proinflammatory Cytokine Production Including IL-23-Induced IL-17 on Activated CD4+ T Cells Partially Through STAT3-Dependent Mechanism","volume":"177","author":"Yoshimura","year":"2006","journal-title":"J. Immunol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"43441","DOI":"10.1038\/srep43441","article-title":"Interleukin-27 Enhances the Potential of Reactive Oxygen Species Generation from Monocyte-derived Macrophages and Dendritic cells by Induction of p47phox","volume":"7","author":"Sowrirajan","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1182\/blood-2006-02-001578","article-title":"Noninfectious papilloma virus-like particles inhibit HIV-1 replication: Implications for immune control of HIV-1 infection by IL-27","volume":"109","author":"Fakruddin","year":"2007","journal-title":"Blood"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1864","DOI":"10.1182\/blood-2009-03-211540","article-title":"Interleukin-27 inhibition of HIV-1 involves an intermediate induction of type I interferon","volume":"114","author":"Jin","year":"2009","journal-title":"Blood"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1084\/jem.20120572","article-title":"IL-27 inhibits HIV-1 infection in human macrophages by down-regulating host factor SPTBN1 during monocyte to macrophage differentiation","volume":"210","author":"Dai","year":"2013","journal-title":"J. Exp. Med."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/j.cytogfr.2013.07.001","article-title":"Evaluating the potential of IL-27 as a novel therapeutic agent in HIV-1 infection","volume":"24","author":"Swaminathan","year":"2013","journal-title":"Cytokine Growth Factor Rev."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/j.bbrc.2013.03.046","article-title":"Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties","volume":"434","author":"Swaminathan","year":"2013","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"164","DOI":"10.4049\/jimmunol.200.Supp.164.7","article-title":"IL-27 induces autophagy during monocyte-to-macrophage differentiation through a novel LC3-independent pathway","volume":"200","author":"Laverdure","year":"2018","journal-title":"J. Immunol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Hu, X., Chen, Q., Sowrirajan, B., Bosche, M., Imamichi, T., and Sherman, B.T. (2017). Genome-Wide Analyses of MicroRNA Profiling in Interleukin-27 Treated Monocyte-Derived Human Dendritic Cells Using Deep Sequencing: A Pilot Study. Int. J. Mol. Sci., 18.","DOI":"10.3390\/ijms18050925"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Goswami, S., Hu, X., Chen, Q., Qiu, J., Yang, J., Poudyal, D., Sherman, B.T., Chang, W., and Imamichi, T. (2020). Profiles of MicroRNAs in Interleukin-27-Induced HIV-Resistant T cells: Identification of a Novel Anti-Viral MicroRNA. J. Acquir. Immune Defic. Syndr., Online Ahead of Print.","DOI":"10.1097\/QAI.0000000000002565"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"eLife"},{"key":"ref_32","unstructured":"Kanellos, I., Vergoulis, T., Sacharidis, D., Dalamagas, T., Hatzigeorgiou, A., Sartzetakis, S., and Sellis, T. (July, January 30). MR-microT: A MapReduce-based MicroRNA target prediction method. Proceedings of the 26th International Conference on Scientific and Statistical Database Management, Aalborg, Denmark."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., and Marks, D.S. (2004). Human MicroRNA Targets. PLoS Biol., 2.","DOI":"10.1371\/journal.pbio.0020363"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"D127","DOI":"10.1093\/nar\/gkz757","article-title":"miRDB: An online database for prediction of functional microRNA targets","volume":"48","author":"Chen","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1002\/art.24436","article-title":"MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins","volume":"60","author":"Tang","year":"2009","journal-title":"Arthritis Rheum."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1002\/JLB.3MR0218-079R","article-title":"MicroRNA miR-223 as regulator of innate immunity","volume":"104","author":"Yuan","year":"2018","journal-title":"J. Leukoc. Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1007\/978-1-4939-1538-5_19","article-title":"Overcoming the challenges of siRNA activation of innate immunity: Design better therapeutic siRNAs","volume":"1218","author":"Sioud","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1093\/nar\/gkt844","article-title":"siRNA enhances DNA-mediated interferon lambda-1 response through crosstalk between RIG-I and IFI16 signalling pathway","volume":"42","author":"Sui","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.cyto.2011.08.022","article-title":"Autophagy and cytokines","volume":"56","author":"Harris","year":"2011","journal-title":"Cytokine"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1016\/0092-8674(95)90076-4","article-title":"Vaccinia virus encodes a soluble type I interferon receptor of novel structure and broad species specificity","volume":"81","author":"Symons","year":"1995","journal-title":"Cell"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1126\/science.1152725","article-title":"Identification of host proteins required for HIV infection through a functional genomic screen","volume":"319","author":"Brass","year":"2008","journal-title":"Science"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1016\/j.chom.2008.10.004","article-title":"Genome-scale RNAi screen for host factors required for HIV replication","volume":"4","author":"Zhou","year":"2008","journal-title":"Cell Host Microbe"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.cell.2008.07.032","article-title":"Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication","volume":"135","author":"Konig","year":"2008","journal-title":"Cell"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Chen, Q., Swaminathan, S., Yang, D., Dai, L., Sui, H., Yang, J., Hornung, R.L., Wang, Y., Huang, D.W., and Hu, X. (2013). Interleukin-27 is a potent inhibitor of cis HIV-1 replication in monocyte-derived dendritic cells via a type I interferon-independent pathway. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0059194"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1089\/jir.2009.0093","article-title":"Interleukin-27, an anti-HIV-1 cytokine, inhibits replication of hepatitis C virus","volume":"30","author":"Frank","year":"2010","journal-title":"J. Interferon Cytokine Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1097\/QAD.0000000000002288","article-title":"IL-27 posttranslationally regulates Y-box binding protein-1 to inhibit HIV-1 replication in human CD4+ T cells","volume":"33","author":"Poudyal","year":"2019","journal-title":"AIDS"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"287","DOI":"10.4161\/auto.22831","article-title":"IFNB1\/interferon-\u03b2-induced autophagy in MCF-7 breast cancer cells counteracts its proapoptotic function","volume":"9","author":"Ejlerskov","year":"2013","journal-title":"Autophagy"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1126\/science.1136880","article-title":"Autophagy-dependent viral recognition by plasmacytoid dendritic cells","volume":"315","author":"Lee","year":"2007","journal-title":"Science"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/s41590-019-0556-1","article-title":"Regulation of cGAS- and RLR-mediated immunity to nucleic acids","volume":"21","author":"Ablasser","year":"2020","journal-title":"Nat. Immunol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"334","DOI":"10.3389\/fimmu.2015.00334","article-title":"MicroRNA as Type I Interferon-Regulated Transcripts and Modulators of the Innate Immune Response","volume":"6","author":"Forster","year":"2015","journal-title":"Front. Immunol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"ra74","DOI":"10.1126\/scisignal.2001614","article-title":"Short RNA duplexes elicit RIG-I-mediated apoptosis in a cell type- and length-dependent manner","volume":"4","author":"Ishibashi","year":"2011","journal-title":"Sci. Signal."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1093\/cvr\/cvn156","article-title":"Role of microRNAs in vascular diseases, inflammation, and angiogenesis","volume":"79","author":"Urbich","year":"2008","journal-title":"Cardiovasc. Res."},{"key":"ref_54","first-page":"161","article-title":"The Role of MicroRNAs in Human Diseases","volume":"2","author":"Ardekani","year":"2010","journal-title":"Avicenna J. Med. Biotechnol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-94-007-5590-1_1","article-title":"MicroRNAs in human cancer","volume":"774","author":"Farazi","year":"2013","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.molmed.2012.12.002","article-title":"IL-27 in tumor immunity and immunotherapy","volume":"19","author":"Murugaiyan","year":"2013","journal-title":"Trends Mol. Med."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"3958069","DOI":"10.1155\/2017\/3958069","article-title":"Dual Roles of IL-27 in Cancer Biology and Immunotherapy","volume":"2017","author":"Fabbi","year":"2017","journal-title":"Mediat. Inflamm."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1089\/aid.1996.12.191","article-title":"Construction and characterization of a stable full-length macrophage-tropic HIV type 1 molecular clone that directs the production of high titers of progeny virions","volume":"12","author":"Theodore","year":"1996","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1006\/viro.1995.1016","article-title":"Vpr is required for efficient replication of human immunodeficiency virus type-1 in mononuclear phagocytes","volume":"206","author":"Connor","year":"1995","journal-title":"Virology"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"6705","DOI":"10.1128\/jvi.69.11.6705-6711.1995","article-title":"Human immunodeficiency virus type 1 viral protein R (Vpr) arrests cells in the G2 phase of the cell cycle by inhibiting p34cdc2 activity","volume":"69","author":"He","year":"1995","journal-title":"J. Virol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1093\/bib\/bbv019","article-title":"Optimization of miRNA-seq data preprocessing","volume":"16","author":"Tam","year":"2015","journal-title":"Brief. Bioinform."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"1000 Genome Project Data Processing Subgroup The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"D140","DOI":"10.1093\/nar\/gkj112","article-title":"miRBase: MicroRNA sequences, targets and gene nomenclature","volume":"34","author":"Grocock","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: A flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/nar\/gkr688","article-title":"miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades","volume":"40","author":"Friedlander","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: The reference human genome annotation for The ENCODE Project","volume":"22","author":"Harrow","year":"2012","journal-title":"Genome Res."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"D130","DOI":"10.1093\/nar\/gku1063","article-title":"Rfam 12.0: Updates to the RNA families database","volume":"43","author":"Nawrocki","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1748-7188-2-6","article-title":"RNAstrand: Reading direction of structured RNAs in multiple sequence alignments","volume":"2","author":"Reiche","year":"2007","journal-title":"Algorithms Mol. Biol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1038\/s41598-018-19259-4","article-title":"A novel microRNA, hsa-miR-6852 differentially regulated by Interleukin-27 induces necrosis in cervical cancer cells by downregulating the FoxM1 expression","volume":"8","author":"Poudyal","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"10958","DOI":"10.1128\/JVI.74.23.10958-10964.2000","article-title":"Relative replication fitness of a high-level 3\u2032-azido-3\u2032-deoxythymidine-resistant variant of human immunodeficiency virus type 1 possessing an amino acid deletion at codon 67 and a novel substitution (Thr-->Gly) at codon 69","volume":"74","author":"Imamichi","year":"2000","journal-title":"J. Virol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/3\/1290\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:16:41Z","timestamp":1760159801000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/3\/1290"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,1,28]]},"references-count":77,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2021,2]]}},"alternative-id":["ijms22031290"],"URL":"https:\/\/doi.org\/10.3390\/ijms22031290","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,1,28]]}}}