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      Dual role of the miR‐146 family in rhinovirus‐induced airway inflammation and allergic asthma exacerbation

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          Abstract

          Rhinovirus (RV) infections are associated with asthma exacerbations. MicroRNA‐146a and microRNA‐146b (miR‐146a/b) are anti‐inflammatory miRNAs that suppress signaling through the nuclear factor kappa B (NF‐κB) pathway and inhibit pro‐inflammatory chemokine production in primary human bronchial epithelial cells (HBECs). In the current study, we aimed to explore whether miR‐146a/b could regulate cellular responses to RVs in HBECs and airways during RV‐induced asthma exacerbation. We demonstrated that expression of miR‐146a/b and pro‐inflammatory chemokines was increased in HBECs and mouse airways during RV infection. However, transfection with cell‐penetrating peptide (CPP)‐miR‐146a nanocomplexes before infection with RV significantly reduced the expression of the pro‐inflammatory chemokines CCL5, IL‐8 and CXCL1, increased interferon‐λ production, and attenuated infection with the green fluorescent protein (GFP)‐expressing RV‐A16 in HBECs. Concordantly, compared to wild‐type ( wt) mice, Mir146a/b −/− mice exhibited more severe airway neutrophilia and increased T helper (Th)1 and Th17 cell infiltration in response to RV‐A1b infection and a stronger Th17 response with a less prominent Th2 response in house dust mite extract (HDM)‐induced allergic airway inflammation and RV‐induced exacerbation models. Interestingly, intranasal administration of CPP‐miR‐146a nanocomplexes reduced HDM‐induced allergic airway inflammation without a significant effect on the Th2/Th1/Th17 balance in wildtype mice. In conclusion, the overexpression of miR‐146a has a strong anti‐inflammatory effect on RV infection in HBECs and a mouse model of allergic airway inflammation, while a lack of miR‐146a/b leads to attenuated type 2 cell responses in mouse models of allergic airway inflammation and RV‐induced exacerbation of allergic airway inflammation. Furthermore, our data indicate that the application of CPP‐miR‐146a nanocomplexes has therapeutic potential for targeting airway inflammation.

          Abstract

          miR‐146a has anti‐inflammatory properties in human bronchial epithelial cells and mouse airways during rhinovirus infection and in case of allergic inflammation. Particular cell penetrating peptide(CPP)‐miR‐146a nanocomplexes have therapeutic potential for targeting of airway inflammation.

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          The Molecular Signatures Database (MSigDB) hallmark gene set collection.

          The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of "hallmark" gene sets as part of MSigDB. Each hallmark in this collection consists of a "refined" gene set, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.
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            Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

            Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
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              Predicting effective microRNA target sites in mammalian mRNAs

              MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks. DOI: http://dx.doi.org/10.7554/eLife.05005.001
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                Author and article information

                Contributors
                ana.rebane@ut.ee
                Journal
                Clin Transl Med
                Clin Transl Med
                10.1002/(ISSN)2001-1326
                CTM2
                Clinical and Translational Medicine
                John Wiley and Sons Inc. (Hoboken )
                2001-1326
                28 May 2021
                June 2021
                : 11
                : 6 ( doiID: 10.1002/ctm2.v11.6 )
                : e427
                Affiliations
                [ 1 ] Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
                [ 2 ] School of Medicine and Public Health University of Wisconsin‐Madison Madison Wisconsin USA
                [ 3 ] Department of Molecular and Cellular Biology Beckman Research Institute of City of Hope National Medical Center Duarte California USA
                [ 4 ] Institute of Technology University of Tartu Tartu Estonia
                [ 5 ] National Heart and Lung Institute Imperial College London London UK
                [ 6 ] Imperial College Healthcare NHS Trust London UK
                [ 7 ] Department of Microbiology Tumor and Cell Biology (MTC) Karolinska Institutet Stockholm Sweden
                [ 8 ] Nucleic Acid Center Department of Physics Chemistry and Pharmacy University of Southern Denmark Odense Denmark
                [ 9 ] Department of Pulmonary Medicine University of Tartu Tartu Estonia
                [ 10 ] Lung Clinic of the Tartu University Hospital Tartu Estonia
                [ 11 ] Department of Medicine Jagiellonian University Medical College Krakow Poland
                Author notes
                [*] [* ] Correspondence

                Ana Rebane, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 14B, 50414 Tartu, Estonia.

                Email: ana.rebane@ 123456ut.ee

                Author information
                https://orcid.org/0000-0002-3648-1139
                Article
                CTM2427
                10.1002/ctm2.427
                8161513
                34185416
                6c12a725-8d87-4785-87db-0dad3d8d0103
                © 2021 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 29 April 2021
                : 11 November 2020
                : 04 May 2021
                Page count
                Figures: 10, Tables: 0, Pages: 22, Words: 11400
                Funding
                Funded by: NIHR Imperial Biomedical Research Centre , open-funder-registry 10.13039/501100013342;
                Funded by: European Research Council , open-funder-registry 10.13039/501100000781;
                Award ID: 788575
                Funded by: Eesti Teadusagentuur , open-funder-registry 10.13039/501100002301;
                Award ID: PUT1669
                Award ID: PRG1259
                Award ID: PUT1617
                Funded by: Polish National Science Center
                Award ID: UMO‐2014/13/B/NZ3/02393
                Award ID: UMO‐2014/15/B/NZ5/01539
                Funded by: National Institute of Health Research
                Funded by: European Regional Development Fund , open-funder-registry 10.13039/501100008530;
                Award ID: 2014‐2020.4.01.15‐0012
                Funded by: STOP CANCER Foundation
                Funded by: National Institutes of Health , open-funder-registry 10.13039/100000002;
                Award ID: R01AI125615
                Funded by: Asthma UK Clinical Chair
                Award ID: CH11SJ
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                June 2021
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.0.2 mode:remove_FC converted:28.05.2021

                Medicine
                asthma,bronchial epithelial cell,house dust mite,microrna,neutrophils,noncoding rna,viral infection

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