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      A dysregulated sebum–microbial metabolite–IL-33 axis initiates skin inflammation in atopic dermatitis

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          Abstract

          This study demonstrates that a dysregulated sebum–microbial metabolite–IL-33 axis is involved in the pathogenesis of atopic dermatitis, possibly by playing an initiating role in the induction of skin inflammation.

          Abstract

          Microbial dysbiosis in the skin has been implicated in the pathogenesis of atopic dermatitis (AD); however, whether and how changes in the skin microbiome initiate skin inflammation, or vice versa, remains poorly understood. Here, we report that the levels of sebum and its microbial metabolite, propionate, were lower on the skin surface of AD patients compared with those of healthy individuals. Topical propionate application attenuated skin inflammation in mice with MC903-induced AD-like dermatitis by inhibiting IL-33 production in keratinocytes, an effect that was mediated through inhibition of HDAC and regulation of the AhR signaling pathway. Mice lacking sebum spontaneously developed AD-like dermatitis, which was improved by topical propionate application. A proof-of-concept clinical study further demonstrated the beneficial therapeutic effects of topical propionate application in AD patients. In summary, we have uncovered that the dysregulated sebum–microbial metabolite–IL-33 axis might play an initiating role in AD-related skin inflammation, thereby highlighting novel therapeutic strategies for the treatment of AD.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

            Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
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              KEGG for linking genomes to life and the environment

              KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ValidationRole: VisualizationRole: Writing - original draft
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: Writing - original draft
                Role: InvestigationRole: ResourcesRole: Validation
                Role: Investigation
                Role: Formal analysis
                Role: Project administrationRole: Resources
                Role: Investigation
                Role: Formal analysis
                Role: Investigation
                Role: Resources
                Role: Investigation
                Role: ConceptualizationRole: Methodology
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing
                Journal
                J Exp Med
                J Exp Med
                jem
                The Journal of Experimental Medicine
                Rockefeller University Press
                0022-1007
                1540-9538
                03 October 2022
                16 August 2022
                : 219
                : 10
                : e20212397
                Affiliations
                [1 ] Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, PR China
                [2 ] Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, PR China
                [3 ] Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, PR China
                [4 ] Department of Dermatology, Kaifeng People’s Hospital, Kaifeng, PR China
                [5 ] Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Institutes of Integrative Medicine, Shanghai Medical College, Fudan University, Shanghai, PR China
                [6 ] Department of Cell Biology, School of Life Science, Anhui Medical University, Hefei, PR China
                [7 ] Children’s Hospital and Institute of Biomedical Sciences, Fudan University, Shanghai, PR China
                Author notes
                Correspondence to Wei Li: liweiderma@ 123456fudan.edu.cn

                Disclosures: The authors declare no competing financial interests.

                Author information
                https://orcid.org/0000-0002-4073-4194
                https://orcid.org/0000-0001-8518-8222
                https://orcid.org/0000-0002-6012-8802
                https://orcid.org/0000-0003-2777-9475
                https://orcid.org/0000-0001-9354-4899
                https://orcid.org/0000-0002-5467-4671
                https://orcid.org/0000-0003-4423-8873
                https://orcid.org/0000-0002-2253-9539
                https://orcid.org/0000-0001-9470-2705
                https://orcid.org/0000-0001-8324-0007
                https://orcid.org/0000-0001-5350-4681
                https://orcid.org/0000-0002-6050-4951
                https://orcid.org/0000-0003-3509-4775
                https://orcid.org/0000-0003-1186-8609
                Article
                jem.20212397
                10.1084/jem.20212397
                9375142
                35977109
                057259fe-bd45-48e5-aa9d-e8208f6d5bd1
                © 2022 Qiu et al.

                This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

                History
                : 29 November 2021
                : 12 May 2022
                : 07 July 2022
                Funding
                Funded by: Key Project of the Innovation Program of Shanghai Municipal Education Commission;
                Award ID: 2021-01-07-00-07-E00078
                Funded by: National Natural Science Foundation of China, DOI http://dx.doi.org/10.13039/501100001809;
                Award ID: 81972939
                Award ID: 82073446
                Award ID: 82003349
                Award ID: 82003357
                Funded by: Milstein Medical Asian American Partnership Foundation, DOI http://dx.doi.org/10.13039/100014354;
                Funded by: Nanjing Incubation Program for National Clinical Research Centre;
                Award ID: 2019060001
                Funded by: Key Project of Social Development in Jiangsu Province;
                Award ID: BE2020632
                Funded by: CAMS Innovation Fund for Medical Sciences;
                Award ID: 2021-I2M-1-059
                Categories
                Article
                Innate Immunity and Inflammation

                Medicine
                Medicine

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