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      The OSMR Gene Is Involved in Hirschsprung Associated Enterocolitis Susceptibility through an Altered Downstream Signaling

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          Abstract

          Hirschsprung (HSCR) Associated Enterocolitis (HAEC) is a common life-threatening complication in HSCR. HAEC is suggested to be due to a loss of gut homeostasis caused by impairment of immune system, barrier defense, and microbiome, likely related to genetic causes. No gene has been claimed to contribute to HAEC occurrence, yet. Genetic investigation of HAEC by Whole-Exome Sequencing (WES) on 24 HSCR patients affected (HAEC) or not affected (HSCR-only) by enterocolitis and replication of results on a larger panel of patients allowed the identification of the HAEC susceptibility variant p.H187Q in the Oncostatin-M receptor ( OSMR) gene (14.6% in HAEC and 5.1% in HSCR-only, p = 0.0024). Proteomic analysis on the lymphoblastoid cell lines from one HAEC patient homozygote for this variant and one HAEC patient not carrying the variant revealed two well distinct clusters of proteins significantly up or downregulated upon OSM stimulation. A marked enrichment in immune response pathways ( q < 0.0001) was shown in the HAEC H187 cell line, while proteins upregulated in the HAEC Q187 lymphoblasts sustained pathways likely involved in pathogen infection and inflammation. In conclusion, OSMR p.H187Q is an HAEC susceptibility variant and perturbates the downstream signaling cascade necessary for the gut immune response and homeostasis maintenance.

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          Most cited references49

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          PLINK: a tool set for whole-genome association and population-based linkage analyses.

          Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.
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            The Perseus computational platform for comprehensive analysis of (prote)omics data.

            A main bottleneck in proteomics is the downstream biological analysis of highly multivariate quantitative protein abundance data generated using mass-spectrometry-based analysis. We developed the Perseus software platform (http://www.perseus-framework.org) to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiple-hypothesis testing. A machine learning module supports the classification and validation of patient groups for diagnosis and prognosis, and it also detects predictive protein signatures. Central to Perseus is a user-friendly, interactive workflow environment that provides complete documentation of computational methods used in a publication. All activities in Perseus are realized as plugins, and users can extend the software by programming their own, which can be shared through a plugin store. We anticipate that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
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              Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1beta production.

              Systems for protein degradation are essential for tight control of the inflammatory immune response. Autophagy, a bulk degradation system that delivers cytoplasmic constituents into autolysosomes, controls degradation of long-lived proteins, insoluble protein aggregates and invading microbes, and is suggested to be involved in the regulation of inflammation. However, the mechanism underlying the regulation of inflammatory response by autophagy is poorly understood. Here we show that Atg16L1 (autophagy-related 16-like 1), which is implicated in Crohn's disease, regulates endotoxin-induced inflammasome activation in mice. Atg16L1-deficiency disrupts the recruitment of the Atg12-Atg5 conjugate to the isolation membrane, resulting in a loss of microtubule-associated protein 1 light chain 3 (LC3) conjugation to phosphatidylethanolamine. Consequently, both autophagosome formation and degradation of long-lived proteins are severely impaired in Atg16L1-deficient cells. Following stimulation with lipopolysaccharide, a ligand for Toll-like receptor 4 (refs 8, 9), Atg16L1-deficient macrophages produce high amounts of the inflammatory cytokines IL-1beta and IL-18. In lipopolysaccharide-stimulated macrophages, Atg16L1-deficiency causes Toll/IL-1 receptor domain-containing adaptor inducing IFN-beta (TRIF)-dependent activation of caspase-1, leading to increased production of IL-1beta. Mice lacking Atg16L1 in haematopoietic cells are highly susceptible to dextran sulphate sodium-induced acute colitis, which is alleviated by injection of anti-IL-1beta and IL-18 antibodies, indicating the importance of Atg16L1 in the suppression of intestinal inflammation. These results demonstrate that Atg16L1 is an essential component of the autophagic machinery responsible for control of the endotoxin-induced inflammatory immune response.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                07 April 2021
                April 2021
                : 22
                : 8
                : 3831
                Affiliations
                [1 ]Laboratory of Developmental Neurobiology, Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università di Genova, Viale Benedetto XV, 5, 16132 Genova, Italy; tiziana.bachetti@ 123456unige.it (T.B.); valentinaobino@ 123456gmail.com (V.O.); candiani@ 123456unige.it (S.C.)
                [2 ]UOSD Laboratorio di Genetica e Genomica delle Malattie Rare, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, 5, 16148 Genova, Italy; GiuseppeSantamaria@ 123456gaslini.org (G.S.); isa.c@ 123456unige.it (I.C.)
                [3 ]Health Science Department (DISSAL), Biostatistics Unit, Università di Genova, Via Pastore 1, 16132 Genova, Italy; rosamilia.francesca@ 123456libero.it
                [4 ]Core Facilities-Clinical Proteomics and Metabolomics, IRCCS, Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; martinabartolucci@ 123456gaslini.org (M.B.); andreapetretto@ 123456gaslini.org (A.P.)
                [5 ]Fetal and Perinatal Pathology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Via Gerolamo Gaslini 5, 16147 Genova, Italy; ManuelaMosconi@ 123456gaslini.org
                [6 ]COSR-Center for Omics Sciences, IRCCS Hospital San Raffaele, Dibit2-Basilica, 3A3, Via Olgettina 58, 20132 Milano, Italy; sartori.serenella@ 123456hsr.it (S.S.); defilippo.maria1983@ 123456gmail.com (M.R.D.F.)
                [7 ]Laboratorio di Fisiopatologia dell’ Uremia, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; marco.diduca@ 123456unige.it
                [8 ]Pediatric Surgery Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; StefanoAvanzini@ 123456gaslini.org
                [9 ]Department of Medical Biotechnologies and Translational Medicine, University of Milan, Via Manzoni 113, 20089 Milan, Italy; domenico.mavilio@ 123456humanitas.it
                [10 ]Laboratory of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano Milan, Italy
                [11 ]Centro Bosio per la Patologia Digestiva Pediatrica, Ospedale Infantile AON SS Antonio e Biagio e Cesare Arrigo, 15121 Alessandria, Italy; apini@ 123456ospedale.al.it
                Author notes
                [* ]Correspondence: f.lantieri@ 123456unige.it ; Tel.: +39-010-3538471; Fax: +39-010-3538441
                [†]

                T.B. and F.R. contributed equally to this work as first authors.

                Author information
                https://orcid.org/0000-0003-4979-9397
                https://orcid.org/0000-0001-5289-4219
                https://orcid.org/0000-0002-4453-5475
                https://orcid.org/0000-0002-8923-0165
                Article
                ijms-22-03831
                10.3390/ijms22083831
                8067804
                33917126
                8cc36e3f-f419-410b-b465-183d20badf22
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 11 March 2021
                : 28 March 2021
                Categories
                Article

                Molecular biology
                mucosal immunity,gut inflammation,proteomics,whole-exome sequencing (wes),hirschsprung associated enterocolitis (haec),oncostatin-m receptor (osmr)

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