Integrative analysis of Paneth cell proteomic data from intestinal organoids reveals functional processes affected in Crohn’s disease due to autophagy impairment
Integrative analysis of Paneth cell proteomic data from intestinal organoids reveals functional processes affected in Crohn’s disease due to autophagy impairment
Abstract Crohn’s disease (CD) is associated with Paneth cell dysfunctions such as altered antimicrobial secretion that is dependent on autophagy which recycles cellular components. Patients carrying the CD risk allele in ATG16L1 – an important component of the autophagy machinery - have Paneth cell abnormalities, as reproduced in Atg16l1-deficient mouse models. However, the direct effect of Atg16l1-deficiency and autophagy-impairment in Paneth cells has not been analyzed. To investigate this, we generated a mouse model lacking Atg16l1 specifically in intestinal epithelial cells making these cells impaired in autophagy. Using a 3D intestinal organoid culture model that we enriched for Paneth cells, we compared the proteomic profiles of organoids derived from the wild-type (WT) and mice. We used an integrated computational approach combining protein-protein interaction networks, autophagy targeted proteins and functional information to identify the mechanistic link between autophagy-impairment and disrupted cellular processes. Of the 284 altered proteins, 198 (70%) were more abundant in autophagy-impaired organoids compared to WT organoids indicating a reduced protein degradation. Interestingly, the 284 differentially abundant proteins comprised 116 proteins (41%), which are potentially targeted by selective autophagy proteins such as p62, LC3 and ATG16l1. Our integrative analysis revealed autophagy-mediated mechanisms which degrade essential proteins belonging to key Paneth cell functions such as exocytosis, apoptosis and DNA damage repair. We performed validation experiments focusing on Paneth cell-derived lysozyme to confirm our inferred observation of down-regulated exocytosis. Our observations could explain how protein level alterations in CD as a result of autophagy impairment could affect Paneth cell functions. Summary statementUsing an integrative approach encompassing intestinal organoid culture, proteomics and protein-protein interaction networks, we link Paneth cell biological functions often found affected in Crohn’s disease to autophagy impairment.
Korcsmaros Tamas、Jones Emily J、Divekar Devina、Jefferson Matthew、Mayer Ulrike、Powell Penny P、Wileman Tom、Matthews Zoe J、Gul Lejla、Watson Alastair JM、Buck Jasmine、Sudhakar Padhmanand、Armstrong Stuart D、Hautefort Isabelle、Carding Simon R
Earlham Institute||Quadram InstituteEarlham Institute||Quadram Institute||Norwich Medical School, University of East AngliaQuadram Institute||Norwich Medical School, University of East AngliaNorwich Medical School, University of East AngliaSchool of Biological Sciences, University of East AngliaNorwich Medical School, University of East AngliaQuadram Institute||Norwich Medical School, University of East AngliaNorwich Medical School, University of East AngliaEarlham InstituteQuadram Institute||Norwich Medical School, University of East AngliaNorwich Medical School, University of East AngliaEarlham Institute||Quadram InstituteNational Institute of Health Research, University of LiverpoolEarlham InstituteQuadram Institute||Norwich Medical School, University of East Anglia
基础医学生物科学研究方法、生物科学研究技术生理学
Paneth cellsATG16L1intestinal organoidsquantitative proteomicsselective autophagyCrohn’s disease
Korcsmaros Tamas,Jones Emily J,Divekar Devina,Jefferson Matthew,Mayer Ulrike,Powell Penny P,Wileman Tom,Matthews Zoe J,Gul Lejla,Watson Alastair JM,Buck Jasmine,Sudhakar Padhmanand,Armstrong Stuart D,Hautefort Isabelle,Carding Simon R.Integrative analysis of Paneth cell proteomic data from intestinal organoids reveals functional processes affected in Crohn’s disease due to autophagy impairment[EB/OL].(2025-03-28)[2025-05-28].https://www.biorxiv.org/content/10.1101/410027.点此复制
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