Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy

Disease Models & Mechanisms

Wilfried Haerty¹  Emily J. Jones¹  Isabelle Hautefort¹  Lejla Gul¹  Tomasz Wrzesinski¹  Federica Di Palma¹  Padhmanand Sudhakar¹  Tamas Korcsmaros¹  Agatha Treveil¹  Stuart D. Armstrong²  Penny P. Powell³  Matthew Jefferson³  Jasmine Buck³  Zoe J. Matthews³  Lindsay J. Hall⁴  Devina Divekar⁴  Tom Wileman⁴  Alastair J. M. Watson⁴  Simon R. Carding⁴  Ulrike Mayer⁵ 

[1] Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK;National Institute of Health Research, University of Liverpool, Liverpool L3 5RF, UK;Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK;Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK;School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK;

关键词: Paneth cells;    Atg16l1;    Intestinal organoids;    Quantitative proteomics;    Selective autophagy;   

DOI  :  10.1242/dmm.037069

来源: DOAJ

【 摘 要 】

Paneth cells are key epithelial cells that provide an antimicrobial barrier and maintain integrity of the small-intestinal stem cell niche. Paneth cell abnormalities are unfortunately detrimental to gut health and are often associated with digestive pathologies such as Crohn's disease or infections. Similar alterations are observed in individuals with impaired autophagy, a process that recycles cellular components. The direct effect of autophagy impairment on Paneth cells has not been analysed. To investigate this, we generated a mouse model lacking Atg16l1 specifically in intestinal epithelial cells, making these cells impaired in autophagy. Using three-dimensional intestinal organoids enriched for Paneth cells, we compared the proteomic profiles of wild-type and autophagy-impaired organoids. 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 pathways. Of the 284 altered proteins, 198 (70%) were more abundant in autophagy-impaired organoids, suggesting reduced protein degradation. Interestingly, these differentially abundant proteins comprised 116 proteins (41%) that are predicted targets of the selective autophagy proteins p62, LC3 and ATG16L1. Our integrative analysis revealed autophagy-mediated mechanisms that degrade key proteins in Paneth cell functions, such as exocytosis, apoptosis and DNA damage repair. Transcriptomic profiling of additional organoids confirmed that 90% of the observed changes upon autophagy alteration have effects at the protein level, not on gene expression. We performed further validation experiments showing differential lysozyme secretion, confirming our computationally inferred downregulation of exocytosis. Our observations could explain how protein-level alterations affect Paneth cell homeostatic functions upon autophagy impairment. This article has an associated First Person interview with the joint first authors of the paper.

【 授权许可】

Unknown