Inflammatory bowel disease (IBD) is a complex, multifactorial disease with genetic, microbial and environmental risk factors combining to result in recurrent inflammation of the intestine. Genetic analyses have uncovered a cluster of IBD risk genes, which regulate a cell stress response called autophagy. Functional studies of these autophagy‐related genes highlight contributions of disease‐associated dysregulation to several aspects of IBD pathology, which include alterations in microbiome composition and bacterial responses (xenophagy), antimicrobial peptide production by Paneth cells (crinophagy), enhanced levels of proinflammatory cytokines and enhanced T‐cell subset responses. This suite of autophagy‐gene regulated responses is modulated not only by the cell type or stimulus, but also by environmental context, with the overall balance of responses critical to the maintenance of health or induction of disease. These findings have opened up new avenues for the development of IBD therapeutics and increased understanding of disease mechanisms to facilitate a more personalised approach to the treatment of IBD.
Key Concepts:
Susceptibility to IBD disease is associated with genetic variants in a spectrum of autophagy‐related genes.
Autophagy is a tightly regulated catabolic degradative pathway implicated in a number of disease‐associated processes.
Autophagy‐dependent processes altered in IBD include intracellular bacterial killing by xenophagy, Paneth cell antimicrobial peptide secretion via crinophagy, production of proinflammatory cytokines by macrophages, antigen presentation and endoplasmic reticulum (ER) stress responses in enterocytes.
Xenophagy is impaired by IBD‐associated polymorphisms in
ATG16L1
,
IRGM
,
NOD2
,
RIP2
,
PTPN2
and
XBP1
resulting in chronic inflammation due to defective clearance of intracellular pathogens.
Both impaired and enhanced crinophagy are observed in Paneth cells from IBD patients. Alterations in crinophagy supress secretion of antimicrobial peptides by these cells.
Proinflammatory cytokine production by macrophages is enhanced in IBD. This process is regulated by a balance between autophagy and inflammasome responses. Genetic variants in both pathways are associated with increased IBD susceptibility.
Defective autophagy in dendritic cells, through gene knockdown or carriage of disease risk alleles in
ATG16L1
,
IRGM
or
NOD2
, alters antigen presentation and enhances T‐cell stimulation.
ER stress activates autophagy through stimulation of the unfolded protein response mediated by XBP1. Disease‐associated alleles of
XBP1
are implicated in Paneth cell dysfunction and decreased xenophagy.