Autophagy and Crohn's disease

Abstract

Advances in genetics have shed light on the molecular basis of Crohn's disease (CD) predisposition and pathogenesis, via linkage disequilibrium analysis to genome-wide association studies. The discovery of genetic variants of NOD2, an intracellular pathogen molecular sensor, as risk factors for CD has paved the way for further research on innate immunity in this disease. Remarkably, polymorphisms in autophagy genes, such as ATG16L1 and IRGM, have been identified, allowing the pivotal role of autophagy in innate immunity to be uncovered. In this review, we summarize recent studies on the CD-associated NOD2, ATG16L1 and IRGM risk variants and their contribution to the autophagy functions that have most influenced our understanding of CD pathophysiology.

Fig. 1

Impact of the CD-associated ATG16L1/Ala300 variant on xenophagy-mediated intracellular bacteria clearance during CD onset. a, b Paneth cells with the ATG16L1/Ala300 risk allele exhibit abnormalities in structure and function compared to Paneth cells with the ATG16L1/Thr300 protective allele such as decreased and disorganized granule compartments with disrupted granule exocytosis pathway (grey dotted arrow) and degraded mitochondria, leading to reduced lysozymes in the mucus layer. This could probably confer the intestinal epithelial layer susceptibility to microbial infection, leading to bacterial overgrowth and the invasion of commensal bacteria, and predominantly of pathogenic bacteria with invasive properties. c Invading bacteria are detected by macrophages and dendritic cells. NOD2 in macrophages senses MDP and recruits ATG16L1 to the plasma membrane at the bacterial entry site, initiating functional xenophagy with the recruitment of the ATG16-ATG5-ATG12 complex to the membrane of autophagosomes. Bacteria are degraded inside autophagolysosomes and the produced peptides are loaded to the MHC class II for antigen presentation, which will be recognized by CD4⁺ T cells. Wild-type macrophages and dendritic cells detecting invasive bacteria also secrete inflammatory cytokines IL-1β and IL-18. d In macrophages and dendritic cells with the ATG16L1/Ala300 risk alleles, the mutated ATG16L1 protein is still able to bind to NOD2 upon MDP stimulation and able to recruit the ATG12-ATG5 complex, but fails to induce xenophagy. Autophagy-deficient macrophages fail to kill intracellular bacteria and to present antigen by MHC class II, leading to inappropriate activation of the adaptive immune system (grey dotted arrow). Autophagy-deficient macrophages produce high levels of IL-1β and IL-18 (red arrow). These result in severe inflammation and consequently chronic inflammatory status, which occur during CD development.

Fig. 2

Impact of the CD-associated NOD2 (L1007fsinsC) risk variant on xenophagy-mediated intracellular bacteria clearance during CD onset. a Induction of functional xenophagy in macrophages with wild-type NOD2 allele in response to bacterial invasion. MDP-activated NOD2 recruits and interacts with ATG16L1 at bacterial entry sites in the plasma membrane, inducing functional xenophagy with the consequent killing of intracellular bacteria and antigen presentation by MHC class II. b Impaired xenophagy in macrophages with the NOD2 (L1007fsinsC) risk variant in response to invasive bacteria. NOD2 (L1007fsinsC) fails to recruit ATG16L1 to the bacterial entry sites or to induce xenophagy. Consequently, intracellular bacterial degradation and MHC class II-mediated antigen presentation are defective.

Fig. 3

Hypothetical model for the involvement of the CD-associated IRGM (c.313C>T) in autophagy, bacterial clearance and CD. a MicroRNA 196 (miR-196) normally targets IRGM mRNA within RISC for a negative regulation. The IRGM (c.313C>T)risk allele mRNA, however, lacks the binding site for miR-196 and therefore is not regulated by this microRNA. The IRGM risk variant does not cause alterations in autophagy during healthy states. b During CD, expression of miR-196 is increased, which leads to a downregulation of IRGM expression. This results in a decrease in autophagic flux accompanied by a decrease in autophagosome-associated intracellular bacteria (upper panel). In subjects with the IRGM risk variant (bottom panel), IRGM expression is not inhibited by miR-196 and is upregulated, leading to defective xenophagy with a decrease in the percentage of intracellular bacteria captured in functional acidic vacuoles (violet circle) in comparison with that in IRGM (c.313C) protective variant-bearing subjects. Most intracellular bacteria replication occurs in nonmature vacuoles (yellow dotted circle). This consequently results in intracellular bacteria overload, which could further worsen disease status.