With 163 genetic loci identified to date, genome wide association studies have revealed the significant genetic complexity associated with risk for IBD.1 Autophagy, pinpointed through the discovery of risk variants in ATG16L1 2 and other autophagy genes,1 remains one of the most interesting disease-specific revelations of Crohn’s disease genetics. Around a fifth of the overall genetic risk yet known for Crohn's disease may lie in genes that are directly involved in autophagy,1 including NOD2, which has recently been exposed as an autophagy inducer,3 a decade after it was reported as the first Crohn's disease risk gene.4 Given this, chances are that further autophagy regulators might hide in the many currently unexplored genetic risk loci. As an ostensibly disease-specific, genetically affected biological process, autophagy stands out within all the genetic heterogeneity of IBD,1 where the vast majority of risk loci (and computationally inferred genes and pathways) is shared between Crohn's disease and UC,1 and with other immune-related diseases that have phenotypically little in common with Crohn's disease.5 Understanding how autophagy risk genes and their variants contribute to Crohn's disease pathogenesis holds the promise of unravelling some of the secrets of this disease.

Autophagy (or ‘self-eating’) represents a basic function of all cell types wherein it serves an essential homeostatic function or is induced by the needs associated with metabolic changes such as starvation or the removal of microbes (xenophagy) (reviewed …