Among the many CD-related risk genes, ATG16L1, IRGM, nucleotide-binding oligomerization domain 2 (NOD2), protein tyrosine phosphatase non-receptor type 2 (PTPN2), leucine-rich repeat kinase 2 (LRRK2), and transcription factor EB (TFEB) have essential roles in maintaining colonic immune homeostasis and correlate highly with defective autophagy in immune cells and intestinal epithelial cells, providing strong support for autophagy in the development of IBD (Table 1) (98). Here, PTPN2 is linked to inflammatory bowel disease.