Cumulative Risk Variant SNPs in ATG16L1 Locus are Associated with Reduced Ability of Salmonella Infected Dendritic Cells to Generate Autologous Bacterial-Specific Foxp3+ Regulatory T (Treg) cells

Atg16l1 SNPs may associate with Crohn’s disease(CD) via impaired autophagy and bacterial clearance resulting in compromised bacterial antigen presentation by dendritic cells(DC). We hypothesize that immune-function modulation results from the cumulative effects of several SNP variants rather than by a single SNP of atg16l1. Our aim was to assess whether cumulative SNPs are associated with changes in the ability of DC to generate bacterial-specific T cell subsets upon in vitro bacterial infection.

Genotypes of CD and healthy controls (HC) were analyzed using the Goldengate® assay. Individuals(13 CD and 11 HC) with homozygous in IL-23R(rs11209026,R381G) and wildtype in NOD2, PTPN22 and IRGM were enrolled in this study.  Monocyte-derived DC were differentiated from peripheral blood of the study participants using IL-4/GM-CSF and infected with Salmonella Typhimurium for 24 hours. The infected DC were co-cultured with autologous T cells for an additional 7-days and T cell polarization assessed using FACS.

Participants were categorized into 3 groups based on genotype at atg16l1 locus:  H1-all heterozygous, H2-homozygous in 2 SNPs(rs12994997 and s2241880,T300A) and wildtype in other 3 SNPs (rs13391356, rs2289472, and rs10192702), and H3-the reversed case of H2. No individuals with all homozygous nor all wildtype were found in this study.  Among T cell subsets, Foxp3+ Treg were significantly decreased in the total cohort with H3 and CD patients with H3 compared to those with H1. This suggests that reduced bacterial-specific Treg generation is not disease specific, but cumulative risk variants in atg16l1 locus are associated with reduced ability to generate Foxp3+ (Treg) cells.