The ZIP8 A391T Crohn’s disease-linked risk variant induces colonic metal ion dyshomeostasis, microbiome compositional shifts, and inflammation

ABSTRACT The pathogenesis of Crohn’s disease involves genetic and environmental factors, with the gut microbiome playing a crucial role. The Crohn’s disease-associated variant rs13107325 in the SLC39A8 gene results in an A391T substitution in the ZIP8 metal ion transporter and has previously been linked to alterations in the colonic microbiome in variant carriers. We hypothesized that the A391T substitution alters metal ion homeostasis in the colonic mucosal-luminal interface, thereby inducing dysbiosis which may promote intestinal inflammation. To evaluate this hypothesis, we generated a SLC39A8 A393T mouse model (matching human A391T). Consistent with an effect of the variant on ZIP8 function, homozygous A393T mice exhibited increased cobalt in the colonic mucosa, but reduced iron, zinc, manganese, cobalt, copper, and cadmium in the colonic lumen. We performed 16S rRNA gene sequencing of colon samples and histological scoring of colon tissue collected from the SLC39A8 A393T mouse model at different ages. We identified variant-linked effects on microbiome beta diversity in 2-month, 3-4 month, and 12-month old mice and spontaneous intestinal inflammation in 10-month but not 5-month old mice. Predicted pathway analysis of the microbiome samples revealed differential enrichment of iron-, zinc- and cobalt-dependent pathways in A393T mice compared to wild-type controls. These results suggest that the variant in SLC39A8 primarily restricts metal availability to the microbiota, resulting in compositions that can adapt to the environment, and that A393T-linked dysbiosis occurs prior to the onset of inflammation. This study paves the way for future studies investigating risk variants as microbiome-disease modifiers. NEW & NOTEWORTHY Mice recapitulating the human A391T Crohn’s disease-linked risk variant in the SLC39A8-encoded ZIP8 transporter exhibit reduced luminal trace metals and an altered microbiome composition. The microbiome compositional shift occurs prior to the onset of spontaneous colonic inflammation. This study supports an emerging paradigm by which genetic risk for inflammatory bowel disease may confer disease susceptibility through modulation of the gut microbiome.