The IBD risk gene<i>PTPN2</i>maintains the spatial distribution of small intestinal antimicrobial peptides in mice

Background: Defective intestinal barrier function and microbiome alterations are major contributors to the pathogenesis of inflammatory Bowel Disease (IBD), which afflicts ~3.2 million Americans. Loss-of-function SNPs within the protein tyrosine phosphatase non-receptor type 2 (PTPN2) locus have been strongly linked to IBD pathogenesis. PTPN2 deficiency is associated with gut microbiota dysbiosis and the expansion of IBD-relevant bacteria like adherent-invasive E. coli (AIEC). Moreover, we recently reported that PTPN2 promotes small intestinal Paneth cell antimicrobial peptide expression in vivo, a critical mechanism to maintain gut microbial equilibrium. Here we tested how PTPN2 regulates the spatial expression of antimicrobial peptides along the intestinal crypt-villus axis. Methods: Tamoxifen (TMX)-inducible intestinal epithelial-specific Ptpn2 disruption ( Ptpn2 ΔIEC ) mice and Ptpn2 fl/fl littermate controls were treated with TMX for four days. Four weeks post-injection, paraffin-embedded tissues collected from the ileocecal junction were analyzed using RNAscope in situ hybridization. Spatial localization of genes coding for antimicrobial peptides ( Lyz1, Reg3g, and Reg3b) was performed on a total of 1,134,052 detected epithelial cells using QuPath. Cell nuclei were stained with DAPI. Results: Loss of PTPN2 from epithelial cells significantly reduced expression of Reg3g, Reg3b, and Lyz1 in the ileocecal junction. Ptpn2 ΔIEC mice had disrupted colocalization of Reg3g and Reg3b in the mid-villus and villus tips. Reg3b co-localization with Lyz1 at the crypt-villus junction, a key site for Paneth cell-mediated antimicrobial defense, was also reduced in Ptpn2 ΔIEC mice. Conclusions: : These findings suggest impaired spatial regulation of antimicrobial peptide production with PTPN2 loss. This disrupted distribution may contribute to dysbiosis by reducing luminal clearance of bacteria at the villus tips and compromising antimicrobial defense at the crypt base, potentially increasing bacterial penetration into the crypts and altering overall microbial community dynamics along the crypt-villus axis. These findings provide new insights into how PTPN2 deficiency likely drives dysbiosis and alters host-microbiota interactions in IBD. NIH The Diversity Supplement R01DK091281 This abstract was presented at the American Physiology Summit 2025 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.