Epithelial antigen compartmentalization dictates CD4+ T cell fate during C. rodentium infection

Introduction/Rationale: While intestinal epithelial cells (IECs) upregulate MHCII during inflammation and can serve as non-professional antigen-presenting cells, their specific contribution to pathogen-specific CD4+ T cell immunity and immunological memory formation remains poorly defined.

Methods: We utilized Citrobacter rodentium infection (murine model of EPEC) with single-cell RNA-seq, engineered bacteria expressing model antigens in distinct compartments, and proximity-labeling approaches. Conditional IEC-specific MHCII deletion and inducible post-infection deletion strategies assessed functional requirements for CD4+ T cell responses.

Results: C. rodentium triggered sustained MHCII expression across all IEC lineages persisting >2 months post-clearance. IEC MHCII proved essential for pathogen-specific CD4+ TRM formation—conditional knockout shifted CD4+ T cell fate from TRM to TCM populations. scRNA-seq revealed MHCII deletion induced aberrant expression of central memory genes (Tcf7, Lef1, Bcl6) in residual TRM cells, while WT TRM showed robust TCR activation signatures (Fos, Jun, Jund) and Runx3 expression. Type III secretion-delivered cytosolic antigens drove TRM via autophagy-dependent IEC processing, whereas surface antigens promoted TFH differentiation in lymphoid tissues. Proximity labeling confirmed direct, MHCII-dependent IEC-CD4+ TRM synapses, particularly with CD103+ subsets.

Conclusion: We establish IECs as orchestrators of mucosal memory, demonstrating that IEC-MHCII actively suppresses TCM programming while promoting TRM differentiation through sustained TCR signaling. This antigen compartmentalization paradigm redefines CD4+ fate decisions—cytoplasmic antigen targeting via epithelial presentation could selectively generate protective TRM. These mechanisms illuminate IBD pathogenesis where dysregulated epithelial antigen presentation may disrupt TRM/TCM balance, perpetuating chronic inflammation.