Mechanisms of commensal- specific CD8+ t cell differentiation, restraint and dysregulation in intestinal inflammation

The National Institute of Allergy and Infectious Diseases awarded $886,942 to Benaroya Research Institute At Virginia Mason on June 17, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to investigate mechanisms of commensal-specific CD8+ T cell differentiation, restraint, and dysregulation in intestinal inflammation. The award supports research into how CD8+ intraepithelial lymphocytes respond to gut microbiota under homeostasis and become dysregulated in inflammatory bowel disease, with the long-term goal of translating findings into new therapeutic approaches. The project runs through May 31, 2031, with place of performance in Seattle, Washington. Benaroya, a nonprofit biomedical research institute and subsidiary of Virginia Mason Health System, operates as a prime recipient on investigator-initiated immunology and autoimmune disease research funded predominantly through National Institutes of Health mechanisms.

Abstract

Our understanding of immunity largely stems from models of infection with pathogenic microbes. However, the vast majority of microbial-immune encounters occur as a symbiotic relationship with the commensal microbiota. Recently, the contribution of commensal-specific t cells to host physiology has received significant attention. These commensal-specific responses not only control microbiota containment but also promote immune tolerance within the gastrointestinal tract. While commensal-specific CD4+ t cell responses in the lamina propria have dominated models of mucosal immune regulation, these are vastly outnumbered by CD8+ intraepithelial lymphocytes within the epithelium. How CD8+ t cell responses to GUT microbiota are primed, differentiate and function under homeostasis has not been addressed. Conversely, aberrant immunity to commensal microbes has been proposed to underlie pathologies of barrier tissues, including inflammatory bowel disease (IBD), where commensal-specific t cells accumulate in blood and intestinal tissues of afflicted patients. A better understanding of the properties and functions of commensal-specific t cell responses is therefore fundamental to studies of tissue immunity in health and disease. Our long term goal is to better understand how commensal-specific t cell responses contribute to barrier tissue homeostasis, and the objective in this application is to investigate the mechanisms regulating induction of commensal-specific CD8+ t cells in homeostasis and how they become dysregulated in IBD. Our rationale for the proposed work is that uncovering these mechanisms has the potential to translate into new therapeutic approaches. Our central hypothesis is that commensal-specific CD8+ t cells develop as functionally restrained intraepithelial lymphocytes (IEL) under homeostasis, but that perturbation of local immune regulation within the intestinal epithelium, in the case of patients with ulcerative colitis, by autoantibody-mediated blockade of integrin AVB6 results in aberrant CD8+ effector t cell responses in IBD. Based on strong preliminary data, we will test three specific aims: (1) determine key antigen-presenting cells (APC) priming SFB-specific CD8⍺β+ IEL. (2) identify how cell-intrinsic pathways drive differentiation, maintenance and restraint of SFB-specific CD8⍺β+ piel. (3) determine how pathogenic KLRG1+eomes+ CD8+ t cells arise and contribute to inflammation in murine models of ulcerative colitis our approach is innovative as IT investigates new mechanisms of immunity unique to commensal-specific CD8+ t cell responses. The proposed work is significant because IT will establish new insights into the interaction and communication between commensal microbes and immune cells in the GUT environment and identify potential targets for therapeutic intervention in conditions of chronic intestinal inflammation.