Antigen-specific induction of CD4⁺CD8αα⁺intraepithelial T lymphocytes byBacteroidetesspecies

Abstract

The microbiome contributes to the development and maturation of the immune system1–3 In response to commensal bacteria, CD4+ T cells can differentiate into distinct functional subtypes with regulatory or effector functions along the intestine. Peripherally-induced Foxp3+-regulatory T cells (pTregs) maintain immune homeostasis at the intestinal mucosa by regulating effector T cell responses against dietary antigens and microbes4. Similarly to pTregs, a subset of small intestine intraepithelial lymphocytes CD4+CD8αα+ (CD4IELS) exhibit regulatory properties and promote tolerance against dietary antigens5. Development of CD4IELS from conventional CD4+ T cells or from Treg precursors depends on the microbiota5,6. However, the identity of the microbial antigens recognized by CD4IELs remains unknown. We identified species belonging to the Bacteroidetes phylum as commensal bacteria capable of generating CD4IEL from naïve CD4+ T cells expressing the pTreg transnuclear (TN) monoclonal TCR6 as well as from polyclonal WT T cells. We found that β-hexosaminidase, a widely conserved carbohydrate-metabolizing enzyme in the Bacteroidetes phylum, is recognized by TN T cells, which share their TCR specificity with CD4+ T cells found in the intraepithelial compartment of polyclonal specific-pathogen-free (SPF) mice. In a mouse model of colitis, β-hexosaminidase-specific CD4IELs provided protection from ulceration of the colon and weight loss. Thus, a single T cell clone can recognize a variety of abundant commensal bacteria and elicit a regulatory immune response at the intestinal epithelial surface.

T Cell Receptor Is Required for Differentiation, but Not Maintenance, of Intestinal CD4+ Intraepithelial Lymphocytes

“…To further address whether TCR identity controls the differentiation of migrating CD4 + T cells into pre-IELs and CD4 + CD8aa + IELs, we took advantage of the transnuclear (TN) monoclonal strain harboring a commensal-specific Va2Vb6 TCR rearrangement that predisposes cells to become CD4 + CD8aa + IELs in the epithelium in a microbiota-dependent manner (Bilate et al, 2016;Bousbaine et al, 2020). We crossed these mice to wild-type (WT) animals to obtain mice carrying only the Vb6 chain (referred as fixed-Vb6 mice) from their offspring, as a means to interrogate TCRa diversity in a diverse setting yet with an imposed repertoire bias dictated by the fixed TCRb chain.…”

Mapping the T cell repertoire to a complex gut bacterial community

“…Instead, it suggests that in the physiological setting of a complex microbial community, expanded TCR clonotypes play ‘zone defense’—instead of recognizing a single colonist they mediate the response to a group of colonists that share a conserved epitope. Most polyreactive TCRs targeted strains of Firmicutes or Bacteroidetes, as observed recently in a different setting 32 and a distinction from previous work reporting poly-reactive immunoglobulin A (IgA) that recognizes strains of Proteobacteria 39 . Future experiments are needed to find dietary antigens for the four TCRs that were specific to chow and fecal pellets from germ-free mice.…”

“…Screening pools of genomic clones against pooled hybridomas made it possible to test 43,200 clones against 13 hybridomas (561,600 combinations) in just 1,440 ELISA assays (arrayed across 15 plates), leading to the identification of three clones-one from each genomic library-which encoded overlapping fragments of orthologous SBPs from an ABC transport system. The SBP is extracellular, widely conserved among Firmicutes, and presumably highly expressed, features that are likely to be found in other epitopes recognized by polyspecific T cells that patrol the gut microbiome 32 .…”

“…A variety of T cell epitopes from other gut commensals have been discovered and characterized 1,2,4,[31][32][33][34][35] . We started by testing 20 such antigens against the 92 hybridomas using dendritic cells for antigen presentation (Extended Data Fig.…”

Deciphering the interdependent labyrinth between gut microbiota and the immune system

“…In comparison to pathogen‐free organisms, germ‐free organisms produce lesser IELs (Bousbaine et al . 2020), Tregs (Rogala et al . 2020) and even lesser IgA‐secreting plasma cells in the lamina propria (Crabbe et al .…”