T-cell receptor repertoire alterations drive pathological gut immunological and microbial signatures in humans and mice with hypomorphic RAG deficiency

Mechanistic knowledge about the homeostatic interplay between T cell-mediated immunity and gut microbiota is still limited. We aimed to investigate how restriction of the T-cell receptor (TCR) repertoire (VDJ region) may influence gut microbiota composition, causing tissue inflammation and disruption of peripheral immune tolerance. Based on the clinical observation of colonic inflammation in patients with partial RAG deficiency (pRD), we applied a multi-omics strategy to study a mouse model of hypomorphic Rag1 deficiency (Rag1 mutant mice) with spontaneous development of colitis. To characterize the transcriptomic and immune repertoire differences between the wild-type and Rag1 mutant mice at 3 weeks and 12 weeks of age, with and without ANMV (ampicillin, neomycin, metronidazole and vancomycin) treatment (only at 12 weeks for the Rag1 mutant mice), we performed scRNA-seq and TCR repertoire (VDJ region) sequencing of colonic lamina propria-specific CD4+ T cells. The scRNA-seq and TCR libraries were coupled with hashtag oligo (HTO) libraries for labeling the samples in order to demultiplex the pooled libraries into wild-type and Rag1 mutant mice at 3/12 weeks of age and with/without ANMV treatment cell populations for downstream analysis. The number of libraries sequenced is six for scRNA-seq, six for TCR (VDJ) repertoire, and six for HTOs.