Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque

• Published in: Clinical & translational immunology 2024, Vol.13 (5), p.e1508-n/a
• Main Authors: Castro Dopico, Xaquin, Guryleva, Mariia, Mandolesi, Marco, Corcoran, Martin, Coquet, Jonathan M, Murrell, Ben, Karlsson Hedestam, Gunilla B
• Format: Article
• Language: English
• Subjects: Antigens; caecum; CD4 antigen; CD45 antigen; CD8 antigen; Cell differentiation; Colon; Effector cells; Endoscopy; Flow cytometry; GATA-3 protein; Gene expression; Genes; Genomics; Genotype & phenotype; Germinal centers; gut homeostasis; Helper cells; Homeostasis; Immunoglobulin A; Immunological memory; Immunoregulation; Inflammatory bowel disease; Insulin-like growth factor I; Lamina propria; Large intestine; Leukocytes; Lymphocytes; Lymphocytes B; Lymphocytes T; Macaca mulatta; Medicin och hälsovetenskap; Memory cells; Metabolism; Natural killer cells; Neutropenia; Original; Plasma cells; rhesus macaque; single‐cell RNA sequencing; Somatic hypermutation; Thymus; tissue atlas; Transcriptomics
• ISSN: 2050-0068; 2050-0068
• DOI: 10.1002/cti2.1508

Objectives The caecum bridges the small and large intestine and plays a front‐line role in discriminating gastrointestinal antigens. Although dysregulated in acute and chronic conditions, the tissue is often overlooked immunologically. Methods To address this issue, we applied single‐cell transcriptomic‐V(D)J sequencing to FACS‐isolated CD45+ caecal patch/lamina propria leukocytes from a healthy (5‐year‐old) female rhesus macaque ex vivo and coupled these data to VDJ deep sequencing reads from haematopoietic tissues. Results We found caecal NK cells and ILC3s to co‐exist with a spectrum of effector T cells partially derived from SOX4+ recent thymic emigrants. Tolerogenic Vγ8Vδ1‐T cells, plastic CD4+ T helper cells and GZMK+EOMES+ and TMIGD2+ tissue‐resident memory CD8+ T cells were present and differed metabolically. An IL13+GATA3+ Th2 subset expressing eicosanoid pathway enzymes was accompanied by IL1RL1+GATA3+ regulatory T cells and a minor proportion of IgE+ plasma cells (PCs), illustrating tightly regulated type 2 immunity devoid of ILC2s. In terms of B lymphocyte lineages, caecal patch antigen‐presenting memory B cells sat alongside germinal centre cells undergoing somatic hypermutation and differentiation into IGF1+ PCs. Prototypic gene expression signatures decreased across PC clusters, and notably, expanded IgA clonotypes could be traced in VDJ deep sequencing reads from additional compartments, including the bone marrow, supporting that these cells contribute a steady stream of systemic antibodies. Conclusions The data advance our understanding of caecal immunological function, revealing processes involved in barrier maintenance and molecular networks relevant to disease. The caecal mucosa plays a front‐line role discriminating pathogens from commensals at the start of the large intestine, yet how the tissue contributes to acute and inflammatory gastrointestinal conditions is poorly understood, especially in primates. To this end, we used top‐down single‐cell sequencing to illustrate a diverse network of T and B lymphocytes that patrol barrier in the steady state, pin‐pointing distinct tolerogenic and inflammatory cell types, and immunological mechanisms of clinical relevance.