16S rRNA sequencing of stool sample from B cell-depleted animals compared with controls

Little is known about the pro-resolution role of immune cells recruited to damaged tissue. Using an experimental model of intestinal epithelial damage and repair, we identified B cells as the dominant cell type in the healing colon. Single-cell RNA-sequencing (scRNAseq) revealed the expansion of an IFN-induced B cell subset during experimental mucosal healing which was predominantly located in damaged areas and associated with colitis severity. In line with this, B cell depletion during mucosal healing resulted in accelerated recovery upon injury, decreased epithelial ulceration and enhanced gene expression programs associated with tissue remodeling. scRNA-seq from the epithelial and stromal compartment combined with spatial transcriptomics and multiplex immunostaining showed that B cells decreased potential interactions between stromal and epithelial cells during mucosal. Using primary fibroblast-organoid co-cultures, we demonstrated that activated B cells disrupt the epithelial-stroma crosstalk required for organoid survival. Conversely, organoids from mice in which total or IFN-induced B cells were depleted in vivo during mucosal healing showed enhanced regenerative capacity. Thus, we identified a previously undescribed role of B cells impairing epithelium-stroma cell interactions required for proper mucosal healing.