Effects of B cell depletion on bulk RNAseq on colonic tissue repair after acute inflammation

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. CD19-cre x iDTR mice were kindly provided by Prof. Dr. Nadine Hövelmeyer (University of Mainz, Germany), imported from Germany and bred locally. Animals were maintained under specific pathogen-free conditions at Astrid Fagraeus Laboratory or AKM animal facility and handled according to protocols approved by the Institutional Animal Care and Use Committee at the Karolinska Institutet (Stockholm, Sweden). All experimental procedures were performed according to national and institutional regulations and guidelines. Mice of C57BL/6J background, aged 8–12 weeks at the beginning of experiments, were used for all experiments. Murine colitis was induced by administration of 2-3% of dextran sodium sulfate (DSS, company, Alfa Aesar) dissolved in drinking water ad libitum for 7 days, followed by 7 days of regular water, when samples were collected. For B cell-depletion experiments CD45.1 mice were irradiated with 2x 6Gy with a time interval of 3 hours in between. Within 24hours after the second irradiation mice received 3 x 106 bone marrow cells (CD45.2) intravenously. 6 weeks after bone marrow transfer reconstitution of cells was analysed by flow cytometric analysis of the blood. 8-10 weeks after BM transfer mice were subjected to DSS and were injected i.p. with 25ng/g BW diphtheria toxin (Sigma-Aldrich) or PBS on days 9, 10, 12 and 13 during DSS-induced colitis. Success of B cell depletion was analysed at the end of the experiment by flow cytometry of splenic B cells.