Single-cell RNA-Seq analysis of colonic mesenchyme lacking tumor necrosis factor receptor 1

Our study reports a role for tumor necrosis factor receptor 1 (TNFR1) in maintaining colonic mesenchymal cell diversity. Through scRNA-seq profiling, we show that a TNFR1-deficient mesenchyme has a reduced transcriptional diversity of mesenchymal cell populations, with a near complete loss of a cluster enriched in TNF, IFN, and cytokine signaling genes, which include MMP9, CD200, TNFRSF9, and TRAF1. We show that the transcriptional clustering of mesenchymal cells is consistently distinct and unique to the TNFR1-/- genotype. TNFR1-/- mesenchymal cells cluster as a single population, compared to control mesenchymal cells that cluster into 3 sub-populations. Through in vivo immunostaining in control and TNFR1-/- mice we show that the TNF signaling cluster localizes to the sub-epithelial niche and therefore may play an important role in the crosstalk between epithelial stem cells and mesenchyme-driven immune signaling in health and disease. Overall design: To assess the role of TNFR1 signaling in the colonic mesenchyme and its interaction with the epithelial stem cell niche, we investigated primary sub-epithelial mesenchymal cell populations isolated from control (TNFR1+/-) or TNFR1-/- mice and grown in vitro for 5 days. These populations were dissociated into a single-cell suspension and profiled using single-cell RNA-Seq.