Blimp-1 and c-Maf regulate common and unique immune gene networks to protect against distinct pathways of pathobiont-induced colitis [bulk tissue RNA-seq]

Using single-cell RNA-seq and bulk tissue RNA-seq of colon lamina propria leukocytes (LPL), together with ATAC-seq, ChIP-seq and RNA-seq from colon LPL and sorted CD4+ T from colon lamina propria during oral infection with the pathobiont Helicobacter hepaticus we show that Blimp-1 and c-Maf both positively regulate Il10 gene expression, but also cooperate to negatively regulate a large network of proinflammatory effector genes in T cells. While T cell-specific deletion of either Prdm1, Maf or both transcription factors did not result in overt inflammation of the colon at steady state, H. hepaticus infection resulted in mild/moderate colitis in both the Prdm1fl/flCd4Cre and Maffl/flCd4Cre single T cell-specific transcription factor deficient mice, while the double knockout Prdm1fl/flMaffl/flCd4Cre infected mice suffered severe colitis and showed a massive increase in T cell effector genes in colonic LPL. Blimp-1 and c-Maf cooperate to negatively regulate genes including Ifng, Csf2, Il23r, Stat4, Il18r1 and Il2rg, and deletion of both these transcription factors in T cells translated to an exacerbated pathogenic TH1, IFN-g+GM-CSF+ effector cell response. c-Maf, additionally negatively regulated Il17a expression which was elevated in the LPL as assessed by bulk RNA-seq and scRNA-Seq analysis in the H. hepaticus infected Maffl/flCd4Cre mice. Overall design: RNA-seq analysis (in 2-5 biological replicates) of colon lamina propria leukocytes isolated from mice with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 Maf on Day 14 following infection with Helicobacter hepaticus in the presence anti-IL-10R blocking mAb or matched isotype control