Single-cell RNA sequencing revealed the transcriptional landscape and heterogeneity of macrophages in the intestinal tissues of WT and RUNX3 macrophage conditional knockout mice.

CD11b+ cell populations, especially macrophages, are highly heterogeneous tissue-resident immune cells in mice and humans. The exact subpopulation and its phenotype remain unknown. Here, we analyzed intestinal CD11b+ cell populations from normal and Runx3 macrophage conditionally deficient mice using scRNA-seq. We found that the transcription factor RUNX3 plays a key role in the entry of inflammatory monocytes into resident macrophages. Decreased resident macrophages and elevated ZFP36 in RUNX3flow/flowlyz2-Cre mice, leading to cytokine and chemokine degradation in colon tissue-resident macrophages. RUNX3 promotes the expression of NR4A1, thereby inducing the differentiation of inflammatory monocytes into resident macrophages. Single-cell population analysis revealed that the ERK1/2/MAPK pathway plays a key role in NR4A1-mediated gut-resident macrophage differentiation. Overall design: 10X Genomics scRNA-seq was performed to better assess immune cell heterogeneity in gut lamina propria (LP).