Single-cell RNAseq analysis (10X Genomics Chromium) of cMAF- and Mafb-deficent lung monocytes and interstium macrophages

Lung interstitium macrophages (IMs) are non-alveolar resident tissue macrophages which contribute to the lung homeostasis. These cells were reported to be heterogeneous by our group and other teams, which contains two main distinct subpopulations: CD206+ IMs and CD206- IMs. However, the exact origin of IMs and the transcriptional programs that regulate IM differentiation remains unclear. In recent report, we analyzed the refilled IMs in the course of time after induced IM depletion with single-cell RNA sequencing (10X Genomics Chromium) and bulk RNA sequencing. The lung IMs and monocytes from either Lyz2-Cre Mafflox/flox mice (cMAF-KO), Lyz2-Cre Mafbflox/flox (MAFb-KO), Lyz2-Cre Mafflox/flox Mafbflox/flox (dKO) or control litermate mice without floxp locus (Control) were analyzed and compared using single-cell RNA sequencing. All the main substs, i.e. Ly6C+ classical monocytes, Ly6C- patrolling monocytes, CD206+ IMs, CD206- IMs were found in control sample, while IMs are absent in both MAFb-KO and dKO sample accompied by a new intermediate population independent of Mafb expression. CMAF-KO sample show less impact in cell population composition with a lower freqency of CD206+ IM population. The lung IMs and monocytes were sorted from four groups of mice: Group “MAFb-KO” contains 3 Lyz2-Cre Mafbflox/flox (MAFb-KO) mice; Group “cMAF-KO” contains 3 Lyz2-Cre Maflox/flox (cMAF-KO) mice; Group “dKO” contains 3 Lyz2-Cre Mafflox/flox Mabflox/flox (dKO) mice. Cells from each group were barcoded with different Biolegend anti-mouse Hastags before being pooled for library construction. Processed data then were analyzed with Bioconductor and Seurat package. The cells from different sample were demultiplexed with the barcode detected in each cell.