Comparison of de novo refilled to original lung interstitial macrophages by bulk RNA-sequencing

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. In this study, the de novo refilled CD206+ and CD206- IMs on Day 14 post-depletion were compared to those without depletion. Alvelar macrophages (AMs) samples were also included in this analysis and served as a reference. Results of clustering and PCA analyses showed high similarity between de novo refilled and original IMs for both CD206+ and CD206- subsets. Only 9 genes were find upregulated in refilled IMs: AA467197, Cd109, Igf2r, Rarb and S100a4. Both CD206+ and CD206- lung IM subsets were FACS sorted from two groups of mice. Mice in Group “refilled” were IM-DTR mice that were treated with 50 ng diphtheria toxin (DT) 14 days before sacrifice. Group “control” was with litternate control mice without DT treatment. On the day of sacrifice, cells sorted by FACS and directly subjected to RNA extraction and library construction. Processed data then were analyzed with Bioconductor.