Panel A shows heatmaps of fatty acid homeostasis related genes dysregulated in control and Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel B shows a gene set enrichment analysis plot demonstrating reduced fatty acid metabolism pathway enrichment in Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel C shows heatmaps of apoptosis related genes differentially expressed between control and Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel D shows a gene set enrichment analysis plot demonstrating positive enrichment of apoptosis pathways in Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel E shows a heatmap of differentially expressed genes comparing control mature alveolar macrophages, Cd11cCre positive Rxrab deficient mature alveolar macrophages, and immature alveolar macrophages. Panel F shows a principal component analysis plot separating transcriptomic profiles of control mature alveolar macrophages, Cd11cCre positive Rxrab deficient mature alveolar macrophages, and immature alveolar macrophages. Panel G shows a volcano plot highlighting significantly upregulated and downregulated genes between immature alveolar macrophages and control mature alveolar macrophages. Panel H shows gene set enrichment analysis plots demonstrating reduced DNA repair and E2F pathway activity in immature alveolar macrophages compared with control mature alveolar macrophages. Panel I shows heatmaps of proliferation associated genes differentially expressed between control mature alveolar macrophages and immature alveolar macrophages. Panel J shows a bubble plot of significantly enriched Gene Ontology biological processes associated with altered proliferation, apoptosis, migration, and DNA replication pathways in immature alveolar macrophages.
Bulk RNA-seq analysis reveals that RXR signaling is necessary for AM identity, metabolism, and proliferation. (A) Heatmap showing dysregulated genes related to fatty acid homeostasis in Cd11cCre+Rxrabfl/fl mAMs (n = 3 mice) versus Rxrabfl/fl mAMs (n = 4 mice). (B) GSEA plot showing a negative normalized enrichment score (NES = −1.30) for the fatty acid metabolism gene set in Cd11cCre+Rxrabfl/fl mAMs versus Rxrabfl/fl mAMs. (C) Heatmap showing dysregulated apoptosis-related genes in Cd11cCre+Rxrabfl/fl mAMs (n = 3 mice) versus Rxrabfl/fl mAMs (n = 4 mice). (D) GSEA plot showing positive enrichment (NES = 1.26) for the apoptosis gene set. (E) Heatmap representing all DEGs obtained after the comparison of Rxrabfl/fl mAMs (n = 4 mice) versus Cd11cCre+Rxrabfl/fl mAMs (n = 3 mice) versus Cd11cCre+Rxrabfl/fl ImmAMs (n = 3 mice) sorted from 9-wk-old mice. (F) PCA plot obtained using the transcriptomes of the previous samples. (G) Volcano plot showing global transcriptomic differences between Rxrabfl/fl mAMs (n = 4 mice) and Cd11cCre+Rxrabfl/fl ImmAMs (n = 3 mice). Colored dots represent DEGs with significant upregulation (p-adj <0.05 and FC >0; red) or significant downregulation (p-adj <0.05 and FC <0; blue). (H) GSEA plots showing negative enrichment for the DNA repair and E2F pathway gene sets in Cd11cCre+Rxrabfl/fl ImmAMs versus Rxrabfl/fl mAMs. (I) Heatmap showing proliferation-related dysregulated genes in the previous samples. (J) Significantly enriched GO terms derived from the bulk RNA-seq data comparison of Cd11cCre+Rxrabfl/fl ImmAMs versus Rxrabfl/fl mAMs, detected with the PANTHER statistical enrichment test tool (P < 0.05 with Bonferroni correction).