(A) Volcano plot of differential gene expression identified by RNA-Seq in KO macrophages relative to WT controls. The x axis represents the log₂ fold-change, and the y axis represents the –log₁₀ P value. The significant genes are depicted in red, indicating that they exhibit both a P value (–log10) < 10^–4 and an absolute log₂ fold-change > 0.6. (B–E) Gene set enrichment analysis (GSEA) plots and heatmaps for efferocytosis-related gene sets in WT macrophages compared with KO macrophages. Enriched efferocytosis-related Gene Ontology (GO) terms in genes repressed in KO macrophages, including (B) positively regulated phagocytosis, (C) phagocytosis engulfment, (D) apoptotic cell clearance, and (E) lysosome lumen. Green curves indicate enrichment scores. The normalized enrichment score (NES), false discovery rate (FDR) q value, and FWER P value are indicated within each graph. NES > 1.1 and P < 0.05 were considered statistically significant. Representative genes were listed in the heatmap of each enrichment plot. Green and red color indicate down- versus upregulated genes, respectively. The genes written in red beside each heatmap are known to be controlled by LXRα. (F and G) RT-qPCR analysis validates that these efferocytosis-related genes are downregulated in KO macrophages but are upregulated by stimulation with GW3965, an agonist of LXRα (n = 3; *, P < 0.05). Expression of β-actin was used as the internal control for RT-qPCR. (H) Flow cytometry assay showing that the impaired efferocytosis in KO macrophages can be rescued by GW3965 treatment (n = 5; *, P < 0.05). All data are presented as mean ± SEM and analyzed by 2-way ANOVA (F and H).