Integrated Single-Cell and Bulk RNA Sequencing Identifies Macrophage Heterogeneity and Mitophagy-Related Biomarkers in Idiopathic Pulmonary Fibrosis

Mitophagy clears damaged mitochondria and maintains normal macrophage function. Clarifying the associations between idiopathic pulmonary fibrosis (IPF), macrophages, and mitophagy is crucial for early diagnosis and clinical management. Core macrophage subsets were identified as M2 macrophages via single-cell RNA sequencing and immune infiltration analysis. Differentially expressed genes related to this subset were obtained. Integrated differential expression analysis, weighted gene co-expression network analysis, machine learning, and expression verification were applied to screen biomarkers. CD163 and SPP1 were identified through biomarker screening, both showing significantly increased expression in IPF. Functional enrichment showed that these biomarkers are mainly involved in cell cycle checkpoints and ciliopathies. Immune microenvironment analysis identified 16 immune cell types with significant differences between IPF and control groups, among which T helper 2 cells were strongly positively correlated with CD163. A total of nine drugs were found to be associated with CD163 and SPP1. The expression of these biomarkers changed dynamically during M2 macrophage differentiation. This study integrates single-cell and bulk transcriptomics analysis to reveal the critical roles of CD163 and SPP1 in the IPF macrophage–mitochondrial autophagy axis, a novel framework for understanding the macrophage–mitophagy axis in IPF pathogenesis.