Multiomic Analysis of Monocyte-Derived Alveolar Macrophages in Idiopathic Pulmonary Fibrosis

Abstract

Abstract Background Monocyte-derived alveolar macrophages (Mo_AMs) are increasingly recognised as potential pathogenic factors for idiopathic pulmonary fibrosis (IPF). While single-cell RNA sequencing (scRNAseq) analysis has proven valuable in the transcriptome profiling of Mo_AMs at single-cell resolution, the integration of scRNAseq with bulk RNA sequencing (bulkseq) and single-cell assay for transposase-accessible chromatin sequencing (scATACseq) may provide additional dimensions of understanding of these cellular populations involved in IPF. Methods We analysed 116 scRNAseq samples, 119 bulkseq samples, and five scATACseq samples of lung tissue. We built a large-scale IPF scRNAseq atlas and then performed the trajectory analysis to explore the developmental path and differences of Mo_AMs subpopulations. Additionally, to determine whether Mo_AMs affected pulmonary function, we projected clinical phenotypes (forced vital capacity, FVC%pred) from the bulkseq dataset onto the scRNAseq atlas using the R package Scissor. To gain a deeper insight into the cell–cell interaction of Mo_AMs, we used the R package CellChat and further validated the downstream mechanism. Finally, we used scATATCseq to uncover the upstream regulatory mechanisms and determine key drivers of transcription factors in Mo_AMs. Results We identified three Mo_AMs clusters: Mon_macs, CCL2_RecMacs, and SPP1_RecMacs. The trajectory analysis further validated the origin and differentiation of these three clusters, and APOE was found to be essential for differentiation of the trajectory. Moreover, the CXCL12/CXCR4 axis was found to be involved in the molecular basis of reciprocal interactions between Mo_AMs and fibroblasts through the activation of the ERK pathway in Mo_AMs. Subsequently, the proportions of CCL2_RecMacs and SPP1_RecMacs were found to be higher in the low-FVC group than in the high-FVC group. Additionally, SPIB (PU.1), JUNB, JUND, BACH2, FOSL2, and SMARCC1 showed stronger association with open chromatin of Mo_AMs than tissue-resident alveolar macrophages. SMAD2 and PPARγ could be the potential drivers during Mo_AM differentiation. Conclusion Mo_AMs may influence FVC% pred and aggravate pulmonary fibrosis through the communication with fibroblasts. Furthermore, Mo_AM differentiation may be regulated by distinctive transcriptional regulators. Overall, through multiomic analysis, this work provides a global overview of how Mo_AMs govern IPF and also helps determine better approaches and intervention therapies.