Integrative single-cell and bulk transcriptomic analysis identifies monocyte/macrophage senescence-associated...

Pulmonary arterial hypertension (PAH) is a progressive vascular disorder characterized by immune dysregulation and vascular remodeling. Cellular senescence modulates immune responses, but its role in PAH, particularly in monocytes/macrophages, remains unclear. Here, we integrated single-cell and bulk transcriptomic data to identify senescence-associated candidate genes associated with monocytes/macrophages in PAH.

Publicly available single-cell RNA-seq data from PAH and control pulmonary vascular tissues were analyzed. A senescence-associated score was calculated for each cell based on MSigDB gene sets. Senescence-associated genes in monocytes/macrophages were identified through correlation and differential expression screening, and further examined in bulk transcriptomic datasets. Bulk transcriptomic discovery used GSE113439, GSE117261, and GSE254617. A sample-title audit identified 68 shared PHBI identifiers between GSE117261 and GSE254617; therefore, the merged data represented 257 expression profiles from 189 unique subjects. LASSO, Random Forest, and XGBoost were used as complementary feature-selection approaches, and genes jointly retained by the three algorithms were defined as candidates for evaluation in independent cohorts.

Single-cell RNA-seq identified 14 cell types in PAH pulmonary vascular tissues, with dendritic cells, T cells, and monocytes/macrophages exhibiting the highest senescence-associated scores. Integrative screening identified 405 senescence-associated genes enriched in monocytes/macrophages. Multi-algorithm screening prioritized 10 candidate genes for subsequent evaluation. After within-cohort multiple-testing correction, external cohort analyses reproduced the discovery-stage expression directions for RGS1, PHLDA1, MAFB, and RNF13 in lung tissue cohorts, and for MAFB in a PBMC cohort. With nominal P values, RGS1 was significantly upregulated in GSE48149 and GSE53408 (both lung), and PHLDA1 was upregulated in GSE48149 (lung). MAFB was significantly downregulated in GSE33463 (PBMC) and GSE48149 (lung), whereas RNF13 was downregulated in GSE15197 and GSE48149 (both lung). Functional analysis revealed significant enrichment of immune-inflammatory and phagocytosis-related pathways among the candidate genes. Consensus clustering based on the candidate genes classified PAH patients into two exploratory transcriptomic groups with distinct expression and pathway activity profiles. In vivo evaluation in an MCT-induced PAH rat model showed seven significant direction-consistent changes, two direction-consistent nonsignificant trends, and one discordant gene (PDE4B), supporting tissue-level expression concordance.

These analyses identify a Mono.Macs-associated senescence-related candidate gene set in PAH. Independent expression analyses provide additional support for RGS1, PHLDA1, MAFB, and RNF13 as candidate genes for subsequent mechanistic and functional validation.