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Integrated Single-Cell and Machine-Learning Analysis Identifies Antigen-Presenting Macrophage-Associated Genes in
Chu Chu1, Yuqin Li1, Qian Qian2
1Department of Infectious Disease, Children's Hospital of Soochow University, Suzhou, 215003, China.
Introduction:
Community-Acquired Pneumonia (CAP) is a major global threat with mortality driven by immune dysregulation. The potential role of antigen-presenting macrophages in coordinating immune responses remains poorly defined in CAP. This study aimed to characterize their cellular landscape and intercellular communication and to identify candidate CAP-associated genes through an integrated computational framework.
Methods:
Single-cell RNA-seq (scRNA-seq) data were analyzed using Seurat, followed by functional enrichment, CellChat, and hdWGCNA analyses. Four machine-learning classifiers were trained and evaluated using a stratified training/test split and repeated cross-validation. Gene set enrichment analysis was performed using the MSigDB Hallmark collection. Molecular docking and a 100-ns molecular dynamics simulation were conducted to explore the predicted interaction between estradiol and SAT1. The expression of SAT1, SERPINB1, and IFITM3 was further examined by qRT-PCR in an LPS/ IFN-γ-stimulated THP-1-derived macrophage model.
Results:
Antigen-presenting macrophages were identified, whose markers were enriched in antigen processing pathways. CellChat indicated extensive communication between these macrophages and other immune cells. hdWGCNA identified M9/M10 as key modules, while XGBoost achieved the highest test-set performance and prioritized SAT1, SERPINB1, and IFITM3 as candidate genes associated with interferon and inflammatory pathways. Molecular docking predicted interactions of estradiol with SAT1 and SERPINB1, and the 100-ns simulation suggested relative dynamic stability of the predicted SAT1-estradiol complex. qRT-PCR showed that LPS/IFN-γ stimulation significantly increased SAT1, SERPINB1, and IFITM3 mRNA expression in THP-1-derived macrophages.
Discussion:
This study characterized antigen-presenting macrophages as potentially important immune-cell populations in pediatric CAP and prioritized three candidate genes. The estradiol findings remain exploratory and require direct mechanistic and functional validation.
Conclusion:
Antigen-presenting macrophages were identified as potential immune regulators in CAP. SAT1, SERPINB1, and IFITM3 represent candidate CAP-associated genes supported by preliminary in vitro transcriptional validation, whereas the predicted interaction with estradiol should be regarded as a hypothesis warranting further investigation.