Integrative single-cell and bulk transcriptomic analysis identify R-loop-associated gene signatures driving immune-inflammatory networks in acute pancreatitis

Abstract

R-loop dysregulation has been implicated in chronic inflammation via DNA damage and cytoplasmic ssDNA release, yet its role in acute pancreatitis (AP) remains to be systematically investigated. This study aimed to identify R-loop-related biomarkers in AP and elucidate their potential roles in immune-inflammatory networks through integrative bioinformatics analysis and in vitro experimental validation. Single-cell and bulk transcriptomic datasets from the GEO database were integrated to calculate R-loop-related gene (RLRG) scores across cell types using multiple scoring algorithms. High-dimensional weighted gene co-expression network analysis (hdWGCNA), differential expression analysis, and machine learning algorithms (LASSO, SVM-RFE, and Boruta) were applied to screen candidate gene signatures. Immune infiltration and functional enrichment analyses were performed to investigate the regulatory mechanisms of identified gene signatures. A caerulein-induced AR42J cell model was established for experimental validation, and siRNA-mediated knockdown was conducted to assess functional roles. Fibroblasts emerged as the primary cell type with elevated RLRG scores and significant differences between AP and control groups. Pseudotime analysis revealed that AP promotes fibroblast progression toward terminal differentiation, with high-RLRG-score cells exhibiting greater stemness and intercellular communication activity. Three candidate gene signatures—Anp32b, Myl12a, and Nras—were identified and showed markedly increased expression in the AP cohort. These genes exhibited significant correlations with immune cell populations and were enriched in immune-inflammatory, apoptotic, cytoskeletal, and proteasome pathways. The upregulation of Anp32b and Myl12a was confirmed in the caerulein-induced AR42J cell model. siRNA-mediated Myl12a knockdown attenuated trypsin activation and reduced inflammatory cytokine release, while immunofluorescence staining with the S9.6 antibody demonstrated that Myl12a knockdown significantly reduced nuclear R-loop accumulation. These findings highlight R-loop-associated gene signatures and functionally validated Myl12a as plausible candidates for dissecting AP pathogenesis. This work provides mechanistic clues for AP-related immune-inflammatory, which need further researches to verify.