Integrative Analysis of Single-cell and Bulk RNA Sequencing Reveals Macrophage Heterogeneity in Lyme Arthritis
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Introduction
Lyme arthritis (LA) is a chronic inflammatory joint disease caused by Borrelia burgdorferi infection, with approximately 10-20% of patients developing antibiotic resistance. Macrophages in the synovial microenvironment play a crucial role in disease progression, but their precise regulatory mechanisms remain unclear.
Methods
scRNA-seq data of synovial tissue from LA patients was obtained from the GEO database (GSE233850) and integrated with transcriptome data from our research team’s LA mouse model and the GSE125503 dataset. Multiple analytical strategies, including cell clustering, differential gene analysis, GO and KEGG enrichment analysis, pseudotime trajectory analysis, and cell-cell communication analysis, were employed to systematically investigate macrophage characteristics in LA. In vitro experiments using RAW cell lines were conducted to validate the role of key genes in response to Borrelia burgdorferi infection.
Results
Through single-cell transcriptome analysis of 78,015 cells in the GSE233850 dataset, we identified and annotated 27,843 macrophages, further classifying them into 4 functional subgroups. Differential expression analysis revealed 387 macrophage-specific genes. Cell-cell communication network analysis showed that macrophages interact with other immune cells, including T cells and B cells, through multiple signaling pathways. GO and KEGG enrichment analyses indicated that these differentially expressed genes were mainly enriched in biological processes such as inflammatory response regulation, pathogen recognition, and cytokine signaling. By integrating transcriptome data from our team’s LA mouse model and the GSE125503 dataset, we screened and validated three potential diagnostic marker genes (SIRPB1C, FABP5, and PEPD). In vitro experiments using the RAW264.7 macrophage cell line showed significant expression changes in these genes following Borrelia burgdorferi stimulation ( P < 0.05).
Conclusion
This study provides the first systematic characterization of macrophage transcriptome in the LA synovial microenvironment, revealing their functional heterogeneity and identifying potential diagnostic markers, offering new targets for targeted therapeutic strategies.
