Integration of single-cell and bulk RNA data to identify key cell types and biomarkers in viral myocarditis: An...

Viral myocarditis (VMC), a multifaceted pathological condition predominantly triggered by viral infections, has emerged as a major worldwide healthcare concern due to its intricate pathogenesis and substantial disease burden. Although the centrality of immune dysregulation in driving VMC progression is well-established, the precise identities of distinct immune cell subsets and their molecular mediators governing pathological progression continue to present significant knowledge gaps. Single-cell datasets were integrated using quality control, batch correction, and normalization. The FindAllMarkers function identified marker genes for each cluster. Cell types were annotated based on literature-derived marker genes. DESeq2 was employed to identify differentially expressed genes in T cells. CellChat was used to explore intercellular communication and identify key ligand-receptor signaling pathways. Receiver operating characteristic curves assessed the predictive performance of key factors in a validation cohort. T cells were re-annotated for higher-resolution subtyping, and pseudotime analysis depicted the cell trajectories of T cell subtypes. Integrated single-cell data revealed a comprehensive single-cell atlas of VMC. Mechanistic delineation of T cell as principal pathogenic effectors emerged through multi-omics interrogation incorporating single-cell transcriptomic profiling and pathological trajectory reconstruction; functional genomics analyses further substantiated their cardinal involvement in cardiotropic viral pathogenesis. Additionally, communication analysis highlighted CCL as a critical immune regulatory pathway for T cell interactions in VMC. Significant upregulation of CCL3 was confirmed in the validation cohort, establishing it as a potential biomarker and therapeutic target for VMC. Pseudotime analysis and re-annotation of T cell subpopulations revealed significant enrichment of T.8EFF.OT1LISO and T.Tregs in VMC. This study identifies T cells as key immune players in VMC, with CCL3 proposed as a novel biomarker for the condition.