Transcriptomic signatures and immune microenvironment of acute rejection after heart transplantation: an integrated bioinformatics analysis.

BACKGROUND

Histologic assessment of endomyocardial biopsy (EMB) remains the standard for diagnosing acute cardiac allograft rejection, yet molecular profiling may provide complementary quantitative insights.

METHODS

Microarray data (GSE2596; GPL1053) were obtained from the Gene Expression Omnibus. Acute rejection (R, n = 16) and non-rejection (N, n = 27) samples were analyzed after excluding infection-related groups. Probes were mapped to gene symbols and summarized per gene. Differential expression was assessed using Welch's t-test with Benjamini-Hochberg false discovery rate control. Reactome over-representation analysis was performed for significant genes. Immune cell scores were estimated using MCP-counter markers. An L1-penalized logistic regression model was evaluated by 5-fold cross-validation. Experimental validation was performed by quantitative PCR in a cervical heterotopic cardiac xenotransplantation model (BALB/c to C57), including normal control and sham groups.

RESULTS

Among 3,968 genes, 1,032 were differentially expressed (FDR<0.05), including 135 with |log2FC|>1. Upregulated genes included HLA-DMA, DEF6, TRB@, and CD74. Enrichment analysis highlighted interferon signaling, T-cell receptor signaling, chemokine pathways, and antigen presentation. Immune scoring indicated increased monocytic, B-lineage, and T/cytotoxic lymphocyte signals in rejection. The diagnostic model achieved strong discrimination (5-fold AUC=0.993). qPCR confirmed coordinated upregulation of interferon-related (Ifng, Stat1), chemokine (Cxcl10), and cytotoxic (Prf1) genes in transplanted grafts.

CONCLUSIONS

Acute rejection EMB transcriptomes demonstrate coordinated interferon-driven immune activation. A compact gene signature shows strong internal diagnostic performance, supported by experimental validation, warranting external confirmation.