Single-cell RNA-sequencing identifies unique cell-specific gene expression profiles in high-grade cardiac allograft vasculopathy.

Background: Cardiac allograft vasculopathy (CAV) is the leading cause of late graft failure and mortality after heart transplantation (HT). Current strategies for early diagnosis and effective treatment of CAV are lacking. Using single-cell RNA-sequencing in peripheral blood mononuclear cells (PBMCs), we sought to investigate cell-specific gene expression profiles and T cell receptor repertoires in CAV that may inform novel biomarkers and pathways to interrupt CAV pathogenesis.

Methods: Whole blood was collected from 22 HT recipients with angiographically-confirmed CAV and 18 HT recipients without CAV. PBMCs were isolated and subjected to single-cell RNA-sequencing using a 10X Genomics microfluidic platform. Downstream analyses focused on differential expression of genes, cell compositional changes, and T cell receptor repertoire analyses.

Results: Across 40 PBMC samples, we isolated 134,984 cells spanning 31 cell types. Compositional analyses showed subtle, but significant increases in CD4+ T central memory cells, and CD14+ and CD16+ monocytes in high-grade CAV (CAV-2 and CAV-3). 745 genes were differentially expressed in a cell-specific manner in high-grade CAV, enriched for putative pathways involved in inflammation and angiogenesis. Intersection with the druggable genome prioritized 68 targets, including targets with approved drugs in cardiovascular disease (e.g., canakinumab). There were no significant differences in T cell clonality or diversity with increasing CAV severity.

Conclusions: Unbiased whole transcriptomic analyses at single-cell resolution identify unique, cell-specific gene expression patterns in CAV, suggesting the potential utility of peripheral gene expression biomarkers in diagnosing CAV. Furthermore, precision targeting of these pathways may offer opportunities to mitigate CAV pathogenesis.