Clinical Trails of Transplantation (CTOT)-03 RNAseq datasets. Pseudo-time trajectory differential expression analysis of bulk expression data uncovers dynamic mechanism of acute rejection post-heart transplant

We applied pseudo-time analysis to longitudinal bulk RNAseq differential expression analyses of 110 prospectively endomyocardial biopsies collected from 26 heart transplant recipients from the Clinical Trials in Organ Transplant-03 study. We detected two lineages amongst our samples after our pseudo-time analyses. Samples with biopsy confirmed acute cellular rejection (ACR) fall along a distinct lineage within the same pseudo-time interval versus a separate lineage without ACR. Differential expression analyses of these two lineages reveals signatures related to immunization mechanisms of allograft rejection with 10 differentially expressed genes (DEGs) associated with rejection episodes along the reconstructed pseudo time on the lineage and 343 DEGs between the two lineages. Recipients with downstream ACR fall into the distinct ACR lineage from the initial biopsy despite no pathological evidence of rejection at that point. Pathway enrichment analysis and comparative analyses link these genes to known processes for allograft rejection but also implicate novel processes in early ACR manifestation.