*Purpose: Whole blood and graft biopsy RNA expression analyses are limited by the heterogeneous cell composition of the samples. Cell coding is an analytical tool that allows to differentiate gene enrichments in different cell subsets from single samples and provides more granular information on transcriptional profile.

*Methods: We used public datasets of single-cell RNA sequencing of peripheral blood and kidney tissues along with sorted-cell RNAseq and microarray datasets to identify transcriptomic meta-markers specific for immune and renal cells. We next carried out gene set enrichment analysis (GSEA) with these markers to analyze the gene expression of immune and renal cell subsets in bulk expression profiles of serial whole blood (month 0 and 3) and surveillance biopsies (month 3 and 12) from 241 kidney transplant recipients enrolled in the GOCAR study.

*Results: We found that, in patients who developed acute rejection (AR), pre-transplant whole blood showed low expression of NK or CD8 cell markers, which were significantly increased at 3 month after transplant. In the 3-month surveillance biopsy, the high expression of immune cell markers (NK, CD8, CD4, B cell and monocytes) was associated with both AR and fibrosis while mast cell and fibroblast markers were associated with fibrosis only. Interestingly, low expression of tubular cell markers (collecting duct, proximal tubule) was associated with fibrosis but not AR. In patients who developed acute rejection (AR) or fibrosis at 12 month, the expression of immune cell markers was increased and tubular cell markers decreased at 12 month compared to 3 month. From our analysis, we also observed a trend towards decreased expression of podocyte markers in patients who showed AR or fibrosis at m3 and m12 biopsies. Lastly in each cell type, the key hub genes associated with AR or fibrosis were identified and the gene expression regulation networks of these hub genes among different cell types were built to reveal the important immune-renal cell crosstalks that may drive development of AR/fibrosis.

*Conclusions: The study portrayed a picture of gene expression regulation in immune and renal graft cells that is changing over the time of kidney transplant. This work has the potential to identify pathogenic pathways and novel therapeutic target at the cellular level.

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