Differentially expressed genes and functional categories in biopsy, peripheral blood and urine from kidney transplant patients with acute and chronic rejection

Kidney transplantation is the treatment of choice for patients with end-stage chronic kidney disease (ESKD). Despite the usefulness of transplantation as replacement therapy, long-term graft survival represents a major challenge for transplant immunology. Although nowadays there has been an advance in understanding immunological mechanisms mediating rejection, and the improvement of immunomodulation therapies, there are still underlying molecular processes marking an important variability among patients, and presumably influencing allograft rejection. With our analysis we explored differences in gene expression by Next Generation Sequencing implementing RNA-Seq in biopsies, blood and urine from kidney transplant patients with acute and chronic rejection. For this, we performed an intra-outcome analysis simultaneously in acute and chronic rejection, with which we sought: 1. To identify differences in gene expression between peripheral blood vs renal tissue and peripheral blood vs urine in acute rejection and chronic rejection; 2. To identify the level of agreement in gene expression between renal tissue and urine in acute rejection and chronic rejection and 3. To identify genes and biological processes associated with acute rejection and chronic rejection that could be potentially detected in blood, and simultaneously in urine and biopsy in acute rejection and in chronic rejection. Kidney transplant patients diagnosed with either acute and chronic rejection were recruited, and blood, biopsy, and urine samples were obtained. RNA was obtained from each sample applying standard protocols and under nuclease-free conditions. RNA was sequenced and raw data was analyzed to obtain the table of raw counts, from which differential expression analyzes were performed. Comparisons were made separately for acute rejection and chronic rejection, using blood libraries as a baseline. This allowed the identification of DEGs in biopsy and in urine in relation to peripheral blood. *** Raw sequencing data are not provided (cannot be recovered). ***