Background: Congenital anomalies of the kidney and urinary tract (CAKUT) cause more than 50% of significant chronic kidney disease (CKD) in children. These children typically do no undergo biopsy and there are few markers for CKD progression in children. Cell-free DNA (cfDNA) methylation studies enable one to exam organ specific methylation changes in disease and urinary cfDNA may provide a window into kidney specific changes not otherwise easily studied. While plasma cfDNA is clinically used in kidney transplantation, there are few studies that have examined cfDNA in urine and no studies performed in children with CKD. Objective: We aim in this study to identify differential methylation regions (DMRs) in urinary cfDNA in patients with CKD secondary to CAKUT compared to children without CKD to identify changes that may be involved in both development of CAKUT and progression of CKD. Additionally, we will identify DMRs in urinary cfDNA in patients with CKD and CAKUT compared to pediatric transplant patients with acute kidney injury (AKI) associated with acute transplant rejection and pediatric patients without rejection to identify overlapping gene expression profiles of kidney injury and identify potential trajectories between AKI and CKD. Design/Methods: This study will utilize urine samples from IRB approved studies, 00000849, 00000188, and 11120514. Urine was obtained from patients with CAKUT/CKD (N=5), nocturnal enuresis normal controls (N=7), transplant patients with AR (N=7) and w/out AR (N=7). DNA methylation status of cfDNA was assessed using whole genome bisulfite sequencing. Note sequencing is complete or near complete for all samples. We are currently analyzing DMCs using logistic regression. DMCs will be defined as >20% methylation difference and q-value of < 0.05. Depending on the number of DMCs we will determine what method we use for DMR identification. We will use DMC/DMRs to perform a Gene Ontology (GO) analysis to identify pathways that are enriched in those with CKD secondary to CAKUT.
