Abstract: TH-OR096
Urinary Cell-Free DNA Methylation Signatures of CKD Progression of Congenital Anomalies of the Kidney and Urinary Tract in Pediatric Patients
Session Information
- Shaping Pediatric Kidney Disease: Developmental Insights, Stem Cell Systems, Novel Biomarkers, and More
October 22, 2026 | Location: Room 603, Convention Center
Abstract Time: 05:20 PM - 05:30 PM
Category: Pediatric Nephrology
- 1800 Pediatric Nephrology
Authors
- Bakhoum, Christine Y., Yale School of Medicine, New Haven, Connecticut, United States
- Kavaliauskaite, Ieva, Yale School of Medicine, New Haven, Connecticut, United States
- Demkowicz, Patrick Christopher, Yale School of Medicine, New Haven, Connecticut, United States
- Furth, Susan L., The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
- Bakhoum, Mathieu F., Yale School of Medicine, New Haven, Connecticut, United States
Background
Congenital anomalies of the kidney and urinary tract (CAKUT) are the leading cause of pediatric CKD, yet progression trajectories vary widely. Urinary cell-free DNA (cfDNA) carries methylation marks from kidney cells shed into urine, providing a window into the chromatin and transcriptional state of the injured kidney. We used whole-genome enzymatic methylation sequencing (EM-seq) on banked urine from the Chronic Kidney Disease in Children (CKiD) cohort to derive and validate a cfDNA methylation signature of CKD progression.
Methods
We selected 120 baseline urine specimens from CKiD participants with CAKUT (60 rapid progressors, 60 slow progressors defined by extreme tertiles of eGFR slope). cfDNA was sequenced by EM-seq at 30X target coverage. After QC, 55 samples were used for discovery and 65 were held out for validation. Analyses adjusted for cell-lineage composition, age, sex, baseline eGFR, and proteinuria. We derived a direction-weighted methylation risk score from top differentially methylated loci and evaluated it for a composite endpoint (≥40% eGFR decline or kidney replacement therapy/KRT) by Cox regression.
Results
We identified 61 differentially methylated CpGs (FDR<0.25). The resulting methylation risk score achieved held-out AUC 0.70 (95% CI 0.57-0.82) for classifying rapid vs. slow progressors. Prognostic CpGs were enriched at kidney development genes (RET, FOXC1/2, BMP4, GDNF; FDR=0.003) and fibrosis-axis genes (TGFB1, CCN2/CTGF, SMAD7), with 96% hypermethylated in rapid progressors. For the composite endpoint (≥40% eGFR decline/KRT), the per-1-SD Cox HR was 1.97 in discovery (95% CI 1.45-2.67, p<0.001) and 1.61 in held-out validation (95% CI 1.10-2.37, p=0.015). Extreme-tertile contrast (T3 vs. T1) showed HR 3.09 in validation (p=0.038; Figure). The signature was robust across CAKUT subtypes (AUC 0.73-0.87) and sexes.
Conclusion
A 61-CpG urinary cfDNA methylation signature predicts kidney outcomes in held-out validation in pediatric CAKUT using methylation alone. The signature is enriched in kidney development and fibrosis pathways, supporting its potential as a non-invasive prognostic tool.
Acknowledgment
Data was collected by the CKiD prospective cohort study with clinical coordinating centers (Principal Investigators) at Children's Mercy Hospital and the University of Missouri – Kansas City (Bradley Warady, MD) and Children's Hospital of Philadelphia (Susan Furth, MD, PhD), Central Biochemistry Laboratory (Jesse Seegmiller, PhD) at the University of Minnesota, and data coordinating center (Derek Ng, PhD) at the Johns Hopkins Bloomberg School of Public Health.
Funding
- NIDDK Support