Diagnostic performances and longitudinal trajectories of gene expression profiling and donor-derived cell-free DNA in pediatric kidney transplant recipients with rejection

Abstract Background Timely diagnosis of allograft rejection is crucial for preventing premature graft loss. This pilot study aimed to evaluate the diagnostic performance of blood gene expression profile (GEP) and donor-derived cell-free DNA (dd-cfDNA) in detecting rejection in pediatric kidney transplant recipients. Methods We prospectively recruited pediatric kidney transplant recipients (<21 years) who underwent a for-cause biopsy (August 20, 2023–February 6, 2025). Blood samples for GEP and dd-cfDNA were collected at biopsy (week 0) and at weeks 4 and 8. Descriptive statistics were used to summarize cohort characteristics. Diagnostic accuracy of biomarkers (sensitivity, specificity, positive predictive value [PPV], and negative predictive value [NPV]) was calculated against the gold-standard biopsy. Results Our pilot study included 27 biopsies performed in 23 recipients. The median age of participants was 6.1 (IQR: 3.9, 13.7) years; 55.6% were male, and 92.6% were white. At week 0, GEP detected rejection with 40.0% sensitivity, 82.0% specificity, 57.0% PPV, and 70.0% NPV. A GEP score >0.4 yielded higher sensitivity (86% vs. 43%) and NPV (80% vs. 67%) compared to a score >0.5. Using a dd-cfDNA threshold of >1.0%, dual-positivity (positive dd-cfDNA and GEP) yielded a 33.0% sensitivity, 94.0% specificity, 75.0% PPV, and 73.0% NPV. Overall, the combined AUC of dd-cfDNA and GEP probability scores was 0.62 (95% CI, 0.31–0.93). Unlike serum creatinine, GEP probability scores and dd-cfDNA trended toward quiescent levels on serial assessment. Conclusion Combining GEP and dd-cfDNA improved their diagnostic performance. GEP and dd-cfDNA levels showed a downward trend after rejection treatment initiation. Graphical Abstract A higher resolution version of the Graphical abstract is available as Supplementary information.