A Pre-Kidney Transplant Blood-Based Next-Generation Sequencing Assay to Predict Early Acute Rejection

KEY POINTS: Pretransplant early acute rejection risk stratification offers a novel approach to personalized immunosuppression management in patients who received a kidney transplant. Stratifying immunologic risk independent of donor characteristics may help guide immunosuppression management in patients who received a kidney transplant. The pretransplant risk assessment gene set reflects metabolic and immune pathways involved in T-cell- and antibody-mediated mechanisms of transplant rejection. BACKGROUND: Although donor and recipient characteristics are used to estimate graft failure risk, they remain limited in predicting early acute rejection (EAR). We developed and validated a next-generation sequencing assay targeting the pretransplant immunologic profile to predict EAR following kidney transplantation. METHODS: This prospective, international study enrolled 321 kidney transplant participants across 13 sites, forming discovery and validation cohorts. Peripheral blood was collected before transplant and at 1, 3, 6, 12, and 24 months post-transplant, with protocol biopsies performed at 3 and 12 months, as well as any indication biopsies. Biopsies were assessed by a blinded central pathologist according to the 2019 Banff criteria. The pretransplant risk assessment (PTRA) test to evaluate RNA expression of a 29-gene signature algorithm designed to predict EAR risk was clinically validated using 122 deceased donor kidney transplant recipients. RESULTS: PTRA classified 31 of 122 participants (25%) as high risk and 91 (75%) as low risk. There were nine EAR events in the first 60 days post-transplant: 6/31 (19%) in the high-risk group and 3/91 (3%) in the low-risk group. PTRA discrimination for EAR at 60 days post-transplant yielded an area under the curve of 0.78 (95% confidence interval [CI], 64.4 to 91.5), P < 0.001. A cutoff of ≤45 was defined as low risk and >45 as high risk for EAR within 60 days post-transplant. Sensitivity was 0.67 (95% CI, 0.36 to 0.97), specificity 0.78 (95% CI, 0.70 to 0.86), positive predictive value 0.19 (95% CI, 0.05 to 0.33), and negative predictive value 0.97 (95% CI, 0.93 to 1.00). The odds ratio comparing patients identified as high versus low risk by PTRA was 7.04 (95% CI, 1.64 to 30.2), P = 0.009. CONCLUSIONS: This study validates the ability of PTRA to stratify kidney transplant recipients as high or low risk for EAR using a pretransplant transcriptomic profile, with implications for graft health and personalized treatment management.