Correlation of Donor-derived Cell-free DNA With Histology and Molecular Diagnoses of Kidney Transplant Biopsies

Background. Circulating donor-derived cell-free DNA (cfDNA), a minimally invasive diagnostic tool for kidney transplant rejection, was validated using traditional histology. The molecular microscope diagnostic system (MMDx) tissue gene expression platform may provide increased precision to traditional histology. Methods. In this single-center prospective study of 208 biopsies (median = 5.8 mo) posttransplant, we report on the calibration of cfDNA with simultaneous biopsy assessments using MMDx and histology by area under the curve (AUC) analyses for optimal criterion, as well as for, previously published cfDNA cutoffs <= 0.21% to rule-out rejection and >= 1% to rule-in rejection. Results. There were significant discrepancies between histology and MMDx, with MMDx identifying more antibody-mediated rejection (65; 31%) than histology (43; 21%); the opposite was true for T cell-mediated rejection [TCMR; histology: 27 (13%) versus MMDx: 13 (6%)]. Most of the TCMR discrepancies were seen for histologic borderline/1A TCMR. AUC for cfDNA and prediction of rejection were slightly better with MMDx (AUC = 0.80; 95% CI: 0.74-0.86) versus histology (AUC = 0.75; 95% CI: 0.69-0.81). A cfDNA <= 0.21% had similar sensitivity (similar to 91%) to rule-out rejection by histology and MMDx. Specificity was slightly higher with MMDx (92%) compared with histology (85%) to rule-in rejection using cfDNA criterion >= 1%. Strong positive quantitative correlations were observed between cfDNA scores and molecular acute kidney injury for both rejection and nonrejection biopsies. Conclusions. Molecular diagnostics using tissue gene expression and blood-based donor-derived cell-free DNA may add precision to some cases of traditional histology. The positive correlation of cfDNA with molecular acute kidney injury suggests a dose-dependent association with tissue injury irrespective of rejection characteristics.

Automated summary

This single-center prospective study examines the application of circulating donor-derived cell-free DNA (cfDNA), molecular microscope diagnostic system (MMDx), and traditional histology in kidney transplant rejection. The results show that MMDx provides higher precision than histology, but there are discrepancies between the two methods. Additionally, cfDNA correlates strongly with molecular acute kidney injury, indicating an association with tissue injury regardless of rejection characteristics.