Extracellular vesicle-bound DNA in urine is indicative of kidney allograft injury

Abstract

Extracellular vesicle-bound DNA (evDNA) is an understudied extracellular vesicle (EV) cargo, particularly in cancer-unrelated fundamental and biomarker research. Although evDNA has been detected in urine, little is known about its characteristics, localization, and biomarker potential for kidney pathologies. To address this, we enriched EVs from urine of well-characterized kidney transplant recipients undergoing allograft biopsy, characterized their evDNA and its association to allograft injury. Using DNase treatment and immunogold labelling TEM, we show that DNA is bound to the surface of urinary EVs. Although the urinary evDNA and cell-free DNA correlated in several characteristics, the DNA integrity index showed evDNA was less fragmented (P < 0.001). Urinary EVs from patients with rejection and non-rejection allograft injury were significantly larger (mean: P = 0.045, median: P = 0.031) and have bound more DNA as measured by normalized evDNA yield (P = 0.018) and evDNA copy number (P = 0.007), compared to patients with normal histology. Urinary evDNA characteristics associated with the degree of interstitial inflammation, combined glomerulitis and peritubular capillaritis, and inflammation in areas of fibrosis (all P < 0.050). The normalized dd-evDNA copy numbers differed between the antibody- and T cell-mediated rejection (P = 0.036). Our study supports the importance of DNA as urine EV cargo, especially as potential non-invasive kidney allograft injury biomarker.