Design and development of a urinary cell pellet mRNA PCR-based assay for progressive kidney disease: Nephro-Dx

Progressive chronic kidney disease (CKD) is a major source of public health spending. Current non-invasive tests estimate CKD but provide a minimal understanding of cell- or compartment-specific injury. The gold standard for CKD diagnosis is a kidney biopsy, which affords risks and is impractical to repeat multiple times. Hence, repeatable, non-invasive tests to estimate pathologic kidney injury for diagnoses, prognosis and follow-up of CKD represent a knowledge gap. We hypothesized that urinary shedding of specific cells is proportional to injury of those cells on biopsy, and that tracking cell-specific urine mRNA will correlate with ongoing injury. Informed by apriori biopsy and urine single cell RNA studies, we developed a targeted 10-gene urine mRNA assay to estimate kidney injury non-invasively (Nephro-Dx). In a pilot study of 48 patients with diverse kidney pathology on biopsy and 20 controls, we confirmed our assays utility in differentiating any kidney disease from controls. Within biopsied cases, we confirmed correlations of cell-specific urinary gene expression with corresponding compartment injury on biopsy using a validated quantitative digital pathology platform. We show that the gene signatures including individual genes associate with subsequent loss of kidney function within our cases providing an advantage over existing non-invasive tests. Our parsimonious set of gene signatures in Nephro-Dx shows advantages in early diagnosis, monitoring, and prognosis to impact this public health problem.