Flow-Cytometric Quantification of Urine Kidney Epithelial Cells Specifically Reflects Tubular Damage in Acute Kidney Diseases

Introduction: Tubular injury is one of the main mechanisms driving acute kidney injury (AKI); however, clinicians still have a limited diagnostic repertoire to precisely monitor damage to tubular epithelial cells (TECs). In our previous study, we used single-cell sequencing to identify TEC subsets as the main components of the urine signature of AKI. This study aimed to establish TECs as clinical markers of tubular damage. Methods: A total of 243 patients were analyzed. For sequencing, we collected 8 urine samples from patients with AKI and glomerular disease. We developed a protocol for the flow cytometric quantification of CD10/CD13⁺ proximal TECs (PTECs) and CD227/CD326⁺ distal TECs (DTECs) in urine by aligning urinary single-cell transcriptomes and TEC surface proteins using Cellular Indexing of Transcriptome and Epitope Sequencing (CITE-Seq). Marker combinations were confirmed in kidney biopsies. We validated our approach in 4 cohorts of 235 patients as follows: patients with AKI (n = 63), COVID-19 infection (n = 47), antineutrophil cytoplasmic autoantibody (ANCA)–associated vasculitis (AAV) with active disease or stable remission (n = 110), and healthy controls (n = 15). Results: Our findings demonstrated that CD10/CD13 and CD227/CD326 adequately identified PTECs and DTECs, respectively. Distal urinary TEC counts correlate with the severity of AKI based on Kidney Disease: Improving Global Outcomes (KDIGO) stage and acute estimated glomerular filtration rate (GFR) loss in 2 separate cohorts and can successfully discriminate AKI from healthy controls and glomerular disease. Conclusion: We propose that urinary CD227/CD326⁺ TEC count is a specific, noninvasive marker for tubular injury in AKI. Our protocol provides a basis for a deeper phenotypic analysis of urinary TECs.