Urinary Transcriptomics Identified Inflammatory Signals Associated With COVID-19-Related AKI

ABSTRACT

Background: SARS-CoV-2, associated with COVID-19, can include dysfunction in many organs including the kidney. Early in the pandemic, a high incidence of acute kidney injury (AKI), with an associated increase in mortality, was observed, particularly in those with severe respiratory failure. Given the effect on the kidney and limited availability of biopsied tissue, we designed a non-invasive protocol to isolate and sequence renal cells from the urine of patients with COVID-19 to identify the cellular and molecular mechanisms of COVID-19-related AKI, and the impact of immunomodulatory treatment. Method(s) Three groups of hospitalized patients, AKI with and without COVID-19 and COVID-19 without AKI, were recruited at Michigan Medicine (N=48). We documented >90 clinical parameters, including serum creatinine trends, treatment exposure to IL-6 inhibitors, and patient outcomes. Urine samples near peak AKI were collected and immediately processed for single cell RNA sequencing (scRNAseq);profiles were generated on the 10x Genomics platform and clustered using Seurat. Differentially expressed gene profiles were generated in a cell type selective manner. Result(s) Urine scRNAseq profiles from 44,440 cells clustered into 5 major celltypes, based on cell marker assignment. Renal cells comprised 12% of the recovered cells. Comparing renal cells from COVID-19-related AKI group to either of the two other groups identified 129 up-regulated and 89 down-regulated genes in common (q<0.05). The COVID-19-related AKI renal cell profile was consistent with activation of one or more inflammatory cytokines including IFN-gamma, IL-6, and IL-1beta. Conversely, patients exposed to IL-6 inhibitors had a reduced expression of inflammatory marker genes. Conclusion(s) This study demonstrates the successful isolation and generation of cell type transcriptional profiles of renal cells in the urine of patients with COVID-19, with or without AKI, and non-COVID-19 AKI. Expression profiles in renal cells were consistent with intra-renal inflammatory activation in COVID-19-related AKI. Association of profiles with renal function and patient outcomes may identify predictive markers of COVID-19-related AKI and potential targets for therapeutic modulation.