Single-Cell RNA Sequencing Of Urinary Cells Reveals Distinct Cellular Diversity in COVID-19–Associated AKI

Discussion 

A limitation of this study is the small number of patients sampled. Sample collections were restricted to new hospital admissions to control for other variables, such as the various medications used as treatments for COVID-19. Hospitalized patients with COVID-19 and without AKI were used as controls because healthy controls do not secrete many cells in urine. An additional limitation is having to process urine before sequencing; however, this greatly increased the proportion of live cells obtained. Here, cells were readily detectable in the urine of infected patients without kidney injury. This is significant because most scRNAseq studies have focused on damaged kidneys, leading to few datasets available to study uninjured kidney cells. AKI has many different causes, and only a subset may be caused by direct kidney infection by SARS-CoV-2, making it difficult to draw broad conclusions about AKI in COVID-19. Additionally, it is possible that direct viral infection of kidney cells occurs later in the infection process than was captured in this study. Subsequent studies will investigate urinary cell changes throughout the illness with sequential samples taken before, during, and after AKI.

ORGANIC HERBS FOR KIDNEY DISEASE PATIENTS HEALTH

We successfully performed scRNAseq on urinary sediment from hospitalized patients with COVID-19. This allowed for noninvasive studies of cellular changes occurring during AKI, a frequent manifestation of COVID-19.The urinary cell composition and upregulated pathways in hospitalized patients with COVID-19 drastically differ in those with AKI versus those without AKI. We also provide preliminary evidence of a potential case of viral cystitis through direct infection of urinary bladder cells. Analysis of urinary cells may provide a useful avenue to understanding the pathophysiology and cellular alterations that occur in kidney diseases.

Disclosures

A. Agarwal reports consultancy agreements with Akebia Therapeutics (served on an expert panel to review new therapeutics on the basis of the hypoxia-inducible factor pathway for AKI), Dynamed (reviewed content related to AKI for Dynamed and reviewed and updated materials prepared by the Dynamed editorial team for AKI topics), and Reata Pharmaceuticals (served as a consultant); ownership interest in Goldilocks Therapeutics, Inc.;research funding from the Genzyme/Sanofi Fabry fellowship award; and honoraria from Akebia Therapeutics, Emory, the University of Southern California, and Vanderbilt. A. Agarwal also reports scientific advisor or membership as an editorial board member for American Journal of Physiology–Renal Physiology, Kidney International, and Laboratory Investigation; as an advisory board member of Goldilocks Therapeutics, Inc. (a New York–based company investigating the delivery of drugs in the kidney using nanotechnology for acute kidney disease and CKD); as an external evaluation panel member for the Kidney Precision Medicine Program; and as an advisory board member of Alpha Young, LLC and Angion. All remaining authors have nothing to disclose.

Funding

This work was supported by National Institute of Diabetes and Digestive and Kidney Diseases grants P30 DK079337 (to A. Agarwal), R01 DK118932 (to A. Agarwal), and R01 DK59600 (to A. Agarwal); National Institute of Allergy and Infectious Diseases grant T32 AI007051 (to M.D. Cheung); National Institute of General Medical Sciences grant T32-GM-008361 (to M.D. Cheung); American Heart Association grant 827257 (to E.N. Erman); and Anderson Innovation Award (to J.F. George). 

Acknowledgments

The authors thank Ms. Wanda Hall, Ms. Rachael Shevin, and Dr. Chiao-Wang Sun for assistance in collection and processing of urine specimens; Mr. Robert Johnson and the Center for Clinical and Translational Sciences (CCTS) Informatics for Integrating Biology and the Bedside (i2b2) team for processing the clinical data; Dr. Katie Bean, Dr. Winn Seay, Dr. Clare Lyas, and the Acute Nephrology Consult Team for collection of non–COVID-19 AKI urine; Dr. Caroline Kelly for diligent proofreading; and Dr. Kelly Andringa and Ms. Mozella Kerley for administrative assistance. We acknowledge the UAB Flow Cytometry and Single Cell Core (National Institutes of Health [NIH] grant P30-AR- 04831), the UAB Heflin Genomics Core (NIH grant 5P30CA013148-48), and CCTS, National Center for Advancing

Translational Sciences (NIH grant UL1TR003096). 

Author Contributions

N.B. Erdmann, E.N. Erman, J.F. George, G. Ghajar-Rahimi, S. Liu, and K.H. Moore reviewed and edited the manuscript

Data 

Sharing Statement 

The scRNAseq data generated in this paper are available in the Gene Expression Omnibus under accession number GSE180595. Supplemental Material This article contains the following supplemental material online at http://kidney360.asnjournals.org/lookup/suppl/doi:10.34067/ KID.0005522021/-/DCSupplemental. Supplemental Figure 1. Heterogeneity of cells captured from each patient sample. Supplemental Figure 2. Gene Set Enrichment Analysis of hallmark pathways in both AKI and no AKI control clusters. Supplemental Figure 3. Heat map of differentially expressed genes from cells from patient 7.

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