HCA Data Explorer

Single-cell RNA sequencing of urinary cells reveals distinct cellular diversity in COVID-19-associated AKI

Updated August 30, 2022

Background: Acute kidney injury (AKI) is a common sequela of infection with SARS-CoV-2 and contributes to the severity and mortality from COVID-19. Here, we tested the hypothesis that kidney alterations induced by COVID-19-associated AKI could be detected in cells collected from urine. Methods: We performed single-cell RNA sequencing (scRNAseq) on cells recovered from the urine of eight hospitalized COVID-19 patients with (n=5) or without AKI (n=3) as well as four non-COVID-19 AKI patients (n=4) to assess differences in cellular composition and gene expression during AKI. Results: Analysis of 30,076 cells revealed a diverse array of cell types, most of which were kidney, urothelial, and immune cells. Pathway analysis of tubular cells from patients with AKI showed enrichment of transcripts associated with damage-related pathways compared to those without AKI. ACE2 and TMPRSS2 expression were highest in urothelial cells amongst cell types recovered. Notably, in one patient we detected SARS-CoV-2 viral RNA in urothelial cells. These same cells were enriched for transcripts associated with anti-viral and anti-inflammatory pathways. Conclusions: We successfully performed scRNAseq on urinary sediment from hospitalized patients with COVID-19 to noninvasively study cellular alterations associated with AKI and established a dataset that includes both injured and uninjured kidney cells. Additionally, we provide preliminary evidence of direct infection of urinary bladder cells by SARS-CoV-2. The urinary sediment contains a wealth of information and is a useful resource for studying the pathophysiology and cellular alterations that occur in kidney diseases. Overall design: Single-cell RNA sequencing of cells obtained from urine of patients with COVID-19. There are 12 total samples from 12 separate patients, 5 with COVID19 AKI, 3 with COVID19 without AKI, and 4 with non COVID19 AKI

Anupam AgarwalUniversity of Alabama at Birminghamagarwal@uab.edu
James F GeorgeUniversity of Alabama at Birminghamjgeorge@uab.edu
Anupam Agarwal (Experimental Scientist)1
James F George (Experimental Scientist)1
1University of Alabama at Birmingham
Parisa Nejad
Brittney D Wick
Rachel Schwartz

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/c6a50b2a-3dfd-4ca8-9b48-3e682f568a25
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Analysis Portals

None

Project Label

humanUrinaryCellsCovidAKI

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

urine

Organ Part

Unspecified

Selected Cell Types

Unspecified

Disease Status (Specimen)

2 disease statuses

Disease Status (Donor)

2 disease statuses

Development Stage

human adult stage

Library Construction Method

10x 3' V3

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis_protocol_1

File Format

4 file formats

Cell Count Estimate

30.1k

Donor Count

12
fastq28 file(s)fastq.gz72 file(s)RAW.tar1 file(s)xlsx1 file(s)