Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury

Klocke, J.; Kim, S. J.; Skopnik, C. M.; Hinze, C.; Boltengagen, A.; Metzke, D.; Grothgar, E.; Prskalo, L.; Wagner, L.; Freund, P.; Görlich, N.; Muench, F.; Schmidt-Ott, K. M.; Mashreghi, M.-F.; Kocks, C.; Eckardt, K.-U.; Rajewsky, N.; Enghard, P.

doi:10.1101/2022.02.15.479234

bioRxiv · 10.1101/2022.02.15.479234

Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury

Klocke, J.·Kim, S. J.·Skopnik, C. M.·Hinze, C.·Boltengagen, A.·Metzke, D.·Grothgar, E.·Prskalo, L.·Wagner, L.·Freund, P.·Görlich, N.·Muench, F.·Schmidt-Ott, K. M.·Mashreghi, M.-F.·Kocks, C.·Eckardt, K.-U.·Rajewsky, N.·Enghard, P.

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Abstract

Acute kidney injury (AKI) is a major health issue, the outcome of which depends primarily on damage and reparative processes of tubular epithelial cells (TEC). Mechanisms underlying AKI remain incompletely understood, specific therapies are lacking and monitoring the course of AKI in clinical routine is confined to measuring urine output and plasma levels of filtration markers. Here we demonstrate feasibility and potential of a novel approach to assess the cellular and molecular dynamics of AKI by establishing a robust urine-to-single cell RNA sequencing (scRNAseq) pipeline for excreted kidney cells via flow cytometry sorting. We analyzed 42,608 single cell transcriptomes of 40 urine samples from 32 AKI patients and compared our data with reference material from human AKI post-mortem biopsies and published mouse data. We demonstrate that TEC transcriptomes mirror intrarenal pathology and reflect distinct injury and repair processes, including oxidative stress, inflammation, and tissue rearrangement. We also describe an AKI-specific abundant urinary excretion of progenitor-like cells. In conclusion, single cell transcriptomics of kidney cells excreted in urine provides non-invasive, unprecedented insight into cellular processes underlying AKI, thereby opening novel opportunities for target identification, AKI sub-categorization and monitoring of natural disease course and interventions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/479234v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@e7175corg.highwire.dtl.DTLVardef@1aed1e6org.highwire.dtl.DTLVardef@5655f4org.highwire.dtl.DTLVardef@2512a7_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Klocke, J., Kim, S. J., Skopnik, C. M., Hinze, C., Boltengagen, A., Metzke, D., Grothgar, E., Prskalo, L., Wagner, L., Freund, P., Görlich, N., Muench, F., Schmidt-Ott, K. M., Mashreghi, M.-F., Kocks, C., Eckardt, K.-U., Rajewsky, N., Enghard, P.. 2022-02-16. Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury. https://doi.org/10.1101/2022.02.15.479234

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