Using human iPSC-derived kidney organoids to decipher SARS-CoV-2 pathology on single cell level

Katharina C. Reimer; Jitske Jansen; Gijs J. Overheul; Pascal Miesen; Ronald P. van Rij; Sergio H. Triana; Bart Smeets; Rebekka K. Schneider; Rafael Kramann

STAR Protocols (Sep 2022)

Using human iPSC-derived kidney organoids to decipher SARS-CoV-2 pathology on single cell level

Katharina C. Reimer,
Jitske Jansen,
Gijs J. Overheul,
Pascal Miesen,
Ronald P. van Rij,
Sergio H. Triana,
Bart Smeets,
Rebekka K. Schneider,
Rafael Kramann

Affiliations

Katharina C. Reimer: Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany; Institute of Cell and Tumor Biology, RWTH Aachen University, Aachen, Germany; Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Corresponding author
Jitske Jansen: Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany; Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Pediatric Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Amalia Children’s Hospital, Nijmegen, the Netherlands
Gijs J. Overheul: Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
Pascal Miesen: Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
Ronald P. van Rij: Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
Sergio H. Triana: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
Bart Smeets: Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
Rebekka K. Schneider: Institute of Cell and Tumor Biology, RWTH Aachen University, Aachen, Germany; Department of Developmental Biology, Erasmus Medisch Centrum, Rotterdam, the Netherlands; Oncode Institute, Erasmus Medisch Centrum, Rotterdam, the Netherlands; Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medisch Centrum, Rotterdam, the Netherlands
Rafael Kramann: Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany; Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medisch Centrum, Rotterdam, the Netherlands; Corresponding author

Journal volume & issue: Vol. 3, no. 3
p. 101612

Abstract

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Summary: We describe a protocol for single-cell RNA sequencing of SARS-CoV-2-infected human induced pluripotent stem cell (iPSC)-derived kidney organoids. After inoculation of kidney organoids with virus, we use mechanical and enzymatic disruption to obtain single cell suspensions. Next, we process the organoid-derived cells into sequencing-ready SARS-CoV-2-targeted libraries. Subsequent sequencing analysis reveals changes in kidney cells after virus infection. The protocol was designed for kidney organoids cultured in a 6-well transwell format but can be adapted to organoids with different organ backgrounds.For complete details on the use and execution of this protocol, please refer to Jansen et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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