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

doi:10.1016/j.xpro.2022.101612

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^*

^*Corresponding author for this work

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Abstract

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).

Original language	English
Article number	101612
Journal	STAR Protocols
Volume	3
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2022.101612
Publication status	Published - 16 Sept 2022

Bibliographical note

Acknowledgments:
This work was supported by grants of the German Research Foundation (DFG: KR 4073/11-1 ; SFBTRR219 , 322900939 ; and CRU344 , 428857858 , and CRU5011 InteraKD 445703531 ), a grant of the European Research Council ( ERC-StG 677448 ), the Federal Ministry of Research and Education (BMBF NUM-COVID19, Organo-Strat 01KX2021 ), the Dutch Kidney Foundation (DKF) TASK FORCE consortium (CP1805), the Else Kroener Fresenius Foundation ( 2017_A144 ), and the ERA-CVD MENDAGE consortium ( BMBF 01KL1907 ) all to R.K.; DFG ( CRU344 P2 to R.K.S.); and the BMBF eMed Consortium Fibromap (to R.K., and R.K.S.). R.K.S. received support from the KWF Kankerbestrijding ( 11031/2017–1 , Bas Mulder Award) and a grant by the ERC (deFiber; ERC-StG 757339 ). J.J. is supported by the Netherlands Organization for Scientific Research ( NWO Veni grant no: 091 501 61 81 01 36 ) and the DKF (grant no. 19OK005 ). B.S. is supported by the DKF (grant: 14A3D104 ) and the NWO (VIDI grant: 016.156.363 ). R.P.V.R. and G.J.O. are supported by the NWO VICI (grant: 16.VICI.170.090 ).

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@article{70643bb3f7f147d488210c574bc69153,

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

abstract = "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).",

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

note = "Acknowledgments: This work was supported by grants of the German Research Foundation (DFG: KR 4073/11-1 ; SFBTRR219 , 322900939 ; and CRU344 , 428857858 , and CRU5011 InteraKD 445703531 ), a grant of the European Research Council ( ERC-StG 677448 ), the Federal Ministry of Research and Education (BMBF NUM-COVID19, Organo-Strat 01KX2021 ), the Dutch Kidney Foundation (DKF) TASK FORCE consortium (CP1805), the Else Kroener Fresenius Foundation ( 2017_A144 ), and the ERA-CVD MENDAGE consortium ( BMBF 01KL1907 ) all to R.K.; DFG ( CRU344 P2 to R.K.S.); and the BMBF eMed Consortium Fibromap (to R.K., and R.K.S.). R.K.S. received support from the KWF Kankerbestrijding ( 11031/2017–1 , Bas Mulder Award) and a grant by the ERC (deFiber; ERC-StG 757339 ). J.J. is supported by the Netherlands Organization for Scientific Research ( NWO Veni grant no: 091 501 61 81 01 36 ) and the DKF (grant no. 19OK005 ). B.S. is supported by the DKF (grant: 14A3D104 ) and the NWO (VIDI grant: 016.156.363 ). R.P.V.R. and G.J.O. are supported by the NWO VICI (grant: 16.VICI.170.090 ). Publisher Copyright: {\textcopyright} 2022 The Author(s)",

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AU - Reimer, Katharina C.

AU - Jansen, Jitske

AU - Overheul, Gijs J.

AU - Miesen, Pascal

AU - van Rij, Ronald P.

AU - Triana, Sergio H.

AU - Smeets, Bart

AU - Schneider, Rebekka K.

AU - Kramann, Rafael

N1 - Acknowledgments: This work was supported by grants of the German Research Foundation (DFG: KR 4073/11-1 ; SFBTRR219 , 322900939 ; and CRU344 , 428857858 , and CRU5011 InteraKD 445703531 ), a grant of the European Research Council ( ERC-StG 677448 ), the Federal Ministry of Research and Education (BMBF NUM-COVID19, Organo-Strat 01KX2021 ), the Dutch Kidney Foundation (DKF) TASK FORCE consortium (CP1805), the Else Kroener Fresenius Foundation ( 2017_A144 ), and the ERA-CVD MENDAGE consortium ( BMBF 01KL1907 ) all to R.K.; DFG ( CRU344 P2 to R.K.S.); and the BMBF eMed Consortium Fibromap (to R.K., and R.K.S.). R.K.S. received support from the KWF Kankerbestrijding ( 11031/2017–1 , Bas Mulder Award) and a grant by the ERC (deFiber; ERC-StG 757339 ). J.J. is supported by the Netherlands Organization for Scientific Research ( NWO Veni grant no: 091 501 61 81 01 36 ) and the DKF (grant no. 19OK005 ). B.S. is supported by the DKF (grant: 14A3D104 ) and the NWO (VIDI grant: 016.156.363 ). R.P.V.R. and G.J.O. are supported by the NWO VICI (grant: 16.VICI.170.090 ). Publisher Copyright: © 2022 The Author(s)

PY - 2022/9/16

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N2 - 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).

AB - 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).

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ER -

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

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