Optimized protocol for the multiomics processing of cryopreserved human kidney tissue

Sydney E. Gies; Sonja Hänzelmann; Dominik Kylies; Moritz Lassé; Simon Lagies; Fabian Hausmann; Robin Khatri; Nikolay Zolotarev; Manuela Poets; Tianran Zhang; Fatih Demir; Anja M. Billing; Josephine Quaas; Elisabeth Meister; Jonas Engesser; Anne K. Mühlig; Shun Lu; Shuya Liu; Silvia Chilla; Ilka Edenhofer; Jan Czogalla; Fabian Braun; Bernd Kammerer; Victor G. Puelles; Stefan Bonn; Markus M. Rinschen; Maja Lindenmeyer; Tobias B. Huber

doi:10.1152/ajprenal.00404.2023

Optimized protocol for the multiomics processing of cryopreserved human kidney tissue

Sydney E. Gies^*, Sonja Hänzelmann, Dominik Kylies, Moritz Lassé, Simon Lagies, Fabian Hausmann, Robin Khatri, Nikolay Zolotarev, Manuela Poets, Tianran Zhang, Fatih Demir, Anja M. Billing, Josephine Quaas, Elisabeth Meister, Jonas Engesser, Anne K. Mühlig, Shun Lu, Shuya Liu, Silvia Chilla, Ilka EdenhoferJan Czogalla, Fabian Braun, Bernd Kammerer, Victor G. Puelles, Stefan Bonn, Markus M. Rinschen, Maja Lindenmeyer, Tobias B. Huber

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

1 Citationer (Scopus)

Abstract

Biobanking of tissue from clinically obtained kidney biopsies for later analysis with multiomic approaches, such as single-cell technologies, proteomics, metabolomics, and the different types of imaging, is an inevitable step to overcome the need of disease model systems and toward translational medicine. Hence, collection protocols that ensure integration into daily clinical routines by the usage of preservation media that do not require liquid nitrogen but instantly preserve kidney tissue for both clinical and scientific analyses are necessary. Thus, we modified a robust single-nucleus dissociation protocol for kidney tissue stored snap-frozen or in the preservation media RNAlater and CellCover. Using at first porcine kidney tissue as a surrogate for human kidney tissue, we conducted single-nucleus RNA sequencing with the widely recognized Chromium 10X Genomics platform. The resulting datasets from each storage condition were analyzed to identify any potential variations in transcriptomic profiles. Furthermore, we assessed the suitability of the preservation media for additional analysis techniques such as proteomics, metabolomics, and the preservation of tissue architecture for histopathological examination including immunofluorescence staining. In this study, we show that in daily clinical routines, the preservation medium RNAlater facilitates the collection of highly preserved human kidney biopsies and enables further analysis with cutting-edge techniques like single-nucleus RNA sequencing, proteomics, and histopathological evaluation. Only metabolome analysis is currently restricted to snap-frozen tissue. This work will contribute to build tissue biobanks with well-defined cohorts of the respective kidney disease that can be deeply molecularly characterized, opening up new horizons for the identification of unique cells, pathways and biomarkers for the prevention, early identification, and targeted therapy of kidney diseases.

Originalsprog	Engelsk
Tidsskrift	American Journal of Physiology - Renal Physiology
Vol/bind	327
Nummer	5
Sider (fra-til)	F822-F844
ISSN	1931-857X
DOI	https://doi.org/10.1152/ajprenal.00404.2023
Status	Udgivet - nov. 2024

Adgang til dokumentet

10.1152/ajprenal.00404.2023

Andre filer og links

Link to publication in Scopus

Citationsformater

Gies, S. E., Hänzelmann, S., Kylies, D., Lassé, M., Lagies, S., Hausmann, F., Khatri, R., Zolotarev, N., Poets, M., Zhang, T., Demir, F., Billing, A. M., Quaas, J., Meister, E., Engesser, J., Mühlig, A. K., Lu, S., Liu, S., Chilla, S., ... Huber, T. B. (2024). Optimized protocol for the multiomics processing of cryopreserved human kidney tissue. American Journal of Physiology - Renal Physiology, 327(5), F822-F844. https://doi.org/10.1152/ajprenal.00404.2023

@article{4fa2f7d075a442c6a76aa83c78f99943,

title = "Optimized protocol for the multiomics processing of cryopreserved human kidney tissue",

abstract = "Biobanking of tissue from clinically obtained kidney biopsies for later analysis with multiomic approaches, such as single-cell technologies, proteomics, metabolomics, and the different types of imaging, is an inevitable step to overcome the need of disease model systems and toward translational medicine. Hence, collection protocols that ensure integration into daily clinical routines by the usage of preservation media that do not require liquid nitrogen but instantly preserve kidney tissue for both clinical and scientific analyses are necessary. Thus, we modified a robust single-nucleus dissociation protocol for kidney tissue stored snap-frozen or in the preservation media RNAlater and CellCover. Using at first porcine kidney tissue as a surrogate for human kidney tissue, we conducted single-nucleus RNA sequencing with the widely recognized Chromium 10X Genomics platform. The resulting datasets from each storage condition were analyzed to identify any potential variations in transcriptomic profiles. Furthermore, we assessed the suitability of the preservation media for additional analysis techniques such as proteomics, metabolomics, and the preservation of tissue architecture for histopathological examination including immunofluorescence staining. In this study, we show that in daily clinical routines, the preservation medium RNAlater facilitates the collection of highly preserved human kidney biopsies and enables further analysis with cutting-edge techniques like single-nucleus RNA sequencing, proteomics, and histopathological evaluation. Only metabolome analysis is currently restricted to snap-frozen tissue. This work will contribute to build tissue biobanks with well-defined cohorts of the respective kidney disease that can be deeply molecularly characterized, opening up new horizons for the identification of unique cells, pathways and biomarkers for the prevention, early identification, and targeted therapy of kidney diseases.",

keywords = "biobanking, kidney tissue, multiomics, RNAlater, single-nucleus RNA sequencing",

author = "Gies, {Sydney E.} and Sonja H{\"a}nzelmann and Dominik Kylies and Moritz Lass{\'e} and Simon Lagies and Fabian Hausmann and Robin Khatri and Nikolay Zolotarev and Manuela Poets and Tianran Zhang and Fatih Demir and Billing, {Anja M.} and Josephine Quaas and Elisabeth Meister and Jonas Engesser and M{\"u}hlig, {Anne K.} and Shun Lu and Shuya Liu and Silvia Chilla and Ilka Edenhofer and Jan Czogalla and Fabian Braun and Bernd Kammerer and Puelles, {Victor G.} and Stefan Bonn and Rinschen, {Markus M.} and Maja Lindenmeyer and Huber, {Tobias B.}",

note = "Publisher Copyright: {\textcopyright} 2024 the American Physiological Society.",

year = "2024",

month = nov,

doi = "10.1152/ajprenal.00404.2023",

language = "English",

volume = "327",

pages = "F822--F844",

journal = "American Journal of Physiology - Renal Physiology",

issn = "1931-857X",

publisher = "American Physiological Society",

number = "5",

}

Gies, SE, Hänzelmann, S, Kylies, D, Lassé, M, Lagies, S, Hausmann, F, Khatri, R, Zolotarev, N, Poets, M, Zhang, T, Demir, F , Billing, AM, Quaas, J, Meister, E, Engesser, J, Mühlig, AK, Lu, S, Liu, S, Chilla, S, Edenhofer, I, Czogalla, J, Braun, F, Kammerer, B, Puelles, VG, Bonn, S, Rinschen, MM, Lindenmeyer, M & Huber, TB 2024, 'Optimized protocol for the multiomics processing of cryopreserved human kidney tissue', American Journal of Physiology - Renal Physiology, bind 327, nr. 5, s. F822-F844. https://doi.org/10.1152/ajprenal.00404.2023

Optimized protocol for the multiomics processing of cryopreserved human kidney tissue. / Gies, Sydney E.; Hänzelmann, Sonja; Kylies, Dominik et al.
I: American Journal of Physiology - Renal Physiology, Bind 327, Nr. 5, 11.2024, s. F822-F844.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

TY - JOUR

T1 - Optimized protocol for the multiomics processing of cryopreserved human kidney tissue

AU - Gies, Sydney E.

AU - Hänzelmann, Sonja

AU - Kylies, Dominik

AU - Lassé, Moritz

AU - Lagies, Simon

AU - Hausmann, Fabian

AU - Khatri, Robin

AU - Zolotarev, Nikolay

AU - Poets, Manuela

AU - Zhang, Tianran

AU - Demir, Fatih

AU - Billing, Anja M.

AU - Quaas, Josephine

AU - Meister, Elisabeth

AU - Engesser, Jonas

AU - Mühlig, Anne K.

AU - Lu, Shun

AU - Liu, Shuya

AU - Chilla, Silvia

AU - Edenhofer, Ilka

AU - Czogalla, Jan

AU - Braun, Fabian

AU - Kammerer, Bernd

AU - Puelles, Victor G.

AU - Bonn, Stefan

AU - Rinschen, Markus M.

AU - Lindenmeyer, Maja

AU - Huber, Tobias B.

PY - 2024/11

Y1 - 2024/11

N2 - Biobanking of tissue from clinically obtained kidney biopsies for later analysis with multiomic approaches, such as single-cell technologies, proteomics, metabolomics, and the different types of imaging, is an inevitable step to overcome the need of disease model systems and toward translational medicine. Hence, collection protocols that ensure integration into daily clinical routines by the usage of preservation media that do not require liquid nitrogen but instantly preserve kidney tissue for both clinical and scientific analyses are necessary. Thus, we modified a robust single-nucleus dissociation protocol for kidney tissue stored snap-frozen or in the preservation media RNAlater and CellCover. Using at first porcine kidney tissue as a surrogate for human kidney tissue, we conducted single-nucleus RNA sequencing with the widely recognized Chromium 10X Genomics platform. The resulting datasets from each storage condition were analyzed to identify any potential variations in transcriptomic profiles. Furthermore, we assessed the suitability of the preservation media for additional analysis techniques such as proteomics, metabolomics, and the preservation of tissue architecture for histopathological examination including immunofluorescence staining. In this study, we show that in daily clinical routines, the preservation medium RNAlater facilitates the collection of highly preserved human kidney biopsies and enables further analysis with cutting-edge techniques like single-nucleus RNA sequencing, proteomics, and histopathological evaluation. Only metabolome analysis is currently restricted to snap-frozen tissue. This work will contribute to build tissue biobanks with well-defined cohorts of the respective kidney disease that can be deeply molecularly characterized, opening up new horizons for the identification of unique cells, pathways and biomarkers for the prevention, early identification, and targeted therapy of kidney diseases.

AB - Biobanking of tissue from clinically obtained kidney biopsies for later analysis with multiomic approaches, such as single-cell technologies, proteomics, metabolomics, and the different types of imaging, is an inevitable step to overcome the need of disease model systems and toward translational medicine. Hence, collection protocols that ensure integration into daily clinical routines by the usage of preservation media that do not require liquid nitrogen but instantly preserve kidney tissue for both clinical and scientific analyses are necessary. Thus, we modified a robust single-nucleus dissociation protocol for kidney tissue stored snap-frozen or in the preservation media RNAlater and CellCover. Using at first porcine kidney tissue as a surrogate for human kidney tissue, we conducted single-nucleus RNA sequencing with the widely recognized Chromium 10X Genomics platform. The resulting datasets from each storage condition were analyzed to identify any potential variations in transcriptomic profiles. Furthermore, we assessed the suitability of the preservation media for additional analysis techniques such as proteomics, metabolomics, and the preservation of tissue architecture for histopathological examination including immunofluorescence staining. In this study, we show that in daily clinical routines, the preservation medium RNAlater facilitates the collection of highly preserved human kidney biopsies and enables further analysis with cutting-edge techniques like single-nucleus RNA sequencing, proteomics, and histopathological evaluation. Only metabolome analysis is currently restricted to snap-frozen tissue. This work will contribute to build tissue biobanks with well-defined cohorts of the respective kidney disease that can be deeply molecularly characterized, opening up new horizons for the identification of unique cells, pathways and biomarkers for the prevention, early identification, and targeted therapy of kidney diseases.

KW - biobanking

KW - kidney tissue

KW - multiomics

KW - RNAlater

KW - single-nucleus RNA sequencing

UR - http://www.scopus.com/inward/record.url?scp=85208097301&partnerID=8YFLogxK

U2 - 10.1152/ajprenal.00404.2023

DO - 10.1152/ajprenal.00404.2023

M3 - Journal article

C2 - 39361723

AN - SCOPUS:85208097301

SN - 1931-857X

VL - 327

SP - F822-F844

JO - American Journal of Physiology - Renal Physiology

JF - American Journal of Physiology - Renal Physiology

IS - 5

ER -

Optimized protocol for the multiomics processing of cryopreserved human kidney tissue

Abstract

Adgang til dokumentet

Andre filer og links

Fingeraftryk

Citationsformater