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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. Optimized protocol for the multiomics processing of cryopreserved human kidney tissue. Am J Physiol Renal Physiol 2024; 327:F822-F844. [PMID: 39361723 DOI: 10.1152/ajprenal.00404.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 08/19/2024] [Accepted: 09/09/2024] [Indexed: 10/05/2024] Open
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.NEW & NOTEWORTHY In this study, we addressed challenges in integrating clinically obtained kidney biopsies into everyday clinical routines. Using porcine kidneys, we evaluated preservation media (RNAlater and CellCover) versus snap freezing for multi-omics processing. Our analyses highlighted RNAlater's suitability for single-nucleus RNA sequencing, proteome analysis and histopathological evaluation. Only metabolomics are currently restricted to snap-frozen biopsies. Our research established a cryopreservation protocol that facilitates tissue biobanking for advancing precision medicine in nephrology.
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Affiliation(s)
- Sydney E Gies
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sonja Hänzelmann
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominik Kylies
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Moritz Lassé
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Lagies
- Core Competence Metabolomics (Hilde-Mangold-Haus), University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Freiburg, Germany
| | - Fabian Hausmann
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robin Khatri
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nikolay Zolotarev
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manuela Poets
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tianran Zhang
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fatih Demir
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute of Advanced Studies, Aarhus, Denmark
| | - Anja M Billing
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute of Advanced Studies, Aarhus, Denmark
| | - Josephine Quaas
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elisabeth Meister
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonas Engesser
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne K Mühlig
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shun Lu
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shuya Liu
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Silvia Chilla
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ilka Edenhofer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Czogalla
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Braun
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bernd Kammerer
- Core Competence Metabolomics (Hilde-Mangold-Haus), University of Freiburg, Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus M Rinschen
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute of Advanced Studies, Aarhus, Denmark
| | - Maja Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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McRae AN, Ticho AL, Liu Y, Ricardo-Silgado ML, Mangena NN, Jassir FF, Gonzalez-Izundegui D, Calderon G, Rohakhtar FR, Simon V, Li Y, Leggett C, Hurtado D, LaRusso N, Acosta AJ. Regulator of G-protein signaling expression in human intestinal enteroendocrine cells and potential role in satiety hormone secretion in health and obesity. EBioMedicine 2024; 107:105283. [PMID: 39142076 PMCID: PMC11367526 DOI: 10.1016/j.ebiom.2024.105283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Gut L-type enteroendocrine cells (EECs) are intestinal chemosensory cells that secrete satiety hormones GLP-1 and PYY in response to activation of G-protein coupled receptors (GPCRs) by luminal components of nutrient digestion and microbial fermentation. Regulator of G-protein Signaling (RGS) proteins are negative regulators of GPCR signaling. The expression profile of RGS in EECs, and their potential role in satiety hormone secretion and obesity is unknown. METHODS Transcriptomic profiling of RGS was completed in native colonic EECs was completed using single-cell RNA sequencing (scRNA-Seq) in lean and obesity, and human jejunal EECs with data obtained from a publicly available RNAseq dataset (GSE114853). RGS validation studies were completed using whole mucosal intestinal tissue obtained during endoscopy in 61 patients (n = 42 OB, n = 19 Lean); a subset of patients' postprandial plasma was assayed for GLP-1 and PYY. Ex vivo human intestinal cultures and in vitro NCI-H716 cells overexpressing RGS9 were exposed to GLP-1 secretagogues in conjunction with a nonselective RGS-inhibitor and assayed for GLP-1 secretion. FINDINGS Transcriptomic profiling of colonic and jejunal enteroendocrine cells revealed a unique RGS expression profile in EECs, and further within GLP-1+ L-type EECs. In obesity the RGS expression profile was altered in colonic EECs. Human gut RGS9 expression correlated positively with BMI and negatively with postprandial GLP-1 and PYY. RGS inhibition in human intestinal cultures increased GLP-1 release from EECs ex vivo. NCI-H716 cells overexpressing RGS9 displayed defective nutrient-stimulated GLP-1 secretion. INTERPRETATION This study introduces the expression profile of RGS in human EECs, alterations in obesity, and suggests a role for RGS proteins as modulators of GLP-1 and PYY secretion from intestinal EECs. FUNDING AA is supported by the NIH(C-Sig P30DK84567, K23 DK114460), a Pilot Award from the Mayo Clinic Center for Biomedical Discovery, and a Translational Product Development Fund from The Mayo Clinic Center for Clinical and Translational Science Office of Translational Practice in partnership with the University of Minnesota Clinical and Translational Science Institute.
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Affiliation(s)
- Alison N McRae
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Alexander L Ticho
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Yuanhang Liu
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Maria Laura Ricardo-Silgado
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Nothando N Mangena
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Fauzi Feris Jassir
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Daniel Gonzalez-Izundegui
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Gerardo Calderon
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | | | - Vernadette Simon
- Center for Individualized Medicine (CIM), Mayo Clinic, Rochester, MN, USA
| | - Ying Li
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Cadman Leggett
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Daniela Hurtado
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition Mayo Clinic, Jacksonville, FL, USA
| | - Nicholas LaRusso
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Andres J Acosta
- Precision Medicine for Obesity Program and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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