Kidney Week

Abstract: SA-PO1188

Optimized Protocol for the Multiomics Processing of Cryopreserved Human Kidney Tissue

Session Information

• CKD: Mechanisms - 3
  October 26, 2024 | Location: Exhibit Hall, Convention Center
  Abstract Time: 10:00 AM - 12:00 PM

Category: CKD (Non-Dialysis)

• 2303 CKD (Non-Dialysis): Mechanisms

Authors

• Gies, Sydney Elisabeth, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Sydney Elisabeth Gies, MD, DrMed

• Haenzelmann, Sonja, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Sonja Haenzelmann, PhD

• Kylies, Dominik, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Dominik Kylies, MD

• Lassé, Moritz, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Moritz Lassé, PhD

• Zolotarev, Nikolay, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Nikolay Zolotarev, PhD

• Khatri, Robin, Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Robin Khatri

• Poets, Manuela, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Manuela Poets

• Lu, Shun, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Shun Lu, PhD

• Liu, Shuya, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Shuya Liu, PhD

• Hausmann, Fabian, Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Translational Immunology (HCTI), Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Fabian Hausmann

• Czogalla, Jan, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Jan Czogalla, MD

• Braun, Fabian, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Fabian Braun, MD

• Rinschen, Markus M., III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Markus M. Rinschen, MD

• Puelles, Victor G., III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Victor G. Puelles, MD, PhD

• Bonn, Stefan, Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Translational Immunology (HCTI), Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Stefan Bonn, PhD

• Lindenmeyer, Maja, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Maja Lindenmeyer, PhD

• Huber, Tobias B., III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

Tobias B. Huber, MD, FASN

Background

Immediate processing of fresh kidney tissue obtained from needle biopsies is challenging in clinical routines. To address this, tissue samples can be harvested in (cryo-) preservative agents such as RNAlater (Rl) or CellCover (CC), that rapidly preserve the integrity of cellular molecules already at room temperature. In this study, we examined the effects of Rl and CC on the single nucleus transcriptome, on tissue architecture and immunofluorescence stainings and on the proteome.

Methods

Biopsy cores from pig kidneys received from a slaughterhouse were either snapfrozen (sf) or put into Rl or CC. For human kidney tissue, the second core of a kidney needle biopsy and healthy kidney tissue from tumor nephrectomies were either sf or put in Rl. For single nucleus RNA sequencing (snRNAseq) with the Chromium 10X platform, 3-4 mm of a thawed kidney biopsy core was dissociated. For proteomic analysis, 2-3 mm sections of biopsies were analyzed by mass spectrometry. For immunohistochemical analysis, samples were thawed and subjected to fluorescent immunolabeling (IF).

Results

Each data set from sf, Rl and CC stored pig kidney tissue contributed to 31 clusters of both common and rare kidney cell types. Enrichment analysis detected a similar activation of the stress response pathways in all preservation methods. Applying snRNAseq to human kidney tissue stored in Rl resulted in diverse cell type clustering. Proteome analysis of pig kidney tissues showed the highest correlation between Rl and sf tissues. Classical histology with OCT-embedded kidney tissue as control indicated better preservation in Rl stored kidney compared to CC. IF-staining signal quality in Rl and CC preserved tissue was comparable to OCT-embedded kidney tissue.

Conclusion

Our study demonstrates that Rl can facilitate the collection and storage of kidney tissue without the need for snap freezing, supporting snRNAseq, proteome and histopathological analysis. As our optimized protocol requires only 3-4 mm of a biopsy core for high-throughput snRNAseq, the remaining part of a biopsy core can be utilized to generate other omics data.