Kidney tissue pipeline for multi-omics and histological analysis
Biobanking of tissue from clinically obtained kidney biopsies for later analysis with multi-omic 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 towards 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 porcine kidney tissue as 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 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 molecular 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. Overall design: This experimental study focused on cryopreserving pig kidney biopsies using three different methods: snap freezing in liquid nitrogen, preservation in RNAlater solution, and preservation in CellCover solution.