Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations
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Abstract
Different cell isolation techniques exist for transcriptomic and proteotype profiling of brain cells. Here, we provide a systematic investigation of the influence of different cell isolation protocols on transcriptional and proteotype profiles in mouse brain tissue by taking into account single-cell transcriptomics of brain cells, proteotypes of microglia and astrocytes, and flow cytometric analysis of microglia. We show that standard enzymatic digestion of brain tissue at 37 °C induces profound and consistent alterations in the transcriptome and proteotype of neuronal and glial cells, as compared to an optimized mechanical dissociation protocol at 4 °C. These findings emphasize the risk of introducing technical biases and biological artifacts when implementing enzymatic digestion-based isolation methods for brain cell analyses.
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We could not control for all these potential confounders, even though these factors could contribute to gene expression changes.
“We could not control for all these potential confounders, even though these factors could contribute to gene expression changes76,77.”
From Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies (2022) · cites this paper as [76]
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- Authors
- Mattei, D., Ivanov, A., van Oostrum, M., Pantelyushin, S., Richetto, J., Mueller, F., Beffinger, M., Schellhammer, L., vom Berg, J., Wollscheid, B., Beule, D., Paolicelli, R. C., & Meyer, U.
- Affiliations
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, CH-8057 Zurich, Switzerland
- Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitaetsmedizin, 10117 Berlin, Germany
- Institute of Molecular Systems Biology and Department for Health Sciences and Technology, ETH Zürich, 8092 Zurich, Switzerland
- Institute of Laboratory Animal Science, University of Zurich, 8952 Schlieren, Switzerland
- Department of Biomedical Sciences, University of Lausanne, Rue du Bugnon 7, 1005 Lausanne, Switzerland
- ORCID
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2020-10-26
- Volume
- 21
- Issue
- 21
- Pages
- 7944
- ISSN
- 1422-0067
- PMC
- PMC7663484
- Cited by
- 123
- References
- 13
- Language
- en
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_188524; PZ00P3_180099, 31003A_160259)
- European Research Council (804949)
- University of Zurich Forschungskredit (K-51503-05-01)
- ETH (grant ETH-25 15-2)
- Stiftung Synapsis Alzheimer Forschung Schweiz AFS (to RCP)
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