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Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations

Daniele Mattei, Andranik Ivanov, Marc van Oostrum and 10 more (opens in a new tab)

International Journal of Molecular Sciences · 2020 · CC BY

doi:10.3390/ijms21217944 (opens in a new tab)

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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