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Investigating microglia-neuron crosstalk by characterizing microglial contamination in human and mouse patch-seq
Keon Arbabi1,2, Yiyue Jiang1,3, Derek Howard1
1The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
Iscience
|July 31, 2023
Summary
Microglial (immune cell) contamination in Patch-seq data is common and linked to activated microglia. This contamination affects neuronal recordings, influencing excitability and potentially explaining variability in brain slice experiments.
Area of Science:
- Neuroscience
- Immunology
- Molecular Biology
Background:
- Microglia, the brain's resident immune cells, play crucial roles in regulating neuronal function.
- Patch-seq is a technique combining patch-clamp electrophysiology with single-cell RNA sequencing.
- Understanding microglial influence on neuronal recordings is vital for accurate interpretation of brain slice data.
Purpose of the Study:
- To investigate the presence and impact of microglial contamination in Patch-seq datasets of human and mouse neocortical neurons.
- To determine factors influencing microglial contamination levels and their transcriptional signatures.
- To assess the relationship between microglial contamination and neuronal electrophysiological properties.
Main Methods:
- Quantification of microglial transcripts in three human and mouse neocortical Patch-seq datasets.
- Analysis of variation in microglial contamination based on donor and neuronal cell type identity.
- Gene set enrichment analysis to characterize microglial transcriptional signatures.
- Correlation analysis between microglial contamination levels and neuronal electrophysiological measurements.
Main Results:
- Extensive microglial transcript contamination was observed in human and mouse neocortical Patch-seq datasets.
- Microglial contamination levels varied significantly with donor identity (especially in humans) and neuronal cell type (in mice).
- Transcriptional signatures indicated activated microglia, distinct from those found in single-nucleus RNA-seq.
- Increased microglial contamination correlated with altered neuronal electrophysiology, including lower input resistance and more depolarized action potential thresholds.
Conclusions:
- Microglial contamination is a prevalent issue in Patch-seq, reflecting activated microglia in brain slice preparations.
- This contamination can significantly impact neuronal electrophysiological characteristics, contributing to observed variability.
- Findings highlight the need to account for microglial presence and activation when interpreting Patch-seq data and other brain slice studies.
