PT  - JOURNAL ARTICLE
AU  - Keon Arbabi
AU  - Yiyue Jiang
AU  - Derek Howard
AU  - Anukrati Nigam
AU  - Wataru Inoue
AU  - Guillermo Gonzalez-Burgos
AU  - Daniel Felsky
AU  - Shreejoy J. Tripathy
TI  - Investigating microglia-neuron crosstalk by characterizing microglial contamination in human and mouse Patch-seq datasets
AID  - 10.1101/2022.09.07.507009
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.09.07.507009
4099  - http://biorxiv.org/content/early/2022/09/26/2022.09.07.507009.short
4100  - http://biorxiv.org/content/early/2022/09/26/2022.09.07.507009.full
AB  - Microglia are dynamic immune cells with diverse functional roles, including the regulation of neuronal excitability. Here, we leveraged an inconvenient truth of neuronal Patch-seq datasets — that they routinely display evidence of contamination by surrounding microglia — to better understand aspects of microglia-neuronal crosstalk. We first quantified the presence of microglial transcripts in three Patch-seq datasets of human and mouse neocortical neurons and observed extensive off-target contamination by microglia in each. Variation in microglial contamination was explained foremost by donor identity, especially in human samples, and neuronal cell type identity. Differential expression testing and enrichment analyses suggest that microglial contamination in Patch-seq is reflective of activated microglia and that these transcriptional signatures are distinct from those captured via single-nucleus RNAseq. Finally, neurons with greater microglial contamination differed markedly in their electrophysiological characteristics, including lowered input resistances and more depolarized action potential thresholds. Our results suggest microglial contamination contributes to cell- and donor-related electrophysiological variability and sheds light on how microglia might impact neurons in vivo.Competing Interest StatementThe authors have declared no competing interest.