Abstract
Microglia are the tissue macrophages of the central nervous system (CNS) and the first to respond to CNS dysfunction and disease. Gene expression profiling of microglia during development, under homeostatic conditions, and in the diseased CNS provided insight in microglia functions and changes thereof. Single‐cell sequencing studies further contributed to our understanding of microglia heterogeneity in relation to age, sex, and CNS disease. Recently, single nucleus gene expression profiling was performed on (frozen) CNS tissue. Transcriptomic profiling of CNS tissues by (single) nucleus RNA‐sequencing has the advantage that it can be applied to archived and well‐stratified frozen specimens. Here, we give an overview of the significant advances recently made in microglia transcriptional profiling. In addition, we present matched cellular and nuclear microglia RNA‐seq datasets we generated from mouse and human CNS tissue to compare cellular versus nuclear transcriptomes from fresh and frozen samples. We demonstrate that microglia can be similarly profiled with cell and nucleus profiling, and importantly also with nuclei isolated from frozen tissue. Nuclear microglia transcriptomes are a reliable proxy for cellular transcriptomes. Importantly, lipopolysaccharide‐induced changes in gene expression were conserved in the nuclear transcriptome. In addition, heterogeneity in microglia observed in fresh samples was similarly detected in frozen nuclei of the same donor. Together, these results show that microglia nuclear RNAs obtained from frozen CNS tissue are a reliable proxy for microglia gene expression and cellular heterogeneity and may prove an effective strategy to study of the role of microglia in neuropathology.
Highlights
Emma Gerrits and Yang Heng contributed and are alphabetically listed
We present matched cellular and nuclear microglia RNA-seq datasets we generated from mouse and human central nervous system (CNS) tissue to compare cellular versus nuclear transcriptomes from fresh and frozen samples
These results show that microglia nuclear RNAs obtained from frozen CNS tissue are a reliable proxy for microglia gene expression and cellular heterogeneity and may prove an effective strategy to study of the role of microglia in neuropathology
Summary
Emma Gerrits and Yang Heng contributed and are alphabetically listed. Erik W. Comparison with peritoneal macrophages identified 626 differentially expressed transcripts and the top 25 most highly expressed microglia transcripts include the sensome genes: P2ry, P2ry, Tmem119, Gpr, Siglech, Trem, and Cx3cr (Hickman et al, 2013) These microglia signatures were confirmed in two studies that addressed the transcriptomic and epigenetic differences between mouse microglia and other tissue-resident macrophages (Gosselin et al, 2014; Lavin et al, 2014). Expression profiling of bulk population human microglia revealed changes associated with age, neurodegenerative diseases and psychiatric disorders (Galatro, Holtman, et al, 2017; Gosselin et al, 2017), and regional and gender-dependent mouse microglia heterogeneity (Ayata et al, 2018; Grabert et al, 2016; Guneykaya et al, 2018). We generated matched nuclear and cellular microglia cell and nucleus RNA-seq datasets to investigate whether nuclear transcriptomes are a good proxy for the cellular transcriptome
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