The microglial reaction signature revealed by RNAseq from individual mice

Abstract

Microglial cells have a double life as the immune cells of the brain in times of stress but have also specific physiological functions in homeostatic conditions. In pathological contexts, microglia undergo a phenotypic switch called "reaction" that promotes the initiation and the propagation of neuro-inflammation. Reaction is complex, molecularly heterogeneous and still poorly characterized, leading to the concept that microglial reactivity might be too diverse to be molecularly defined. However, it remains unknown whether reactive microglia from different pathological contexts share a common molecular signature. Using improved flow cytometry and RNAseq approaches we studied, with higher statistical power, the remodeling of microglia transcriptome in a mouse model of sepsis. Through bioinformatic comparison of our results with published datasets, we defined the microglial reactome as a set of genes discriminating reactive from homeostatic microglia. Ultimately, we identified a subset of 86 genes deregulated in both acute and neurodegenerative conditions. Our data provide a new comprehensive resource that includes functional analysis and specific molecular markers of microglial reaction which represent new tools for its unambiguous characterization.

RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS + IFNγ

“…This slight difference between the number of genes upregulated and those downregulated, though in accordance with Hirbec et al . 54 , differs from most previous microglial RNA-Seq analysis, where most of the affected genes were upregulated (Table 4 ). These differences may be due to different time points, treatment doses or microglia sources being used.…”

“… M1 transcriptome most distinct from M0 (837 genes were induced, including mir-155, and 618 were reduced). M1 stimuli lead to an almost complete loss of myelin phagocytic activity (Mtgf > M2c > M2a = M0 > M1) 54 Acute isolated cortical microglia from adult mouse Intraperitoneal LPS for 24 or 48 h 10788 genes were detected. Of them, 4179 were significantly altered by LPS (50% ↑, 50% ↓).…”

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

“…Although module mRNA.M15 is enriched with microglial markers (Supplementary Figure 7g), it exhibits a markedly different transcriptional profile 27 than the previously identified ASD upregulated microglial module mRNA.M19 (Figure 2i). Module mRNA.M19 is specifically enriched with genes marking microglial activation 28 , suggesting that it is directly related to neural-immune response. In contrast, module mRNA.M15 is enriched with markers of juvenile or aging glia, suggesting it may be related to glial growth and maturation.…”

“…We downloaded microglial cell-type specific markers (fold change >= 1) from Hammond et al 27 . We downloaded markers of microglial activation from Hirbec et al 28 . For module cell type enrichments, enrichments of co-expression vs co-methylation modules, and enrichment with orthogonal gene lists we used logistic regression to test whether gene set 1 ~ gene set 2 using a background set of genes shared between study 1 and study 2.…”

“…G) Top 30 hub genes and 300 connections for co-expression module mRNA.M15. H) Top gene ontology enrichments for co-expression module mRNA.M15.I) Enrichment of ASD upregulated glial co-expression modules with microglial activated genes28 and microglial cell-type markers27 . FDR corrected p-values are shown in parentheses.…”