Single cell RNA-seq analysis reveals compartment-specific heterogeneity and plasticity of microglia

Abstract

Microglia are heterogeneous and ubiquitous CNS-resident macrophages that maintain homeostasis of neural tissues and protect them from pathogen attacks. Yet, their differentiation in different compartments remains elusive. We performed single cell RNA-seq (scRNA-seq) analysis to compare the transcriptomes of 32760 microglia in adult mouse (C57/Bl) brains and spinal cords to identify microglial subtypes in these CNS compartments. Cortical microglia from 2-month mice consisted of a predominant population of the homeostatic subtype (HOM-M) and a small population (4%) of the inflammatory subtype (IFLAM-M), while spinal microglia consisted of 55% HOM-M and 45% IFLAM-M subtype. Comparison of cortical and spinal microglia at 2, 4 and 8 months revealed consistently a higher composition of the IFLAM-M subtype in the spinal cord. At 8-month, cortical microglia differentiated a small new subtype with interferon response phenotypes (INF-M), while spinal microglia polarized toward a proinflammatory phenotype, as indicated by the increase of microglia expressing IL-1β. To further characterize the differential plasticity of cortical and spinal microglial heterogeneity, we determined the microglial transcriptomes from HIV-1 gp120 transgenic (Tg) mice, a model of HIV-associated neurological disorders. Compared with wilt-type (Wt) cortical microglia, the gp120tg cortical microglia had three new subtypes, with signatures of interferon I response (INF-M), cell proliferation (PLF-M), and myelination or demyelination (MYE-M) respectively; while INF-M and PLF-M subtypes presented at all ages, the MYE-M only at 4-month.In contrast, only the INF-M subtype was observed in the spinal microglia from 2-and 4-month gp120tg mice. Bioinformatic analysis of regulated molecular pathways of individual microglial subtypes indicated that gp120 more severely impaired the biological function of microglia in cortices than in the spinal cord. The results collectively reveal differential heterogeneity and plasticity of cortical and spinal microglia, and suggest functional differentiation of microglia in different CNS compartments.

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“…These imply that cluster #13 represents dividing microglia. These are consistent with reports showing the complex heterogeneity in microglia populations especially during early development, compared with adult stages 54,55 . The smallest cluster of cells (#14, n=125 cells) is distinguished as oligodendrocyte precursor cells owing to expression of PTPRZ1, PMP2 and PDGFRA (Fig.…”

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“…Microglial homeostatic genes (e.g., Tmem119 and Siglech) were down‐regulated, whereas pro‐inflammatory genes (e.g., Ccl2 and Nfkbia) were up‐regulated at the single‐cell level (Sousa et al, 2018). Similarly, using single‐cell RNA sequencing, a distinct microglial population (using C57/Bl and HIV gp120 transgenic mouse models) in the cortex and the spinal cord was found (Zheng et al, 2021). Notably, these microglia showed differential signatures based on the expression of genes involved in homeostasis (e.g., Cx3cr1 and Tmem119), regulation of immune responses (e.g., Il1a and Ccl4), and cytokine and chemokine genes (e.g., Il1b and Ccl2; Zheng et al, 2021).…”

“…Similarly, using single‐cell RNA sequencing, a distinct microglial population (using C57/Bl and HIV gp120 transgenic mouse models) in the cortex and the spinal cord was found (Zheng et al, 2021). Notably, these microglia showed differential signatures based on the expression of genes involved in homeostasis (e.g., Cx3cr1 and Tmem119), regulation of immune responses (e.g., Il1a and Ccl4), and cytokine and chemokine genes (e.g., Il1b and Ccl2; Zheng et al, 2021). Another recent study by Hammond et al (2019) revealed at least nine transcriptionally distinct microglial populations (in C57Bl/6J mice) that express unique sets of genes.…”

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