Type I interferon responsive microglia shape cortical development and behavior

Abstract

Microglia, the innate immune cells of the brain, are exquisitely sensitive to dynamic changes in the brain environment. We used single cell RNA sequencing to define glial responses in the early postnatal somatosensory cortex after partial whisker lesion, revealing transcriptomic shifts in both astrocytes and microglia during the resulting topographic remapping. The most distinct change was the emergence of a type I interferon (IFN-I) responsive microglia population that was rare in the resting cortex but expanded 20-fold after whisker deprivation. The top gene candidate in this cluster, Ifitm3, marked a conserved but transient subset of microglia that were in the process of phagocytosing whole cells. IFITM3 protein identified this subset in vivo, where it was enriched in early microglial phagosomes. Loss of canonical IFN-I signaling in Ifnar1-/- animals resulted in abnormal 'bubble' microglia with deficient phagolysosomal processing. In a meta-analysis of transcriptomes, we identified the IFN-I signature in microglia across a range of pathologies. We identified phagocytic IFITM3+ microglia in two murine disease models: SARS-CoV-2 infection and Alzheimer's Disease. These data reveal the potential of transcriptional profiling after defined perturbation to elicit transient microglial states, and identify a novel role for IFN-I signaling in regulating microglial phagocytosis.

A resource for generating and manipulating human microglial states in vitro

“…S4C-F). These transcriptional signatures have been identified in both mouse and human scRNAseq datasets 6–8, 10–13, 23, 24, 26 , suggesting iMGLs can adopt in vivo -like transcriptional states in a dish (see below for dataset integration). The remaining two unknown clusters (iMGL_13 and iMGL_16) consisted of few cells (1.9% of iMGLs) and exhibited high expression of an artifactual activation gene signature (Fig.…”

“…Although we focus on the DAM signature, the resources provided here will enable the dissection of many other microglial states such as interferon-responsive or proliferative microglia 6, 8, 10, 13, 17, 26, 29, 50 . By combining substrate exposure, scRNAseq, integrative analyses, epigenetics and viral vectors, it will be possible to scalably manipulate the genes or transcription factors that define these cell states and rapidly assay their impact on microglial functions.…”

“…Emerging genetic studies of late onset AD implicate microglia, with a large fraction of AD risk genes specifically expressed in myeloid cells 3,4 , while microglia activation and dysfunction is a hallmark of AD and other neurodegenerative disorders 5 . The application of single-cell RNA sequencing (scRNAseq) has revealed that microglia exhibit multiple states [6][7][8][9][10][11][12][13][14] , subpopulations that express distinct gene signatures, including disease-associated microglia (DAMs) which occur in neurodegenerative disorders. However, the function of these states and their impact on disease remains unknown.Since microglial states are defined by the differential expression of many genes, scalable models are needed to understand the function of transcriptional signatures.…”

Neuronal apoptosis drives remodeling states of microglia and shifts in survival pathway dependence

“…Clusters 7, 8, and 9 represented Cycling microglia and expressed Mki67, Top2a , and Mcm genes. Cluster 10, the smallest, contained 71 cells with high and very specific expression of interferon response genes such as Ccl5, Ifit3, and Ifitm3 ( Dorman et al, 2022 ) and was thus termed Interferon-responsive cluster. Overall, these proportions were consistent with our previous quantification of select homeostatic and DAM-related genes by in situ hybridization ( Anderson et al, 2019a ).…”

“…For lysosomal and lipid metabolism genes we used GO lists of 552 ‘Lysosomal’ genes (GO:0005764) and 1428 ‘Lipid Metabolic Process’ genes (GO:0006629) from the MGI mouse genome database (MGD) ( Bult et al, 2019 ). For comparison to interferon-responsive microglia, we used cluster eight markers from Table 5 of Dorman et al, 2022 . For exAM activation genes, we used 27 genes from Table 4 of Marsh et al, 2020 .…”