Single-cell transcriptomics of the ventral posterolateral nucleus-enriched thalamic regions from HSV-1-infected mice reveal a novel microglia/microglia-like transcriptional response

Abstract

Background Microglia participate in the immune response upon central nervous system (CNS) infections. However, the role of these cells during herpes simplex encephalitis (HSE) has not been fully characterized. We sought to identify different microglia/microglia-like cells and describe the potential mechanisms and signaling pathways involved during HSE. Methods The transcriptional response of CD11b+ immune cells, including microglia/microglia-like cells, was investigated using single-cell RNA sequencing (scRNA-seq) on cells isolated from the ventral posterolateral nucleus (VPL)-enriched thalamic regions of C57BL/6 N mice intranasally infected with herpes simplex virus-1 (HSV-1) (6 × 105 PFUs/20 µl). We further performed scanning electronic microscopy (SEM) analysis in VPL regions on day 6 post-infection (p.i.) to provide insight into microglial functions. Results We describe a novel microglia-like transcriptional response associated with a rare cell population (7% of all analyzed cells), named “in transition” microglia/microglia-like cells in HSE. This new microglia-like transcriptional signature, found in the highly infected thalamic regions, was enriched in specific genes (Retnlg, Cxcr2, Il1f9) usually associated with neutrophils. Pathway analysis of this cell-type transcriptome showed increased NLRP3-inflammasome-mediated interleukin IL-1β production, promoting a pro-inflammatory response. These cells' increased expression of viral transcripts suggests that the distinct “in transition” transcriptome corresponds to the intrinsic antiviral immune signaling of HSV-1-infected microglia/microglia-like cells in the thalamus. In accordance with this phenotype, we observed several TMEM119+/IBA-I+ microglia/microglia-like cells immunostained for HSV-1 in highly infected regions. Conclusions A new microglia/microglia-like state may potentially shed light on how microglia could react to HSV-1 infection. Our observations suggest that infected microglia/microglia-like cells contribute to an exacerbated CNS inflammation. Further characterization of this transitory state of the microglia/microglia-like cell transcriptome may allow the development of novel immunomodulatory approaches to improve HSE outcomes by regulating the microglial immune response.

Brain region- and sex-specific transcriptional profiles of microglia

“…PFC-enriched transcripts were enriched for synapse-related pathways. Prkar1a was enriched in PFC microglia, and this transcript has been shown to be elevated in surveillant microglia ( 57 ). Striatal-enriched microglia were associated with microtubule- and cytoskeleton-related pathways.…”

Microglia at the scene of the crime: what their transcriptomics reveal about brain health

“…Evaluation of microglia transcriptomes in the setting of severe HSV1-encephalitis in mice showed they develop a neutrophil-like transcriptional signature, upregulating genes such as resistin-like gamma (Retnlg), retroviral-like aspartic protease, IL-36γ, and C-X-C chemokine receptor 2, while also expressing classical microglial markers P2RY12, transmembrane protein 119 (TMEM119), CSF1R, and Fc receptor-like S (Fcrls). These microglia arise in highly infected brain regions such as the thalamus and most likely represent a direct antiviral response of infected microglial cells [26 ▪ ].…”

Role of Microglia in Herpesvirus-Related Neuroinflammation and Neurodegeneration

“…Another study by Uyar et al demonstrated that, depending on the infection levels, microglia are highly phagocytic and participate in antigen presentation (moderately infected thalamic areas) or display impaired physiological functions, such as decreased phagocytic activity (highly infected thalamic regions) [ 47 ]. By using single-cell RNA sequencing (scRNA-seq) on cells isolated from highly infected thalamic regions of HSV-1 infected C57BL/6 mice, Uyar et al revealed a novel transcriptional signature of microglia/microglia-like cells, which they defined as “in transition”.…”

“…By using single-cell RNA sequencing (scRNA-seq) on cells isolated from highly infected thalamic regions of HSV-1 infected C57BL/6 mice, Uyar et al revealed a novel transcriptional signature of microglia/microglia-like cells, which they defined as "in transition". Pathway analysis of this cell-type transcriptome showed that "in transition" microglia/microglia-like cells detect the dsRNA of HSV-1 via RIG-I (retinoic acid-inducible gene I, also known as DDX58)/MDA5 in the cytosol), which results in type I IFN production and NLRP3 inflammasome-mediated IL-1β production [47] (Figure 1). Another study by Fekete et al demonstrated a rapid recruitment (within hours) and elimination of HSV-1 infected neurons via microglial P2Y12 receptors in vivo [48].…”