Figure 4

Differential gene expression between subtypes. (a) Representative inflammatory cytokine (Il1b) and anti-inflammatory cytokine (Il10) expression across identified clusters. (b) Identification of proliferative populations by expression of mitotic genes Cdk1 and Pclaf (2810417H13Rik). (c) Expression of representative complement genes (C1qa and Cfh) across clusters. (d) Rod photoreceptor transcripts, including Guca1a and Cngb1, are found in a subset of activated microglia, particularly in several cells from Cluster #5 (activated microglia C). (e) Expression of disease activated (DA) microglia markers from Keren-Shaul et al. 2017, which suggested: Tmem119, Glul, and Serinc3 are downregulated in DA microglia (i.e., are markers of resting microglia); Lyz2, Apoe, and Cstb are upregulated during Stage 1 of disease-related activation; Spp1, Cd63, and Cst7 are upregulated in Stage 2 activation. None of the 5 microglia clusters in the present study completely align with these previously defined activation stages. For example, Cst7 expression is low in activated microglia Clusters #3–5, despite the expression of other Stage 2 markers. Additionally, activated microglia Cluster #2 has lower expression of Cstb despite otherwise strong expression of several Stage 1 and Stage 2 markers. In (a–c,e), the color corresponds to the cluster identity and the extruded shape represents the distribution of cells with the corresponding expression levels.