Identification of a conserved and acute neurodegeneration‐specific microglial transcriptome in the zebrafish

Abstract

Microglia are brain resident macrophages important for brain development, connectivity, homeostasis and disease. However, it is still largely unclear how microglia functions and their identity are regulated at the molecular level. Although recent transcriptomic studies have identified genes specifically expressed in microglia, the function of most of these genes in microglia is still unknown. Here, we performed RNA sequencing on microglia acutely isolated from healthy and neurodegenerative zebrafish brains. We found that a large fraction of the mouse microglial signature is conserved in the zebrafish, corroborating the use of zebrafish to help understand microglial genetics in mammals in addition to studying basic microglia biology. Second, our transcriptome analysis of microglia following neuronal ablation suggested primarily a proliferative response of microglia, which we confirmed by immunohistochemistry and in vivo imaging. Together with the recent improvements in genome editing technology in zebrafish, these data offer opportunities to facilitate functional genetic research on microglia in vivo in the healthy as well as in the diseased brain. GLIA 2016;65:138–149

Gene expression profiling reveals a conserved microglia signature in larval zebrafish

“…In conclusion, out of the 242 annotated zebrafish orthologs of adult mouse microglial genes we detect up to 43% in larval zebrafish microglia (7 dpf) and a strong overall correlation ( r = .57). This is almost the same degree of conservation to mouse microglia as previously shown for adult zebrafish microglia (45% genes in common with mouse microglia; Oosterhof et al, ).…”

“…Larval zebrafish microglia share a significant number of DE genes with adult zebrafish microglia, adult mouse microglia, and human microglia. (a) Venn diagram showing unique and intersecting DE genes from zebrafish microglia transcriptome at 3 (green), 5 (yellow), and 7 (magenta) dpf versus other brain cells in comparison to DE genes from adult zebrafish (AZ) microglia transcriptome versus other brain cells (Oosterhof et al, ; FDR < 0.05, Fold change >2). Significant gene enrichments are shown in bold (FDR < 0.05).…”

“…Normalized data were inspected using Principal Component Analysis (PCA) (Figure ), and inter‐sample correlation plots (Figure S1). Two types of differential expression analyses were performed using DESeq2: (i) microglia at 3 dpf versus 5 dpf, microglia at 5 dpf versus 7 dpf, microglia at 3 dpf versus 7 dpf; (ii) microglia at 3 or 5 dpf or 7 dpf versus brain cells (from Oosterhof et al, ). Differentially expressed genes (DEs) were selected using the following filter criteria: FDR ≤ 0.05 and Fold Change ≥ |2|.…”

Transcriptional control of microglia phenotypes in health and disease

“…Transcriptional control of microglia phenotypes in health and disease matures, microglia acquire a surveilling phenotype and express the TFs Jun, Fos, Mef2a, and Mafb, as well as a set of genes that are highly expressed in microglia such as the characteristic purinergic receptor P2RY12, the transmembrane protein TMEM119, and the chemokine receptor CX3CR1 (31)(32)(33)(34), the expression of which is largely conserved in humans (35)(36)(37) and zebrafish (38).…”

Axonal regeneration in zebrafish spinal cord

“…Similar to other vertebrates, zebrafish microglia express typical vertebrate macrophage genes. Furthermore the expression of many transcriptional regulators, immune pathogen receptors, and pruning associated genes, which are also found in mammals, suggests functional conservation between mammals and fish (Oosterhof et al., ).…”