Transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia [RNA-seq]

The role of the lineage-determining transcription factor IRF8 in microglia remains unelucidated. We report the genome-wide, transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia. Deep-sequencing and subsequent differential analysis revealed the impacts of IRF8 on microglia-specific transcription programs, such as cell identity. Sall1 and Batf3 genes were identified as a downstream transcription factor of IRF8, and Batf3 dependent genes showed correlation with IRF8-dependent genes in microglia. The conditional depletion of IRF8 gene after microglial maturation (P14) increased or decreased the gene expression, most of which were shared with those of IRF8KO. This study provides a novel insight into understanding transcriptional programs in microglia. Transcriptome profiles of adult WT, IRF8KO, 5xFAD, 5xFAD/IRF8KO, IRF8cKO, and Batf3KO mice were analyzed. The conditional deletion of IRF8 gene was achieved with 5 consecutive days of Tamoxifen injection to an IRF8flox-Cx3cr1CreERT2-Rosa26LSL-EYFP mouse at the age of P12-14 and YFP-positive microglia at 3-month-old of age were sorted and analyzed.谱系决定转录因子干扰素调节因子8（Interferon Regulatory Factor 8，IRF8）在小胶质细胞中的调控作用尚未明确。本研究报道了野生型（Wild-type，WT）、IRF8全身敲除（IRF8KO）、IRF8条件性敲除（IRF8cKO）、碱性亮氨酸拉链ATF样转录因子3（Basic Leucine Zipper ATF-Like Transcription Factor 3，Batf3）敲除（Batf3KO）、5xFAD以及5xFAD/IRF8KO小胶质细胞的全基因组转录组图谱。通过深度测序与后续差异表达分析，本研究揭示了IRF8对小胶质细胞特异性转录程序（如细胞身份维持）的调控影响。研究鉴定出Sal样蛋白1（Sal-like Protein 1，Sall1）与Batf3基因为IRF8的下游转录因子，且Batf3依赖型基因与小胶质细胞中IRF8依赖型基因的表达模式具有显著相关性。在小胶质细胞成熟阶段（出生后第14天，P14）条件性敲除IRF8基因，可上调或下调部分基因的表达水平，其中绝大多数差异基因与IRF8全身敲除小鼠的差异基因重合。本研究为解析小胶质细胞的转录调控程序提供了全新视角。本研究分析了成年WT、IRF8KO、5xFAD、5xFAD/IRF8KO、IRF8cKO及Batf3KO小鼠的转录组图谱。IRF8条件性敲除模型的构建方式为：对出生后第12-14天的IRF8flox-Cx3cr1CreERT2-Rosa26LSL-EYFP小鼠连续5天注射他莫昔芬，随后分选3月龄的YFP阳性小胶质细胞进行后续实验分析。