Integrative multi-omics landscape of fluoxetine action across 27 brain regions (single cell profiling for 2 regions)

We constructed a comprehensive multi-omics map of the molecular effects of fluoxetine (an SSRI antidepressant) in 27 rat brain regions. We profiled gene expression (bulk RNA-seq, 210 datasets) and chromatin state (bulk chromatin immunoprecipitation sequencing (ChIP-seq) for the histone marker H3K27ac, 100 datasets) in a broad, unbiased panel of 27 brain regions across the entire rodent brain, in naive and fluoxetine-treated animals. We complemented this approach with single-cell RNA-seq (scRNA-seq) analysis of two brain regions (20 datasets). Remarkably, in the single-cell RNA-seq profiling we observed profound changes in the transcripts of hippocampal dorDG and venDG (~500 DEGs in specific cell types). Using diverse integrative data analysis techniques we characterized the complex and multifaceted effects of fluoxetine on region-specific and cell-type-specific gene regulatory networks and pathways. We leveraged this atlas to identify fluoxetine-modulated genes and gene-regulatory loci, predict enriched motifs that suggest potential upstream regulators, and validate global mechanisms of fluoxetine action.本研究构建了氟西汀（fluoxetine，一种选择性5-羟色胺再摄取抑制剂（Selective Serotonin Reuptake Inhibitor, SSRI）类抗抑郁药）在27个大鼠脑区中发挥分子效应的全面多组学图谱。我们针对覆盖全啮齿类大脑的27个脑区，构建了无偏倚的广谱检测面板，分别在未经干预的动物与氟西汀处理动物中，完成了基因表达（批量RNA测序（bulk RNA-seq），合计210套数据集）与染色质状态（针对组蛋白标记物H3K27ac的批量染色质免疫共沉淀测序（chromatin immunoprecipitation sequencing, ChIP-seq），合计100套数据集）的组学谱分析。本研究还通过对2个脑区的单细胞RNA测序（single-cell RNA-seq, scRNA-seq）分析（共20套数据集）对上述工作进行了补充。值得注意的是，在单细胞RNA测序谱分析中，我们观察到海马背侧齿状回（dorsal dentate gyrus, dorDG）与海马腹侧齿状回（ventral dentate gyrus, venDG）的转录本发生了显著变化——在特定细胞类型中存在约500个差异表达基因（Differentially Expressed Genes, DEGs）。我们借助多种整合数据分析技术，阐明了氟西汀对脑区特异性及细胞类型特异性基因调控网络与通路的复杂多面调控效应。本研究利用该多组学图谱，鉴定了受氟西汀调控的基因与基因调控位点，预测了提示潜在上游调控因子的富集基序，并验证了氟西汀发挥作用的全局分子机制。