Zebrafish screen of schizophrenia risk genes reveals convergent dysregulation of cholesterol metabolism

This repository contains larval behavior data and phospho-Erk whole brain activity mapping stacks for multiple zebrafish knockouts for orthologs of genes linked to schizophrenia risk in humans. In addition, it includes tracking data in a y-maze assay, filipin staining for free cholesterol, and fabp7a staining for mutants at the juvenile 21 dpf stage (sp4-ko, atp1a3a-v129m, atp1a3a-ko). Lastly, additional RNA-seq analysis files are included, including html files with complete analysis code. The manuscript abstract is as follows: Rare coding variants provide a tractable entry point for understanding the molecular mechanisms underlying schizophrenia risk. Here, we generated and characterized zebrafish lines with mutations in the orthologs of >20 human schizophrenia-associated genes, including eight of the top ten SCHEMA genes, genes disrupted in childhood-onset schizophrenia (COS), and genes located within recurrent copy number variants. Whole-brain phospho-Erk activity mapping and behavioral profiling identified phenotypes in multiple mutant lines. We prioritized a protein-truncating mutation in sp4, which encodes an activity-dependent transcription factor, and a COS-associated missense mutation in atp1a3a, which encodes a Na+/K+ ATPase pump, for additional characterization. Both knockout and point mutations in atp1a3a disrupted brain activity and behavior in larvae and impaired navigation of a Y-maze in juveniles. Bulk RNA sequencing data from adult sp4 and atp1a3a brains highlighted convergent upregulation of sterol biosynthesis pathways, including increased expression of srebf2 and msmo1. Analysis of previously published telencephalon single-cell data demonstrated that cholesterol synthesis genes are enriched in astrocyte-like cells and increase in expression during post-larval development. Consistent with transcriptomic findings, filipin staining indicated increased free cholesterol in juvenile sp4 and atp1a3a mutant brains. Our findings identify dysregulation of glial and sterol-associated programs as a shared molecular consequence of two distinct schizophrenia risk mutations. Although whether sterol pathway dysregulation represents a primary pathogenic mechanism or a secondary response to changes in neuronal activity requires further investigation, the convergence observed between genetic models and developmental stages suggests that disruptions to lipid homeostasis could represent a shared feature of schizophrenia disease biology.本数据集仓库包含针对与人类精神分裂症（schizophrenia）风险相关基因的同源基因所构建的多种斑马鱼（zebrafish）敲除模型的幼体行为学数据、全脑磷酸化Erk（phospho-Erk）活性成像堆栈。此外，该仓库还包含Y迷宫实验（Y-maze assay）行为追踪数据、针对游离胆固醇的菲洛平染色（Filipin staining）结果，以及针对幼年期（受精后21天，21 dpf）的sp4敲除（sp4-ko）、atp1a3a V129M突变（atp1a3a-v129m）和atp1a3a敲除（atp1a3a-ko）突变体的fabp7a染色结果。最后，仓库还包含额外的RNA测序（RNA-seq）分析文件，其中包含带有完整分析代码的HTML格式文件。该研究手稿的摘要如下：罕见编码变异为解析精神分裂症风险背后的分子机制提供了可行的研究切入点。本研究构建并鉴定了20余个与人类精神分裂症相关基因的同源基因突变斑马鱼品系，其中包含SCHEMA排名前十的基因中的8个、儿童起病型精神分裂症（childhood-onset schizophrenia, COS）相关致病基因，以及复发性拷贝数变异（recurrent copy number variants）区域内的基因。通过全脑磷酸化Erk活性成像与行为谱分析，我们在多个突变品系中发现了异常表型。我们选取了编码活性依赖型转录因子的sp4基因的蛋白截短突变，以及编码Na+/K+ ATP酶泵的atp1a3a基因的儿童起病型精神分裂症相关错义突变，开展进一步功能鉴定。atp1a3a的敲除模型与点突变模型均会破坏幼体的脑活动与行为，并损害幼体在Y迷宫中的空间导航能力。对成年sp4与atp1a3a突变体脑组织的批量RNA测序数据显示，二者均存在固醇生物合成通路的协同上调，其中包括srebf2与msmo1基因的表达水平升高。对已发表的端脑（telencephalon）单细胞测序数据的分析表明，胆固醇合成基因在星形胶质样细胞中富集，并在幼体发育后期表达量上升。与转录组学结果一致，菲洛平染色结果显示幼年期sp4与atp1a3a突变体脑组织中的游离胆固醇水平升高。本研究结果证实，胶质细胞与固醇相关调控程序的失调是两种不同精神分裂症风险突变共有的分子效应。尽管固醇通路失调究竟是精神分裂症的原发致病机制，还是神经元活动改变引发的继发反应仍需进一步探究，但不同遗传模型与发育阶段中观察到的共性特征提示，脂质稳态紊乱可能是精神分裂症疾病生物学的共有特征。