Unraveling the Genetic Programs Engaged in ASD Neurons Through Coupled Transcriptomic and Phenotypic Readouts

通过耦合转录组和表型读数揭示参与自闭症谱系障碍神经元的遗传程序

• 批准号: 10680485
• 负责人: Samouil Farhi
• 金额: $ 73.14万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-10 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10680485
• 关键词: Affect; Binding; Biological Models; Biological Process; CRISPR interference; Cell Culture Techniques; Cell Differentiation process; Cell model; Cells; Child; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Complement; Coupled; Coupling; Data; Data Analyses; Data Set; Disease; Disease model; Electrophysiology (science); Gene Expression; Gene Expression Profile; Genes; Genetic; Genetic Diseases; Genetic Risk; Genetic Transcription; Genetic study; Human; Human Genetics; Intervention; Investigation; Joints; Link; Machine Learning; Measurement; Measures; Mental disorders; Methods; Molecular; Morphology; Neurobiology; Neurons; Ontology; Optics; Pathway interactions; Patients; Phenotype; Research Personnel; System; Techniques; Testing; Undifferentiated; United States; Variant; Work; autism spectrum disorder; autoencoder; case control; clinical development; cohort; data integration; experience; experimental study; follow-up; genetic signature; genetic variant; high dimensionality; human pluripotent stem cell; innovation; innovative technologies; insight; invention; knock-down; multimodality; multiple omics; multiplexed imaging; postsynaptic; programs; protein protein interaction; rare variant; recruit; response; risk variant; scale up; stem cells; success; tool; transcriptomics

Autism spectrum disorders (ASD) are genetically diverse, characterized by both rare variants of large effect size and common variants of small effect size. Identifying the molecular mechanisms resulting from these variants presents a key challenge for the development of clinical interventions. Human pluripotent stem-cell derived neurons (hPSC-Ns) allow studies against a human genetic background, and show altered morphology and electrophysiology in ASD conditions. However, identifying mechanisms remains difficult with small numbers of lines, especially for common genetic variants. To overcome this challenge, we will leverage multi-omic characterization of hPSC-Ns perturbed with CRISPRi knockdown of both large effect size ASD risk genes and genes related to neuronal morphology (Aim 1) and electrophysiology (Aim 2). We will complement these screens with a characterization (Aim 3) of a larger, diverse cohort of 46 ASD lines and 46 matched controls which do not harbor coding variants in the genes perturbed in the previous Aims. An integrative analysis of this data (Aim 4) will generate interpretable genetic signatures related to each of these phenotypes and will show how these signatures interact with ASD risk genes. This approach is made possible by new techniques for pooled stem cell culture developed in Dr. Ralda Nehme’s lab, high content optical profiling methods developed by Dr. Samouil Farhi’s team, and data integration tools developed by Dr. Ernest Fraenkel’s group. The overall project will provide a basic neurobiological understanding of hPSC-Ns; provide valuable insight into how both common and rare variants induce observed cell-intrinsic phenotypes; and define an analytic framework and genetic signatures which can be used to understand mechanistic recruitment of new genetic risk loci and other psychiatric diseases.

自闭症谱系障碍 (ASD) 具有遗传多样性，其特点是具有大效应量的罕见变异 以及小效应大小的常见变体，识别这些变体产生的分子机制。 对人类多能干细胞衍生的临床干预措施的发展提出了关键挑战。 神经元 (hPSC-Ns) 允许针对人类遗传背景进行研究，并显示形态和结构的改变 然而，在 ASD 条件下确定机制仍然很困难。 为了克服这一挑战，我们将利用多组学。 CRISPRi 敲除大效应 ASD 风险基因和扰乱 hPSC-N 的特征 与神经元形态（目标 1）和电生理学（目标 2）相关的基因我们将补充这些筛选。 具有 46 个 ASD 系和 46 个匹配对照的更大、多样化群体的特征（目标 3） 对该数据进行综合分析（目标 4）。 将生成与每个表型相关的可解释的遗传特征，并将显示这些表型如何 特征与 ASD 风险基因相互作用，这种方法是通过混合干细胞新技术实现的。 Ralda Nehme 博士实验室开发的培养物，Samouil 博士开发的高内涵光学分析方法 Farhi 的团队和 Ernest Fraenkel 博士的团队开发的数据集成工具将提供整个项目。 对 hPSC-N 的基本神经生物学了解，为了解常见和罕见的 hPSC-N 提供了宝贵的见解； 变异诱导观察到的细胞内在表型；并定义分析框架和遗传特征； 它可用于了解新遗传风险位点和其他精神疾病的机制招募。

项目成果

Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits.

同时 CRISPR 筛选和空间转录组学揭示了细胞内、细胞间和功能性转录回路。

• 发表时间: 2023-12-01
• 作者: Binan, Loϊc;Danquah, Serwah;Valakh, Vera;Simonton, Brooke;Bezney, Jon;Nehme, Ralda;Cleary, Brian;Farhi, Samouil L
• 通讯作者: Farhi, Samouil L

Robust induction of functional astrocytes using NGN2 expression in human pluripotent stem cells.

使用人类多能干细胞中的 NGN2 表达强力诱导功能性星形胶质细胞。

• 发表时间: 2023-07-21
• 影响因子: 5.8
• 作者: Berryer, Martin H;Tegtmeyer, Matthew;Binan, Loïc;Valakh, Vera;Nathanson, Anna;Trendafilova, Darina;Crouse, Ethan;Klein, Jenny A;Meyer, Daniel;Pietiläinen, Olli;Rapino, Francesca;Farhi, Samouil L;Rubin, Lee L;McCarroll, Steven A;Nehme, Ralda
• 通讯作者: Nehme, Ralda