Defining gene-by-environment interactions using multiplex single-cell genomics

使用多重单细胞基因组学定义基因与环境的相互作用

• 批准号: 10657595
• 负责人: Jose Luis McFaline-Figueroa
• 金额: $ 46.07万
• 依托单位: COLUMBIA UNIV NEW YORK MORNINGSIDE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-24 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10657595
• 关键词: Alzheimer' s Disease; Cells; Clustered Regularly Interspaced Short Palindromic Repeats; Couples; Disease; Environment; Epilepsy; Exposure to; Genes; Genetic; Genetic Screening; Genetic Transcription; Genomics; Goals; In Situ; In Vitro; Individual; Malignant neoplasm of brain; Methods; Molecular; Mus; Mutate; Mutation; Neurobiology; Neurons; Nuclear; Oxidative Stress; Peptides; Research; Resolution; Risk; Sampling; Severity of illness; System; Technology; Therapeutic Intervention; Virus Receptors; cell type; clinically actionable; disorder prevention; flexibility; gene environment interaction; genetic makeup; in vivo; individual response; preventive intervention; programs; receptor expression; response; single-cell RNA sequencing; tool; tumor

PROJECT SUMMARY The proposed research program aims to develop systems for the multiplex assessment of the effect of genetic perturbation on the response of cells to exogenous and endogenous exposures at the resolution of individual cells . Specifically, we will develop a flexible and scalable in vitro platform for high-throughput single-cell gene- by-environment interaction screens that couples CRISPR-based single-cell pooled genetic screens to a “nuclear hashing”-based sample multiplexing strategy and a single-cell genomic readout. This platform will allow for the simultaneous molecular description of 1,000s-10,000s of unique conditions (i.e. gene and exposure combinations) at the resolution of individual cell types and cell states. In addition, we propose to develop a set of tools based on heterologous viral receptor expression for the in situ and cell-type specific delivery of CRISPR- based genetic perturbations in a manner compatible with single-cell RNA-seq. We highlight the versatility and generalizability of our approach across three applications of our technologies that aim to define gene-by- environment interactions in neurobiological disease. We propose to dissect the genetic interactions between mutations associated with Alzheimer’s disease and the transcriptional response of neural cell types to oxidative stress and peptide aggregates; to characterize the transcriptional effects associated with cell-type specific modulation of genetic modifier activity in response to mutations in genes that cause epilepsy disorder and; to determine how genes that are commonly mutated in brain cancer alter the response of murine tumors to therapies in vivo. Our goal is to arrive at clinically actionable molecular descriptions of how individual genes contribute to the response of individuals to exposure.

项目概要 拟议的研究计划旨在开发对遗传影响进行多重评估的系统 在个体分辨率下对细胞对外源性和内源性暴露的反应的扰动 细胞 。具体来说，我们将开发一个灵活且可扩展的高通量单细胞基因体外平台—— 环境相互作用筛选，将基于 CRISPR 的单细胞汇集遗传筛选与“核 基于散列的样本复用策略和单细胞基因组读数。该平台将允许 对 1,000-10,000 个独特条件（即基因和暴露）进行同步分子描述 组合）在单个细胞类型和细胞状态的分辨率。此外，我们建议开发一套 基于异源病毒受体表达的工具，用于原位和细胞类型特异性递送 CRISPR- 以与单细胞 RNA-seq 兼容的方式进行基于遗传扰动的研究。我们强调多功能性和 我们的方法在我们的技术的三种应用中的普遍性，旨在逐个定义基因 神经生物学疾病中的环境相互作用。我们建议剖析之间的遗传相互作用 与阿尔茨海默病相关的突变以及神经细胞类型对氧化的转录反应 应激和肽聚集体；表征与细胞类型特异性相关的转录效应 调节基因修饰剂活性以响应引起癫痫病的基因突变；到 确定脑癌中常见突变的基因如何改变小鼠肿瘤的反应 体内疗法。我们的目标是对个体基因如何进行临床可行的分子描述 有助于个人对暴露的反应。