Development of a platform for spatial functional genomics

空间功能基因组学平台的开发

• 批准号: 10250339
• 负责人: Brian D Brown
• 金额: $ 72.4万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10250339
• 关键词: Address; Affect; Antibodies; Architecture; Area; Bar Codes; Behavior; Biological; Biological Process; Biology; CRISPR library; Cell Adhesion Molecules; Cell Communication; Cell Nucleus; Cell Proliferation; Cells; Cellular Morphology; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Cytoplasm; Development; Dimensions; Disease; Drug resistance; Environment; Epitopes; Exclusion; Gene Expression; Genes; Genetic; Genome; Genomic approach; Goals; Guide RNA; Hormones; Human Genome; Image; Immune; Immunity; Immunooncology; Immunotherapy; Inflammatory; Knock-out; Libraries; Malignant Neoplasms; Malignant neoplasm of lung; Maps; Medicine; Methods; Motivation; Necrosis; Neoplasm Metastasis; Outcome; Pharmaceutical Preparations; Pharmacotherapy; Phenotype; Population; Process; Proteins; Publishing; Reporter; Research; Resistance; Resolution; Role; Set protein; Software Tools; Stains; Structure; System; T-Lymphocyte; Technology; Tissues; Tumor Immunity; Tumor Tissue; Tumor-infiltrating immune cells; Work; antibody detection; base; cancer biomarkers; cancer cell; cancer immunotherapy; cell killing; cell motility; cell type; chemokine; combinatorial; cytokine; density; drug development; extracellular; functional genomics; gene function; genetic signature; genome annotation; high dimensionality; immune clearance; immunoregulation; in vivo; innovation; insight; interest; knockout gene; malignant breast neoplasm; multiplexed imaging; new technology; novel; overexpression; predicting response; preservation; prevent; recruit; response; targeted cancer therapy; tumor; tumor microenvironment; vector

PROJECT SUMMARY There are >20,000 genes in the genome and though there has been progress in assigning many gene functions, we still do not know the function of numerous genes or their specific roles in affecting disease. Genes can direct diverse phenotypes in different cell types, cell states, or tissues, which makes gene annotation a staggering task. Studies are needed to determine each gene’s function in different contexts, but the scope of the problem is a challenge – it is necessary to assess many possible functions of 100s of genes and within the context of a complex cellular and extracellular milieu whose spatial architecture is an essential component of system behavior. In addition, some genes work coordinately or redundantly with other genes, making phenotypic annotation more challenging. Establishing the role of every gene in different normal and disease states would have an incalculable impact on biology and medicine. It would elicit novel intrinsic components of different diseases and thus facilitate the development of drugs to treat some of these diseases. The objective of this project is to establish a first-of-its-kind platform for spatial functional genomics (Perturb- map), which will enable 100s of genetic perturbations, including multi-gene knockouts, to be generated in parallel in tissues and tumors, and the effect of each perturbation on multiple intrinsic and extrinsic biological processes to be revealed at cellular, subcellular, and tissue level resolution. To reach our objective, we will develop novel technologies, methods, and software tools that will permit 100s of CRISPRs, along with dozens of biological phenotypes, to be spatially resolved within a tissue by high-dimensional imaging. To establish the potential of Perturb-map to address urgent unmet needs, we will apply the platform to one of the most pressing questions in immune oncology, namely how tumors prevent immune infiltration and subvert immunity. We will use Perturb- map to identify factors that regulate immune recruitment and exclusion from the tumor microenvironment and uncover genes controlling tumor resistance to immune clearance. The outcome of this project will be a transformative technology for functional genomics with spatial cellular and sub-cellular resolution and high-dimensional phenotyping. This would have unmatched capabilities to answer numerous questions in a broad array of biological areas, and to investigate entire classes of genes and phenotypes that could not be studied with existing functional genomics approaches; enabling highly scaled studies to identify genes that control processes such as: tissue and tumor organization, cell migration, invasion and metastasis, cell-cell interactions, and local immune cell recruitment and crosstalk. By being able to interrogate multiple gene perturbations within the same cell, Perturb-map will also enable genetic redundancies and synthetic lethal relationships to be identified, a major area of interest for development of targeted cancer therapies. Thus, the platform will have broad utility in numerous areas of basic and translational biology.

项目概要 基因组中有超过 20,000 个基因，尽管在分配许多基因方面已经取得了进展 功能，我们仍然不知道许多基因的功能或它们在影响疾病中的具体作用。 可以在不同的细胞类型、细胞状态或组织中指导不同的表型，这使得基因注释成为一种 需要进行研究来确定每个基因在不同情况下的功能，但其范围是巨大的。 问题就是挑战——有必要评估数百个基因的许多可能功能，并在 复杂的细胞和细胞外环境的背景，其空间结构是细胞和细胞外环境的重要组成部分 此外，一些基因与其他基因协调或冗余地发挥作用，从而形成表型。 确定每个基因在不同正常和疾病状态下的作用将更具挑战性。 它将对生物学和医学产生不可估量的影响。 疾病，从而促进治疗其中一些疾病的药物的开发。 该项目的目标是建立首个空间功能基因组学平台（Perturb- 图），这将能够并行生成数百个遗传扰动，包括多基因敲除 组织和肿瘤中的变化，以及每种扰动对多种内在和外在生物过程的影响 为了实现我们的目标，我们将开发新的细胞、亚细胞和组织水平的分辨率。 技术、方法和软件工具将允许数百个 CRISPR 以及数十个生物 表型，通过高维成像在组织内进行空间解析。 为了解决紧迫的未满足需求，扰动图，我们将应用该平台来解决最紧迫的问题之一 免疫肿瘤学，即如何防止肿瘤免疫浸润和颠覆免疫。 绘制图谱以识别调节免疫募集和排除肿瘤微环境的因素 揭示控制肿瘤抵抗免疫清除的基因。 该项目的成果将是一种具有空间细胞功能基因组学的变革性技术 以及亚细胞分辨率和高维表型分析，这将具有无与伦比的能力。 回答广泛的生物学领域中的众多问题，并研究整个类别的基因和 现有功能基因组学方法无法研究的表型； 研究鉴定控制组织和肿瘤组织、细胞迁移、侵袭等过程的基因 以及转移、细胞间相互作用以及局部免疫细胞招募和串扰。 询问同一细胞内的多个基因扰动，扰动图还将实现遗传冗余 和有待确定的合成致死关系，这是开发靶向癌症的主要兴趣领域 因此，该平台将在基础和转化生物学的许多领域具有广泛的用途。