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.

项目总结 基因组中有20,000个基因，尽管在分配许多基因方面取得了进展 虽然我们还不知道许多基因的功能，也不知道它们在影响疾病中的具体作用。基因 可以在不同的细胞类型、细胞状态或组织中指示不同的表型，这使得基因注释成为 艰巨的任务。需要研究来确定每个基因在不同背景下的功能，但 问题是一个挑战--有必要评估100个基因的许多可能的功能 复杂的细胞和细胞外环境的背景，其空间架构是 系统行为。此外，一些基因与其他基因协同或冗余地工作，使其具有表型。 批注更具挑战性。确定每个基因在不同的正常和疾病状态下的作用 对生物学和医学产生了不可估量的影响。它将引发不同的新的内在成分 这将有助于开发治疗其中一些疾病的药物。 该项目的目标是建立一个首创的空间功能基因组学平台。 MAP)，这将使包括多基因敲除在内的数百种遗传扰动能够并行产生 以及每种扰动对多种内在和外在生物过程的影响 将在细胞、亚细胞和组织水平上揭示。为了达到我们的目标，我们将开发小说 技术、方法和软件工具将允许100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分辨。确立…的潜力 为了解决紧急的未得到满足的需求，我们将应用该平台来解决 免疫肿瘤学，即肿瘤如何防止免疫渗透和破坏免疫。我们将使用扰乱- MAP以确定调节免疫募集和从肿瘤微环境中排除的因素 发现控制肿瘤抵抗免疫清除的基因。 该项目的成果将是空间细胞功能基因组学的一项变革性技术 以及亚细胞分辨率和高维表型。这将具有无与伦比的能力 在广泛的生物学领域回答大量问题，并研究整个基因和 无法用现有功能基因组学方法研究的表型；使高度规模化 研究确定控制组织和肿瘤组织、细胞迁移、侵袭等过程的基因 和转移，细胞间的相互作用，以及局部免疫细胞的募集和串扰。通过能够 询问同一细胞内的多个基因扰动，扰动图谱也将实现遗传冗余 和合成致死关系有待确定，这是开发靶向癌症的主要兴趣领域 治疗。因此，该平台将在基础生物学和翻译生物学的众多领域具有广泛的实用价值。