Chemical toolbox for multiscale, integrative imaging: Connecting cellular gene expression to organ-scale phenotype

用于多尺度综合成像的化学工具箱：将细胞基因表达与器官尺度表型联系起来

• 批准号: 10709587
• 负责人: Hee-Sun Han
• 金额: $ 39.65万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-24 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10709587
• 关键词: Abnormal Cell; Address; Affect; Biological; Biology; Brain; Cell Communication; Cell physiology; Cells; Cellular Morphology; Chemicals; Chemistry; Clustered Regularly Interspaced Short Palindromic Repeats; Defect; Development; Disease; Environment; Functional disorder; Gene Expression; Gene Expression Profile; Genes; Genetic; Genotype; Health; Human; Image; Imaging Device; In Situ; In Vitro; Individual; Link; Molecular; Molecular Abnormality; Multimodal Imaging; Mutation; Near-infrared optical imaging; Neurons; Organ; Organism; Pathogenicity; Phenotype; Proteomics; Quantum Dots; RNA; Research Personnel; Science; Series; Shapes; System; Technology; Thick; Tissue Engineering; Tissue imaging; Tissues; Translating; autistic; cell type; complex biological systems; genetic manipulation; imaging platform; in vivo; innovation; intercellular communication; multiple omics; protein profiling; single cell sequencing; tool; transcriptome; transcriptomics

PROJECT SUMMARY The biology of multicellular organisms is organized on multiple levels. Molecular abundance and interactions regulate cell function; Communication of cells with nearby cells and environments further shapes cellular states and functions; Cells form highly interconnected functional networks organ-wide. Thus, a function or a dysfunction of an organ is manifested through the orchestrated action of individual cells comprising the organ. To mechanistically comprehend how a disease develops, we need to understand how the abnormal alteration in a cell is translated into system-level dysfunctions. With remarkable progress in sequencing, imaging, and genetic manipulation, researchers are now a step closer to decipher how cellular genotype gives rise to system-level phenotype in vivo. Single-cell sequencing probes the genetic profile of individual cells comprising a tissue. Organ-scale phenotyping, such as CLARITY, probes the detailed morphology of cells, cellular wiring, and the spatial organization of cells throughout an organ. CRISPR-based genetic perturbation establishes causal links between genes and phenotype in vitro at unprecedented throughput. However, these technologies mostly probe a single facet of a complex biological system. This limitation makes it challenging to integrate information obtained from different molecular types and scales, and to extract the mechanistic underpinning of system-level phenotype, especially in vivo. We aim to address this critical gap by developing a transformational, multiscale, multimodal imaging platform that screens a large tissue volume to identify cells with abnormal phenotype and characterize the complete and quantitative molecular contents or the abnormal cells as well as nearby cells. This platform will identify how the abnormal genetic change in a cell alters its phenotype, affects nearby cells, and contributes to disease development. Despite its immense potential, streamlining organ-scale proteomic phenotyping and in situ single cell transcriptomics is impossible due to the incompatibility of chemistry and imaging requirements. We propose to develop a series of chemical tools to enable multiscale, integrative profiling of proteins and RNAs: reversible protection of RNAs in an intact tissue; tissue transformation chemistry for multi- omic profiling; and quantum dot-based NIR imaging platform for thick-tissue imaging. Integrating these tools, we will develop and implement the multiscale, integrative imaging platform to characterize phenotypic abnormalities in autistic brains, such as ectopic neuronal connections, and profile cellular transcriptome at the region of phenotypic defects. Such study will provide a holistic view of diseased tissues to decipher pathogenic mechanisms behind a phenotypic abnormality at a molecular level, through the identification of altered gene expression patterns near an abnormal phenotype, intercellular communication network that leads to the system- level phenotype, and the spatial organization of differential cell types in healthy versus diseased tissues. In addition to enabling new biological studies, the newly developed chemical tools will drive innovations in a wide range of biomedical science, including RNA biology, genetics, imaging, and tissue engineering.

项目概要 多细胞生物的生物学是在多个层面上组织的。分子丰度和相互作用 调节细胞功能；细胞与附近细胞和环境的通信进一步塑造细胞状态 和功能；细胞在整个器官内形成高度互连的功能网络。因此，功能或功能障碍 器官的功能是通过组成该器官的各个细胞的精心策划的行动来体现的。到 从机制上理解疾病是如何发展的，我们需要了解体内的异常改变是如何发生的。 细胞转化为系统级功能障碍。在测序、成像和遗传方面取得了显着进展 通过操纵，研究人员现在距离破译细胞基因型如何产生系统水平又近了一步 体内表型。单细胞测序可探测构成组织的单个细胞的遗传特征。 器官规模表型分析，例如 CLARITY，可探测细胞的详细形态、细胞布线和 整个器官中细胞的空间组织。基于 CRISPR 的遗传扰动建立了因果关系 以前所未有的通量在体外研究基因和表型之间的关系。然而，这些技术大多探测 复杂生物系统的一个方面。这种限制使得整合信息变得具有挑战性 从不同的分子类型和尺度获得，并提取系统级的机制基础 表型，尤其是在体内。我们的目标是通过开发一个变革性的、多尺度的、 多模态成像平台，可筛选大体积组织以识别具有异常表型的细胞和 全面、定量地表征异常细胞及其附近细胞的分子含量。这 平台将识别细胞中的异常遗传变化如何改变其表型、影响附近的细胞，以及 有助于疾病的发展。尽管其潜力巨大，但简化器官规模的蛋白质组学 由于化学和化学的不相容性，表型分析和原位单细胞转录组学是不可能的。 成像要求。我们建议开发一系列化学工具来实现多尺度、综合分析 蛋白质和 RNA：完整组织中 RNA 的可逆保护；多组织转化化学 组学分析；以及基于量子点的近红外成像平台，用于厚组织成像。整合这些工具，我们 将开发和实施多尺度综合成像平台来表征表型异常 在自闭症大脑中，例如异位神经元连接，并分析该区域的细胞转录组 表型缺陷。此类研究将提供患病组织的整体视图，以破译致病组织 通过识别改变的基因，在分子水平上揭示表型异常背后的机制 异常表型附近的表达模式，导致系统的细胞间通讯网络 水平表型，以及健康组织与患病组织中差异细胞类型的空间组织。在 除了实现新的生物学研究之外，新开发的化学工具还将推动广泛领域的创新 生物医学科学的范围，包括RNA生物学、遗传学、成像和组织工程。