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: 10797662
• 负责人: Hee-Sun Han
• 金额: $ 23.97万
• 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/10797662
• 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.

项目摘要 多细胞生物的生物学在多个层面上组织。分子丰度和相互作用 调节细胞功能；细胞与附近的细胞和环境的通信进一步塑造了细胞状态 和功能；细胞形成高度相互连接的功能网络。因此，功能或功能障碍 器官通过包含器官的单个细胞的精心策划表现出来。到 从机械上理解疾病的发展方式，我们需要了解一个异常改变 细胞被翻译成系统级功能障碍。在测序，成像和遗传方面取得了显着进展 操纵，研究人员现在更近于解密的细胞基因型如何产生系统级 体内表型。单细胞测序探测包含组织的单个细胞的遗传特征。 器官尺度的表型，例如清晰度，探测细胞，细胞接线的详细形态和 整个器官中细胞的空间组织。基于CRISPR的遗传扰动建立因果关系 在前所未有的吞吐量下的基因和表型之间。但是，这些技术主要是探测 复杂的生物系统的单个方面。这种限制使整合信息具有挑战性 从不同的分子类型和鳞片中获得，并提取系统级的机械基础 表型，尤其是体内。我们旨在通过发展一个变革型的，多尺度， 多模式成像平台筛选大型组织体积，以鉴定具有异常表型和异常的细胞 表征完整和定量的分子内容物或异常细胞以及附近的细胞。这 平台将确定细胞中异常的遗传变化如何改变其表型，影响附近的细胞，并且 有助于疾病的发展。尽管具有巨大的潜力，但可以简化器官规模的蛋白质组学 由于化学不兼容，表型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，以实现多尺度，集成分析 蛋白质和RNA：完整组织中RNA的可逆保护；组织转化化学多数 莫基分析；和基于量子点的NIR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的集成成像平台，以表征表型异常 在自闭症大脑中，例如异位神经元连接和剖面的细胞转录组 表型缺陷。这样的研究将为患病的组织提供全面的视野，以破译致病性 通过鉴定改变基因，在分子水平上表型异常背后的机制 在异常表型附近的表达模式，细胞间通信网络，导致系统 - 水平表型，以及健康组织与患病组织中差分细胞类型的空间组织。在 除了启用新的生物学研究，新开发的化学工具将推动创新 生物医学科学范围，包括RNA生物学，遗传学，成像和组织工程。

项目成果

Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT).

细胞内空间转录组分析工具包 (InSTAnT)。

• DOI: 10.21203/rs.3.rs-2481749/v1
• 发表时间: 2023
• 期刊: Research square
• 作者: Kumar,Anurendra;Schrader,AlexW;Boroojeny,AliEbrahimpour;Asadian,Marisa;Lee,Juyeon;Song,YouJin;Zhao,SihaiDave;Han,Hee-Sun;Sinha,Saurabh
• 通讯作者: Sinha,Saurabh