Highly scalable and sensitive spatial transcriptomic and epigenomic sequencing of brain tissues from human and non-human primate

对人类和非人类灵长类动物的脑组织进行高度可扩展且灵敏的空间转录组和表观基因组测序

• 批准号: 10370074
• 负责人: Rong Fan
• 金额: $ 289.65万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-15 至 2024-09-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10370074
• 关键词: 3-Dimensional; ATAC-seq; Address; Adopted; Aging; Area; Atlases; BRAIN initiative; Bar Codes; Biological; Biological Assay; Biomedical Engineering; Brain; Brain Mapping; Brain region; Cell Nucleus; Cells; Censuses; Characteristics; Chromatin; Collection; Communities; Complex; Consumption; Coupled; DNA; Data; Data Set; Development; Devices; Disease; Epigenetic Process; Fluorescent in Situ Hybridization; Gene Expression; Genetic Transcription; Genomics; Grant; Health; Heterogeneity; Human; Knowledge; Longevity; Macaca; Maps; Measures; Messenger RNA; Methods; Microfluidics; Molecular; Morphology; Motivation; Nervous system structure; Neurosciences; Organ; Outcome; Proteins; Protocols documentation; Public Health; Quality Control; RNA; Reagent; Research; Research Personnel; Resolution; Running; Sampling; Slide; Small Nuclear RNA; Solid; Suspensions; Technology; Time; Tissue Sample; Tissues; Validation; base; brain cell; brain tissue; cell type; cost; epigenome; epigenomics; experience; genome-wide; high throughput technology; histone modification; human tissue; imaging modality; improved; interest; molecular imaging; multiple omics; new technology; next generation sequencing; nonhuman primate; novel; relating to nervous system; single molecule; synergism; tool; transcriptome; transcriptome sequencing; transcriptomics

SUMMARY The human nervous system is possibly the most complex biological tissue, organized into multiple functionally distinct regions and comprised of over 200 billion neural and non-neural cells, requiring novel scalable tools to profile cell types and relationships in the tissue context with high spatial resolution. Recently, we developed DBiT-seq (high-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue), which has demonstrated (i) high sensitivity (~5,000 UMIs per 10µm pixel), (ii) versatility as it does not require micropatterned DNA barcode arrays but only a set of reagents, and (iii) adoptability by potential users with no experience in advanced single molecule imaging or microfluidics. This BICCN project is capitalized on this novel technology developed by PI Rong Fan (Biomedical Engineer) and the long-standing experience of MPI Nenad Sestan (Neuroscience) in genomic analysis of human and non-human primate brain tissues, to further develop DBiT-seq into a highly scalable tool for BICCN to perform high-throughput, high-sensitivity, high- spatial-resolution, genome-wide mapping of brain tissues. Uniquely, we propose to develop a groundbreaking first-of-its-kind spatial epigenome sequencing technology based on deterministic barcoding in tissue, which may open up a new direction in the field of spatial omics research. We will apply spatial transcriptomics and spatial epigenomics to the mapping of 6 brain regions in human and non-human primate. Spatial omics data will be integrated with single-nucleus RNA-seq and ATAC-seq to generate spatially-resolved transcriptomic and epigenomic cell census at an unprecedented level. The contributions of this project to the BICCN consortium include: (1) fundamental knowledge on diverse cell types and their transcriptional and epigenomic characteristics in the context of 3D tissue organization in the brain and (2) validated high throughput and scalable approaches to characterizing cell diversity in human and/or non-human primate brain tissues. The resulting data will lead to a better understanding of the relationship between brain tissue organization, function, and epigenetic underpinnings. The technologies can be readily adopted by a BRAIN Initiative community and the data can be compared or integrated with datasets generated by other BICCN investigators

概括 人类神经系统可能是最复杂的生物组织，组织成多种功能 不同的区域由超过 2000 亿个神经和非神经细胞组成，需要新颖的可扩展工具来 最近，我们开发了具有高空间分辨率的组织环境中的细胞类型和关系。 DBiT-seq（通过组织中确定性条形码进行高空间分辨率多组学测序）， 证明了 (i) 高灵敏度（每 10μm 像素约 5,000 个 UMI），(ii) 多功能性，因为它不需要 微图案 DNA 条形码阵列，但只有一套试剂，以及 (iii) 潜在用户无需任何操作即可采用 该 BICCN 项目充分利用了先进单分子成像或微流体技术的经验。 PI荣范（生物医学工程师）开发的新技术和MPI的长期经验 Nenad Sestan（神经科学）对人类和非人类灵长类动物脑组织进行基因组分析，以进一步 将 DBiT-seq 开发为 BICCN 的高度可扩展工具，以执行高通量、高灵敏度、高通量 独特的是，我们建议开发一种突破性的脑组织全基因组图谱。 首创的基于组织确定性条形码的空间表观基因组测序技术， 可能会在空间组学研究领域开辟一个新的方向，我们将应用空间转录组学和 空间表观基因组学绘制人类和非人类灵长类动物 6 个大脑区域的空间组学数据。 将与单核 RNA-seq 和 ATAC-seq 集成，生成空间分辨的转录组 该项目对 BICCN 的贡献达到了前所未有的水平。 联盟包括：（1）关于不同细胞类型及其转录和表观基因组的基础知识 大脑 3D 组织组织背景下的特征，以及 (2) 验证了高通量和 表征人类和/或非人类灵长类动物脑组织中细胞多样性的可扩展方法。 由此产生的数据将有助于更好地理解脑组织组织、功能、 这些技术可以很容易地被 BRAIN Initiative 社区采用，并且 数据可以与其他 BICCN 研究人员生成的数据集进行比较或集成