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

总结 人类神经系统可能是最复杂的生物组织，组织成多个功能 不同的区域，由超过2000亿个神经和非神经细胞组成，需要新的可扩展工具来 以高空间分辨率描绘组织背景中的细胞类型和关系。最近，我们开发了 DBiT-seq（通过组织中的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 UMI），（ii）多功能性，因为它不需要 微图案化的DNA条形码阵列，但只有一套试剂，和（iii）可采用的潜在用户没有 在先进的单分子成像或微流体方面的经验。这个BICCN项目就是利用了这一点 PI Rong Fan（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）在人类和非人类灵长类动物脑组织的基因组分析中， 将DBiT-seq开发成为BICCN的高度可扩展工具，以执行高通量、高灵敏度、高通量 空间分辨率，脑组织的全基因组映射。独特的是，我们建议开发一种开创性的 首个基于组织中确定性条形码的空间表观基因组测序技术， 可能为空间组学研究开辟一个新的方向。我们将应用空间转录组学， 空间表观基因组学用于人类和非人类灵长类动物6个脑区的映射。空间组学数据 将与单核RNA-seq和ATAC-seq整合，以产生空间分辨的转录组学。 和表观基因组细胞普查达到了前所未有的水平。该项目对BICCN的贡献 该联盟包括：（1）关于不同细胞类型及其转录和表观基因组的基础知识 在脑中的3D组织组织的背景下的特征和（2）经验证的高通量和 表征人和/或非人灵长类动物脑组织中细胞多样性的可扩展方法。的 由此产生的数据将导致更好地理解脑组织组织，功能， 和表观遗传学的基础。这些技术可以很容易地被BRAIN Initiative社区采用， 这些数据可以与其他BICCN调查人员生成的数据集进行比较或整合