Ultrasensitive device for epigenomic profiling of stem cell differentiation

用于干细胞分化表观基因组分析的超灵敏装置

• 批准号: 8699399
• 负责人: Chang Lu
• 金额: $ 23.66万
• 依托单位: UNIVERSITY OF IOWA
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-04-01 至 2016-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8699399
• 关键词: Adult; Algorithms; Animal Model; Aorta; Bioinformatics; Biological Assay; Biological Markers; Biopsy Specimen; Bone Marrow; Cell Count; Cell Ontogeny; Cells; ChIP-seq; Coupled; DNA; DNA Sequence; Data Analyses; Development; Device Designs; Devices; Disease; Disease Marker; Embryo; Epigenetic Process; Fetal Liver; Flow Cytometry; Foundations; Gene Expression Regulation; Genome; Goals; Gonadal structure; Hematopoiesis; Hematopoietic; Hematopoietic stem cells; Histones; Hour; Human Cell Line; K-562; Knowledge; Lead; Manuals; Maps; Mesonephric structure; Microfluidic Microchips; Microfluidics; Molecular; Mus; Noise; Play; Protocols documentation; Reading; Regenerative Medicine; Regulation; Reproducibility; Research; Role; Sampling; Staging; Stem cells; System; Technology; Time; base; cell type; chromatin immunoprecipitation; epigenome; epigenomics; genome-wide; histone modification; improved; insight; instrumentation; novel; novel therapeutics; prevent; public health relevance; research study; stem; stem cell biology; stem cell differentiation

DESCRIPTION (provided by applicant): Epigenetic regulation of gene expression plays a pivotal role in normal and disease development. A better understanding of epigenetic regulation will lead to better strategies for manipulating cell fate for regenerative medicine, novel epigenetics-based disease markers and biomarkers, and novel therapeutics. Despite of its widespread application in epigenomics, traditional ChIP-Seq technology suffers from several limitations. It requires a large number of cells (typically >10^6 per experiment), involves extensive manual handling of the samples, and takes 3-4 days (not including sequencing) to finish. The requirement of a large number of cells prevents application of ChIP-Seq to biologically important but rare cell types, such as stem cells and cells purified from biopsy samples. To overcome such hurdles, we will develop a novel microfluidics-based ChIP- Seq technology that uses two orders of magnitude fewer cells than state-of-the-art protocols and can be completed in hours. As a proof-of-principle, we will apply our transformative technology to profile the epigenomes of hematopoietic stem and progenitor cells (HSPCs) from various stages of embryonic hematopoiesis. Little is known about the dynamics of the epigenome during HSC fate specification since embryonic HSPCs are extremely rare, precluding application of current ChIP-Seq protocols to these cell types. If successful, our proposed technology will revolutionize research in epigenomics by enabling ChIP-Seq studies using rare cells and in fast and multiplex format.

描述（由申请人提供）：基因表达的表观遗传调控在正常和疾病发展中起着关键作用。对表观遗传调控的更好理解将导致更好的策略，用于操纵再生医学的细胞命运，基于表观遗传学的新型疾病标志物和生物标志物，以及新型治疗方法。尽管其在表观基因组学中的广泛应用，但传统的ChIP-Seq技术受到若干限制。它需要大量的细胞（通常每个实验>10^6个），涉及大量的手动处理样品，需要3-4天（不包括测序）才能完成。大量细胞的需求阻碍了ChIP-Seq应用于生物学上重要但稀有的细胞类型，例如干细胞和从活检样品中纯化的细胞。为了克服这些障碍，我们将开发一种新的基于微流体的ChIP-Seq技术，该技术使用的细胞比最先进的方案少两个数量级，并且可以在几个小时内完成。作为原理证明，我们将应用我们的变革性技术来分析胚胎造血不同阶段的造血干细胞和祖细胞（HSPC）的表观基因组。关于HSC命运特化期间表观基因组的动态知之甚少，因为胚胎HSPC极其罕见，排除了当前ChIP-Seq方案对这些细胞类型的应用。如果成功的话，我们提出的技术将通过使用稀有细胞并以快速和多重格式进行ChIP-Seq研究来彻底改变表观基因组学的研究。