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

基本信息

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
项目类别：
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

项目摘要

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节在正常和疾病发育中起关键作用。对表观遗传调节的更好理解将为操纵细胞命运，新型表观遗传学标志物和生物标志物以及新型治疗剂提供更好的策略。尽管在表观基因组学中广泛应用，但传统的CHIP-SEQ技术仍有几个局限性。它需要大量的单元格（通常每个实验> 10^6），涉及大量手动处理样品，并且需要3-4天（不包括测序）才能完成。大量细胞的需求阻止了芯片seq在生物学上重要但罕见的细胞类型中的应用，例如干细胞和从活检样品中纯化的细胞。为了克服此类障碍，我们将开发一种新型的基于微流体的芯片SEQ技术，该技术使用两个数量级的细胞比最先进的协议少，并且可以在数小时内完成。作为原则证明，我们将应用转化技术来介绍造血茎和祖细胞（HSPC）的表观基因组，从胚胎造血的各个阶段。关于HSC命运规范期间表观基因组的动力学知之甚少，因为胚胎HSPC极为罕见，因此排除了当前的芯片seq方案在这些细胞类型中的应用。如果成功，我们提出的技术将通过使用稀有细胞以及快速和多重形式的芯片序列进行研究来彻底改变表观基因组学的研究。