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控在正常和疾病发展中发挥着关键作用。对表观遗传调控的更好理解将为再生医学、基于表观遗传学的新型疾病标志物和生物标志物以及新疗法提供更好的操纵细胞命运的策略。尽管传统 ChIP-Seq 技术在表观基因组学中广泛应用，但仍存在一些局限性。它需要大量细胞（通常每个实验 >10^6），涉及大量的样本手动处理，并且需要 3-4 天（不包括测序）才能完成。由于需要大量细胞，ChIP-Seq 无法应用于生物学上重要但罕见的细胞类型，例如干细胞和从活检样本中纯化的细胞。为了克服这些障碍，我们将开发一种基于微流体的新型 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，并且可以在数小时内完成。作为原理验证，我们将应用我们的变革性技术来分析胚胎造血各个阶段的造血干细胞和祖细胞 (HSPC) 的表观基因组。由于胚胎 HSPC 极其罕见，因此人们对 HSC 命运规范过程中表观基因组的动态知之甚少，这妨碍了当前 ChIP-Seq 方案对这些细胞类型的应用。如果成功，我们提出的技术将通过使用稀有细胞以快速和多重格式进行 ChIP-Seq 研究，彻底改变表观基因组学的研究。