Ultrasensitive device for epigenomic profiling of stem cell differentiation

描述（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。更好地理解表观遗传调控将导致更好的策略来操纵细胞命运的再生医学，新的基于表观遗传学的疾病标志物和生物标志物，以及新的治疗方法。尽管在表观基因组学中得到了广泛的应用，但传统的ChIP-Seq技术仍存在一些局限性。它需要大量的细胞（每次实验通常需要10 × 10^6个细胞），需要大量的人工处理样品，需要3-4天（不包括测序）才能完成。对大量细胞的要求阻碍了ChIP-Seq应用于生物学上重要但罕见的细胞类型，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，可以在几个小时内完成。作为一项原理验证，我们将应用我们的转化技术来分析胚胎造血不同阶段的造血干细胞和祖细胞（HSPCs）的表观基因组。由于胚胎造血干细胞极为罕见，因此对胚胎造血干细胞命运确定过程中表观基因组的动态知之甚少，这妨碍了当前ChIP-Seq协议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和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。

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.