Ultrasensitive device for epigenomic profiling of stem cell differentiation

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的发展中起着关键作用。更好地理解表观遗传调控将为再生医学、新的基于表观遗传学的疾病标记物和生物标记物以及新的治疗方法带来更好的策略。尽管它在表观基因组学中得到了广泛的应用，但传统的芯片序列技术受到了一些限制。它需要大量的细胞(通常每个实验需要106个细胞)，需要大量的人工处理样本，需要3-4天(不包括测序)才能完成。由于需要大量的细胞，CHIP-SEQ无法应用于生物学上重要但稀有的细胞类型，如干细胞和从活检样本中提纯的细胞。为了克服这些障碍，我们将开发一种基于微流控技术的新型芯片--SEQ技术，它使用的细胞比最先进的协议少两个数量级，可以在几个小时内完成。作为一项原则证明，我们将应用我们的变革性技术来描述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。由于胚胎HSPC极其罕见，排除了当前芯片-序列协议在这些细胞类型中的应用，因此对HSC命运指定过程中表观基因组的动态变化知之甚少。如果成功，我们建议的技术将通过使用稀有细胞并以快速和多重格式实现芯片序列研究，从而使表观基因组学研究发生革命性变化。

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 >106 per experiment), involves extensiv 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.