Epigenomic drivers of human muscle progenitor cells in development and disease

描述（由申请人提供）：Duchenne肌营养不良症（DMD）是一种目前无法治愈的退行性肌肉疾病，每3500例男性中就有1例受到影响，因此非常需要新的治疗方法。有希望的选择包括移植正常或“基因校正”的肌肉祖细胞，这可以移植受影响的肌肉纤维以纠正潜在的遗传缺陷，以及基于小分子的疗法，可以纠正中断的生肌过程以支持改善肌肉功能。不幸的是，再生肌肉前体细胞的稀缺性和缺乏强烈模拟人类DMD进展和严重程度的相关模型，给理解疾病机制造成了许多障碍，并阻碍了治愈性疗法的发展。然而，我们相信，表观基因组分析和肌肉干细胞生物学方面的新创新，部分是在我们的实验室中开发的，为发现和推进DMD的新疗法创造了新的机会。该项目将利用Wagers和Rinn研究小组的综合专业知识，他们在哈佛大学干细胞和再生生物学系共享共同的实验室空间。Wagers实验室的研究已经建立了新的策略，从人类肌肉中分离高度富集的骨骼肌祖细胞（卫星细胞）群体，并从人类诱导多能干细胞中获得可移植的肌源性前体细胞。Rinn实验室的研究已经定义了新的计算管道，用于注释和分析指定细胞命运和功能的基因调控元件。该项目将联合收割机这些创新的进步与NIH表观基因组学路线图计划提供的独特资源相结合，以确定驱动人类肌肉祖细胞身份的表观遗传调节因子，并确定那些可能在启动或促进DMD病理学中发挥作用的调节因子。我们的分析将特别集中在调节增强剂（例如，“延伸”或“超级”增强子，SE），其代表经常与表观遗传和转录机制相互作用以控制基因表达的调节“枢纽”。我们将使用ChIP-Seq和转录数据集来定义肌肉祖细胞特异性SE及其靶基因，包括肌肉祖细胞命运的候选“主”转录调节因子。还将在源自健康或DMD患者诱导的多能干细胞（iPSC）的骨骼肌祖细胞和终末肌细胞中定义调节性SE及其靶点，使用等基因iPSC系和基于培养的新策略，用于在肌肉分化的不同阶段产生和鉴定肌原性前体及其后代。总之，这项工作将定义独特地强制骨骼肌祖细胞命运的核心调控和转录景观，识别可能驱动疾病进展的增强子活性中的DMD相关改变，并进一步应用基于iPSC的技术来发现DMD和其他肌肉疾病的新疗法。

DESCRIPTION (provided by applicant): There is great need for new therapies for Duchenne Muscular Dystrophy (DMD), a currently incurable degenerative muscle disorder that affects 1 in every 3500 male births. Promising options include the transplantation of normal or "gene-corrected" muscle progenitors, which could engraft affected muscle fibers to correct the underlying genetic defects, as well as small molecule based therapies that could correct disrupted myogenic processes to support improved muscle function. Unfortunately, the rarity of regenerative muscle precursor cells and lack of relevant models that strongly mimic the progression and severity of human DMD has created many obstacles to understanding disease mechanisms and hindered the development of curative therapies. However, we believe that new innovations in epigenomic analysis and muscle stem cell biology, developed in part in our laboratories, have created new opportunities to discover and advance novel therapies in DMD. This project will exploit the combined expertise of the Wagers and Rinn research groups, which share common laboratory space in the Department of Stem Cell and Regenerative Biology at Harvard University. Studies in the Wagers lab have established novel strategies to isolate highly enriched populations of skeletal muscle progenitors (satellite cells) from human muscle and to derive engraftable myogenic precursor cells from human induced pluripotent stem cells. Studies in the Rinn lab have defined novel computational pipelines for the annotation and analysis of gene regulatory elements that specify cell fate and function. This project will combine these innovative advances with the unique resources provided by the NIH Epigenomics Roadmap Program to identify epigenetic regulators that drive human muscle progenitor cell identity and pinpoint those that may play a role in initiating or promoting DMD pathology. Our analyses will concentrate particularly on regulatory enhancers (e.g., "Stretch" or "Super" Enhancers, SEs), which represent regulatory "hubs" that frequently interact with the epigenetic and transcriptional machinery to control gene expression. We will use ChIP-Seq and transcriptional datasets to define muscle progenitor-specific SEs and their target genes, including candidate "master" transcriptional regulators of the muscle progenitor fate. Regulatory SEs and their targets will also be defined in skeletal muscle progenitors and terminal muscle cells derived from healthy or DMD patient induced pluripotent stem cells (iPSCs), using isogenic iPSC lines and novel culture-based strategies for generating and identifying myogenic precursors and their progeny at distinct stages of muscle differentiation. Together, this work will define the core regulatory and transcriptional landscapes that uniquely enforce the skeletal muscle progenitor cell fate, identify DMD-related alterations in enhancer activity that may drive disease progression, and further the application of iPSC-based technologies for the discovery of novel therapies for DMD and other muscle disorders.