Epigenomic mapping of myogenic regulation in human muscle development

先天性肌病和先天性肌营养不良是一组遗传性肌肉疾病，临床上以肌肉张力低下和无力为特征，临床病程为静止或缓慢进展。在过去的十年中，全外显子组测序(WES)的广泛使用导致了许多不同先天性肌营养不良症的潜在遗传原因的确定，但这些病例中的一大部分未能进行所有分子诊断的尝试。我们专注于先天性肌病和肌营养不良症患者的Charité队列，在这些患者中，Wes在蛋白质编码序列中没有发现遗传原因，并着手在基因组的非编码或调节序列中寻找致病变异。这些区域含有增强子和转录因子结合位点(TFBs)，控制着肌肉特异的基因表达程序，其功能障碍是发病的原因。在我们的合作研究计划中，我们对肌肉细胞分化的连续发育阶段进行了一系列全面的表观基因组和转录批量和单细胞分析。同时，我们开发了多通道数据集成的计算模型。在第一个资助期工作的基础上，我们现在将开发计算方法来分类不同的增强子亚群，并识别成肌调节区域内的相关DNA序列信息。我们将使用这些模型来确定预测会改变先天性肌病患者转录程序的变异。我们将利用CRISPRi/a筛选来验证数十个候选增强子以及序列变异对靶基因表达的影响，最终确认非编码变异对分化的影响。通过这种方式，我们的项目将能够将基础分子生物学转化为罕见肌肉疾病患者的诊断。

Congenital myopathies and congenital muscle dystrophies are a group of genetic muscle disorders clinically characterized by muscle hypotonia and weakness and a static or slowly progressive clinical course. Widespread use of Whole Exome Sequencing (WES) over the course of the last decade has led to the identification of the underlying genetic cause of many different congenital myopathies muscular dystrophies, but a large subset of these cases has eluded all attempts to make a molecular diagnosis. We focused on a Charité cohort of patients with congenital myopathy and muscular dystrophy in whom WES had found no genetic cause in protein coding sequences and set out to find disease-causing variants in the non-coding or regulatory sequences of the genome. These regions, which harbor enhancers and transcription factor binding sites (TFBSs), control muscle-specific gene expression programs whose dysfunction is the cause of pathogenesis. In our collaborative research program, we have embarked on a series of comprehensive epigenomic and transcriptional bulk and single-cell analyses of successive developmental stages of muscle cell differentiation. At the same time, we have developed computational models for multimodal data integration. Building on this work from the first funding period, we will now develop computational approaches to classify distinct enhancer subgroups and to identify relevant DNA sequence information within myogenic regulatory regions. We will use these models to identify variants predicted to alter the transcriptional programs in patients with congenital myopathy. We will validate the impact of dozens of enhancer candidates, as well as sequence variations on target gene expression using CRISPRi/a screens, and finally confirm the impact of non-coding variation on differentiation. In this way, our project will enable the translation of the basic molecular biology into diagnoses for patients with rare muscle diseases.