Exploratory genomic investigations of mesial temporal lobe epilepsy

简介（由申请人提供）：中颞叶癫痫是部分性癫痫最常见的形式，也是最耐药的。海马硬化存在于大多数耐药内侧颞叶癫痫患者中，使其成为该疾病重要的病理生物标志物，并可能是破译疾病病理生理的有价值的工具。了解影响基因在有或没有海马病理的中颞叶癫痫患者中表达的细胞特异性过程，是发现相关致病过程的重要一步。因此，本应用程序的目标是优化和应用方法来研究可能有助于海马硬化发展的两个关键基因组过程（体细胞突变和mRNA表达）。为此，我们首先将优化一种新的下一代测序方法，对小群齿状颗粒细胞的转录组进行测序，这种细胞群被认为与海马硬化症的发展有关。其次，我们将从从少量同质细胞中获得的微量基因组DNA开始，评估全基因组下一代测序方案的变异调用准确性，以探索准确检测体细胞变异的可行性。最后，这些方法将被应用于从一组海马硬化的内侧颞叶癫痫患者和一组没有海马硬化的患者中收集的齿状颗粒细胞的细胞转录组和体细胞基因组的特征。如果这些方法能够被优化并应用于一种能够检测与疾病病理相关的细胞特异性基因组变化的方式，我们将有宝贵的工具和必要的初步数据来设计额外的，更全面的内侧颞叶癫痫基因组研究。其次，这项工作也可能为激发其他疾病中细胞特异性基因组的研究提供重要的基础，其中组织标本是可用的。

DESCRIPTION (provided by applicant): Mesial temporal lobe epilepsy is the most common form of partial epilepsy, and also the most drug-resistant. Hippocampal sclerosis is observed in the majority of drug-resistant mesial temporal lobe epilepsy patients, making it an important pathological biomarker in this disease, and possibly a valuable tool for deciphering disease pathophysiology. Understanding cell-specific processes that influence how genes are expressed in mesial temporal lobe epilepsy patients with and without the hippocampal pathology is an important step towards discovering the pathogenic processes involved. Accordingly, the goal of this application is to optimize and apply methodologies to investigate two key genomic processes (somatic mutations and mRNA expression) that may contribute to the development of hippocampal sclerosis. To do this, we first will optimize a novel next-generation sequencing method to sequence the transcriptome of small populations of dentate granule cells, a cellular population believed to be integrally involved in the development of hippocampal sclerosis. Second, we will evaluate variant calling accuracy of whole-genome next-generation sequencing protocols starting from minute amounts of genomic DNA procured from small numbers of homogenous cells to explore the feasibility of accurate detection of somatic variants. Finally, these methods will be applied to characterize the cellular transcriptome and somatic genome of dentate granule cells collected from a set of mesial temporal lobe epilepsy patients with hippocampal sclerosis compared to a set of patients without hippocampal sclerosis. If these methodologies can be optimized and applied in a way to be able to detect cell- specific genomic changes associated with the disease pathology, we will have valuable tools and the necessary preliminary data to design additional, more comprehensive genomic studies in mesial temporal lobe epilepsy. Secondarily, this work may also provide an important foundation to motivate the study of the cell- specific genome in other diseases where tissue specimens are available.