Exploratory genomic investigations of mesial temporal lobe epilepsy

说明(申请人提供)：内侧颞叶癫痫是部分性癫痫最常见的形式，也是最耐药的。在大多数耐药的内侧颞叶癫痫患者中均可观察到海马硬化，使其成为该病重要的病理生物标志物，并可能成为破译疾病病理生理学的有价值的工具。了解影响内侧颞叶癫痫患者基因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，这项应用的目标是优化和应用方法学来研究可能有助于海马硬化症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，对齿状颗粒细胞的小群体的转录组进行测序，齿状颗粒细胞被认为与海马硬化症的发展密切相关。其次，我们将从从少量同源细胞获取的微量基因组DNA入手，评估全基因组下一代测序协议的变体调用准确性，以探索准确检测体细胞变体的可行性。最后，这些方法将被应用于从一组患有海马硬化症的内侧颞叶癫痫患者和一组非海马硬化症患者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和应用，能够检测到与疾病病理相关的细胞特异性基因组变化，我们将拥有宝贵的工具和必要的初步数据来设计更多、更全面的内侧颞叶癫痫基因组研究。其次，这项工作也可能为在其他可获得组织标本的疾病中推动细胞特异性基因组的研究提供重要的基础。 公共卫生相关性：这项工作旨在优化和应用下一代测序技术，以调查与内侧颞叶癫痫有关的基因组过程。在这些概念验证实验的基础上，我们相信这些努力最终将导致更好地理解海马硬化症和这种癫痫表型之间的关系，增强对内侧颞叶癫痫潜在病理生理学的知识，最重要的是在这一人群中产生更好的治疗选择。

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. PUBLIC HEALTH RELEVANCE: This work seeks to optimize and apply next-generation sequencing technologies to investigate genomic processes involved in mesial temporal lobe epilepsy. Building from these proof-of-concept experiments, we believe that ultimately these efforts will lead to an improved understanding of the relationship between hippocampal sclerosis and this epilepsy phenotype, enhanced knowledge of the underlying pathophysiology of mesial temporal lobe epilepsy, and most importantly result in better treatment options in this population.