Exploratory genomic investigations of mesial temporal lobe epilepsy

描述（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。在大多数耐药内侧颞叶癫痫患者中观察到海马硬化，使其成为这种疾病的重要病理生物标志物，并可能成为解读疾病病理生理学的有价值的工具。了解细胞特异性的过程，影响基因表达的内侧颞叶癫痫患者与海马病理和没有发现的致病过程是一个重要的一步。因此，本申请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）。要做到这一点，我们首先将优化一种新的下一代测序方法，对小群体齿状颗粒细胞的转录组进行测序，这种细胞群体被认为与海马硬化的发展密切相关。第二，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识别准确性，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表征的齿状颗粒细胞的细胞转录组和体细胞基因组收集从一组内侧颞叶癫痫患者海马硬化相比，一组患者没有海马硬化。如果这些方法可以优化和应用的方式，能够检测与疾病病理相关的细胞特异性基因组变化，我们将有宝贵的工具和必要的初步数据，设计额外的，更全面的基因组研究内侧颞叶癫痫。其次，这项工作也可能提供一个重要的基础，以激励研究的细胞特异性基因组在其他疾病的组织标本是可用的。

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.