Differential gene expression in dentate granule cells in mesial temporal lobe epilepsy with and without hippocampal sclerosis.
Differential gene expression in dentate granule cells in mesial temporal lobe epilepsy with and without hippocampal sclerosis.
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DOI：
10.1111/epi.13305
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发表时间：
2016-03
期刊：
影响因子：
5.6
通讯作者：
Heinzen EL
中科院分区：
文献类型：
--
作者：
Griffin NG;Wang Y;Hulette CM;Halvorsen M;Cronin KD;Walley NM;Haglund MM;Radtke RA;Skene JH;Sinha SR;Heinzen EL
海马区硬化症是内科难治性内侧颞叶癫痫最常见的神经病理表现。在这项研究中，我们分析了患有和不患有海马硬化的内侧颞叶癫痫患者齿状颗粒细胞的基因表达谱，以表明下一代测序方法可以从从小的同质细胞群收集的RNA中产生可解释的基因组数据，并阐明与海马硬化相关的转录变化。从手术切除的内侧颞叶癫痫伴和不伴海马区硬化患者的海马齿状回颗粒细胞中提取RNA，制备并扩增互补DNA(CDNAs)。对测序文库进行测序，并将得到的测序读数与参考基因组进行比对。差异表达分析被用来确定有和没有海马硬化症患者之间的表达差异。超过90%的RNA-Seq读数与参考序列对齐。重复样本的转录图谱之间有很高的一致性。主成分分析显示，海马区硬化的存在或不存在是数据内差异的主要决定因素。在海马区硬化症样本中上调的基因中，参与氧化磷酸化的基因显著丰富。通过分析手术切除的患有和不伴有海马硬化的内侧颞叶癫痫患者的海马齿状颗粒细胞的基因表达谱，我们已经证明了下一代测序方法的有效性，可以从少量同质细胞中产生生物学相关的结果，并对与这种病理相关的转录变化提供了洞察力。
Hippocampal sclerosis is the most common neuropathological finding in medically intractable cases of mesial temporal lobe epilepsy. In this study, we analyzed the gene expression profiles of dentate granule cells of mesial temporal lobe epilepsy patients with and without hippocampal sclerosis to show that next-generation sequencing methods can produce interpretable genomic data from RNA collected from small homogenous cell populations and to shed light on the transcriptional changes associated with hippocampal sclerosis. RNA was extracted, and complementary DNA (cDNA) was prepared and amplified from dentate granule cells that had been harvested by laser capture microdissection from surgically resected hippocampi from mesial temporal lobe epilepsy patients with and without hippocampal sclerosis. Sequencing libraries were sequenced, and the resulting sequencing reads were aligned to the reference genome. Differential expression analysis was used to ascertain expression differences between patients with and without hippocampal sclerosis. Greater than 90% of the RNA-Seq reads aligned to the reference. There was high concordance between transcriptional profiles obtained for duplicate samples. Principal component analysis revealed that the presence or absence of hippocampal sclerosis was the main determinant of the variance within the data. Among the genes upregulated in the hippocampal sclerosis samples, there was significant enrichment for genes involved in oxidative phosphorylation. By analyzing the gene expression profiles of dentate granule cells from surgically resected hippocampal specimens from mesial temporal lobe epilepsy patients with and without hippocampal sclerosis, we have demonstrated the utility of next-generation sequencing methods for producing biologically relevant results from small populations of homogeneous cells, and have provided insight on the transcriptional changes associated with this pathology.