伴或不伴海马硬化的颞叶内侧癫痫患者齿状颗粒细胞基因的差异表达分析_Journal of Epilepsy

Authors：

Nicole G.Griffin , YuWang , Christine M.Hulette , 张颖颖　译 , 慕洁　审

Corresponding author：

Keywords：

颞叶癫痫; 海马; 颞叶内侧硬化; RNA 测序

DOI：

10.7507/2096-0247.20180017

Video：

Export PDF Favorites Scan Get Citation

Abstract Full text Figures/Tables Video References Cited by

海马硬化（Hippocampal sclerosis, HS）是难治性颞叶内侧型癫痫中最常见的神经病理学改变。在研究中，分析了伴或不伴 HS 的颞叶内侧癫痫患者齿状颗粒细胞的基因表达谱，揭示下一代测序方法可以从小同源细胞群收集的 RNA 产生可解释的基因组数据以及与 HS 相关的转录变化。手术切除伴或不伴有 HS 的颞叶内侧癫痫患者的海马，并通过激光捕获显微切割技术获得手术切除海马的齿状颗粒细胞，从而提取 RNA，制备并扩增互补 DNA（cDNA）。对测序文库进行测序，将所得测序读数与参照基因组进行比对。差异表达分析用于确定伴或不伴 HS 患者之间的表达差异。结果发现，超过 90% 的 RNA-Seq 读数与参考对齐。获得的复样转录谱之间存在高度一致性。主成分分析显示，HS 的存在与否是数据差异的主要决定因素。HS 样本中上调的基因中，参与氧化磷酸化的基因有显著的富集。通过分析来自伴或不伴 HS 的颞叶内侧癫痫患者的手术切除的海马标本的齿状颗粒细胞的基因表达谱，已经证明了下一代测序方法用于从小均匀细胞群产生生物学相关结果的实用性，并提供了与该病理学变化相关的转录变化的一些见解。

Citation： Nicole G.Griffin, YuWang, Christine M.Hulette, 张颖颖　译, 慕洁　审. 伴或不伴海马硬化的颞叶内侧癫痫患者齿状颗粒细胞基因的差异表达分析. Journal of Epilepsy, 2018, 4(1): 72-80. doi: 10.7507/2096-0247.20180017 Copy

1.	Blumcke I, Kistner I, Clusmann H, et al. Towards a clinico-pathological classification of granule 2 cell dispersion in human mesial temporal lobe epilepsies. Acta Neuropathol, 2009, 117(5): 535-544.
2.	Bernasconi A. Magnetic resonance imaging in intractable epilepsy: focus on structural image analysis. Adv Neurol, 2006, 97: 273-278.
3.	Blumcke I, Thom M, Aronica E, et al. International consensus classification of hippocampal sclerosis in temporal lobe epilepsy: a Task Force report from the ILAE Commission on Diagnostic Methods. Epilepsia, 2013, 54(7): 1315-1329.
4.	Kaalund SS, Veno MT, Bak M, et al. Aberrant expression of miR-218 and miR-204 in human mesial temporal lobe epilepsy and hippocampal sclerosis-convergence on axonal guidance. Epilepsia, 2014, 55(12): 2017-2027.
5.	Miller-Delaney SF, Bryan K, Das S, et al. Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy. Brain, 2015, 138(Pt 3): 616-631.
6.	Engel T, Henshall DC. Apoptosis, Bcl-2 family proteins and caspases: the ABCs of seizure-damage and epileptogenesis?. Int J Physiol Pathophysiol Pharmacol, 2009, 1(2): 97-115.
7.	Xu S, Pang Q, Liu Y, et al. Neuronal apoptosis in the resected sclerotic hippocampus in patients with mesial temporal lobe epilepsy. J Clin Neurosci, 2007, 14(9): 835-840.
8.	Dericioglu N, Soylemezoglu F, Gursoy-Ozdemir Y, et al. Cell death and survival mechanisms are concomitantly active in the hippocampus of patients with mesial temporal sclerosis. Neuroscience, 2013, 237: 56-65.
9.	Johnson MR, Behmoaras J, Bottolo L, et al. Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus. Nat Commun, 2015, 6: 6031.
10.	Houser CR. Granule cell dispersion in the dentate gyrus of humans with temporal lobe epilepsy. Brain Res, 1990, 535(2): 195-204.
11.	Scharfman HE, Sollas AL, Berger RE, et al. Electrophysiological evidence of monosynaptic excitatory transmission between granule cells after seizure-induced mossy fiber sprouting. J Neurophysiol, 2003, 90(4): 2536-2547.
12.	Zucchini S, Marucci G, Paradiso B, et al. Identification of miRNAs differentially expressed in human epilepsy with or without granule cell pathology. PLoS ONE, 2014, 9(8): e105521.
13.	Kim D, Pertea G, Trapnell C, et al. Top Hat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol, 2013, 14(4): R36.
14.	Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 2010, 28(5): 511-515.
15.	Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol, 2010, 11(10): R106.
16.	Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 2014, 15(12): 550.
17.	Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by " surrogate variable analysis”. PLoS Genet, 2005 3(9): 1724-1735.
18.	Robinson MD, McCarthy DJ, Smyth GK. EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010, 26(1): 139-140.
19.	Chen YM, Robinson MD, Smyth GK. EdgeR: differential expression analysis of digital gene expression data. Bioconductor: User Guide, 2015.
20.	Rapaport F, Khanin R, Liang Y, et al. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol, 2013, 14(9): R95.
21.	Thomas PD, Campbell MJ, Kejariwal A, et al. Panther: a library of protein families and subfamilies indexed by function. Genome Res, 2003, 13(9): 2129-2141.
22.	Laan MP, KS. Hybrid clustering of gene expression data with visualization and the bootstrap. J Stat Plan Inference, 2003, 117: 275-303.
23.	Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta DeltaC(T)) method. Methods, 2001, 25(4): 402-408.
24.	Xu S, Pang Q, Liu Y, et al. Neuronal apoptosis in the resected sclerotic hippocampus in patients with mesial temporal lobe epilepsy. J Clin Neurosci, 2007, 14(9): 835-840.
25.	Crevecoeur J, Kaminski RM, Rogister B, et al. Expression pattern of synaptic vesicle protein 2 (SV2) isoforms in patients with temporal lobe epilepsy and hippocampal sclerosis. Neuropathol Appl Neurobiol, 2014, 40(2): 191-204.
26.	Abe R, Yamamoto K, Sakamoto H. Target specificity of neuronal RNA-binding protein, Mel-N1: direct binding to the 30 untranslated region of its own mRNA. Nucleic Acids Res, 1996, 24(11): 2011-2016.
27.	Xiao Z, Peng J, Yang L, et al. Interleukin-1beta plays a role in the pathogenesis of mesial temporal lobe epilepsy through the PI3K/Akt/mTOR signaling pathway in hippocampal neurons. J Neuroimmunol, 2015, 282: 110-117.
28.	Elliott RC, Miles MF, Lowenstein DH. Overlapping microarray profiles of dentate gyrus gene expression during development- and epilepsy-associated neurogenesis and axon outgrowth. J Neurosci, 2003, 23(6): 2218-2227.
29.	Ristic AJ, Savic D, Sokic D, et al. Hippocampal antioxidative system in mesial temporal lobe epilepsy. Epilepsia, 2015, 56(5): 789-799.
30.	Winden KD, Bragin A, Engel J, et al. Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy.Neurobiol Dis, 2015, 78(6): 35-44.
31.	Feenstra B, Pasternak B, Geller F, et al. Common variants associated with general and MMR vaccine-related febrile seizures. Nat Genet, 2014, 46(12): 1274-1282.
32.	Cavazos JE, Das I, Sutula TP. Neuronal loss induced in limbic pathways by kindling: evidence for induction of hippocampal sclerosis by repeated brief seizures. J Neurosci, 1994, 14(5): 3106-3121.
33.	Kotloski R, Lynch M, Lauersdorf S, et al. Repeated brief seizures induce progressive hippocampal neuron loss and memory deficits.Prog Brain Res, 2002, 135: 95-110.

1. Blumcke I, Kistner I, Clusmann H, et al. Towards a clinico-pathological classification of granule 2 cell dispersion in human mesial temporal lobe epilepsies. Acta Neuropathol, 2009, 117(5): 535-544.
2. Bernasconi A. Magnetic resonance imaging in intractable epilepsy: focus on structural image analysis. Adv Neurol, 2006, 97: 273-278.
3. Blumcke I, Thom M, Aronica E, et al. International consensus classification of hippocampal sclerosis in temporal lobe epilepsy: a Task Force report from the ILAE Commission on Diagnostic Methods. Epilepsia, 2013, 54(7): 1315-1329.
4. Kaalund SS, Veno MT, Bak M, et al. Aberrant expression of miR-218 and miR-204 in human mesial temporal lobe epilepsy and hippocampal sclerosis-convergence on axonal guidance. Epilepsia, 2014, 55(12): 2017-2027.
5. Miller-Delaney SF, Bryan K, Das S, et al. Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy. Brain, 2015, 138(Pt 3): 616-631.
6. Engel T, Henshall DC. Apoptosis, Bcl-2 family proteins and caspases: the ABCs of seizure-damage and epileptogenesis?. Int J Physiol Pathophysiol Pharmacol, 2009, 1(2): 97-115.
7. Xu S, Pang Q, Liu Y, et al. Neuronal apoptosis in the resected sclerotic hippocampus in patients with mesial temporal lobe epilepsy. J Clin Neurosci, 2007, 14(9): 835-840.
8. Dericioglu N, Soylemezoglu F, Gursoy-Ozdemir Y, et al. Cell death and survival mechanisms are concomitantly active in the hippocampus of patients with mesial temporal sclerosis. Neuroscience, 2013, 237: 56-65.
9. Johnson MR, Behmoaras J, Bottolo L, et al. Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus. Nat Commun, 2015, 6: 6031.
10. Houser CR. Granule cell dispersion in the dentate gyrus of humans with temporal lobe epilepsy. Brain Res, 1990, 535(2): 195-204.
11. Scharfman HE, Sollas AL, Berger RE, et al. Electrophysiological evidence of monosynaptic excitatory transmission between granule cells after seizure-induced mossy fiber sprouting. J Neurophysiol, 2003, 90(4): 2536-2547.
12. Zucchini S, Marucci G, Paradiso B, et al. Identification of miRNAs differentially expressed in human epilepsy with or without granule cell pathology. PLoS ONE, 2014, 9(8): e105521.
13. Kim D, Pertea G, Trapnell C, et al. Top Hat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol, 2013, 14(4): R36.
14. Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 2010, 28(5): 511-515.
15. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol, 2010, 11(10): R106.
16. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 2014, 15(12): 550.
17. Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by " surrogate variable analysis”. PLoS Genet, 2005 3(9): 1724-1735.
18. Robinson MD, McCarthy DJ, Smyth GK. EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010, 26(1): 139-140.
19. Chen YM, Robinson MD, Smyth GK. EdgeR: differential expression analysis of digital gene expression data. Bioconductor: User Guide, 2015.
20. Rapaport F, Khanin R, Liang Y, et al. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol, 2013, 14(9): R95.
21. Thomas PD, Campbell MJ, Kejariwal A, et al. Panther: a library of protein families and subfamilies indexed by function. Genome Res, 2003, 13(9): 2129-2141.
22. Laan MP, KS. Hybrid clustering of gene expression data with visualization and the bootstrap. J Stat Plan Inference, 2003, 117: 275-303.
23. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta DeltaC(T)) method. Methods, 2001, 25(4): 402-408.
24. Xu S, Pang Q, Liu Y, et al. Neuronal apoptosis in the resected sclerotic hippocampus in patients with mesial temporal lobe epilepsy. J Clin Neurosci, 2007, 14(9): 835-840.
25. Crevecoeur J, Kaminski RM, Rogister B, et al. Expression pattern of synaptic vesicle protein 2 (SV2) isoforms in patients with temporal lobe epilepsy and hippocampal sclerosis. Neuropathol Appl Neurobiol, 2014, 40(2): 191-204.
26. Abe R, Yamamoto K, Sakamoto H. Target specificity of neuronal RNA-binding protein, Mel-N1: direct binding to the 30 untranslated region of its own mRNA. Nucleic Acids Res, 1996, 24(11): 2011-2016.
27. Xiao Z, Peng J, Yang L, et al. Interleukin-1beta plays a role in the pathogenesis of mesial temporal lobe epilepsy through the PI3K/Akt/mTOR signaling pathway in hippocampal neurons. J Neuroimmunol, 2015, 282: 110-117.
28. Elliott RC, Miles MF, Lowenstein DH. Overlapping microarray profiles of dentate gyrus gene expression during development- and epilepsy-associated neurogenesis and axon outgrowth. J Neurosci, 2003, 23(6): 2218-2227.
29. Ristic AJ, Savic D, Sokic D, et al. Hippocampal antioxidative system in mesial temporal lobe epilepsy. Epilepsia, 2015, 56(5): 789-799.
30. Winden KD, Bragin A, Engel J, et al. Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy.Neurobiol Dis, 2015, 78(6): 35-44.
31. Feenstra B, Pasternak B, Geller F, et al. Common variants associated with general and MMR vaccine-related febrile seizures. Nat Genet, 2014, 46(12): 1274-1282.
32. Cavazos JE, Das I, Sutula TP. Neuronal loss induced in limbic pathways by kindling: evidence for induction of hippocampal sclerosis by repeated brief seizures. J Neurosci, 1994, 14(5): 3106-3121.
33. Kotloski R, Lynch M, Lauersdorf S, et al. Repeated brief seizures induce progressive hippocampal neuron loss and memory deficits.Prog Brain Res, 2002, 135: 95-110.

Previous Article
癫痫、痫性发作、体育锻炼和运动：ILAE 运动与癫痫工作组的报告
Next Article
颞叶癫痫术后并发短暂性精神异常一例

Journal of Epilepsy

伴或不伴海马硬化的颞叶内侧癫痫患者齿状颗粒细胞基因的差异表达分析

Abstract Full text Figures/Tables Video References Cited by

Previous Article

Next Article

Format

Content