[1]李茜雨,鲍 娟.基于GEO数据库的生物信息学分析筛选结节性硬化症和复杂性热性惊厥共有癫痫相关差异基因[J].现代检验医学杂志,2026,41(03):104-107+141.[doi:10.3969/j.issn.1671-7414.2026.03.019]
 LI Qianyu,BAO Juan.Bioinformatics Analysis Based on GEO Database Identifies Epilepsy-Related Differentially Expressed Genes Common to Tuberous Sclerosis Complex and Complex Febrile Seizures[J].Journal of Modern Laboratory Medicine,2026,41(03):104-107+141.[doi:10.3969/j.issn.1671-7414.2026.03.019]
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基于GEO数据库的生物信息学分析筛选结节性硬化症和复杂性热性惊厥共有癫痫相关差异基因()

《现代检验医学杂志》[ISSN:/CN:]

卷:
第41卷
期数:
2026年03期
页码:
104-107+141
栏目:
论著
出版日期:
2026-05-13

文章信息/Info

Title:
Bioinformatics Analysis Based on GEO Database Identifies Epilepsy-Related Differentially Expressed Genes Common to Tuberous Sclerosis Complex and Complex Febrile Seizures
文章编号:
1671-7414(2026)03-104-05
作者:
李茜雨鲍 娟
湖北医药学院公共卫生与健康学院,湖北十堰442000
Author(s):
LI QianyuBAO Juan
School of Public Health and Health, Hubei University of Medicine,Hubei Shiyan 442000,China
关键词:
生物信息学癫痫结节性硬化症复杂性热性惊厥差异表达基因
分类号:
R741.1;Q786
DOI:
10.3969/j.issn.1671-7414.2026.03.019
文献标志码:
A
摘要:
目的?基于生物信息学探讨结节性硬化症(TSC)与复杂性热性惊厥(CFS)的癫痫相关基因及其作用的分子机制,挖掘出癫痫诊断的生物标志物和发病机制方面的相关线索。方法从基因表达综合(GEO)数据库下载TSC的基因芯片数据GSE16969和CFS的CA3转录组谱GSE28674。借助R语言里的limma包来筛选出各自对应的差异表达基因(DEGs)。运用Venny平台,筛选出两组差异基因中共有的部分。通过R语言中的clusterProfiler软件包,针对这些DEGs展开基因本体(GO)以及京都基因与基因组百科全书(KEGG)的富集分析工作。利用STRING数据库与Cytoscape软件对相关蛋白之间的相互作用情况进行分析,找出共有的关键基因。结果从数据GSE16969和GSE28674中分别筛选出1136个和455个DEGs,其中共有的差异基因41个。GO分析显示DEGs主要涉及囊泡介导的突触转运、突触囊泡周期、运输小泡、离子通道调节器活性等生物学过程。KEGG分析结果表明其在氮素代谢、钙信号通路、皮质醇的合成和分泌路等通路中富集。对共有差异基因进行蛋白相互作用关系图制作,并找出共有的关键基因ATP2B3、SNCB和NEFL。结论通过生物信息学手段筛选出的关键基因,可能参与癫痫的发生和发展,可作为相关候选药物筛选的理论依据。
Abstract:
Objective To explore epilepsy-related genes and their molecular mechanisms in tuberous sclerosis complex (TSC) and complex febrile seizures (CFS) based on bioinformatics, and to identify potential biomarkers for epilepsy diagnosis and clues to its pathogenesis. Methods Gene expression microarray data (GSE16969) for TSC and CA3 transcriptome profiles (GSE28674) for CFS were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) for each dataset were screened using the limma package in R language. Venny platform was used to identify the common DEGs between the two groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of these DEGs were performed using the clusterProfiler package in R. Protein-protein interaction (PPI) networks were analyzed via the STRING database and Cytoscape software to identify shared key genes. Results A total of 1,136 DEGs were screened from GSE16969, and 455 DEGs from GSE28674, with 41 common DEGs identified between the two groups. GO analysis showed that the DEGs were primarily in-volved in biological processes such as vesicle-mediated synaptic transport, synaptic vesicle cycle, transport vesicles, and ion channel regulator activity. KEGG analysis revealed enrichment in pathways including nitrogen metabolism, calcium signaling pathway, and cortisol synthesis and secretion. A PPI network was constructed for the common DEGs, identifying three shared key genes: ATP2B3, SNCB, and NEFL. Conclusions The key genes identified through bioinformatics methods may be involved in the occurrence and development of epilepsy, providing a theoretical basis for screening related candidate drugs.

参考文献/References:

[1] ZHANG S N, LI H M, LIU Q, et al. Eucommiae folium and active compounds protect against mitochondrial dysfunction-calcium overload in epileptic hippocampal neurons through the hypertrophic cardiomyopathy path-way[J]. Neurochemical Research, 2023, 48(9): 2674-2686.
[2] PONG A W, XU K J, KLEIN P. Recent advances in pharmacotherapy for epilepsy[J] . Current Opinion in Neurology, 2023, 36(2): 77-85.
[3] 张孟周,孙英富,侯伟良,等.癫痫发作伴发急性心肌梗死死亡法医学鉴定1例[J].中国法医学杂志,2023, 38(1):95-96. ZHANG M Z, SUN Y F, HOU W L, et al. Forensic iden-tification of death due to acute myocardial infarction com-plicated with epileptic seizure: a case report[J]. Chinese Journal of Forensic Medicine, 2023, 38(1): 95-96.
[4] PFIRMANN P, COMBE C, RIGOTHIER C. Tuberous sclerosis complex: a review] [J]. La Revue de Méde-cine Interne, 2021 , 42(10): 714-721..
[5] 杨智全,王海青,支更花,等.外周血UCH-L1?NSE表达水平对热性惊厥患儿脑损伤及预后的评估价值[J].临床和实验医学杂志,2020,19(2):162-164. YANG Z Q, WANG H Q, ZHI G H, et al. Evaluation value of UCH-L1 and NSE expression levels in periph-eral blood on brain injury and prognosis in children with convulsions[J]. Journal of Clinical and Experi-mental Medicine, 2020, 19(2): 162-164.
[6] FALCO-WALTER J. Epilepsy-definition, classification, pathophysiology, and epidemiology[J]. Seminars in Neurology, 2020, 40(6): 617-623.
[7] CROSS J H, COCK H. A perspective on cannabinoids for treating epilepsy: do they really change the land-scape? [J]. Neuropharmacology, 2020, 170: 107861.
[8] DJULBEGOVIC M B, UVERSKY V N. Expanding the understanding of the heterogeneous nature of melanoma with bioinformatics and disorder-based proteomics[J]. International Journal of Biological Macromolecules, 2020, 150:1281-1293.
[9] ZHU Z A, LI Y Y, XU J, et al. CDKL5 deficiency in adult glutamatergic neurons alters synaptic activity and causes spontaneous seizures via TrkB signaling[J]. Cell Reports, 2023, 42(10):113202.
[10] PERUCCA E, PERUCCA P, WHITE H S, et al. Drug resistance in epilepsy[J]. The Lancet Neurology, 2023 , 22(8):723-734.
[11] LIM?N I D, ANGULO-CRUZ I, S?NCHEZ-ABDON L, et al. Disturbance of the glutamate-glutamine cycle, secondary to hepatic damage, compromises memory func-tion[J]. Frontiers in Neuroscience, 2021, 15: 578922.
[12] MEDEIROS A T, GRATZ S J, DELGADO A, et al. Ca2+channel and active zone protein abundance intersects with input-specific synapse organization to shape functional synaptic diversity[J]. eLife, 2024, 12: RP88412.
[13] BAVELIER S. Synaptic transmission: a comprehensive re-view[J]. Journal of Cognitive Neuroscience, 2024, 7(1): 192.
[14] CHEN C P, LU X. Gonadotropin-releasing hormone receptor inhibits triple-negative breast cancer prolifera-tion and metastasis[J]. Journal of International Medical Research, 2022, 50(3):3000605221082895.
[15] VALLESE F, MASO L, GIAMOGANTE F, et al. The ataxia-linked E1081Q mutation affects the sub-plasma membrane Ca2+-microdomains by tuning PMCA3 ac-tivity[J]. Cell Death & Disease, 2022, 13(10): 855.
[16] ZANNI G, CAL? T, KALSCHEUER V M, et al. Mutation of plasma membrane Ca2+ ATPase isoform 3 in a family with X-linked congenital cerebellar ataxia impairs Ca2+ homeosta-sis[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(36): 14514-14519.
[17] TAUBER P, AICHINGER B, CHRIST C, et al. Cellular pathophysiology of an adrenal adenoma-associated mu-tant of the plasma membrane Ca2+-ATPase ATP2B3[J]. Endocrinology, 2016, 157(6): 2489-2499.
[18] LAVEDAN C, LEROY E, TORRES R, et al. Genomic organization and expression of the human beta-synucle-in gene (SNCB)[J]. Genomics, 1998, 54(1): 173-175.
[19] No Authors Listed . NDEL length and haplotypes in the β-synuclein gene: a key to differentiate dementia with lewy bodies? [J]. Journal of Alzheimer’s Disease , 2021, 81(2):853.
[20] LEREBOURS F, OLSCHWANG S, THUILLE B, et al. Deletion mapping of the tumor suppressor locus involved in colorectal cancer on chromosome band 8p21[J]. Genes, Chromosomes and Cancer, 1999, 25(2): 147-153.
[21] HADDAD L A, SMITH N, BOWSER M, et al. The TSC1 tumor suppressor hamartin interacts with neuro-filament-L and possibly functions as a novel integrator of the neuronal cytoskeleton[J]. The Journal of Biologi-cal Chemistry, 2002, 277(46): 44180-44186.
[22] CHEN R, MASUO K J, YOGO A, et al. SNAIL reg-ulates gastric carcinogenesis through CCN3 and NE-FL[J]. Carcinogenesis, 2021, 42(2): 190-201.
[23] LI X Q, LI L, XIAO C H, et al. NEFL mRNA expres-sion level is a prognostic factor for early-stage breast cancer patients[J]. PLoS One, 2012, 7(2): e31146.

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备注/Memo

备注/Memo:
作者简介:李茜雨(2000-),女,研究生在读,E-mail:2625261285@qq.com。
通讯作者:鲍娟(1983-),女,博士,教授,E-mail:bao_0203@126.com。
更新日期/Last Update: 2026-05-15