中山大学附属第一医院麻醉科,广东 广州 510080
于瑜,硕士,研究方向:脑缺血再灌注损伤的保护,E-mail:sysuyuyu@163.com
纸质出版日期:2021-01-20,
收稿日期:2020-12-03,
扫 描 看 全 文
于瑜,王钟兴.基于生物信息学途径筛选缺血性脑卒中关键基因及药物预测[J].中山大学学报(医学科学版),2021,42(01):42-50.
YU Yu,WANG Zhong-xing.Screening of Key Genes and Prediction of Drugs for Ischemic Stroke Based on Bioinformatics Approach[J].Journal of Sun Yat-sen University(Medical Sciences),2021,42(01):42-50.
目的
2
筛选缺血性脑卒中的关键基因及重要信号通路,预测可能对脑卒中有用的药物。
方法
2
从GEO数据库下载GSE98319基因芯片数据,该数据包含了假手术组、大脑中动脉梗塞组(MCAO)小鼠的基因芯片检测结果。用R语言的Limma包对数据进行差异表达分析,
P
<
0.05且|log
2
FC|
>
0.6的基因为差异表达基因。借助STRING网站构建差异表达基因的蛋白质相互作用网络(PPIN)后由Cytoscape软件进行核心子网络筛选及可视化输出。筛选出核心基因后用实时荧光定量PCR(qRT- PCR)验证核心基因在脑缺血小鼠大脑皮层的表达情况。基因集富集分析(GSEA)算法用于京都基因与基因组百科全书(KEGG)和基因本体(GO)富集分析,以FDR
<
0.05作为富集标准。最后用Connectivity Map数据库预测脑卒中的潜在作用药物。
结果
2
共筛出521个差异mRNA,其中421个上调、100个下调,其中2个关键基因
Drd4
(
P
=0.000 019)和
Hcar2
(
P
=0.000 094)经qRT-PCR实验证实在脑缺血后表达均升高。4种小分子化合物艾司洛尔(Esmolol)、甲巯咪唑(Methimazole)、吐根酚碱(Cephaeline)、水仙环素(Narciclasine)可能对缺血性卒中有治疗作用。
结论
2
Drd4
和
Hcar2
可能与缺血性卒中的发生发展密切相关。预测出的4种药物可为后续药物研究提供参考。
Objective
2
To screen out key genes and important signal pathways of ischemic stroke to predict potential drugs that might be useful for stroke.
Methods
2
We obtained GSE98319 Microarray data from GEO database which contained sequencing results from control (Sham group) and experimental (middle cerebral artery occlusion, MCAO) mice. Limma package of R language was used to analyze Microarray data. Differentially expressed genes were selected with
P
<
0.05 and |log
2
FC|
>
0.6 as the criteria. Protein-Protein Interaction Network (PPIN) of differentially expressed genes was constructed by STRING online website and visualized by Cytoscape software. Quantitative real-time polymerase chain reaction(qRT-PCR)was performed to testify hub genes expression level. Gene Set enrichment analysis (GSEA) algorithm was used in functional enrichment analysis of Kyoto Encyclopedia of Genes and Genomics (KEGG) and Gene Ontology (GO) with FDR
<
0.05 as the enrichment standard. Finally, potential agents for stroke were predicted by Connectivity Map.
Results
2
A total of 521 differentially expressed genes were identified, 421 up-regulated and 100 down-regulated. Two hub genes:
Drd4
(
P
=0.000 019)and
Hcar2
(
P
=0.000 094)expression level upregulated in stroke mice cortex validated by qRT- PCR. Finally, four small molecule compounds:Esmolol, Methimazole, Cephaeline and Narciclasine were predicted to have potential therapeutic effects on ischemic stroke.
Conclusions
2
Drd4
and
Hcar2
may be closely related to the occurrence and development of ischemic stroke. Four potential therapeutic drugs are predicted, providing reference for the subsequent research on drug therapy.
缺血性脑卒中基因集富集分析生物信息学药物预测
ischemic strokeGSEAbioinformaticsdrugs prediction
Campbell BCV, Silva DAD, Macleod MR, et al. Ischaemic stroke[J]. Nat Rev Dis Primers, 2019, 5(1): 1-22.
Simats A, Ramiro L, Berrocoso TG, et al. A mouse brain-based multi-omics integrative approach reveals potential blood biomarkers for ischemic stroke[J]. Mol Cell Proteomics, 2020, 19(12): 1921-1935.
Gu L, Wu YL, Hu SY, et al. Analysis of association between MAP2K4 gene polymorphism rs3826392 and IL-1b serum level in Southern Chinese Han ischemic stroke patients[J]. J Stroke Cerebrovasc Dis, 2016, 25(5): 1096-1101.
Chin CH, Chen SH, Wu HH, et al. cytoHubba: identifying hub objects and sub-networks from complex interactome[J]. BMC Syst Biol, 2014, Suppl 4(Suppl 4): S11.
Bader GD, Hogue CWV. An automated method for finding molecular complexes in large protein interaction networks[J]. BMC Bioinformatics, 2003, 4: 2.
Yu GC, Wang LG, Han YY, et al. clusterProfiler: an R package for comparing biological themes among gene clusters[J]. OMICS, 2012, 6(5): 284-7.
Subramanian A, Narayan R, Corsello SM, et al. A next generation connectivity map: L1000 platform and the first 1,000,000 profiles[J]. Cell, 2017, 171(6): 1437-1452.
Chen HS, Guan BH, Wang B, et al. Glycyrrhizin prevents hemorrhagic transformation and improves neurological outcome in ischemic stroke with delayed thrombolysis through targeting peroxynitrite-mediated HMGB1 signaling[J]. Transl Stroke Res, 2020, 11(5): 967-982.
Li X, Huang LL, Liu G, et al. Ginkgo diterpene lactones inhibit cerebral ischemia/reperfusion induced inflammatory response in astrocytes via TLR4/NF-κB pathway in rats[J]. J Ethnopharmacol, 2020, 249: 112365.
Tajalli-Nezhad S, Karimian M, Beyer C, et al. The regulatory role of Toll-like receptors after ischemic stroke: neurosteroids as TLR modulators with the focus on TLR2/4[J]. Cell Mol Life Sci, 2019, 76(3): 523-537.
Li PY, Wang L, Zhou YX, et al. C-C chemokine receptor type 5 (CCR5)-mediated docking of transferred tregs protects against early blood-brain barrier disruption after stroke[J]. J Am Heart Assoc, 2017, 6(8): e006387.
Georgakis MK, Gill D, Rannikmäe K, et al. Genetically determined levels of circulating cytokines and risk of Stroke[J]. Circulation, 2019, 139(2): 256-268.
Urra X, Villamor N, Amaro S, et al. Monocyte subtypes predict clinical course and prognosis in human stroke[J]. J Cereb Blood Flow Metab, 2009, 29(5): 994-1002.
Nakka VP, Lang BT, Lenschow DJ, et al. Increased cerebral protein ISGylation after focal ischemia is neuroprotective[J]. J Cereb Blood Flow Metab, 2011, 31(12): 2375-2384.
Clausen BH, Lundberg L, Yli-Karjanmaa M, et al. Fumarate decreases edema volume and improves functional outcome after experimental stroke[J]. Exp Neurol, 2017, 295: 144-154.
Hwang CK, Chaurasia SS, Jackson CR, et al. Circadian rhythm of contrast sensitivity is regulated by a dopamine-neuronal PAS-domain protein 2-adenylyl cyclase 1 signaling pathway in retinal ganglion cells[J]. J Neurosci, 2013, 33(38): 14989-14997.
Goyagi T, Nishikawa T, Tobe Y. Neuroprotective effects and suppression of ischemia-induced glutamate elevation by β1-adrenoreceptor antagonists administered before transient focal ischemia in rats[J]. J Neurosurg Anesthesiol, 2011, 23(2): 131-137.
Lee CH, Yoo KY, Hwang IK, et al. Hypothyroid state does not protect but delays neuronal death in the hippocampal CA1 region following transient cerebral ischemia: focus on oxidative stress and gliosis[J]. J Neurosci Res, 2010, 88(12): 2661-2668.
0
浏览量
0
下载量
2
CSCD
关联资源
相关文章
相关作者
相关机构