正常和帕金森病患者基底神经节的转录差异分析  

Differential expression analysis of the transcriptome for hurnan basal ganglia from normal donors and Parkinson’s disease patients

作　　者：俎高钰 李凤娇 咸伟伟 郭旸洋 赵百成 李文生 尤琳雅 ZU Gao-yu;LI Feng-jiao;XIAN Wei-wei;GUO Yang-yang;ZHAO Bai-cheng;LI Wen-sheng;YOU Lin-ya(Department of Human Anatomy and Histoembryology,School of Basic Medical Sciences,Fudan University,Shanghai200032,China;Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention,Shanghai200032,China)

机构地区：[1]复旦大学基础医学院人体解剖学与组织学胚胎学系,上海200032 [2]上海市医学图像处理与计算机辅助手术重点实验室,上海200032

出　　处：《解剖学报》2024年第4期482-492,共11页Acta Anatomica Sinica

基　　金：人脑组织资源库及地区脑库协作网络平台/脑科学重大项目(2021ZD0201100,2021ZD0201104)。

摘　　要：目的分析人基底神经节各核团的分子标志物以及不同核团间、不同性别、疾病相关的差异表达,探讨差异表达基因的生物学功能。方法针对来源于10具人尸脑45个基底神经节核团样本,按是否有神经疾病分为对照组和帕金森病组,对照组按性别分为女性和男性组,提取各样本RNA进行高通量转录组测序。生物信息学分析鉴定对照组各核团的分子标志物、不同核团间、不同性别以及帕金森病相关的差异表达基因,并对差异表达基因进行基因富集分析和功能注释。结果测序分析发现,top差异表达基因包含尾状核的DRD1、FOXG1、FAM183A;黑质的SLC6A3、EN1、SLC18A2、TH;苍白球的MEPE、FGF10;底丘脑的SLC17A6、PMCH、SHOX2等。其中,壳核top差异表达基因与尾状核存在部分重叠,如DRD1、FOXG1等。对照组不同核团间鉴定出大量差异表达基因,尾状核与苍白球间存在数量最多的差异表达基因(9321),其次是壳核与苍白球间(6341),尾状核与黑质间(6054)。黑质与底丘脑间存在数量最少的差异表达基因(44)。基因富集分析发现,尾状核与苍白球间下调基因显著富集在神经元髓鞘形成、细胞迁移调节等;壳核与苍白球上调基因富集在化学突触传递、膜电位调节、金属离子转运、神经递质转运等,而下调基因富集在神经元髓鞘形成、细胞黏附等;尾状核与黑质上调基因富集在化学突触传递、轴突传导等,而下调基因富集在神经元髓鞘形成等。另外,尾状核、壳核、黑质、苍白球和底丘脑分别鉴定到性别差异上调基因468、548、1402、333和341个,以及下调基因756、988、2532、444和1372个。基因富集分析发现,上调基因大多富集在免疫反应相关通路,下调基因富集在化学突触传递等。最后,尾状核、壳核、黑质、苍白球和底丘脑分别鉴定出帕金森病特异上调基因709、852、276、507和416个,以及下调基因830、2014、1218、836�Objective To analyze the molecular markers of various nuclei in the human basal ganglia and the differentially expressed genes(DEGs)among different nuclei,gender,and Parkinson’s disease(PD),followed by the biological function annotations of the DEGs.Methods Forty-five specimens of basal ganglia from 10 human postmortem brains were divided into control and PD groups,and the control group was further categorized into female and male groups.RNA from each sample was extracted for high-throughput transcriptome sequencing.Bioinformatic analysis was conducted to identify molecular markers of each nuclei in the control group,nuclei-specific,gender-specific,and PD-specific DEGs,followed by gene enrichment analysis and functional annotation.Results Sequencing analysis revealed top DEGs such as DRD1,FOXG1,and FAM183A in the caudate;SLC6A3,EN1,SLC18A2,and TH in the substantia nigra;MEPE and FGF10 in the globus pallidus;and SLC17A6,PMCH,and SHOX2 in the subthalamic nucleus.In them,putamen showed some overlapping DEGs with caudate,such as DRD1 and FOXG1.A significant number of DEGs were identified among different nuclei in the control group,with the highest number between caudate and globus pallidus(9321),followed by putamen and globus pallidus(6341),caudate and substantia nigra(6054),and substantia nigra and subthalamic nucleus(44).Gene enrichment analysis showed that downregulated DEGs between caudate and globus pallidus were significantly enriched in processes like myelination of neurons and cell migration.Upregulated DEGs between putamen and globus pallidus were enriched processes like chemical synaptic transmission and regulation of membrane potential,while downregulated DEGs were enriched in myelination and cell adhesion.Upregulated DEGs between caudate and substantia nigra were enriched in processes like chemical synaptic transmission and axonal conduction,while downregulated DEGs were enriched in myelination of neurons.Totally 468,548,1402,333,and 341 gender-specific upregulated DEGs and 756,988,2532,444,and 1372 dow

关 键 词：基底神经节 帕金森病 高通量转录组测序 差异表达分析 人 

分 类 号：R322[医药卫生—人体解剖和组织胚胎学]