基于生物信息学方法鉴定灯盏花治疗脑缺血再灌注的 mA 甲基化相关基因。

Identification of mA methylation-related genes in cerebral ischaemia‒reperfusion of Breviscapus therapy based on bioinformatics methods.

机构信息

Department of Interventional Radiology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China.

Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China.

出版信息

BMC Med Genomics. 2023 Sep 5;16(1):210. doi: 10.1186/s12920-023-01651-3.

DOI:10.1186/s12920-023-01651-3

PMID:37670341

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10478429/

Abstract

BACKGROUND

Cerebral ischaemia‒reperfusion (I/R) frequently causes late-onset neuronal damage. Breviscapine promotes autophagy in microvascular endothelial cells in I/R and can inhibit oxidative damage and apoptosis. However, the mediation mechanism of breviscapine on neuronal cell death is unclear.

METHODS

First, transcriptome sequencing was performed on three groups of mice: the neuronal normal group (Control group), the oxygen-glucose deprivation/ reoxygenation group (OGD/R group) and the breviscapine administration group (Therapy group). Differentially expressed genes (DEGs) between the OGD/R and control groups and between the Therapy and OGD/R groups were obtained by the limma package. N-methyladenosine (mA) methylation-related DEGs were selected by Pearson correlation analysis. Then, prediction and confirmation of drug targets were performed by Swiss Target Prediction and UniProt Knowledgebase (UniProtKB) database, and key genes were obtained by Pearson correlation analysis between mA-related DEGs and drug target genes. Next, gene set enrichment analysis (GSEA) and Ingenuity pathway analysis (IPA) were used to obtain the pathways of key genes. Finally, a circRNA-miRNA‒mRNA network was constructed based on the mRNAs, circRNAs and miRNAs.

RESULTS

A total of 2250 DEGs between the OGD/R and control groups and 757 DEGs between the Therapy and OGD/R groups were selected by differential analysis. A total of 7 mA-related DEGs, including Arl4d, Gm10653, Gm1113, Kcns3, Olfml2a, Stk26 and Tfcp2l1, were obtained by Pearson correlation analysis. Four key genes (Tfcp2l1, Kcns3, Olfml2a and Arl4d) were acquired, and GSEA showed that these key genes significantly participated in DNA repair, e2f targets and the g2m checkpoint. IPA revealed that Tfcp2l1 played a significant role in human embryonic stem cell pluripotency. The circRNA-miRNA‒mRNA network showed that mmu_circ_0001258 regulated Tfcp2l1 by mmu-miR-301b-3p.

CONCLUSIONS

In conclusion, four key genes, Tfcp2l1, Kcns3, Olfml2a and Arl4d, significantly associated with the treatment of OGD/R by breviscapine were identified, which provides a theoretical basis for clinical trials.

摘要

背景

脑缺血再灌注（I/R）常导致迟发性神经元损伤。灯盏花素可促进 I/R 中微血管内皮细胞自噬，并能抑制氧化损伤和细胞凋亡。然而，灯盏花素对神经元细胞死亡的介导机制尚不清楚。

方法

首先，对三组小鼠进行转录组测序：神经元正常组（对照组）、氧葡萄糖剥夺/复氧组（OGD/R 组）和灯盏花素给药组（治疗组）。通过 limma 包获得 OGD/R 组与对照组、治疗组与 OGD/R 组之间的差异表达基因（DEGs）。通过 Pearson 相关分析筛选 N6-甲基腺苷（m6A）甲基化相关 DEGs。然后，通过 SwissTargetPrediction 和 UniProtKnowledgebase（UniProtKB）数据库进行药物靶点的预测和验证，并通过 m6A 相关 DEGs 与药物靶点基因的 Pearson 相关分析获得关键基因。接下来，通过基因集富集分析（GSEA）和 IPA 获得关键基因的通路。最后，基于 mRNAs、circRNAs 和 miRNAs 构建 circRNA-miRNA-mRNA 网络。

结果

差异分析共筛选出 2250 个 OGD/R 组与对照组之间的 DEGs 和 757 个治疗组与 OGD/R 组之间的 DEGs。通过 Pearson 相关分析获得 7 个 m6A 相关 DEGs，包括 Arl4d、Gm10653、Gm1113、Kcns3、Olfml2a、Stk26 和 Tfcp2l1。获得 4 个关键基因（Tfcp2l1、Kcns3、Olfml2a 和 Arl4d），GSEA 显示这些关键基因显著参与 DNA 修复、e2f 靶标和 g2m 检查点。IPA 显示 Tfcp2l1 在人类胚胎干细胞多能性中发挥重要作用。circRNA-miRNA-mRNA 网络表明 mmu_circ_0001258 通过 mmu-miR-301b-3p 调控 Tfcp2l1。