Key copper homeostasis genes and inflammatory mechanisms in ischemic stroke: A bioinformatics and experimental study

IF 3.1 4区生物学 Q1 GENETICS & HEREDITY

Functional & Integrative Genomics Pub Date : 2025-09-10 DOI:10.1007/s10142-025-01692-0

Ting Shi, Zhifeng Wang, Jiao Yang, Pengfen He, Daman Tian, Junfeng Lan, Shuangfeng Xu, Aiming Yang, Liwei Xing, Yujiang Xi, Jian Wang

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Abstract

Ischemic stroke (IS) has high morbidity/mortality with limited treatments. This study screened core copper homeostasis-related genes in IS and validated their function as precise intervention targets. Human IS gene chip data were retrieved from GEO, and copper homeostasis genes from multiple databases. After data correction/normalization, IS differentially expressed genes (DEGs) were identified and intersected with copper genes. DAVID for GO/KEGG enrichment, STRING for PPI network, CytoHubba for key genes, and ROC curves for diagnostic value. MCAO rat models were established; after 14-day rearing, protein expression was validated via relevant assays. 1,425 IS DEGs and 2,610 copper genes intersected to 235 genes, enriched in inflammatory response, innate immunity, and TNF/NOD-like/Toll-like receptor pathways. Key genes HIF-1α, TNF, TLR4, IL-1β had IS diagnostic AUC 0.70–0.80. MCAO rats showed worse neurological deficits, larger infarcts, neuronal damage, brain copper accumulation, and upregulated key genes linked to neuroinflammation, BBB disruption, and neuronal injury. Bioinformatics and animal studies revealed copper homeostasis imbalance-related genes mediate inflammation, oxidative stress, and mitochondrial regulation, supporting the "copper accumulation–inflammation–oxidative stress" cascade. These genes may be novel IS targets. Further study on dynamic expression across ischemic time windows/brain regions and interactions with other cell death modes is needed.

Graphical abstract

This study used a system approach: bioinformatics screening → experimental validation → mechanism elucidation. Three cerebral ischemia datasets from GEO (GSE16561, GSE22255, GSE58294) underwent DEG analysis; Venn diagram identified core shared DEGs. GO/KEGG enrichment, STRING for PPI network, Cytoscape for hub genes, ROC curves for diagnostic potential. Rat MCAO model was established; validity verified via relevant staining; Cu2+ accumulation detected; molecular expression validated by assays.

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关键铜稳态基因和缺血性卒中炎症机制：生物信息学和实验研究

缺血性脑卒中（IS）发病率/死亡率高，治疗有限。本研究筛选了IS中核心铜稳态相关基因，并验证了其作为精确干预靶点的功能。人类IS基因芯片数据来源于GEO，铜稳态基因来源于多个数据库。数据校正/归一化后，鉴定出IS差异表达基因（DEGs）并与铜基因交叉。DAVID表示GO/KEGG富集，STRING表示PPI网络，CytoHubba表示关键基因，ROC曲线表示诊断价值。建立MCAO大鼠模型；饲养14 d后，通过相关检测验证蛋白表达。1425个IS DEGs和2610个铜基因与235个基因相交，在炎症反应、先天免疫和TNF/ nod样/ toll样受体途径中富集。关键基因HIF-1α、TNF、TLR4、IL-1β的诊断AUC为0.70 ~ 0.80。MCAO大鼠表现出更严重的神经功能缺损、更大的梗死、神经元损伤、脑铜积累以及与神经炎症、血脑屏障破坏和神经元损伤相关的关键基因上调。生物信息学和动物研究表明，铜稳态失衡相关基因介导炎症、氧化应激和线粒体调节，支持“铜积累-炎症-氧化应激”级联反应。这些基因可能是新的IS目标。需要进一步研究缺血时间窗/脑区域的动态表达以及与其他细胞死亡模式的相互作用。本研究采用生物信息学筛选→实验验证→机制阐明的系统方法。GEO的三个脑缺血数据集（GSE16561、GSE22255、GSE58294）进行DEG分析；维恩图确定了核心共享deg。GO/KEGG富集，STRING用于PPI网络，Cytoscape用于枢纽基因，ROC曲线用于诊断潜力。建立大鼠MCAO模型；通过相关染色验证有效性；Cu2+积累检测；通过实验验证分子表达。

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来源期刊

Functional & Integrative Genomics 生物-遗传学

CiteScore

3.50

自引率

3.40%

发文量

审稿时长

2 months

期刊介绍： Functional & Integrative Genomics is devoted to large-scale studies of genomes and their functions, including systems analyses of biological processes. The journal will provide the research community an integrated platform where researchers can share, review and discuss their findings on important biological questions that will ultimately enable us to answer the fundamental question: How do genomes work?