采用生物信息学和实验验证方法鉴定和分析缺氧缺血性脑损伤中的氧化应激相关基因。

Identification and analysis of oxidative stress-related genes in hypoxic-ischemic brain damage using bioinformatics and experimental verification.

机构信息

Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.

Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China.

出版信息

Immun Inflamm Dis. 2024 Aug;12(8):e70000. doi: 10.1002/iid3.70000.

DOI:10.1002/iid3.70000

PMID:39172048

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11340634/

Abstract

BACKGROUND

Oxidative stress (OS) plays a major role in the progress of hypoxic-ischemic brain damage (HIBD). This study aimed to investigate OS-related genes and their underlying molecular mechanisms in neonatal HIBD.

METHODS

Microarray data sets were acquired from the Gene Expression Omnibus (GEO) database to screen the differentially expressed genes (DEGs) between control samples and HIBD samples. OS-related genes were drawn from GeneCards and OS-DEGs in HIBD were obtained by intersecting with the DEGs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were conducted to determine the underlying mechanisms and functions of OS-DEGs in HIBD. Moreover, the hub genes were screened using the protein-protein interaction network and identified in the GSE144456 data set. CIBERSORT was then performed to evaluate the expression of immunocytes in each sample and perform a correlation analysis of the optimal OS-DEGs and immunocytes. Finally, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and immunohistochemistry were performed to validate the expression levels of the optimal OS-DEGs.

RESULTS

In total, 93 OS-DEGs were identified. GO, KEGG, and GSEA enrichment analyses indicated that these genes were predominantly enriched in OS and inflammation. Four OS-related biomarker genes (Jun, Fos, Tlr2, and Atf3) were identified and verified. CIBERSORT analysis revealed the dysregulation of six types of immune cells in the HIBD group. Moreover, 47 drugs that might target four OS-related biomarker genes were screened. Eventually, RT-qPCR and immunohistochemistry results for rat samples further validated the expression levels of Fos, Tlr2, and Atf3.

CONCLUSIONS

Fos, Tlr2 and Atf3 are potential OS-related biomarkers of HIBD progression. The mechanisms of OS are associated with those of neonatal HIBD.

摘要

背景

氧化应激（OS）在缺氧缺血性脑损伤（HIBD）的进展中起着重要作用。本研究旨在探讨 OS 相关基因及其在新生儿 HIBD 中的潜在分子机制。

方法

从基因表达综合数据库（GEO）数据库中获取微阵列数据集，以筛选对照样本和 HIBD 样本之间的差异表达基因（DEGs）。从 GeneCards 中提取 OS 相关基因，并通过与 DEGs 相交获得 HIBD 中的 OS-DEGs。随后，进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）以及基因集富集分析（GSEA），以确定 OS-DEGs 在 HIBD 中的潜在机制和功能。此外，使用蛋白质-蛋白质相互作用网络筛选枢纽基因，并在 GSE144456 数据集中进行鉴定。然后进行 CIBERSORT 以评估每个样本中免疫细胞的表达，并对最佳 OS-DEGs 和免疫细胞进行相关性分析。最后，进行定量逆转录聚合酶链反应（RT-qPCR）和免疫组织化学以验证最佳 OS-DEGs 的表达水平。

结果

共鉴定出 93 个 OS-DEGs。GO、KEGG 和 GSEA 富集分析表明，这些基因主要富集在 OS 和炎症中。鉴定并验证了 4 个 OS 相关生物标志物基因（Jun、Fos、Tlr2 和 Atf3）。CIBERSORT 分析显示 HIBD 组中六种免疫细胞类型失调。此外，筛选出 47 种可能针对 4 个 OS 相关生物标志物基因的药物。最终，大鼠样本的 RT-qPCR 和免疫组织化学结果进一步验证了 Fos、Tlr2 和 Atf3 的表达水平。