通过生物信息学分析鉴定神经管缺陷胚胎中与免疫相关的生物标志物。
Identification of immune-related biomarkers in embryos with neural tube defects via a bioinformatics analysis.
作者信息
Huang Qingli, Yang Li, Nong Binbin, Gan Haisi, Wu Huizhen, Li Meiyan, Jin Mingyang, Xie Liling
机构信息
Department of Obstetrics, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.
Department of Gynecology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.
出版信息
Ann Transl Med. 2022 May;10(9):521. doi: 10.21037/atm-22-1273.
BACKGROUND
Neural tube defects (NTDs) are one of the most common types of birth defects. Oral folic acid (FA) prophylaxis is currently available, but the pathogenesis of NTDs is not fully understood. We conducted this study to examine the role of the immune landscape of NTDs and identify novel diagnostic and therapeutic biomarkers.
METHODS
We downloaded the GSE33111 data set of 12 NTD embryos and 12 healthy embryos in the same period of fetal development from the Gene Expression Omnibus (GEO) database. We compared the healthy embryos and NTD embryos to identify the differentially expressed genes (DEGs). We also performed a functional enrichment analysis of the DEGs using the clusterProfiler package. We extracted the top 10 ranked genes as hub immune-related biomarkers. We then used receiver operating characteristic (ROC) curves to determine the expression levels of the hub immune-related genes and the accuracy of the diagnosis of NTDs. Finally, we analyzed the immune landscape of the NTD embryos and healthy embryos via a single-sample gene set enrichment analysis (ssGSEA).
RESULTS
A total of 611 DEGs were identified by the differential analysis, including 95 immune genes. The functional enrichment analysis indicated that Epstein-Barr virus infection, antigen processing and presentation, inflammatory bowel disease, and type I diabetes mellitus were associated with NTDs. The results of the expression level analysis showed that the hub immune-related genes were more highly expressed in the NTD embryos than the healthy embryos. Additionally, the ROC curve analysis also indicated that the expression levels of the 10 hub immune-related genes were highly accurate in the diagnosis of NTDs [area under the curve (AUC) range, 0.708-0.812]. The immune infiltration analysis demonstrated that 20 of the 28 immune cell types were more highly infiltrated in the NTD embryos than the healthy embryos.
CONCLUSIONS
Immune-related genes are important regulators of the occurrence and development of NTDs.
背景
神经管缺陷（NTDs）是最常见的出生缺陷类型之一。目前已有口服叶酸（FA）预防措施，但NTDs的发病机制尚未完全明确。我们开展本研究以探讨NTDs免疫格局的作用，并识别新的诊断和治疗生物标志物。
方法
我们从基因表达综合数据库（GEO）下载了12个NTD胚胎和12个处于胎儿发育同期的健康胚胎的GSE33111数据集。我们比较了健康胚胎和NTD胚胎以识别差异表达基因（DEGs）。我们还使用clusterProfiler软件包对DEGs进行了功能富集分析。我们提取排名前十的基因作为核心免疫相关生物标志物。然后我们使用受试者工作特征（ROC）曲线来确定核心免疫相关基因的表达水平以及NTDs诊断的准确性。最后，我们通过单样本基因集富集分析（ssGSEA）分析了NTD胚胎和健康胚胎的免疫格局。
结果
通过差异分析共识别出611个DEGs，其中包括95个免疫基因。功能富集分析表明，爱泼斯坦-巴尔病毒感染、抗原加工与呈递、炎症性肠病和1型糖尿病与NTDs相关。表达水平分析结果显示，核心免疫相关基因在NTD胚胎中的表达高于健康胚胎。此外，ROC曲线分析还表明，10个核心免疫相关基因的表达水平在NTDs诊断中具有较高的准确性[曲线下面积（AUC）范围为0.708 - 0.812]。免疫浸润分析表明
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