采用生物信息学方法研究特纳综合征相关的枢纽基因。

Investigation of hub genes involved in Turner syndrome using biological informatics methods.

机构信息

Department of Internal Medicine, School of Clinical Medicine, North China University of Science and Technology, Tangshan, Hebei, China.,Department ofEndocrinology and Metabolic Diseases, Hebei General Hospital, Shijiazhuang, Hebei, China.,Department of Internal Medicine, Hebei Medical University, Shijiazhuang,Hebei, China.,Hebei Key Laboratory of Metabolic Diseases, Hebei General Hospital, Shijiazhuang, Hebei, China.

出版信息

Medicine (Baltimore). 2022 Mar 18;101(11). doi: 10.1097/MD.0000000000029069.

DOI:10.1097/MD.0000000000029069

PMID:35356930

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10684194/

Abstract

BACKGROUND

This study aimed to explore candidate genes and their potential interaction mechanism critical to the pathophysiology of Turner syndrome by using the Gene Expression Omnibus database.

METHODS

GSE58435 data set was obtained by querying the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened using R and subsequently annotated by Gene Ontology. Functional enrichment analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes database for annotation, visualization, and integrated discovery. A protein-protein interaction network of different genes was constructed based on the STRING database, in which hub genes were explored through Cytoscape software. The expression of the hub genes was verified by analyzing the gene expression in the GSE46687 data set.

RESULTS

A total of 733 differential genes were identified. These differentially expressed genes were significantly enriched in nucleoplasm and nucleus. Their molecular function was concentrated on DNA binding and transcription, coronary artery, and adipose tissue development. According to the annotation of Kyoto Encyclopedia of Genes and Genomes, the identified DEGs were mainly enriched in inflammatory mediator regulation of TRP channels, osteoclast differentiation. A total of 10 hub genes (HIST1H2BA, TRIM71, HIST1H2BB, HIST1H4D, TNF, TP53BP1, CDCA8, EGF, HMG20B, and BCL9) were identified from the constructed protein-protein interaction network. These genes were discovered to be highly expressed in osteoclasts, ovaries, digestive tract, blood, and lymphatic tissues through the online application of human protein atlas.

CONCLUSION

In this study, 733 DEGs and 10 hub genes were identified. They would be new candidate targets in Turner syndrome.

摘要

背景

本研究旨在通过使用基因表达综合数据库（Gene Expression Omnibus database），探索特纳综合征病理生理学的候选基因及其潜在的相互作用机制。

方法

通过查询基因表达综合数据库（Gene Expression Omnibus database），获得 GSE58435 数据集。使用 R 筛选差异表达基因（Differentially expressed genes，DEGs），并进行基因本体论（Gene Ontology）注释。基于京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes database）进行功能富集分析，用于注释、可视化和综合发现。基于 STRING 数据库构建不同基因的蛋白质-蛋白质相互作用网络，利用 Cytoscape 软件探索枢纽基因。通过分析 GSE46687 数据集的基因表达，验证枢纽基因的表达。

结果

共鉴定出 733 个差异基因。这些差异表达基因在核质和核中显著富集。其分子功能主要集中在 DNA 结合和转录、冠状动脉和脂肪组织发育。根据京都基因与基因组百科全书的注释，鉴定出的差异基因主要富集在调节 TRP 通道的炎症介质、破骨细胞分化。从构建的蛋白质-蛋白质相互作用网络中鉴定出 10 个枢纽基因（HIST1H2BA、TRIM71、HIST1H2BB、HIST1H4D、TNF、TP53BP1、CDCA8、EGF、HMG20B 和 BCL9）。通过人类蛋白质图谱（human protein atlas）的在线应用，发现这些基因在破骨细胞、卵巢、消化道、血液和淋巴组织中高表达。