加权基因共表达网络分析鉴定出与滑膜肉瘤转移相关的五个枢纽基因。

Weighted Gene Co-expression Network Analysis Identifies Five Hub Genes Associated with Metastasis in Synovial Sarcoma.

机构信息

Department of Orthopedics, The Fourth Hospital of Hebei Medical University, 12 Health Road, Shijiazhuang, Hebei 050011, P.R. China.

Hebei Medical University, 361 Zhongshan East Road, Shijiazhuang, Hebei 050011, P. R. China.

出版信息

Comb Chem High Throughput Screen. 2022;25(10):1767-1777. doi: 10.2174/1386207324666210628112429.

DOI:10.2174/1386207324666210628112429

PMID:34182903

Abstract

BACKGROUND

Synovial Sarcoma (SS) refers to a malignant Soft Tissue Sarcoma (STS) which often comes about to children and adults and has a poor prognosis in elderly patients. Patients with local lesions can be treated with extensive surgical resection combined with adjuvant or radiotherapy, whereas about half of the cases have recurrent diseases and metastatic lesions, and five-year survival ratio is assessed within the range of 27% - 55% only.

METHODS

We downloaded a set of expression profile data (GSE40021) related to SS metastasis based on the Gene Expression Omnibus (GEO) database, and selected distinctly represented genes (DEGs) related to tumor metastasis. WGCNA was used to emphasize the DEGs related to tumor metastasis, and obtain co-expression modules. Then, the module most related to SS metastasis was screened out. The genes of enriched in this module were analyzed by Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway improvement analysis. Cytoscape software was used for constructing protein-protein interaction (PPI) networks, and screening hub genes were made in virtue of Oncomine analysis.

RESULT

We selected 514 DEGs, consisting of 210 up-regulated genes and 304 down-regulated genes. Through WGCAN, we got seven co-expression modules and the module most related to SS metastasis was turquoise module, which contained 66 genes. Finally, we screened out five hub genes (HJURP, NCAPG, TPX2, CENPA, NDC80) through CytoHubba and Oncomine analysis.

CONCLUSION

In this study, we screened out five hub genes to help clinical diagnosis and serve as the latent purpose of SS treatment.

摘要

背景

滑膜肉瘤（SS）是一种常见于儿童和成人的恶性软组织肉瘤（STS），其预后在老年患者中较差。局部病变的患者可以通过广泛的手术切除联合辅助或放疗进行治疗，而大约一半的病例会出现复发和转移病变，五年生存率评估仅在 27%-55%范围内。

方法

我们从基因表达综合数据库（GEO）中下载了一组与 SS 转移相关的表达谱数据（GSE40021），并选择了与肿瘤转移相关的具有明显代表性的基因（DEGs）。我们使用 WGCNA 强调与肿瘤转移相关的 DEGs，并获得共表达模块。然后，筛选出与 SS 转移最相关的模块。对这个模块中富集的基因进行基因本体论（GO）功能和京都基因与基因组百科全书（KEGG）通路富集分析。使用 Cytoscape 软件构建蛋白质-蛋白质相互作用（PPI）网络，并通过 Oncomine 分析筛选枢纽基因。

结果

我们选择了 514 个 DEGs，包括 210 个上调基因和 304 个下调基因。通过 WGCNA，我们得到了七个共表达模块，与 SS 转移最相关的模块是绿松石模块，包含 66 个基因。最后，我们通过 CytoHubba 和 Oncomine 分析筛选出五个枢纽基因（HJURP、NCAPG、TPX2、CENPA、NDC80）。