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European Journal of Gynaecological Oncology  2021, Vol. 42 Issue (1): 50-65    DOI: 10.31083/j.ejgo.2021.01.2151
Original Research Previous articles | Next articles
Bioinformatic analysis identifies potential key genes in the pathogenesis of uterine leiomyoma
Yi-Chao Jin1, Tong-Hui Ji1, Xiong Yuan1, Ying Sun1, Yu-Jie Sun2, Jie Wu1, *()
1Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu, P. R. China
2Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126 Jiangsu, P. R. China
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Abstract  

Objective: The present study aimed to screen hub genes for pathology of uterine leiomyoma. Methods: The microarray data of GSE31699, containing 16 uterine leiomyoma tissue samples and 16 matched normal myometrium samples, were downloaded from the Gene Expression Omnibus database (GEO). The “limma” R language package was used to identify differently-expressed genes (DEGs) between uterine leiomyoma and myometrium. Gene Ontology (GO) and pathway enrichment analyses were performed by using clusterprofiler, the DEGs were mostly enriched in post-synapse assembly, response to glucocorticoid, extracellular matrix receptor interaction and coagulation cascades. Subsequently, a protein-protein interaction (PPI) network of DEGs was constructed by Search Tool for the Retrieval of Interacting Genes Database (STRING) and visualized by utilizing Cytoscape software. We screened hub clusters of PPI network by the plug-in Molecular Complex Detection (MCODE) in Cytoscape, then clusterprofiler was also utilized to analyze functions and pathways enrichment of the genes in the hub clusters. Furthermore, we employed the “WGCNA” package in R to conduct co-expression network for all genes in GSE31699. Ultimately, we selected the overlapped genes in hub clusters of DEGs’ PPI network and WGCNA. Results: Five genes (COL5A2, ALDH1A1, GNG11, EFEMP1, ANXA1) were finally validated in other GEO datasets (GSE64763, GSE764, GSE593) and Oncomine database. Gene set enrichment analysis (GSEA) was also performed for the hub genes. The expression of COL5A2 was significantly higher in uterine leiomyoma compared with that in myometrium, while the expression of the other hub genes was significantly lower in uterine leiomyoma. Conclusion: The results indicated that COL5A2, ALDH1A1, GNG11, EFEMP1 and ANXA1 may be the key pathological genes in uterine leiomyoma.

Key words:  Bioinformatics analysis      Uterine leiomyoma      PPI      WGCNA     
Submitted:  25 May 2020      Revised:  12 August 2020      Accepted:  28 August 2020      Published:  15 February 2021     
*Corresponding Author(s):  Jie Wu     E-mail:  wujiemd@126.com

Cite this article: 

Yi-Chao Jin, Tong-Hui Ji, Xiong Yuan, Ying Sun, Yu-Jie Sun, Jie Wu. Bioinformatic analysis identifies potential key genes in the pathogenesis of uterine leiomyoma. European Journal of Gynaecological Oncology, 2021, 42(1): 50-65.

URL: 

https://ejgo.imrpress.com/EN/10.31083/j.ejgo.2021.01.2151     OR     https://ejgo.imrpress.com/EN/Y2021/V42/I1/50

Fig. 1.  Study design and the flow diagram of study.

Fig. 2.  Heatmap of the top 273 DEGs according to the value of |logFC| after deleting the samples GSM786796 and GSM786789.

Fig. 3.  KEGG and GO enrichment of DEGs. (A) GO enrichment of the up-regulated DEGs. (B) GO enrichment of the down-regulated DEGs. (C) KEGG analysis of the up-regulated DEGs. (D) KEGG analysis of the down-regulated DEGs.

Fig. 4.  PPI network construction and clusters analyses. The red nodes represent the up-regulated genes and the blue nodes represent the down-regulated genes. (A) The PPI network of 273 DEGs was constructed via STRING that contained 267 nodes and 555 edges. (B) Cluster rank 1. This cluster consists of 24 nodes and 69 edges and has the highest score in those clusters. (C) Cluster rank 2. (D) Cluster rank 3. (E) Cluster rank 4.

Fig. 5.  Co-expression network creation and hub modules selection. (A) Dendrogram of all genes in GSE31699 clustered based on a dissimilarity measure (1-TOM). (B) A heatmap of selected genes. The intensity of the yellow color indicates the strength of the correlation between pairs of modules on a linear scale. (C) Correlation between modules and traits. The upper number in each cell refers to the correlation coefficient of each module in the trait, and the lower number is the corresponding P-value. Among them, the blue module was the most relevant modules with uterine leiomyoma traits.

Fig. 6.  Clustering of module eigengenes and eigengene adjacency heatmap (the red color indicates the strong correlation between different modules).

Fig. 7.  Scatter plots of GS for uterine leiomyoma versus the MM in the hub modules. (A) Blue module. (B) Turquoise module. (C) Tan module. (D) Cyan module.

Fig. 8.  PPI network construction of hub modules and identification of hub genes. (A) PPI network for genes in blue module. (B) PPI network for genes in turquoise module. (C) PPI network for genes in tan module. (D) Real hub genes belonging to both the hub modules and the hub clusters in PPI network of DEGs.

Fig. 9.  The relative expression of hub genes in other datasets from GEO (GSE64763, GSE764 and GSE593, *: P < 0.01, **: P < 0.001, ***: P < 0.0001, ****: P < 0.00001).

Fig. 10.  Transcriptional expression of hub genes in 20 different types of cancer diseases (ONCOMINE database). ‘Uterine corpus leiomyoma’ was included in ‘other cancer’. Difference of transcriptional expression was compared by students’ t-test. Cut-off of P value and fold change were as following: P value: 0.01, fold change: 1.5, gene rank: 10%, data type: mRNA. The number in cell means how many studies in the database meet the threshold. Red means higher expression in cancer while blue means lower expression.

Fig. 11.  Gene set enrichment analysis (GSEA) using GSE31699. The most enriched functional gene set in uterine leiomyoma samples with hub genes highly expressed was identified. (A) COL5A2. (B) ALDH1A1. (C) GNG11. (D) EFEMP1. (E) ANXA1.

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