Title:Potential Prognostic Predictors and Molecular Targets for Skin Melanoma Screened by Weighted Gene Co-expression Network Analysis
Volume: 20
Issue: 1
Author(s): Sichao Chen, Zeming Liu, Man Li, Yihui Huang, Min Wang, Wen Zeng, Wei Wei, Chao Zhang, Yan Gong*Liang Guo*
Affiliation:
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan,China
- Department of Plastic Surgery, Zhongnan Hospital of Wuhan University, Wuhan,China
Keywords:
Melanoma, WGCNA, prognosis, CCNB2, ARHGAP30, SEMA4D.
Abstract:
Aims and Objectives: Among skin cancers, malignant skin melanoma is the leading cause
of death. Identification of gene markers of malignant skin melanoma associated with survival may
provide new clues for prognosis prediction and treatment. This research aimed to screen out potential
prognostic predictors and molecular targets for malignant skin melanoma.
Introduction: Information regarding gene expression in skin melanoma and patients’ clinical traits
was obtained from the Gene Expression Omnibus database. Weighted gene co-expression network
analysis (WGCNA) was applied to build co-expression modules and investigate the association between
the modules and clinical traits. Moreover, functional enrichment analysis was performed for
clinically significant co-expression modules. Hub genes of these modules were validated via Gene
Expression Profiling Interactive Analysis (GEPIA) and the Human Protein Atlas (http://
www.proteinatlas.org).
Methods: First, using WGCNA, 9 co-expression modules were constructed by the top 25% differentially
expressed genes (4406 genes) from 77 human melanoma samples. Two co-expression modules
(magenta and blue modules) were significantly correlated with survival months (r = -0.27, p = 0.02;
r = 0.27, p = 0.02, respectively). The results of functional enrichment analysis demonstrated that the
magenta module was mainly enriched in the cell cycle process and the blue module was mainly enriched
in the immune response process. Additionally, the GEPIA and Human Protein Atlas results
suggested that the hub genes CCNB2, ARHGAP30, and SEMA4D were associated with relapse-free
survival and overall survival (all p-values < 0.05) and were differentially expressed in melanoma tumors
and normal skin.
Results and Conclusion: The results provided the framework of co-expression gene modules of skin
melanoma and screened out CCNB2, ARHGAP30, and SEMA4D associated with survival as potential
prognostic predictors and molecular targets of treatment.
