Open Access

Identification of key candidate genes involved in melanoma metastasis

  • Authors:
    • Jia Chen
    • Fei Wu
    • Yu Shi
    • Degang Yang
    • Mingyuan Xu
    • Yongxian Lai
    • Yeqiang Liu
  • View Affiliations

  • Published online on: May 30, 2019     https://doi.org/10.3892/mmr.2019.10314
  • Pages: 903-914
  • Copyright: © Chen et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Metastasis is the most lethal stage of cancer progression. The present study aimed to investigate the underlying molecular mechanisms of melanoma metastasis using bioinformatics. Using the microarray dataset GSE8401 from the Gene Expression Omnibus database, which included 52 biopsy specimens from patients with melanoma metastasis and 31 biopsy specimens from patients with primary melanoma, differentially expressed genes (DEGs) were identified, subsequent to data preprocessing with the affy package, followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. A protein‑protein interaction (PPI) network was constructed. Mutated genes were analyzed with 80 mutated cases with melanoma from The Cancer Genome Atlas. The overall survival of key candidate DEGs, which were within a filtering of degree >30 criteria in the PPI network and involved three or more KEGG signaling pathways, and genes with a high mutation frequency were delineated. The expression analysis of key candidate DEGs, mutant genes and their associated genes were performed on UALCAN. Of the 1,187 DEGs obtained, 505 were upregulated and 682 were downregulated. ‘Extracellular exosome’ processes, the ‘amoebiasis’ pathway, the ‘ECM‑receptor interaction’ pathway and the ‘focal adhesion’ signaling pathway were significantly enriched and identified as important processes or signaling pathways. The overall survival analysis of phosphoinositide‑3‑kinase regulator subunit 3 (PIK3R3), centromere protein M (CENPM), aurora kinase A (AURKA), laminin subunit α 1 (LAMA1), proliferating cell nuclear antigen (PCNA), adenylate cyclase 1 (ADCY1), BUB1 mitotic checkpoint serine/threonine kinase (BUB1), NDC80 kinetochore complex component (NDC80) and protein kinase C α (PRKCA) in DEGs was statistically significant. Mutation gene analysis identified that BRCA1‑associated protein 1 (BAP1) had a higher mutation frequency and survival analysis, and its associated genes in the BAP1‑associated PPI network, including ASXL transcriptional regulator 1 (ASXL1), proteasome 26S subunit, non‑ATPase 3 (PSMD3), proteasome 26S subunit, non ATPase 11 (PSMD11) and ubiquitin C (UBC), were statistically significantly associated with the overall survival of patients with melanoma. The expression levels of PRKCA, BUB1, BAP1 and ASXL1 were significantly different between primary melanoma and metastatic melanoma. Based on the present study, ‘extracellular exosome’ processes, ‘amoebiasis’ pathways, ‘ECM‑receptor interaction’ pathways and ‘focal adhesion’ signaling pathways may be important in the formation of metastases from melanoma. The involved genes, including PIK3R3, CENPM, AURKA, LAMA1, PCNA, ADCY1, BUB1, NDC80 and PRKCA, and mutation associated genes, including BAP1, ASXL1, PSMD3, PSMD11 and UBC, may serve important roles in metastases of melanoma.

Introduction

Melanoma is a common malignancy and has one of the poorest prognoses due to its excessive aggression and metastasis (1). In recent years, the incidence of melanoma has increased significantly and the survival rate of patients with melanoma remains poor (2). As metastasis is the most lethal stage of melanoma progression, identifying its underlying molecular mechanisms and determining its molecular biomarkers is important.

Microarray analysis is able to quickly identify all of the genes expressed at any one time-point and is particularly suited to screen for differentially expressed genes (DEGs) (3). Recently, microarray analysis has been widely applied and has produced large amounts of microarray data, which are deposited in public databases. It may be beneficial for further research to integrate and reanalyze this data (4).

In a previous study, the microarray dataset GSE8401 generated by Xu et al (5) was used to validate a ‘metastasis aggressiveness gene expression signature’ derived from human melanoma cells, selected based on their metastatic potential in an immunodeficient mouse metastasis model, and their correlation with the aggressiveness of melanoma metastases in human patients. However, an integral bioinformatics analysis combined with an expression profile analysis has not been yet been conducted, to the best of the authors' knowledge.

In the present study, the DEGs from the GSE8401 dataset were identified, subsequent to data preprocessing with the affy package, followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. A protein-protein interaction (PPI) network was constructed. Mutated genes were analyzed with 80 mutated cases with melanoma from The Cancer Genome Atlas (TCGA). The overall survival of key candidate DEGs, which were within a filtering of degree >30 criteria in the PPI network and involved three or more KEGG signaling pathways, and genes with a high mutation frequency were delineated. The expression analysis of key candidate DEGs, mutant genes and their associated genes were performed on UALCAN. Of the 1,187 DEGs obtained, 505 were upregulated and 682 were downregulated. ‘Extracellular exosome’ processes, the ‘amoebiasis’ pathway, the ‘ECM-receptor interaction’ pathway and the ‘focal adhesion’ signaling pathway were significantly enriched and identified as important processes or signaling pathways. The overall survival analysis of phosphoinositide-3-kinase regulator subunit 3 (PIK3R3), centromere protein M (CENPM), aurora kinase A (AURKA), laminin subunit α 1 (LAMA1), proliferating cell nuclear antigen (PCNA), adenylate cyclase 1 (ADCY1), BUB1 mitotic checkpoint serine/threonine kinase (BUB1), NDC80, kinetochore complex component (NDC80) and protein kinase C α (PRKCA) in DEGs was statistically significant. Mutation gene analysis identified that BRCA1-associated protein 1 (BAP1) had a higher mutation frequency and survival analysis, and its associated genes in the BAP1-associated PPI network, including ASXL transcriptional regulator 1 (ASXL1), proteasome 26S subunit, non-ATPase 3 (PSMD3), proteasome 26S subunit, non ATPase 11 (PSMD11) and ubiquitin C (UBC), were statistically significantly associated with the overall survival of patients with melanoma. The expression levels of PRKCA, BUB1, BAP1 and ASXL1 were significantly different between primary melanoma and metastatic melanoma. Based on the present study, ‘extracellular exosome’ processes, ‘amoebiasis’ pathways, ‘ECM-receptor interaction’ pathways and ‘focal adhesion’ signaling pathways may be important in the formation of metastases from melanoma. The involved genes, including PIK3R3, CENPM, AURKA, LAMA1, PCNA, ADCY1, BUB1, NDC80 and PRKCA, and mutation associated genes, including BAP1, ASXL1, PSMD3, PSMD11 and UBC, may serve important roles in metastases of melanoma.

Materials and methods

Affymetrix microarray data and clinical information

The gene expression profile dataset GSE8401 was extracted from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) (6). The GSE8401 dataset was deposited by Xu et al (5), including 52 biopsy specimens from patients with melanoma metastasis and 31 biopsy specimens from patients with primary melanoma, and was based on the platform of the GPL96 (HG-U133A) Affymetrix Human Genome U133A Array (Affymetrix; Thermo Fisher Scientific, Inc., Waltham, MA, USA). These 83 fresh melanoma biopsies from patients undergoing surgery were collected between 1992 and 2001 as a part of the diagnostic or therapeutic strategy. Immediately following surgery, half of each specimen was fixed in formalin and processed for routine histology, and the other half was immediately snap-frozen and stored in liquid nitrogen until use for RNA extraction. Histopathological diagnosis of each tissue specimen was performed independently by two histopathologists. All patient specimens were collected and used, according to the approval by the institutional ethics committee and written informed consent was obtained, according to the ethical standards in the 1964 Declaration of Helsinki.

Data preprocessing and DEG screening

The downloaded data in the series matrix file was preprocessed using the affy package (version 1.50.0) (7) in R language, including normalization and expression calculation. Annotations to the probes were performed, and probes that were not matched to the gene symbols were excluded. The average expression values were taken if different probes mapped to the same gene. DEGs in patients with melanoma metastasis compared with patients with primary melanoma were analyzed using the limma package (8) in R language. The cut-off threshold was set as a P<0.05 and log2 (fold change) >1 or <-1.

GO and pathway enrichment analysis

GO (http://www.geneontology.org/) analysis is commonly used for functional studies of large-scale genomic or transcriptomic data and classifies functions with respect to three criteria: Molecular function (MF), cellular component (CC) and biological process (BP) (9,10). The KEGG (http://www.kegg.jp/) pathway database is widely used for the systematic analysis of gene functions, associating genomic data with higher order functional data (11). The Database for Annotation, Visualization and Integrated Discovery (DAVID; http://david.ncifcrf.gov/) is an integrated biological knowledge base with analytical tools used for the systematic and integrative analysis of large gene lists (12). In the present study, GO terms and KEGG signaling pathway enrichment analyses for DEGs were performed using DAVID. The cutoff threshold was set as P<0.05.

Integration analysis of the PPI network and the KEGG pathway network

Search Tool for the Retrieval of Interacting Gene/Proteins (STRING; http://www.string-db.org/) is an online database that assesses and integrates PPIs (13). In the present study, DEGs were mapped onto the STRING database for PPI analysis, with a combined score of 0.4 as the parameter setting. The PPI network generated with the DEGs was constructed with Cytoscape software (version 3.4.0) (14,15) and the topology scores of the nodes in the PPI network were analyzed using the CentiScape plugin (version 3.4.0; Parameter setting: Without weight) (16). The key candidate genes were screened with a filtering of degree >30 criteria in the PPI network. Networks of significantly enriched (P<0.05) KEGG pathways and their associated genes were constructed using the Cytoscape (version 3.4.0) plugin ClueGO (14) and Cluepedia (15). The cross-talk genes were identified with the filtering criteria of association with at least three signaling pathways.

Mutant genes screening

The cBioPortal (http://www.cbioportal.org/) for Cancer Genomics, which provides the visualization, analysis and download of large-scale cancer genomics datasets, was employed for the mutation analysis (17,18). In total, 80 mutated cases were selected from TCGA database (project ID: TCGA_SKCM; http://cancergenome.nih.gov/) to screen for mutated genes (19). The detailed clinical information of the samples is listed in Table I.

Table I.

Information of the cases with metastasis.

Table I.

Information of the cases with metastasis.

A, Deceased patients

Submitter IDBAP1 mutationTumor stageDays to mortality
TCGA-WC-A88AYesIV82
TCGA-WC-A884YesIIIb123
TCGA-WC-A883YesIIIa241
TCGA-WC-A87UYesIIIa581
TCGA-VD-A8KFNoIIIb240
TCGA-VD-A8KDNoIV114
TCGA-V4-A9EXNoIIIa730
TCGA-V4-A9EVNoIIIa1,105
TCGA-V4-A9ESYesIIIa511
TCGA-V4-A9EQYesIIIa355
TCGA-V4-A9EINoIIIb389
TCGA-V4-A9E9YesIIIa1,246
TCGA-V4-A9E8YesIIIa458
TCGA-V4-A9E7NoIIIa565
TCGA-RZ-AB0BNoIV349

B, Alive patients

Submitter IDBAP1 mutationTumor stageDays to last follow-up

TCGA-YZ-A985YesIIIa1,184
TCGA-YZ-A982YesIIIb895
TCGA-YZ-A980YesIIIa862
TCGA-WC-A880YesIIIa1,258
TCGA-VD-A8KKYesIIIa624
TCGA-VD-A8KHNoIIIb1,158
TCGA-VD-A8K7NoIIIa1,459
TCGA-V4-A9F8NoIIIa797
TCGA-V4-A9F5NoIV603
TCGA-V4-A9F4NoIIIa634
TCGA-V4-A9F3NoIIIa1543
TCGA-V4-A9F2NoIIIa934
TCGA-V4-A9F0NoIIIb1,678
TCGA-V4-A9EYNoIIIa837
TCGA-V4-A9EWNoIIIa1,211
TCGA-V4-A9EUNoIIIc709
TCGA-V4-A9ETNoIIIb1,362
TCGA-V4-A9EOYesIIIa973
TCGA-V4-A9EMNoIIIa966
TCGA-V4-A9ELNoIIIa1,082
TCGA-V4-A9EHNoIIIb670
TCGA-V4-A9EFNoIIIb1,165
TCGA-V4-A9EDNoIIIa1,078
TCGA-V4-A9EANoIIIa1,348
TCGA-V4-A9E5NoIIIb1,799

[i] TCGA, The Cancer Genome Atlas; BAP1, BRCA1-associated protein 1.

Overall survival and expression analysis

Overall survival analyses for key candidate DEGs and mutation associated genes were performed using Gene Expression Profiling Interactive Analysis (http://gepia.cancer-pku.cn/index.html) (20). Briefly, by entering the genes of interest to the website, patients were divided into two groups according to the expression level of gene, and the survival rate was statistically analysed. The hazard ratio (HR) with 95% confidence intervals and log rank P-value were calculated and are presented. The expression analysis of key candidate DEGs and mutation-associated genes in melanoma was performed using UALCAN (http://ualcan.path.uab.edu/analysis.html) (21).

Results

Data normalization and analysis of DEGs

The boxplot demonstrated good normalization of the GSE8401 data (Fig. 1A). In total, 22,283 probes were obtained, among which 1,205 probes were differentially expressed. Following annotation, 1,187 DEGs in patients with melanoma metastasis compared with patients with primary melanoma were identified, including 505 upregulated DEGs and 682 downregulated DEGs (Fig. 1B).

GO and signaling pathway enrichment analysis

GO enrichment analysis for the DEGs was performed. The top 10 most significant GO terms of each group are presented in Fig. 2A. For MF, the DEGs were primarily enriched in ‘structural molecule activity’ processes. For CC, the DEGs were primarily enriched in ‘extracellular exosome’ processes and ‘extracellular space’ processes. For BP, the DEGs were primarily enriched in ‘epidermis development’ processes, ‘keratinocyte differentiation’ processes and ‘cell adhesion’ processes.

The top 20 most significant KEGG pathway terms are presented in Fig. 2B. The genes were primarily enriched in ‘amoebiasis’, ‘ECM-receptor interaction’ and ‘focal adhesion’ signaling pathways.

PPI analysis

Using the STRING online database and Cytoscape software, a total of 447 DEGs of the 1,187 DEGs were mapped onto the PPI network complex (Fig. 3), and 740 of 1,187 DEGs did not fall into the PPI network.

Cross-talk genes and key candidate gene screening

The cross-talk genes were identified with the filtering criteria of association with at least three signaling pathways, based on the KEGG pathway analysis (Fig. 4). The key candidate genes were screened, including PIK3R3, CENPM, AURKA, LAMA1, PCNA, ADCY1, BUB1, NDC80 kinetochore complex component (NDC80) and PRKCA. Among these genes, PIK3R3, PRKCA, ADCY1 and LAMA1 were enriched in the ‘amoebiasis’ signaling pathway. ADCY1 was additionally involved in ‘pancreatic secretion’, ‘GnRH signaling pathway’, ‘melanogenesis’ and ‘pathways in cancer’ signaling pathways. The majority of these genes were involved in ‘pathways in cancer’, ‘ECM-receptor interaction’ and ‘focal adhesion’ signaling pathways.

Overall survival analysis of key candidate genes

The survival analysis sourced from TCGA data was performed and the analysis curves demonstrated that the aberrant expressions of the key candidate genes, including PIK3R3, CENPM, AURKA, LAMA1, PCNA, ADCY1, BUB1, NDC80 and PRKCA, were significantly associated with poor overall survival (Fig. 5).

Mutant genes and their associated gene analysis

The mutation analysis of genes was performed on cBioPortal based on 80 patients with melanoma from TCGA database. The results demonstrated that G protein subunit α q, G protein subunit α 11, BAP1 and slicing factor 3b subunit 1 had the highest mutation frequency (Fig. 6). Only the survival analysis of BAP1 was statistically significant (data not shown).

A BAP1-associated PPI network was constructed (Fig. 7), in which the survival analyses of ASXL1, proteasome 26S subunit, non-ATPase 3 (PSMD3), proteasome 26S subunit, non ATPase 11 (PSMD11) and UBC were statistically significant (Fig. 8). Survival analysis was conducted in 40 melanoma cases with metastasis selected from the 80 patients with melanoma in the TCGA database (14 cases with BAP1 mutations and 26 cases without BAP1 mutations) to identify the prognostic value of BAP1 mutations in melanoma cases with metastasis (Fig. 9); information on the cases is provided in Table I.

Discussion

The majority of patients with melanoma are diagnosed at advanced stages and have poor overall survival (22). However, the molecular mechanisms involved in the metastasis and progression of malignant melanoma remain unclear.

In the present study, the raw gene expression data of GSE8401 was obtained from the GEO. The original previous study identified that membrane proteins served an important role in tumor-microenvironment interactions during metastasis (5). However, further investigation is required regarding the clinical value of these genes. In the present study, a comprehensive bioinformatics analysis based on the GSE8401 dataset and TCGA was performed. The results suggested that high expression of PIK3R3, CENPM, AURKA, LAMA1, PCNA, ADCY1, BUB1, NDC80 and PRKCA in patients with melanoma was associated with poor overall survival.

PRKCA serves a critical role in the growth of human melanoma cells and a low expression level of PRKCA promotes cellular proliferation (23). In models of melanoma, activation of PRKCA was associated with increased tumor cell proliferation and invasiveness (24). Small interfering RNA-mediated knockdown of PRKCA resulted in a significant suppression of invasion (25). ADCY1, a member of the adenylate cyclase gene family, encodes adenylate cyclase. ADCY1 demonstrated a downregulated trend in rectal adenocarcinoma metastasis (26). LAMA1 expression was increased in esophageal squamous cell carcinoma tissues, and its overexpression rescued the multiplication suppression and cell apoptosis increases induced by microRNA-202 (27).

In the present study, PRKCA, ADCY1 and LAMA1 were enriched in the ‘amoebiasis’ signaling pathway. Colonic amoebiasis has been commonly demonstrated to mimic colon carcinoma (2830). A rare case of colonic amoebiasis was identified to coexist with signet-ring cell carcinoma (31). All of these results support the hypothesis that PRKCA may contribute to the metastases of melanoma.

A previous study demonstrated that ADCY1 had a downregulated trend in rectal adenocarcinoma metastasis and was significantly enriched in the ‘pancreatic secretion’ pathway (26). In the present study, ADCY1 was identified to be involved in several melanoma-related pathways such as ‘pathways in cancer’ and ‘melanogenesis’. Previous study has shown that melanogenesis plays a key role in regulation of cellular metabolism of melanoma cell (32).

The diagnostic gene BUB1, a discriminator between melanoma, benign nevi and lymph nodes, contributes to the detection of melanoma micrometastasis in sentinel lymph nodes (33). Utilizing gene microarray analysis and real-time quantitative polymerase chain reactions, the expression level of BUB1 has been identified to be high in metastatic melanoma (34). BUB1 is downstream of sirtuin 1 (SIRT1), which is upregulated in human melanoma, and its inhibition causes an anti-proliferative effect in melanoma cells (35). The expression of BUB1 is suppressed by the inhibition of SIRT1 (35). Therefore, high expression of BUB1 promotes melanoma metastasis and results in a poor prognosis.

AURKA is known to induce the formation of the mitotic spindle and to be involved in cell multiplication and migration (22). AURKA was upregulated in malignant melanoma cells and tissues, and AURKA overexpression promoted human melanoma cell growth (22). Activation of AURKA is driven by the forkhead box protein M1 and the mitogen-activated protein kinase/extracellular-regulated kinase signaling pathway, and is associated with a poor prognosis in patients with melanoma (36). A comprehensive gene expression analysis of melanoma metastasis suggested that BUB1 and AURKA may serve crucial roles in the development and progression of melanoma (37).

NDC80 is a novel oncogene that is involved in the occurrence of various tumors. It is highly expressed in a variety of cancer types, including pancreatic cancer, hepatocellular carcinoma, gastric cancer and colorectal cancer (3841). Overexpression of NDC80 in cancer cells and tissues promoted multiplication and migration, and was correlated with poor outcomes in those patients with pancreatic cancer (38). In patients with colorectal cancer, NDC80 overexpression was significantly associated with advanced tumor stage and a poor prognosis (41). NDC80 is a downstream gene of polo-like kinase 1, which is a well-documented oncogene that serves a key role in cell reproduction and invasion (42). In bladder cancer, NDC80 was associated with the regulation of cell reproduction, migration and invasion, and was positively associated with metastasis (43). All of these results suggested that NDC80 serves an important role in the metastases of melanoma.

PIK3R3, which activates the protein kinase B/serine/threonine-protein kinase mTOR signaling pathway, serves a crucial role in the survival, proliferation and motility of various tumors (44,45). PIK3R3 is involved in the regulation of the actin cytoskeleton and regulates triple-negative breast cancer cell migration (46). Its expression is high in human hepatocellular carcinoma tissues and glioma tissues (45,47,48). PIK3R3 overexpression augments tumor migration and aggressiveness, and promotes the metastasis of colorectal cancer (49). The basal expression level of PIK3R3 was upregulated in highly metastatic human non-small-cell lung cancer cells (44).

PCNA is a proliferation marker and regulates cell growth (50). In esophageal tumor tissues, upregulation of MAGE family member D1 promoted cell growth by interacting with PCNA (51). CENPM and UBC were additionally identified as key candidate genes in the present study. However, CENPM and UBC have not been previously identified to be involved in cancer. Their function and roles require further experimental verification.

In addition, it was identified that the somatic mutation frequency of BAP1 was high in patients with melanoma and patients with a low expression level of BAP1 had poor overall survival. Conversely, high expression of ASXL1, PSMD3, PSMD11 and UBC, which are BAP1-associated genes, was associated with poor overall survival.

BAP1 is a novel identified tumor suppressor gene and somatic mutations of BAP1 occur in a variety of malignancies (52). BAP1 serves a key role in stabilizing epigenetic regulators, including O-linked N-acetylglucosamine (GlcNAc) transferase, host cell factor C1 and ASXL1, and thus an ASXL/BAP1 complex may inhibit chronic myelomonocytic leukemia, in which ASXL1 is frequently mutated (53). The frequency of BAP1 mutations may be undervalued, and a number of previously unidentified BAP1 and spliceosome mutations were identified in uveal melanoma (54). Inactivating mutations in BAP1 were associated with a high metastatic risk of uveal melanoma (55). In the clinical setting, anti-BAP-1 has been used to detect the presence of BAP-1 mutation (56). Histologically, the melanocytic lesions are located predominantly in the dermis and are composed of epithelioid melanocytes with abundant cytoplasm and distinct nucleoli. Similar lesions develop in the context of somatically acquired BAP-1 loss (57). Immunohistochemistry analysis with anti-BAP-1 demonstrated loss of nuclear staining in melanocytic lesions with BAP-1 mutations (56,58). In the present study, patients with low expression levels of BAP1 had poor overall survival, and the expression of BAP1 was lower in metastatic melanoma compared with primary melanoma. Moreover, mutation of BAP1 was associated with poor prognosis in 40 melanoma cases with metastasis. These results suggested that mutations of BAP1 may serve a key role in the metastases of melanoma.

ASXL1 is involved in polycomb repressive complex 2-dependent transcriptional repression and nuclear hormone receptor- and BAP1-dependent transcriptional regulation. Somatic mutations of ASXL family members occur in human cancer (59). ASXL1 overexpression was identified in cervical cancer (60) and truncation mutations in ASXL1 were identified in various diseases, including chronic lymphocytic leukemia, malignant myeloid diseases, head and neck squamous cell carcinoma, colorectal cancer, liver cancer, prostate cancer and breast cancer (58,59). Furthermore, truncation mutations in ASXL1 resulted in a poor prognosis of myeloid malignancies (61,62). This is inconsistent with the present result that ASXL1 was highly expressed in metastatic melanoma and associated with poor overall survival in patients with melanoma. ASXL1 may have different functions in the metastases of melanoma. This requires further validation.

Silencing of PSMD3 together with human epidermal growth factor receptor 2 resulted in an additive suppression of cell viability, multiplication and protein kinase B signaling pathway activity (63). PSMD3 is downregulated in the long-term survivor subtype of glioblastoma multiforme, suggesting that a low expression level of PSMD3 results in longer survival (64). PSMD11 was overexpressed in breast cancer tissue, and this may be associated with specific biological processes and pathological types of breast cancer (65). PSMD11 is a short-lived protein, and knockdown of PSMD11 via RNA interference partially resulted in the occurrence of acute apoptosis in pancreatic cancer cells (66). It was identified that high expression of PSMD3 and PSMD11 was associated with poor overall survival in patients with melanoma. Therefore, PSMD3 and PSMD11 may be associated with the occurrence of melanoma metastasis.

Among all of the genes discussed, the key candidate genes and the mutated genes that were identified may serve crucial roles in the metastasis of melanoma. These prognostic markers require further study, and the accuracy of diagnosis may be improved based on multiple gene detection. There are specific limitations to the present bioinformatics analysis. Only a single open GEO dataset was included in the present study, considering that there was no suitable dataset for merge analysis and verification. No functional validation was conducted to support the present findings, although a number of the present observations were supported by previous studies. Biological validation is required in future studies. The survival analysis was conducted based on a TCGA dataset with a limited number of cases. The function and role of the candidate genes in the metastases of melanoma requires further validation. Future studies may aim to validate the gene expression in clinical samples. Additionally, the diagnostic value of BAP1 and its associated genes require validation in clinical samples. Further studies are required to investigate the molecular mechanism of the hub genes, selected in the present study, in melanoma metastasis.

In conclusion, 1,187 DEGs were identified in metastatic melanoma compared with primary melanoma. A total of 447 DEGs were mapped onto a PPI network. Based on the PPI network analysis, gene function enrichment analysis, KEGG network analysis and survival analysis, PIK3R3, CENPM, AURKA, LAMA1, PCNA, ADCY1, BUB1, NDC80 and PRKCA, which were associated with poor overall survival, may serve key roles in the metastasis and invasion processes of melanoma. Additionally, BAP1 and its associated genes may contribute to the metastasis and invasion processes of melanoma. The results of the present study may provide valuable prognostic markers and therapeutic targets for melanoma. Further studies are required to validate the function and role of these DEGs in the metastasis and aggressiveness of melanoma.

Acknowledgements

Not applicable.

Funding

The present study was supported in part by Shanghai Municipal Health Bureau General Project (grant no. 20134381 to Jia Chen) and Science and Technology Commission of Shanghai Municipal Health Bureau Youth Project (grant no. 20114Y057 to Yongxian Lai).

Availability of data and materials

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Authors' contributions

JC, YLa and YLi conceived and designed the study; JC, FW and YS performed data analysis; FW designed the figures. YS and YLa reviewed the literature. JC and YLi wrote the paper. DY and MX participated in the study design and revised the paper critically for important intellectual content.

Ethics approval and consent to participate

All patient specimens were collected and used according to the approval by the institutional Ethics Committee, and written informed consent was obtained, according to the ethical standards in the 1964 Declaration of Helsinki.

Patient consent for publication

Not applicable.

Competing interests

The authors declare no conflict of interest.

References

1 

Palmieri G, Capone M, Ascierto ML, Gentilcore G, Stroncek DF, Casula M, Sini MC, Palla M, Mozzillo N and Ascierto PA: Main roads to melanoma. J Transl Med. 7:862009. View Article : Google Scholar : PubMed/NCBI

2 

Pessina F, Navarria P, Tomatis S, Cozzi L, Franzese C, Di Guardo L, Ascolese AM, Reggiori G, Franceschini D, Del Vecchio M, et al: Outcome evaluation of patients with limited brain metastasis from malignant melanoma, treated with surgery, radiation therapy, and targeted therapy. World Neurosurg. 105:184–190. 2017. View Article : Google Scholar : PubMed/NCBI

3 

Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr and Kinzler KW: Cancer genome landscapes. Science. 339:1546–1558. 2013. View Article : Google Scholar : PubMed/NCBI

4 

Guo Y, Bao Y, Ma M and Yang W: Identification of key candidate genes and pathways in colorectal cancer by integrated bioinformatical analysis. Int J Mol Sci. 18:E7222017. View Article : Google Scholar : PubMed/NCBI

5 

Xu L, Shen SS, Hoshida Y, Subramanian A, Ross K, Brunet JP, Wagner SN, Ramaswamy S, Mesirov JP and Hynes RO: Gene expression changes in an animal melanoma model correlate with aggressiveness of human melanoma metastases. Mol Cancer Res. 6:760–769. 2008. View Article : Google Scholar : PubMed/NCBI

6 

Edgar R, Domrachev M and Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30:207–210. 2002. View Article : Google Scholar : PubMed/NCBI

7 

Gautier L, Cope L, Bolstad BM and Irizarry RA: affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 20:307–315. 2004. View Article : Google Scholar : PubMed/NCBI

8 

Smyth GK: Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. https://doi.org/10.2202/1544-6115.1027

9 

Hulsegge I, Kommadath A and Smits MA: Globaltest and GOEAST: Two different approaches for Gene Ontology analysis. BMC Proc. 3 (Suppl 4):S102009. View Article : Google Scholar : PubMed/NCBI

10 

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al The Gene Ontology Consortium, : Gene ontology: Tool for the unification of biology. Nat Genet. 25:25–29. 2000. View Article : Google Scholar : PubMed/NCBI

11 

Kanehisa M and Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27–30. 2000. View Article : Google Scholar : PubMed/NCBI

12 

Huang W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2009. View Article : Google Scholar : PubMed/NCBI

13 

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, et al: STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43(D1): D447–D452. 2015. View Article : Google Scholar : PubMed/NCBI

14 

Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z and Galon J: ClueGO: A Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 25:1091–1093. 2009. View Article : Google Scholar : PubMed/NCBI

15 

Bindea G, Galon J and Mlecnik B: CluePedia Cytoscape plugin: Pathway insights using integrated experimental and in silico data. Bioinformatics. 29:661–663. 2013. View Article : Google Scholar : PubMed/NCBI

16 

Scardoni G, Petterlini M and Laudanna C: Analyzing biological network parameters with CentiScaPe. Bioinformatics. 25:2857–2859. 2009. View Article : Google Scholar : PubMed/NCBI

17 

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, et al: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 6:pl12013. View Article : Google Scholar : PubMed/NCBI

18 

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, et al: The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2:401–404. 2012. View Article : Google Scholar : PubMed/NCBI

19 

Guan J, Gupta R and Filipp FV: Cancer systems biology of TCGA SKCM: Efficient detection of genomic drivers in melanoma. Sci Rep. 5:78572015. View Article : Google Scholar : PubMed/NCBI

20 

Tang Z, Li C, Kang B, Gao G, Li C and Zhang Z: GEPIA: A web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res 45 (W1). W98–W102. 2017. View Article : Google Scholar

21 

Chandrashekar DS, Bashel B, Balasubramanya SAH, Creighton CJ, Ponce-Rodriguez I, Chakravarthi BVSK and Varambally S: UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia. 19:649–658. 2017. View Article : Google Scholar : PubMed/NCBI

22 

Chang X, Zhang H, Lian S and Zhu W: miR-137 suppresses tumor growth of malignant melanoma by targeting aurora kinase A. Biochem Biophys Res Commun. 475:251–256. 2016. View Article : Google Scholar : PubMed/NCBI

23 

Krasagakis K, Lindschau C, Fimmel S, Eberle J, Quass P, Haller H and Orfanos CE: Proliferation of human melanoma cells is under tight control of protein kinase C alpha. J Cell Physiol. 199:381–387. 2004. View Article : Google Scholar : PubMed/NCBI

24 

Lahn MM and Sundell KL: The role of protein kinase C-alpha (PKC-alpha) in melanoma. Melanoma Res. 14:85–89. 2004. View Article : Google Scholar : PubMed/NCBI

25 

Kabbarah O, Nogueira C, Feng B, Nazarian RM, Bosenberg M, Wu M, Scott KL, Kwong LN, Xiao Y, Cordon-Cardo C, et al: Integrative genome comparison of primary and metastatic melanomas. PLoS One. 5:e107702010. View Article : Google Scholar : PubMed/NCBI

26 

Hua Y, Ma X, Liu X, Yuan X, Qin H and Zhang X: Identification of the potential biomarkers for the metastasis of rectal adenocarcinoma. APMIS. 125:93–100. 2017. View Article : Google Scholar : PubMed/NCBI

27 

Meng X, Chen X, Lu P, Ma W, Yue D, Song L and Fan Q: MicroRNA-202 inhibits tumor progression by targeting LAMA1 in esophageal squamous cell carcinoma. Biochem Biophys Res Commun. 473:821–827. 2016. View Article : Google Scholar : PubMed/NCBI

28 

Fernandes H, D'Souza CR, Swethadri GK and Naik CN: Ameboma of the colon with amebic liver abscess mimicking metastatic colon cancer. Indian J Pathol Microbiol. 52:228–230. 2009. View Article : Google Scholar : PubMed/NCBI

29 

Ayari H, Rebii S, Ghariani W, Daghfous A, Hasni R, Rehaiem R, Rezgui-Marhoul L and Zoghlami A: Colonic amoebiasis simulating a cecal tumor: Case report. Med Sante Trop. 23:274–275. 2013.(In French). PubMed/NCBI

30 

Moorchung N, Singh V, Srinivas V, Jaiswal SS and Singh G: Caecal amebic colitis mimicking obstructing right sided colonic carcinoma with liver metastases: A rare case. J Cancer Res Ther. 10:440–442. 2014. View Article : Google Scholar : PubMed/NCBI

31 

Grosse A: Diagnosis of colonic amebiasis and coexisting signet-ring cell carcinoma in intestinal biopsy. World J Gastroenterol. 22:8234–8241. 2016. View Article : Google Scholar : PubMed/NCBI

32 

Slominski A, Kim TK, Brożyna AA, Janjetovic Z, Brooks DL, Schwab LP, Skobowiat C, Jóźwicki W and Seagroves TN: The role of melanogenesis in regulation of melanoma behavior: Melanogenesis leads to stimulation of HIF-1α expression and HIF-dependent attendant pathways. Arch Biochem Biophys. 563:79–93. 2014. View Article : Google Scholar : PubMed/NCBI

33 

Lewis TB, Robison JE, Bastien R, Milash B, Boucher K, Samlowski WE, Leachman SA, Dirk Noyes R, Wittwer CT, Perreard L and Bernard PS: Molecular classification of melanoma using real-time quantitative reverse transcriptase-polymerase chain reaction. Cancer. 104:1678–1686. 2005. View Article : Google Scholar : PubMed/NCBI

34 

Riker AI, Enkemann SA, Fodstad O, Liu S, Ren S, Morris C, Xi Y, Howell P, Metge B, Samant RS, et al: The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis. BMC Med Genomics. 1:132008. View Article : Google Scholar : PubMed/NCBI

35 

Singh CK, George J, Nihal M, Sabat G, Kumar R and Ahmad N: Novel downstream molecular targets of SIRT1 in melanoma: A quantitative proteomics approach. Oncotarget. 5:1987–1999. 2014. View Article : Google Scholar : PubMed/NCBI

36 

Puig-Butille JA, Vinyals A, Ferreres JR, Aguilera P, Cabré E, Tell-Martí G, Marcoval J, Mateo F, Palomero L, Badenas C, et al: AURKA Overexpression Is Driven by FOXM1 and MAPK/ERK Activation in Melanoma Cells Harboring BRAF or NRAS Mutations: Impact on Melanoma Prognosis and Therapy. J Invest Dermatol. 137:1297–1310. 2017. View Article : Google Scholar : PubMed/NCBI

37 

Quan L, Shi J, Tian Y, Zhang Q, Zhang Y, Zhang Y, Hui Q and Tao K: Identification of potential therapeutic targets for melanoma using gene expression analysis. Neoplasma. 62:733–739. 2015. View Article : Google Scholar : PubMed/NCBI

38 

Meng QC, Wang HC, Song ZL, Shan ZZ, Yuan Z, Zheng Q and Huang XY: Overexpression of NDC80 is correlated with prognosis of pancreatic cancer and regulates cell proliferation. Am J Cancer Res. 5:1730–1740. 2015.PubMed/NCBI

39 

Qu Y, Li J, Cai Q and Liu B: Hec1/Ndc80 is overexpressed in human gastric cancer and regulates cell growth. J Gastroenterol. 49:408–418. 2014. View Article : Google Scholar : PubMed/NCBI

40 

Chen ZH, Wang WT, Huang W, Fang K, Sun YM, Liu SR, Luo XQ and Chen YQ: The lncRNA HOTAIRM1 regulates the degradation of PML-RARA oncoprotein and myeloid cell differentiation by enhancing the autophagy pathway. Cell Death Differ. 24:212–224. 2016. View Article : Google Scholar : PubMed/NCBI

41 

Yan X, Huang L, Liu L, Qin H and Song Z: Nuclear division cycle 80 promotes malignant progression and predicts clinical outcome in colorectal cancer. Cancer Med. 7:420–432. 2018. View Article : Google Scholar : PubMed/NCBI

42 

Ahonen LJ, Kallio MJ, Daum JR, Bolton M, Manke IA, Yaffe MB, Stukenberg PT and Gorbsky GJ: Polo-like kinase 1 creates the tension-sensing 3F3/2 phosphoepitope and modulates the association of spindle-checkpoint proteins at kinetochores. Curr Biol. 15:1078–1089. 2005. View Article : Google Scholar : PubMed/NCBI

43 

Zhang Z, Zhang G, Gao Z, Li S, Li Z, Bi J, Liu X, Li Z and Kong C: Comprehensive analysis of differentially expressed genes associated with PLK1 in bladder cancer. BMC Cancer. 17:8612017. View Article : Google Scholar : PubMed/NCBI

44 

Yu T, Li J, Yan M, Liu L, Lin H, Zhao F, Sun L, Zhang Y, Cui Y, Zhang F, et al: MicroRNA-193a-3p and −5p suppress the metastasis of human non-small-cell lung cancer by downregulating the ERBB4/PIK3R3/mTOR/S6K2 signaling pathway. Oncogene. 34:413–423. 2015. View Article : Google Scholar : PubMed/NCBI

45 

Cao G, Dong W, Meng X, Liu H, Liao H and Liu S: MiR-511 inhibits growth and metastasis of human hepatocellular carcinoma cells by targeting PIK3R3. Tumour Biol. 36:4453–4459. 2015. View Article : Google Scholar : PubMed/NCBI

46 

Klahan S, Wu MS, Hsi E, Huang CC, Hou MF and Chang WC: Computational analysis of mRNA expression profiles identifies the ITG family and PIK3R3 as crucial genes for regulating triple negative breast cancer cell migration. BioMed Res Int. 2014:5365912014. View Article : Google Scholar : PubMed/NCBI

47 

Liu K, Li X, Cao Y, Ge Y, Wang J and Shi B: MiR-132 inhibits cell proliferation, invasion and migration of hepatocellular carcinoma by targeting PIK3R3. Int J Oncol. 47:1585–1593. 2015. View Article : Google Scholar : PubMed/NCBI

48 

Zhu Y, Zhao H, Rao M and Xu S: MicroRNA-365 inhibits proliferation, migration and invasion of glioma by targeting PIK3R3. Oncol Rep. 37:2185–2192. 2017. View Article : Google Scholar : PubMed/NCBI

49 

Wang G, Yang X, Li C, Cao X, Luo X and Hu J: PIK3R3 induces epithelial-to-mesenchymal transition and promotes metastasis in colorectal cancer. Mol Cancer Ther. 13:1837–1847. 2014. View Article : Google Scholar : PubMed/NCBI

50 

Calderón A, Ortiz-Espín A, Iglesias-Fernández R, Carbonero P, Pallardó FV, Sevilla F and Jiménez A: Thioredoxin (Trxo1) interacts with proliferating cell nuclear antigen (PCNA) and its overexpression affects the growth of tobacco cell culture. Redox Biol. 11:688–700. 2017. View Article : Google Scholar : PubMed/NCBI

51 

Yang Q, Ou C, Liu M, Xiao W, Wen C and Sun F: NRAGE promotes cell proliferation by stabilizing PCNA in a ubiquitin-proteasome pathway in esophageal carcinomas. Carcinogenesis. 35:1643–1651. 2014. View Article : Google Scholar : PubMed/NCBI

52 

Kadariya Y, Cheung M, Xu J, Pei J, Sementino E, Menges CW, Cai KQ, Rauscher FJ, Klein-Szanto AJ and Testa JR: Bap1 Is a bona fide tumor suppressor: Genetic evidence from mouse models carrying heterozygous germline Bap1 mutations. Cancer Res. 76:2836–2844. 2016. View Article : Google Scholar : PubMed/NCBI

53 

Dey A, Seshasayee D, Noubade R, French DM, Liu J, Chaurushiya MS, Kirkpatrick DS, Pham VC, Lill JR, Bakalarski CE, et al: Loss of the tumor suppressor BAP1 causes myeloid transformation. Science. 337:1541–1546. 2012. View Article : Google Scholar : PubMed/NCBI

54 

Field MG, Durante MA, Anbunathan H, Cai LZ, Decatur CL, Bowcock AM, Kurtenbach S and Harbour JW: Punctuated evolution of canonical genomic aberrations in uveal melanoma. Nat Commun. 9:1162018. View Article : Google Scholar : PubMed/NCBI

55 

Smit KN, van Poppelen NM, Vaarwater J, Verdijk R, van Marion R, Kalirai H, Coupland SE, Thornton S, Farquhar N, Dubbink HJ, et al: Combined mutation and copy-number variation detection by targeted next-generation sequencing in uveal melanoma. Mod Pathol. 31:763–771. 2018. View Article : Google Scholar : PubMed/NCBI

56 

Pitcovski J, Shahar E, Aizenshtein E and Gorodetsky R: Melanoma antigens and related immunological markers. Crit Rev Oncol Hematol. 115:36–49. 2017. View Article : Google Scholar : PubMed/NCBI

57 

Garfield EM, Walton KE, Quan VL, VandenBoom T, Zhang B, Kong BY, Isales MC, Panah E, Kim G and Gerami P: Histomorphologic spectrum of germline-related and sporadic BAP1-inactivated melanocytic tumors. J Am Acad Dermatol. 79:525–534. 2018. View Article : Google Scholar : PubMed/NCBI

58 

Tetzlaff MT, Torres-Cabala CA, Pattanaprichakul P, Rapini RP, Prieto VG and Curry JL: Emerging clinical applications of selected biomarkers in melanoma. Clin Cosmet Investig Dermatol. 8:35–46. 2015.PubMed/NCBI

59 

Balasubramani A, Larjo A, Bassein JA, Chang X, Hastie RB, Togher SM, Lähdesmäki H and Rao A: Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex. Nat Commun. 6:73072015. View Article : Google Scholar : PubMed/NCBI

60 

Scotto L, Narayan G, Nandula SV, Arias-Pulido H, Subramaniyam S, Schneider A, Kaufmann AM, Wright JD, Pothuri B, Mansukhani M and Murty VV: Identification of copy number gain and overexpressed genes on chromosome arm 20q by an integrative genomic approach in cervical cancer: Potential role in progression. Genes Chromosomes Cancer. 47:755–765. 2008. View Article : Google Scholar : PubMed/NCBI

61 

Katoh M: Functional and cancer genomics of ASXL family members. Br J Cancer. 109:299–306. 2013. View Article : Google Scholar : PubMed/NCBI

62 

Katoh M: Functional proteomics of the epigenetic regulators ASXL1, ASXL2 and ASXL3: A convergence of proteomics and epigenetics for translational medicine. Expert Rev Proteomics. 12:317–328. 2015. View Article : Google Scholar : PubMed/NCBI

63 

Sahlberg KK, Hongisto V, Edgren H, Mäkelä R, Hellström K, Due EU, Moen Vollan HK, Sahlberg N, Wolf M, Børresen-Dale AL, et al: The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells. Mol Oncol. 7:392–401. 2013. View Article : Google Scholar : PubMed/NCBI

64 

Patel VN, Gokulrangan G, Chowdhury SA, Chen Y, Sloan AE, Koyutürk M, Barnholtz-Sloan J and Chance MR: Network signatures of survival in glioblastoma multiforme. PLOS Comput Biol. 9:e10032372013. View Article : Google Scholar : PubMed/NCBI

65 

Deng S, Zhou H, Xiong R, Lu Y, Yan D, Xing T, Dong L, Tang E and Yang H: Over-expression of genes and proteins of ubiquitin specific peptidases (USPs) and proteasome subunits (PSs) in breast cancer tissue observed by the methods of RFDD-PCR and proteomics. Breast Cancer Res Treat. 104:21–30. 2007. View Article : Google Scholar : PubMed/NCBI

66 

Qi T, Zhang W, Luan Y, Kong F, Xu D, Cheng G and Wang Y: Proteomic profiling identified multiple short-lived members of the central proteome as the direct targets of the addicted oncogenes in cancer cells. Mol Cell Proteomics. 13:49–62. 2014. View Article : Google Scholar : PubMed/NCBI

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Spandidos Publications style
Chen J, Wu F, Shi Y, Yang D, Xu M, Lai Y and Liu Y: Identification of key candidate genes involved in melanoma metastasis. Mol Med Rep 20: 903-914, 2019
APA
Chen, J., Wu, F., Shi, Y., Yang, D., Xu, M., Lai, Y., & Liu, Y. (2019). Identification of key candidate genes involved in melanoma metastasis. Molecular Medicine Reports, 20, 903-914. https://doi.org/10.3892/mmr.2019.10314
MLA
Chen, J., Wu, F., Shi, Y., Yang, D., Xu, M., Lai, Y., Liu, Y."Identification of key candidate genes involved in melanoma metastasis". Molecular Medicine Reports 20.2 (2019): 903-914.
Chicago
Chen, J., Wu, F., Shi, Y., Yang, D., Xu, M., Lai, Y., Liu, Y."Identification of key candidate genes involved in melanoma metastasis". Molecular Medicine Reports 20, no. 2 (2019): 903-914. https://doi.org/10.3892/mmr.2019.10314