Exploration and Validation of Metastasis-associated Genes for Skin Cutaneous Melanoma

Abstract Background: Skin cutaneous melanoma is a malignant and highly metastatic skin tumor, and its morbidity and mortality are still rising worldwide. However, the molecular mechanisms that promote melanoma metastasis are unclear. Methods: Two datasets (GSE15605 and GSE46517) were retrieved to identify the differentially expressed genes (DEGs), including 23 normal skin tissues (N), 77 primary melanoma tissues (T) and 85 metastatic melanoma tissues (M). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were performed to explore the functions of the DEGs. The protein–protein interaction (PPI) network was constructed using the STRING tool and Cytoscape software. We used the cytoHubba plugin of Cytoscape to identify the most significant hub genes by five topological analyses (Degree, Bottleneck, MCC, MNC, and EPC). Hub gene expression was validated using the UALCAN website. Clinical relevance was investigated using The Cancer Genome Atlas (TCGA) resources. Finally, we explored the association between metastasis-associated genes and immune infiltrates through the Tumor Immune Estimation Resource (TIMER) database and performed drug-gene interaction analysis using the Drug-Gene Interaction database.Results: A total of 294 specific genes were related to melanoma metastasis and were mainly involved in the positive regulation of locomotion, mitotic cell cycle process, and epithelial cell differentiation. Four hub genes (CDK1, FOXM1, KIF11, and RFC4) were identified from the cytoHubba plugin of Cytoscape. CDK1 was significantly upregulated in metastatic melanoma compared with primary melanoma, and high expression of CDK1 was positively correlated with poor prognosis. We found that CDK1 expression correlated positively with the infiltration levels of macrophage cells (Rho = -0.164, P = 2.02e-03) and neutrophil cells (Rho = 0.269, P = 2.72e-07) in SKCM metastasis. In addition, we identified that CDK1 had a close interaction with 10 antitumor drugs. Conclusions: CDK1 was identified as a hub gene involved in the progression of melanoma metastasis and may be regarded as a therapeutic target for melanoma patients to improve prognosis and prevent metastasis in the future.

Download Full-text

Identification of Metastasis-Associated Gene And Its Correlation With Immune Infiltrates For Skin Cutaneous Melanoma

10.21203/rs.3.rs-1059356/v1 ◽

2021 ◽

Author(s):

Hong Luan ◽

Ye He ◽

Linge Jian ◽

Tuo Zhang ◽

Liping Zhou

Keyword(s):

Metastatic Melanoma ◽

Cutaneous Melanoma ◽

Molecular Mechanisms ◽

Immune Cell ◽

Gene Expression Omnibus ◽

Skin Tumor ◽

Melanoma Metastasis ◽

Hub Genes ◽

P53 Signaling ◽

Genes Expression

Abstract Background: Skin cutaneous melanoma is a malignant and highly metastatic skin tumor. As the most common cause of death in skin cancer, its morbidity and mortality are still rising worldwide. However, the molecular mechanisms of melanoma metastasis are unclear. Methods: Three Gene Expression Omnibus (GEO) datasets (GSE15605, GSE7553 and GSE8401) were downloaded to identify the differentially expressed genes (DEGs) between primary and metastatic melanoma samples. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were performed to explore the functional of DEGs by Metascape. The protein-protein interaction (PPI) network was constructed using STRING tool and Cytoscape software. We used the cytoHubba plugin of Cytoscape to identify the most significant hub genes by four topological analyses (Degree, MCC, DMNC, and MNC). Hub genes expression was validated using UALCAN website. Finally, we explored the association between metastasis-associated genes and immune infiltrates through Tumor Immune Estimation Resource (TIMER) database.Results: In total, we obtained 196 DEGs including 12 upregulated and 184 downregulated genes. GO and KEGG enrichment results indicated that DEGs were mainly concentrated in epidermis development, cornified envelope, structural molecule activity, and p53 signaling pathway. Eight hub genes were identified to be closely related to melanoma metastasis, including SPRR1B, DSC1, PKP1, TGM1, DSG1, IVL, SPRR1A and DSC3. On the ULCAN website, all hub genes expression levels are lower in metastatic tissues than in primary cancers. Results from TIMER database revealed that DSC1 and TGM1 were significantly related with most of immune cell infiltration.Conclusions: SPRR1B, DSC1, PKP1, TGM1, DSG1, IVL, SPRR1A and DSC3 may be hub genes involved in the progression of melanoma metastasis and thus may be regarded as therapeutic targets in the future. DSC1 and TGM1 play an important role in the microenvironment of metastatic melanoma by regulating the tumor infiltration of immune cells.

Download Full-text

Identification of core genes and pathways in melanoma metastasis via bioinformatics analysis

10.21203/rs.3.rs-39969/v1 ◽

2020 ◽

Author(s):

Yumei Li ◽

Bifei Li ◽

Fan Chen ◽

Weiyu Shen ◽

Vladimir L. Katanaev ◽

...

Keyword(s):

Gene Expression ◽

Metastatic Melanoma ◽

Molecular Mechanisms ◽

Therapeutic Targets ◽

Primary Melanoma ◽

Melanoma Cells ◽

Receptor Interaction ◽

Melanoma Metastasis ◽

Hub Genes ◽

Core Genes

Abstract Background Metastasis is the leading cause of melanoma mortality. Current therapies are rarely curative for metastatic melanoma, revealing the urgent need to identify more effective preventive and therapeutic targets. This study aimed to screen for the key core genes and molecular mechanisms related to the metastasis of melanoma. Methods Gene expression profile, GSE8401 including 31 primary melanoma and 52 metastatic melanoma clinical samples, was downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between metastatic melanoma and primary melanoma were screened using GEO2R. Assays of gene ontology (GO), Kyoto Encyclopedia of Gene and Genome (KEGG) pathway and protein-protein interaction (PPI) were performed to visualize these DEGs through Database for Annotation, Visualization and Integrated Discovery (DAVID) software and Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape with Molecular Complex Detection (MCODE) plug-in tools. Top 10 genes with high degree were defined as hub genes. Furthermore, paired post-metastatic melanoma cells and pre-metastatic melanoma cells were established by experimental mouse model of melanoma metastasis to verify the expression of these hub genes. Results 424 DEGs between the metastatic melanoma and primary melanoma were screened, including 60 upregulated genes enriched in ECM-receptor interaction and progesterone-mediated oocyte maturation and 364 downregulated genes enriched in amoebiasis, melanogenesis, and ECM-receptor interaction. CDH1, EGFR, KRT5, COL17A1, KRT14, IVL, DSP, DSG1, FLG and CDK1 were defined as the hub genes. . In addition, paired post-metastatic melanoma cells (A375M) and pre-metastatic melanoma cells (A375) were established and qRT-PCR analysis confirmed the expression of the hub genes during melanoma metastasis. Conclusion This bioinformatic study has provided a deeper understanding of the molecular mechanisms of melanoma metastasis. KRT5, IVL and COL17A1 have emerged as possible biomarkers and therapeutic targets in metastasis of melanoma.

Download Full-text

Identification of Metastasis-Associated MicroRNAs in Metastatic Melanoma by miRNA Expression Profile and Experimental Validation

Frontiers in Genetics ◽

10.3389/fgene.2021.663110 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yunshu Gao ◽

Jiahua Xu ◽

Hongwei Li ◽

Yi Hu ◽

Guanzhen Yu

Keyword(s):

Metastatic Melanoma ◽

Signaling Pathway ◽

Target Genes ◽

Primary Melanoma ◽

Mirna Expression Profile ◽

Melanoma Metastasis ◽

Hippo Signaling ◽

Invasive Ability ◽

Hub Genes ◽

Proliferation And Apoptosis

It is reported that microRNAs (miRNA) have paramount functions in many cellular biological processes, development, metabolism, differentiation, survival, proliferation, and apoptosis included, some of which are involved in metastasis of tumors, such as melanoma. Here, three metastasis-associated miRNAs, miR-18a-5p (upregulated), miR-155-5p (downregulated), and miR-93-5p (upregulated), were identified from a total of 63 different expression miRNAs (DEMs) in metastatic melanoma compared with primary melanoma. We predicted 262 target genes of miR-18a-5p, 904 miR-155-5p target genes, and 1220 miR-93-5p target genes. They participated in pathways concerning melanoma, such as TNF signaling pathway, pathways in cancer, FoxO signaling pathway, cell cycle, Hippo signaling pathway, and TGF-beta signaling pathway. We identified the top 10 hub nodes whose degrees were higher for each survival-associated miRNA as hub genes through constructing the PPI network. Using the selected miRNA and the hub genes, we constructed the miRNA-hub gene network, and PTEN and CCND1 were found to be regulated by all three miRNAs. Of note, miR-155-5p was obviously downregulated in metastatic melanoma tissues, and miR-18a-5p and miR-93-5p were obviously regulated positively in metastatic melanoma tissues. In validating experiments, miR-155-5p's overexpression inhibited miR-18a-5p's and miR-93-5p's expression, which could all significantly reduce SK-MEL-28 cells' invasive ability. Finally, miR-93-5p and its potential target gene UBC were selected for further validation. We found that miR-93-5p's inhibition could reduce SK-MEL-28 cell's invasive ability through upregulated the expression of UBC, and the anti-invasive effect was reserved by downregulation of UBC. The results show that the selected three metastasis-associated miRNAs participate in the process of melanoma metastasis via regulating their target genes, providing a potential molecular mechanism for this disease.

Download Full-text

Identification of Core Genes and Pathways in Melanoma Metastasis via Bioinformatics Analysis

International Journal of Molecular Sciences ◽

10.3390/ijms23020794 ◽

2022 ◽

Vol 23 (2) ◽

pp. 794

Author(s):

Renjian Xie ◽

Bifei Li ◽

Lee Jia ◽

Yumei Li

Keyword(s):

Gene Expression ◽

Molecular Mechanisms ◽

Primary Melanoma ◽

Melanoma Metastasis ◽

Ppi Network ◽

Hub Genes ◽

Receptor Interactions ◽

Upregulated Genes ◽

Core Genes ◽

A375 Cells

Metastasis is the leading cause of melanoma-related mortality. Current therapies are rarely curative for metastatic melanoma, revealing the urgent need to identify more effective preventive and therapeutic targets. This study aimed to screen the core genes and molecular mechanisms related to melanoma metastasis. A gene expression profile, GSE8401, including 31 primary melanoma and 52 metastatic melanoma clinical samples, was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between melanoma metastases and primary melanoma were screened using GEO2R tool. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analyses of DEGs were performed using the Database for Annotation Visualization and Integrated Discovery (DAVID). The Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape with Molecular Complex Detection (MCODE) plug-in tools were utilized to detect the protein–protein interaction (PPI) network among DEGs. The top 10 genes with the highest degrees of the PPI network were defined as hub genes. In the results, 425 DEGs, including 60 upregulated genes and 365 downregulated genes, were identified. The upregulated genes were enriched in ECM–receptor interactions and the regulation of actin cytoskeleton, while 365 downregulated genes were enriched in amoebiasis, melanogenesis, and ECM–receptor interactions. The defined hub genes included CDK1, COL17A1, EGFR, DSG1, KRT14, FLG, CDH1, DSP, IVL, and KRT5. In addition, the mRNA and protein levels of the hub genes during melanoma metastasis were verified in the TCGA database and paired post- and premetastatic melanoma cells, respectively. Finally, KRT5-specific siRNAs were utilized to reduce the KRT5 expression in melanoma A375 cells. An MTT assay and a colony formation assay showed that KRT5 knockdown significantly promoted the proliferation of A375 cells. A Transwell assay further suggested that KRT5 knockdown significantly increased the cell migration and cell invasion of A375 cells. This bioinformatics study provided a deeper understanding of the molecular mechanisms of melanoma metastasis. The in vitro experiments showed that KRT5 played the inhibitory effects on melanoma metastasis. Therefore, KRT5 may serve important roles in melanoma metastasis.

Download Full-text

Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis

10.21203/rs.3.rs-25246/v4 ◽

2020 ◽

Author(s):

Wenxing Su ◽

Yi Guan ◽

Biao Huang ◽

Juanjuan Wang ◽

Yuqian Wei ◽

...

Keyword(s):

Differentially Expressed Gene ◽

Primary Melanoma ◽

Enrichment Analysis ◽

Gene Interaction ◽

Underlying Mechanism ◽

Bioinformatic Analysis ◽

Pathway Enrichment Analysis ◽

Melanoma Metastasis ◽

Ppi Network ◽

Hub Genes

Abstract Background: Melanoma has the highest mortality rate of all skin tumors, and metastases are the major cause of death from it. The molecular mechanism leading to melanoma metastasis is currently unclear. Methods: With the goal of revealing the underlying mechanism, three data sets with accession numbers GSE8401, GSE46517 and GSE7956 were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the differentially expressed gene (DEG) of primary melanoma and metastatic melanoma, three kinds of analyses were performed, namely functional annotation, protein‐protein interaction (PPI) network and module construction, and co-expression and drug-gene interaction prediction analysis. Results: A total of 41 up-regulated genes and 79 down-regulated genes was selected for subsequent analyses. Results of pathway enrichment analysis showed that extracellular matrix organization and proteoglycans in cancer are closely related to melanoma metastasis. In addition, seven pivotal genes were identified from PPI network, including CXCL8, THBS1, COL3A1, TIMP3, KIT, DCN, and IGFBP5, which have all been verified in the TCGA database and clinical specimens, but only CXCL8, THBS1 and KIT had significant differences in expression. Conclusions: To conclude, CXCL8, THBS1 and KIT may be the hub genes in the metastasis of melanoma and thus may be regarded as therapeutic targets in the future.

Download Full-text

Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis

BMC Cancer ◽

10.1186/s12885-020-07372-5 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Wenxing Su ◽

Yi Guan ◽

Biao Huang ◽

Juanjuan Wang ◽

Yuqian Wei ◽

...

Keyword(s):

Differentially Expressed Gene ◽

Primary Melanoma ◽

Enrichment Analysis ◽

Gene Interaction ◽

Underlying Mechanism ◽

Bioinformatic Analysis ◽

Pathway Enrichment Analysis ◽

Melanoma Metastasis ◽

Ppi Network ◽

Hub Genes

Abstract Background Melanoma has the highest mortality rate of all skin tumors, and metastases are the major cause of death from it. The molecular mechanism leading to melanoma metastasis is currently unclear. Methods With the goal of revealing the underlying mechanism, three data sets with accession numbers GSE8401, GSE46517 and GSE7956 were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the differentially expressed gene (DEG) of primary melanoma and metastatic melanoma, three kinds of analyses were performed, namely functional annotation, protein-protein interaction (PPI) network and module construction, and co-expression and drug-gene interaction prediction analysis. Results A total of 41 up-regulated genes and 79 down-regulated genes was selected for subsequent analyses. Results of pathway enrichment analysis showed that extracellular matrix organization and proteoglycans in cancer are closely related to melanoma metastasis. In addition, seven pivotal genes were identified from PPI network, including CXCL8, THBS1, COL3A1, TIMP3, KIT, DCN, and IGFBP5, which have all been verified in the TCGA database and clinical specimens, but only CXCL8, THBS1 and KIT had significant differences in expression. Conclusions To conclude, CXCL8, THBS1 and KIT may be the hub genes in the metastasis of melanoma and thus may be regarded as therapeutic targets in the future.

Download Full-text

Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis

10.21203/rs.3.rs-25246/v3 ◽

2020 ◽

Author(s):

wenxing su ◽

yi guan ◽

biao huang ◽

juanjuan wang ◽

yuqian wei ◽

...

Keyword(s):

Differentially Expressed Gene ◽

Primary Melanoma ◽

Enrichment Analysis ◽

Gene Interaction ◽

Underlying Mechanism ◽

Bioinformatic Analysis ◽

Pathway Enrichment Analysis ◽

Melanoma Metastasis ◽

Ppi Network ◽

Hub Genes

Abstract Background: Melanoma has the highest mortality rate of all skin tumors, and metastases are the major cause of death from it. The molecular mechanism leading to melanoma metastasis is currently unclear. Methods: With the goal of revealing the underlying mechanism, three data sets with accession numbers GSE8401, GSE46517 and GSE7956 were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the differentially expressed gene (DEG) of primary melanoma and metastatic melanoma, three kinds of analyses were performed, namely functional annotation, protein‐protein interaction (PPI) network and module construction, and co-expression and drug-gene interaction prediction analysis. Results: A total of 41 up-regulated genes and 79 down-regulated genes was selected for subsequent analyses. Results of pathway enrichment analysis showed that extracellular matrix organization and proteoglycans in cancer are closely related to melanoma metastasis. In addition, seven pivotal genes were identified from PPI network, including CXCL8, THBS1, COL3A1, TIMP3, KIT, DCN, and IGFBP5, which have all been verified in the TCGA database and clinical specimens, but only CXCL8, THBS1 and KIT had significant differences in expression. Conclusions: To conclude, CXCL8, THBS1 and KIT may be the hub genes in the metastasis of melanoma and thus may be regarded as therapeutic targets in the future.

Download Full-text

LRG1 Promotes Metastatic Dissemination of Melanoma through Regulating EGFR/STAT3 Signalling

Cancers ◽

10.3390/cancers13133279 ◽

2021 ◽

Vol 13 (13) ◽

pp. 3279

Author(s):

Yuet Ping Kwan ◽

Melissa Hui Yen Teo ◽

Jonathan Chee Woei Lim ◽

Michelle Siying Tan ◽

Graciella Rosellinny ◽

...

Keyword(s):

Metastatic Melanoma ◽

Melanoma Cell ◽

Molecular Mechanisms ◽

Complex Disease ◽

Treatment Options ◽

Melanoma Metastasis ◽

Dependent Manner ◽

Promoting Effect ◽

Human Patient ◽

Cell Invasiveness

Although less common, melanoma is the deadliest form of skin cancer largely due to its highly metastatic nature. Currently, there are limited treatment options for metastatic melanoma and many of them could cause serious side effects. A better understanding of the molecular mechanisms underlying the complex disease pathophysiology of metastatic melanoma may lead to the identification of novel therapeutic targets and facilitate the development of targeted therapeutics. In this study, we investigated the role of leucine-rich α-2-glycoprotein 1 (LRG1) in melanoma development and progression. We first established the association between LRG1 and melanoma in both human patient biopsies and mouse melanoma cell lines and revealed a significant induction of LRG1 expression in metastatic melanoma cells. We then showed no change in tumour cell growth, proliferation, and angiogenesis in the absence of the host Lrg1. On the other hand, there was reduced melanoma cell metastasis to the lungs in Lrg1-deficient mice. This observation was supported by the promoting effect of LRG1 in melanoma cell migration, invasion, and adhesion. Mechanistically, LRG1 mediates melanoma cell invasiveness in an EGFR/STAT3-dependent manner. Taken together, our studies provided compelling evidence that LRG1 is required for melanoma metastasis but not growth. Targeting LRG1 may offer an alternative strategy to control malignant melanoma.

Download Full-text