Human skin cutaneous melanoma is the most common and dangerous skin tumour, but its pathogenesis is still unclear. Although some progress has been made in genetic research, no molecular indicators related to the treatment and prognosis of melanoma have been found. In various diseases, dysregulation of lncRNA is common, but its role has not been fully elucidated. In recent years, the birth of the “competitive endogenous RNA” theory has promoted our understanding of lncRNAs.
Methods
To identify the key lncRNAs in melanoma, we reconstructed a global triple network based on the “competitive endogenous RNA” theory. Gene Ontology and KEGG pathway analysis were performed using DAVID (Database for Annotation, Visualization, and Integration Discovery). Our findings were validated through qRT-PCR assays. Moreover, to determine whether the identified hub gene signature is capable of predicting the survival of cutaneous melanoma patients, a multivariate Cox regression model was performed.
Results
According to the “competitive endogenous RNA” theory, 898 differentially expressed mRNAs, 53 differentially expressed lncRNAs and 16 differentially expressed miRNAs were selected to reconstruct the competitive endogenous RNA network. MALAT1, LINC00943, and LINC00261 were selected as hub genes and are responsible for the tumorigenesis and prognosis of cutaneous melanoma.
Conclusions
MALAT1, LINC00943, and LINC00261 may be closely related to tumorigenesis in cutaneous melanoma. In addition, MALAT1 and LINC00943 may be independent risk factors for the prognosis of patients with this condition and might become predictive molecules for the long-term treatment of melanoma and potential therapeutic targets.
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Abkürzungen
ceRNA
Competitive endogenous RNA
SKCM
Skin cutaneous melanoma
lncRNA
Long non-coding RNAs
NCBI GEO
National center for biotechnology information gene expression omnibus
GO
Gene ontology
KEGG
Kyoto encyclopedia of genes and genomes
DAVID
Database for annotation, visualization, and integration discovery
MREs
miRNA-response elements
DEMis
Differential expressed miRNAs
DELs
Differential expressed lncRNAs
DEMs
Differential expressed mRNAs
CNV
Copy number variation
Background
Human skin cutaneous melanoma (SKCM) is the most common and dangerous type of skin tumour [1, 2]. Worldwide, approximately 232,000 (1.7%) cases of cutaneous melanoma are reported among all newly diagnosed primary malignant cancers, and this disease results in approximately 55,500 cancer deaths (0.7% of all cancer deaths) [1, 3]. The incidence of melanoma in Australia, New Zealand, Norway, Sweden, the UK, and the USA from 1982 to 2011 has shown increases of approximately 3% annually and will further increase until 2022 [3]. In 2015, there were 3.1 million people with melanoma, resulting in 59,800 deaths [4]. Nevertheless, 95,710 cases of melanoma in situ will be newly diagnosed in 2020 [5]. The high incidence and high mortality of melanoma indicate that researchers must further study this disease. Although some achievements have been made in the genetic research of melanoma, markers related to diagnosis and treatment are needed.
Tumorigenesis often results from aberrant transcriptomes, including aberrant levels of coding RNA and noncoding RNA [6‐8]. It has been proven that lncRNAs have various effects, including regulation of gene transcription, post-transcriptional regulation and epigenetic regulation [9‐12]. In addition, dysregulation of lncRNAs has been observed in various diseases [13‐16]. Unfortunately, the functions of lncRNAs are more difficult to identify than those of coding RNAs. Until now, only a few lncRNAs have been identified as crucial factors in the tumorigenesis and development of melanoma, including ZNNT1, THOR and SAMMSON [14, 15, 17]. Thus, how to locate them and define their functions is a challenge of current research.
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The effect of miRNAs on malignancies has been verified in many ways. Studies have suggested that lncRNAs can regulate miRNA abundance by binding and sequestering them [18]. Thus, we aimed to study the function of lncRNAs by studying the interactions among lncRNAs, mRNAs and miRNAs. In 2011, the competitive endogenous RNA (ceRNA) hypothesis proposed a novel regulatory mechanism between noncoding RNA and coding RNA [19‐21]. This theory indicated that any RNA transcript harbouring miRNA-response elements (MREs) can sequester miRNAs from other targets sharing the same MREs and thereby regulate their expression [19‐21]. That is, the RNA transcripts that can be cross regulated by each other can be biologically predicted according to their common MREs [20, 22]. Evidence has shown that ceRNAs exist in several species and contexts and might play an important role in various biological processes, such as tumorigenesis [21]. Systematic analysis of the ceRNA network has been performed in multiple tumours, such as gastric cancer, bladder cancer, and ovarian cancer, contributing to a better understanding of tumorigenesis and facilitating the development of lncRNA-directed diagnostics and therapeutics against this disease [23‐25]. Unfortunately, however, such functional interactions have not yet been elucidated in melanoma.
In this study, we used bioinformatics methods to construct the ceRNA network of cutaneous melanoma and to identify the key lncRNAs involved in melanomagenesis. Through the reconstruction of a ceRNA network, we identified and verified that the key ceRNA molecules play a crucial role in the tumorigenesis and prognosis of SKCM. (Work flow was shown in Fig. 1).
Fig. 1
Study flow of this study
×
Methods
Raw data
Human melanoma miRNA expression data were downloaded from the NCBI GEO database (GEO (http://www.ncbi.nlm.nih.gov/geo) [26], including GSE24996, GSE35579, and GSE62372, which are array-based datasets. The GSE24996 dataset consists of 8 benign nevus tissue samples and 23 primary melanoma tissue samples. The GSE35579 dataset consists of 11 benign nevus tissue samples and 20 primary melanoma tissue samples. The GSE62372 dataset consists of 9 benign nevus tissue samples and 92 primary melanoma tissue samples. mRNA and lncRNA expression data were also downloaded from the NCBI GEO database (GSE112509), which is a sequence-based dataset. The GSE112509 dataset consists of 23 benign nevus tissue samples and 57 primary melanoma tissue samples.
Identification of DEMis, DELs and DEMs
For identification of the differentially expressed miRNAs (DEMis) between primary melanoma and benign nevus samples, “R” (version 3.4.2, https://www.r-project.org/) [27] was used with the “limma” package after normalization [28]. For identification of the differentially expressed lncRNAs (DELs) and mRNAs (DEMs) between primary melanoma and benign nevus samples, “R” (version 3.4.2, https://www.r-project.org/) [27] was used with the “DESeq2” package [29]. The DEMis, DELs and DEMs were selected according to |log2FC| > 1 and adjusted P-value < 0.05.
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Prediction of target lncRNAs and mRNAs
For prediction of the target lncRNAs and mRNAs through DEMis, starBase (starbase.sysu.edu.cn) was used in our study [30]. Multiple lncRNA/mRNA-predicting programmes (PITA, RNA22, miRmap, DIANA-microT, miRanda, PicTar and TargetScan) were used in starBase [30]. For accuracy, only when the target mRNA was predicted in at least four predicted programmes on starBase would it be chosen as the predicted target mRNA. Then, these predicted target lncRNAs and mRNAs were merged with DEMs and DELs, respectively.
Reconstruction of the ceRNA network
The ceRNA network was reconstructed based on ceRNA theory [20] and as follows: (1) Expression correlation between DELs and DEMs was evaluated using the Pearson correlation coefficient (PCC). The DEL-DEM pairs with PCC > 0.4 and P-value < 0.01 were considered coexpressed lncRNA-mRNA pairs. (2) Both lncRNAs and mRNAs in the pairs were negatively correlated with their common miRNAs. (3) The ceRNA network was reconstructed and visualized using Cytoscape (version 3.7.1, https://cytoscape.org/) [31, 32].
Functional enrichment analysis
For functional enrichment, Gene Ontology (GO) biological process (BP), cell component (CC), molecular function (MF) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of mRNAs in the ceRNA network were performed using DAVID (version 6.8, https://david.ncifcrf.gov/) [33, 34].
Hub gene selection and reconstruction of key ceRNA subnetworks
To reconstruct our key ceRNA subnetwork, we first selected hub genes according to the node degrees of the ceRNA network we reconstructed above by calculating the number of lncRNA-miRNA and miRNA-mRNA pairs. For these key lncRNAs, GO-BP, GO-CC, GO-MF and KEGG pathway annotation were performed according to their first mRNA neighbours by using DAVID (version 6.8, https://david.ncifcrf.gov/) [33, 34].
Sample selection for qRT-PCR validation
To validate findings in the ceRNA network, we selected the top three hub genes to determine their expression in cutaneous melanoma and skin tissues. Twelve patients with cutaneous melanoma and three healthy patients were included in this study. The study protocol was approved by the Ethics Committee of The First Affiliated Hospital, Sun Yat-sen University. All patients provided written informed consent in compliance with the code of ethics of the World Medical Association (Declaration of Helsinki). The eligible patients for this study had to meet the following criteria: (1) histologically confirmed as melanoma; (2) received no radiotherapy, chemotherapy or biotherapy before surgery. The exclusion criteria were as follows: (1) previous malignancies; (2) concomitant malignancies; (3) serious active infection; and (4) pregnancy or lactation.
Eligible cutaneous melanoma patients were from The First Affiliated Hospital, Sun Yat-sen University (Guangzhou, Guangdong, China) or the Cancer Center of Guangzhou Medical University (Guangzhou, Guangdong, China). Each tumour sample was matched with adjacent apparently normal tissues removed during the same operation. Frozen sections were made from these tissues and examined by at least three pathologists. The clinicopathological features of twelve skin cutaneous melanoma patients (51.67 ± 14.57 years old) for qRT-PCR validation are shown in Table 1. Three healthy patients from The First Affiliated Hospital, Sun Yat-sen University (Guangzhou, Guangdong, China) were included in this study. These patients were scheduled to undergo split-thickness skin grafting due to deep partial burn wounds. Each normal skin sample was obtained from the donor site. All the samples were frozen immediately after the operation and were stored in liquid nitrogen until RNA isolation.
Table 1
The clinicopathological features of twelve SKCM patients for qRT-PCR validation
aPathologic tumor stage is according to AJCC staging for SKCM (8th edition)
RNA isolation and qRT-PCR
Total RNA was extracted from all fresh-frozen samples using TRIzol reagent (Invitrogen, USA). The OD value (260/280) of all RNA extracted samples was greater than 1.8. For each replicate, complementary DNA (cDNA) was synthesized from 2 μg RNA using the GoScript Reverse Transcription System (Promega, USA). The qRT-PCR comprised 10 μl of GoTaq qPCR Master Mix (2×) (Promega, USA), 2 μl of diluted cDNA template (1:10) and 10 μM of each primer contributing to a total volume of 20 μl. Reactions were run in an ABI 7500 real-time PCR system (Applied Biosystems, USA) under the following conditions: 95 °C for 10 mins and 40 cycles of 95 °C for 15 s and 60 °C for 60 s. Melting curves were derived for every reaction to ensure a single product. Relative gene expression was evaluated according to the ddCT method, using the human GAPDH gene as an endogenous control for RNA load and gene expression in the analysis. All experiments were performed in triplicate. GraphPad Prism 8 (GraphPad Software, USA) was used to output figures.
The primers were as follows: MALAT1 Fw.: GACGAGTTGTGCTGCGAT; MALAT1 Rev.: TTCTGTGTTATGCCTGGTTA; LINC00943 Fw.: GGATTGGATTGTGGATTGC; LINC00943 Rev.: CAGGTCTCAGTTCAGTGTT; LINC00261 Fw.: CTTCTTGACCACATCTTACAC; LINC00261 Rev.: GGACCATTGCCTCTTGATT; GAPDH Fw: GAGAGGGAAATCGTGCGTGAC; GAPDH Rev.: CATCTGCTGGAAGGTGGACA.
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Multivariate cox regression model for survival analysis
a The information of exons belongs to the hg19 database
To determine which factors should be included in the multivariate Cox regression model, we first performed the univariate Cox regression model for survival analysis. Factors that were statistically significant (p < 0.05) in the univariate Cox regression model were included in the multivariate Cox regression model, and the multivariate Cox regression model for survival analysis was performed. SPSS 22.0 was used for the analysis of the Cox regression model.
Results
Identification of DEMs, DELs and DEMis and reconstruction of the lncRNA-miRNA-mRNA (ceRNA) network
After standardization of the GEO datasets, 56, 70 and 34 DEMis between benign nevus tissues and primary melanoma tissues were identified in GSE24996, GSE35579 and GSE62372, respectively (Supplementary Table 2, Fig. 2a-f). The candidate 18 miRNAs were shared in at least two datasets (Fig. 3a): hsa-miRNA-378a-3p, hsa-miRNA-23b-3p, hsa-miRNA-140-3p, hsa-miRNA-99a-5p, hsa-miRNA-100-5p, hsa-miRNA-204-5p, hsa-miRNA-211-5p, hsa-miRNA-205-5p, hsa-miRNA-224-5p, hsa-miRNA-200b-3p, hsa-miRNA-200c-3p, hsa-miRNA-125b-5p, hsa-miRNA-149-5p, hsa-miRNA-21-5p, hsa-miRNA-20b-5p, hsa-miRNA-424-5p, hsa-miRNA-203a-3p and hsa-miRNA-1826. According to method 2.3, 2361 mRNAs and 277 lncRNAs were predicted using these miRNAs. We ruled out two of these 18 DEMis, hsa-miRNA-203a-3p and hsa-miRNA-1826, because no predicted gene was found in starBase according to method 2.3. In addition, 5953 DEMs and 665 DELs between benign nevus tissues and primary melanoma tissues were identified in GSE112509 (Fig. 2g and h). As a result, a total of 898 DEMs and 53 DELs were selected for further analysis according to method 2.3 (Fig. 3b and c). Finally, 898 DEMs, 53 DELs and 16 DEMis were selected for further reconstruction of the lncRNA-miRNA-mRNA (ceRNA) network.
Fig. 2
a Heatmap analysis of miRNA differential expressed profiles in GSE24996; (b) Volcano analysis of miRNA expressed profiles in GSE24996; (c) Heatmap analysis of miRNA differential expressed profiles in GSE35579; (d) Volcano analysis of miRNA expressed profiles in GSE35579; (e) Heatmap analysis of miRNA differential expressed profiles in GSE62372; (f) Volcano analysis of miRNA expressed profiles in GSE62372; (g) Heatmap analysis of RNA differential expressed profiles in GSE112509; (h) Volcano analysis of RNA expressed profiles in GSE112509. (These images were produced by R version 3.4.2)
Fig. 3
Venn diagram: (a) DEMis were selected with |log2FC| > 1 and adjusted P-value < 0.05 among the non-coding RNA profiling sets, GSE24996, GSE35579 and GSE62372. The candidates 18 miRNAs were shared in at least two datasets. b DEMs were selected by intersecting mRNAs predicted by DEMis through starbase and differential expressed mRNAs in GSE112509. c DELs were selected by intersecting lncRNAs predicted by DEMis through starbase and differential expressed lncRNAs in GSE112509. (These images were produced by R version 3.4.2)
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The lncRNA-miRNA-mRNA (ceRNA) network, consisting of 53 lncRNA nodes, 16 miRNA nodes, 898 mRNA nodes and 609 edges, was reconstructed and visualized using Cytoscape (Fig. 4a).
Fig. 4
a ceRNA network. The round rectangle represents lncRNAs, the diamond represents miRNAs, and the ellipse represents mRNAs. There are 53 lncRNA nodes, 16 miRNA nodes, 898 mRNA nodes and 609 edges in the network. b-e Biological function and pathway analysis of differentially expressed mRNAs. b The top 15 significant changes in GO-BP. c The top 15 significant changes in the GO-CC. d The top 15 significant changes in the GO-MF. e The top 15 significant changes in the KEGG pathway. Note: more details are shown in Table 3. (Fig. 4a was produced by Cytoscape version 3.7.1)
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KEGG pathway and GO enrichment analysis of lncRNAs based on the ceRNA network
We used DAVID to analyse the biological classification of DEMs according to method 2.5. The results of the top 15 significant GO terms and KEGG pathways are shown in Table 3 and Fig. 4b-e. Sixty pathways were significantly enriched through KEGG pathway analysis, including the PI3K-Akt signalling pathway, focal adhesion, proteoglycans in cancer, pathway in cancer and, most importantly, melanomagenesis. The results of GO-BP analysis revealed 172 enriched terms, particularly in the regulation of transcription, such as positive regulation of transcription from the RNA polymerase II promoter, positive regulation of transcription (DNA-templated), and transcription from the RNA polymerase II promoter.
Table 3
The top 15 significant changes in GO-BP (A), −CC (B), −MF(C) and KEGG pathway (D) according to differentially expressed genes in ceRNA network
A
GO-BP Term
Enrichment Score
Count
%
P-Value
positive regulation of transcription from RNA polymerase II promoter
9.446887
56
13.18
< 0.001
positive regulation of transcription, DNA-templated
4.759462
29
6.824
< 0.001
transcription from RNA polymerase II promoter
3.957811
27
6.353
< 0.001
negative regulation of transcription from RNA polymerase II promoter
3.674737
33
7.765
< 0.001
protein stabilization
3.580807
12
2.824
< 0.001
spinal cord development
3.291952
6
1.412
< 0.001
heart morphogenesis
3.157839
6
1.412
< 0.001
kidney development
3.144958
9
2.118
< 0.001
positive regulation of peptidyl-serine phosphorylation
3.001168
8
1.882
< 0.001
response to cytokine
2.967806
7
1.647
0.001
regulation of protein localization
2.967806
7
1.647
0.001
regulation of cell-matrix adhesion
2.914902
4
0.941
0.001
negative regulation of cell proliferation
2.759652
20
4.706
0.002
cell migration
2.732195
12
2.824
0.002
insulin receptor signaling pathway
2.724648
8
1.882
0.002
B
GO-CC Term
Enrichment Score
Count
%
P-Value
cytosol
5.793638
111
26.12
< 0.001
cytoplasm
4.942099
154
36.24
< 0.001
nucleoplasm
4.725908
93
21.88
< 0.001
nucleus
4.05725
154
36.24
< 0.001
membrane
3.599508
73
17.18
< 0.001
cytoskeleton
2.478053
18
4.235
0.003
cell-cell adherens junction
2.302618
16
3.765
0.005
cis-Golgi network
1.888299
5
1.176
0.013
cell-cell junction
1.877361
10
2.353
0.013
Golgi apparatus
1.852153
30
7.059
0.014
PcG protein complex
1.690927
4
0.941
0.02
receptor complex
1.672147
8
1.882
0.021
lamellipodium
1.616858
9
2.118
0.024
focal adhesion
1.603246
16
3.765
0.025
perinuclear region of cytoplasm
1.496331
22
5.176
0.032
C
GO-MF Term
Enrichment Score
Count
%
P-Value
protein binding
8.364509
260
61.18
< 0.001
sequence-specific DNA binding
4.118515
28
6.588
< 0.001
beta-catenin binding
3.946374
10
2.353
< 0.001
transcription factor activity, sequence-specific DNA binding
3.635935
41
9.647
< 0.001
platelet-derived growth factor receptor binding
3.50464
5
1.176
< 0.001
transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
2.912949
15
3.529
0.001
transcription regulatory region sequence-specific DNA binding
2.667561
7
1.647
0.002
protein channel activity
2.637341
4
0.941
0.002
insulin-like growth factor receptor binding
2.344093
4
0.941
0.005
insulin binding
2.293839
3
0.706
0.005
neurotrophin TRKA receptor binding
2.124416
3
0.706
0.008
microtubule binding
2.037592
12
2.824
0.009
N6-methyladenosine-containing RNA binding
1.984943
3
0.706
0.01
small GTPase binding
1.982255
4
0.941
0.01
RNA polymerase II core promoter proximal region sequence-specific DNA binding
1.726919
16
3.765
0.019
D
KEGG pathway
Enrichment Score
Count
%
P-Value
PI3K-Akt signaling pathway
6.144606
25
5.882
< 0.001
Prostate cancer
5.389517
12
2.824
< 0.001
Focal adhesion
4.815445
17
4
< 0.001
Proteoglycans in cancer
4.365137
16
3.765
< 0.001
Insulin signaling pathway
4.202316
13
3.059
< 0.001
Signaling pathways regulating pluripotency of stem cells
4.141148
13
3.059
< 0.001
Adherens junction
3.732503
9
2.118
< 0.001
Pathways in cancer
3.709619
22
5.176
< 0.001
FoxO signaling pathway
3.670169
12
2.824
< 0.001
Acute myeloid leukemia
3.609095
8
1.882
< 0.001
Thyroid hormone signaling pathway
3.584028
11
2.588
< 0.001
Choline metabolism in cancer
3.353402
10
2.353
< 0.001
Glioma
3.20572
8
1.882
< 0.001
Melanoma
2.973883
8
1.882
0.001
HIF-1 signaling pathway
2.844366
9
2.118
0.001
Hub gene selection
According to the node degree in the ceRNA network, we found that three lncRNAs, MALAT1, LINC00943, and LINC00261, had the highest number of lncRNA-miRNA and miRNA-mRNA pairs, suggesting that these three lncRNAs could be chosen as hub nodes, and the results are shown in Table 4. Therefore, these three lncRNAs might play an essential role in melanomagenesis and might be considered key lncRNAs.
Table 4
The number of the highest lncRNA–miRNA and miRNA–mRNA pairs
lncRNA-miRNA pairs
miRNA-mRNA pairs
Total number
MALAT1
9
200
209
LINC00943
7
202
209
LINC00261
5
158
163
Reconstruction of the MALAT1/LINC00943/LINC00261-miRNA-mRNA subnetworks
MALAT, LINC00943, LINC00261 and their paired miRNAs and mRNAs were used to reconstruct key ceRNA subnetworks. The MALAT1 ceRNA network consists of 1 lncRNA node, 9 miRNA nodes, 158 mRNA nodes and 209 edges, as shown in Fig. 5a. The LINC00943 ceRNA network consists of 1 lncRNA node, 7 miRNA nodes, 182 mRNA nodes and 209 edges, as shown in Fig. 6a. The LINC00261 ceRNA network consists of 1 lncRNA node, 5 miRNA nodes, 123 mRNA nodes and 163 edges, as shown in Fig. 7a. The results of functional analysis revealed that 75 GO-BP, 21 GO-CC, 15 GO-MF and 20 pathways were enriched in the MALAT1-miRNA-mRNA subnetwork; 67 GO-BP, 14 GO-CC, 17 GO-MF and 13 pathways were enriched in the LINC00943-miRNA-mRNA subnetwork; and 42 GO-BP, 7 GO-CC, 10 GO-MF and 7 pathways were enriched in the LINC00261-miRNA-mRNA subnetwork. The results of the top 10 significant GO terms and KEGG pathways of these three lncRNAs are shown in Fig. 5b-e, Fig. 6b-e, Fig. 7b-e, and Tables 5, 6, 7.
Fig. 5
a The ceRNA sub-network of MALAT1. The round rectangle represents lncRNAs, the diamond represents miRNAs, and the ellipse represents mRNAs. There are 1 lncRNA nodes, 9 miRNA nodes, 158 mRNA nodes and 209 edges in the network. b-e Biological function and pathway analysis of MALAT1 paired mRNAs. b The top 10 significant changes in the GO-BP. c The top 10 significant changes in the GO-CC. d The top 10 significant changes in the GO-MF. e The top 10 significant changes in the KEGG pathway. Note: more details are shown in Table 5. (Fig. 5a was produced by Cytoscape version 3.7.1)
Fig. 6
a The ceRNA sub-network of LINC00943. The round rectangle represents lncRNAs, the diamond represents miRNAs, and the ellipse represents mRNAs. There are 1 lncRNA nodes, 7 miRNA nodes, 182 mRNA nodes and 209 edges in the network. b-e Biological function and pathway analysis of LINC00943 paired mRNAs. b The top 10 significant changes in the GO-BP. c The top 10 significant changes in the GO-CC. d The top 10 significant changes in the GO-MF. e The top 10 significant changes in the KEGG pathway. Note: more details are shown in Table 6. (Fig. 6a was generated by Cytoscape version 3.7.1)
Fig. 7
a The ceRNA sub-network of LINC00261. The round rectangle represents lncRNAs, the diamond represents miRNAs, and the ellipse represents mRNAs. There are 1 lncRNA nodes, 5 miRNA nodes, 123 mRNA nodes and 163 edges in the network. b-e Biological function and pathway analysis of LINC00261 paired mRNAs. b The top 10 significant changes in the GO-BP. c The changes in the GO-CC. d The top 10 significant changes in the GO-MF. e The changes in the KEGG pathway. Note: more details are shown in Table 7. (Fig. 7a was generated by Cytoscape version 3.7.1)
Table 5
The top 15 significant changes in GO-BP (A), −CC (B), −MF(C) and KEGG pathway (D) according to differentially expressed genes in MALAT1-ceRNA sub-network
A
GO-BP Term
Enrichment Score
Count
%
P-Value
positive regulation of transcription from RNA polymerase II promoter
3.579259
20
11.43
< 0.001
transcription from RNA polymerase II promoter
3.106442
13
7.429
< 0.001
positive regulation of transcription, DNA-templated
3.091753
13
7.429
< 0.001
neuroepithelial cell differentiation
2.894845
3
1.714
0.001
positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
2.772993
4
2.286
0.002
neural tube formation
2.772164
3
1.714
0.002
in utero embryonic development
2.425229
7
4
0.004
kidney development
2.315189
5
2.857
0.005
camera-type eye morphogenesis
2.158154
3
1.714
0.007
regulation of protein localization
2.092037
4
2.286
0.008
inner ear morphogenesis
2.092037
4
2.286
0.008
positive regulation of branching involved in ureteric bud morphogenesis
2.011071
3
1.714
0.01
positive regulation of neuroblast proliferation
1.967555
3
1.714
0.011
negative regulation of transcription from RNA polymerase II promoter
1.923719
13
7.429
0.012
cell migration
1.922663
6
3.429
0.012
B
GO-CC Term
Enrichment Score
Count
%
P-Value
cytosol
3.530641
45
25.71
< 0.001
nucleus
3.429028
64
36.57
< 0.001
nucleoplasm
3.288165
39
22.29
< 0.001
cell-cell adherens junction
2.341584
9
5.143
0.005
melanosome
2.052614
5
2.857
0.009
filopodium
1.71293
4
2.286
0.019
PcG protein complex
1.707154
3
1.714
0.02
nuclear chromatin
1.705842
6
3.429
0.02
extracellular exosome
1.429256
32
18.29
0.037
cis-Golgi network
1.35117
3
1.714
0.045
spindle microtubule
1.314751
3
1.714
0.048
cytoplasm
1.239444
52
29.71
0.058
perinuclear region of cytoplasm
1.205186
10
5.714
0.062
membrane
1.146558
25
14.29
0.071
spindle
1.134303
4
2.286
0.073
C
GO-MF Term
Enrichment Score
Count
%
P-Value
protein binding
3.880727
95
54.29
< 0.001
sequence-specific DNA binding
3.451663
14
8
< 0.001
transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
3.120112
9
5.143
< 0.001
RNA polymerase II core promoter proximal region sequence-specific DNA binding
2.566023
10
5.714
0.003
poly(A) RNA binding
2.27862
19
10.86
0.005
transcription factor activity, sequence-specific DNA binding
1.893028
16
9.143
0.013
zinc ion binding
1.508313
17
9.714
0.031
cadherin binding involved in cell-cell adhesion
1.481723
7
4
0.033
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
RNA polymerase II regulatory region sequence-specific DNA binding
1.031152
5
2.857
0.093
DNA binding
1.029587
20
11.43
0.093
Table 6
The top significant changes in GO-BP (A), −CC (B), −MF(C) and KEGG pathway (D) according to differentially expressed genes in LINC00943-ceRNA sub-network
A
GO-BP Term
Enrichment Score
Count
%
P-Value
positive regulation of transcription from RNA polymerase II promoter
3.413985
22
12.22
< 0.001
positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
2.5522952
4
2.222
0.003
negative regulation of transcription from RNA polymerase II promoter
2.4555568
16
8.889
0.004
transcription from RNA polymerase II promoter
2.4471842
13
7.222
0.004
positive regulation of transcription, DNA-templated
2.4336944
13
7.222
0.004
apoptotic process
2.1092412
13
7.222
0.008
negative regulation of translational initiation
2.064083
3
1.667
0.009
protein import into mitochondrial matrix
1.95711
3
1.667
0.011
regulation of protein localization
1.8821494
4
2.222
0.013
response to cytokine
1.8821494
4
2.222
0.013
cellular response to cytokine stimulus
1.7404426
3
1.667
0.018
cell morphogenesis
1.6784701
4
2.222
0.021
positive regulation of mesenchymal cell proliferation
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
1.197916
4
2.222
0.063
N6-methyladenosine-containing RNA binding
1.185193
2
1.111
0.065
P-P-bond-hydrolysis-driven protein transmembrane transporter activity
1.129258
2
1.111
0.074
poly(A) RNA binding
1.119963
17
9.444
0.076
chromatin binding
1.08038
8
4.444
0.083
mRNA 5′-UTR binding
1.080159
2
1.111
0.083
D
KEGG pathway
Enrichment Score
Count
%
P-Value
Pathways in cancer
2.26453
11
6.111
0.005
PI3K-Akt signaling pathway
2.145933
10
5.556
0.007
Oocyte meiosis
1.604046
5
2.778
0.025
Pancreatic cancer
1.566902
4
2.222
0.027
Platelet activation
1.386975
5
2.778
0.041
Insulin signaling pathway
1.307592
5
2.778
0.049
Proteoglycans in cancer
1.304184
6
3.333
0.05
Focal adhesion
1.259046
6
3.333
0.055
Rap1 signaling pathway
1.229991
6
3.333
0.059
Hippo signaling pathway
1.190921
5
2.778
0.064
MicroRNAs in cancer
1.179653
7
3.889
0.066
HIF-1 signaling pathway
1.146419
4
2.222
0.071
Vibrio cholerae infection
1.020041
3
1.667
0.095
Table 7
The top significant changes in GO-BP (A), −CC (B), −MF(C) and KEGG pathway (D) according to differentially expressed genes in LINC00261-ceRNA sub-network
A
GO-BP Term
Enrichment Score
Count
%
P-Value
positive regulation of transcription from RNA polymerase II promoter
4.294676
19
14.29
< 0.001
transcription from RNA polymerase II promoter
3.946596
13
9.774
< 0.001
neuroepithelial cell differentiation
3.074302
3
2.256
< 0.001
spinal cord development
3.033527
4
3.008
0.001
neural tube formation
2.951191
3
2.256
0.001
inner ear morphogenesis
2.342119
4
3.008
0.005
regulation of protein localization
2.342119
4
3.008
0.005
regulation of neuron differentiation
2.141452
3
2.256
0.007
regulation of transforming growth factor beta receptor signaling pathway
2.141452
3
2.256
0.007
protein stabilization
1.937969
5
3.759
0.012
fungiform papilla morphogenesis
1.892035
2
1.504
0.013
stem cell differentiation
1.887589
3
2.256
0.013
regulation of signal transduction
1.799832
3
2.256
0.016
negative regulation of transcription from RNA polymerase II promoter
1.756023
11
8.271
0.018
myotome development
1.717328
2
1.504
0.019
B
GO-CC Term
Enrichment Score
Count
%
P-Value
nucleus
4.161906
55
41.35
< 0.001
nucleoplasm
3.062718
32
24.06
< 0.001
cytoplasm
3.032352
50
37.59
< 0.001
membrane
2.306958
25
18.8
0.005
microtubule plus-end
2.297019
3
2.256
0.005
cytosol
1.228885
29
21.8
0.059
cytoplasmic mRNA processing body
1.060323
3
2.256
0.087
C
GO-MF Term
Enrichment Score
Count
%
P-Value
transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
3.752771
9
6.767
< 0.001
protein binding
2.747245
75
56.39
0.002
protein channel activity
2.559552
3
2.256
0.003
transcription regulatory region sequence-specific DNA binding
2.171926
4
3.008
0.007
sequence-specific DNA binding
2.120902
10
7.519
0.008
RNA polymerase II core promoter proximal region sequence-specific DNA binding
2.024814
8
6.015
0.009
chromatin binding
1.812398
8
6.015
0.015
RNA polymerase II transcription coactivator activity
1.602367
3
2.256
0.025
N6-methyladenosine-containing RNA binding
1.341641
2
1.504
0.046
protein kinase activity
1.042052
6
4.511
0.091
D
KEGG pathway
Enrichment Score
Count
%
P-Value
PI3K-Akt signaling pathway
1.809894
7
5.263
0.015
Oocyte meiosis
1.553469
4
3.008
0.028
Platelet activation
1.379399
4
3.008
0.042
Insulin signaling pathway
1.315081
4
3.008
0.048
Hippo signaling pathway
1.219786
4
3.008
0.06
Purine metabolism
1.062637
4
3.008
0.087
ErbB signaling pathway
1.024741
3
2.256
0.094
×
×
×
Expression of MALAT1, LINC00943 and LINC00261 is higher in tumour tissues
To confirm the expression of MALAT1, LINC00943 and LINC00261 in melanoma tissues, we evaluated the MALAT1, LINC00943 and LINC00261 expression levels in the cancer tissues from 12 melanoma patients (see Table 1) and 3 healthy tissues via qRT-PCR, as shown in Fig. 8. The results showed that the expression of MALAT1, LINC00943 and LINC00261 was significantly higher in the tumour tissues than in the healthy tissues (p = 0.0243, p = 0.0005, p < 0.0001, respectively). Additionally, the expression of MALAT1, LINC00943 and LINC00261 was significantly higher in the tumour tissues than in the adjacent normal tissues (p = 0.0002, p < 0.0001, p < 0.0001, respectively). However, no significant difference was observed between the healthy tissues and the adjacent normal skin tissues in the expression of MALAT1, LINC00943 and LINC00261 (p = 0.366, p = 0.379, p = 0.262, respectively). The results are consistent with those discussed above. Thus, the expression of MALAT1, LINC00943 and LINC00261 is increased in melanoma and may be responsible for the tumorigenesis of melanoma.
Fig. 8
The expression level of MALAT1 (a), LINC00943 (b) and LINC00261 (c) in normal skin, adjacent normal skin and melanoma tissues
×
Anzeige
MALAT1 and LINC00943 are independent risk factors for the prognosis of cutaneous melanoma
A univariate Cox regression model for survival analysis of age, sex and stage was performed, and the results are shown in Supplementary Table 3. Then, the multivariate Cox regression model for survival analysis of MALAT1, LINC00943, and LINC00261 was performed. The results showed that the overall survival time and disease-free survival time of the patients with MALAT1 or LINC00943 CNV deficiency were significantly lower than those without it, and the difference was significant (details are shown in Table 8 and Fig. 9a-d), suggesting that MALAT1 and LINC00943 are independent risk factors for the prognosis of cutaneous melanoma. Although the overall survival time and disease-free survival time of patients with LINC00261 deletion were lower than those without it, the difference was not significant (p = 0.535, p = 0.694) (details are shown in Table 8 and Fig. 9e- f).
Table 8
Multivariate COX regression model for overall survival (A) and disease-free survival analysis (B) of MALAT1, LINC00943, and LINC00261
A
Number of cases, Total
Number of cases, Decased
Median Months, Overall
OR
95%CI
p-value
MALAT1
with CNV deficiency
82
53
34.23
0.714
0.524–0.975
0.034
without CNV deficiency
454
243
63.53
LINC00943
with CNV deficiency
54
34
55.59
0.671
0.465–0.969
0.033
without CNV deficiency
482
262
61.05
LINC00261
with CNV deficiency
23
16
17.03
0.612
0.356–1.053
0.076
without CNV deficiency
513
280
61.05
B
Number of cases, Total
Number of cases, Decased
Median Months, Overall
OR
95%CI
p-value
MALAT1
with CNV deficiency
84
69
15.52
0.691
0.528–0.906
0.007
without CNV deficiency
448
331
27.09
LINC00943
with CNV deficiency
55
45
21.37
0.704
0.511–0.971
0.033
without CNV deficiency
477
355
24.82
LINC00261
with CNV deficiency
23
19
13.50
0.842
0.516–1.374
0.491
without CNV deficiency
509
381
25.02
Fig. 9
Multivariate COX regression model for survival analysis of MALAT1 (a, b), LINC00943 (c, d) and LINC00261 (e, f). (This image was generated by SPSS version 22.0)
×
Discussion
In this study, three lncRNAs, MALAT1, LINC00943 and LINC00261, were identified according to the reconstructed ceRNA network. Among these key lncRNAs found in this study, MALAT1 has been demonstrated to be related to various malignant tumours [40‐44]. Studies have confirmed that MALAT1 is a valuable prognostic marker and a promising therapeutic target in lung cancer metastasis [40, 41]. A study also suggested that MALAT1 plays an important role in tumour progression and could serve as a promising therapeutic target [42]. Through the study of the whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer, Fujimoto A. and colleagues discovered that MALAT1 is closely related to liver carcinogenesis.46 In addition, a study revealed a novel mechanism of MALAT1-regulated autophagy-related chemoresistance in gastric cancer [44]. At present, it is believed that MALAT1 is mainly responsible for regulating the proliferation, migration and invasion of tumour cells. According to our findings, MALAT1 might also be a crucial factor in the tumorigenesis and development of melanoma. In this subnetwork, we found nine lncRNA-miRNA pairs: miRNA-378a-3p, miRNA-23b-3p, miRNA-224-5p, miRNA-204-5p, miRNA-205-5p, miRNA-200c-3p, miRNA-200b-3p, miRNA-149-5p, and miRNA-211-5p. Among them, MALAT1 was shown to regulate chemoresistance via miRNA-23b-3p sequestration in gastric cancer [44]. In ovarian cancer, a study suggested that MALAT1-miRNA-211-5p may act as a key mediator in the prevention of this disease [45]. MALAT1 is also involved in promoting renal cell carcinoma through interaction with miRNA-205-5p [46]. Studies have confirmed that MALAT1 functions in liver and lung cancer through miRNA-204-5p [47, 48]. In addition, targeting the MALAT1/miRNA-200c-3p axis in a xenograft endometrial carcinoma model strongly inhibited tumour growth [49].
Moreover, studies have illustrated that these miRNAs are closely related to melanoma in several ways. miRNA-378a-3p can regulate oncogenic PARVA expression in melanoma, preventing its progression [50]. miRNA-23b-3p was shown to be a tumour suppressor gene in melanoma [51]. miRNA-224-5p can be regulated by E2F1 to drive EMT through TXNIP downregulation in melanoma, and it can inhibit uveal melanoma cell proliferation, migration, and invasion by targeting PIK3R3/AKT3 [52, 53]. miRNA-204-5p, known as a tumour suppressor gene in melanoma, was associated with the CDKN2A pathway and NRAS gene and contributed to BRAF inhibitor resistance [51, 54, 55].. miRNA-205-5p suppresses proliferation and induces senescence via regulation of E2F1 in melanoma [51, 56‐58]. miRNA-200b/c-3p act as potential diagnostic and prognostic markers for melanoma [59‐61]. Upregulation of miRNA-149-5p, directly regulated by p53, results in increased expression of Mcl-1 and resistance to apoptosis in melanoma cells [62]. Most importantly, studies have confirmed that miRNA-211-5p plays a major role as a tumour suppressor via various targets in melanoma [51, 55, 59, 63, 64]. Moreover, MALAT1 is an independent risk factor for the prognosis of SKCM according to multivariate Cox regression model analysis. Thus, we believe that MALAT1 may contribute to the tumorigenesis and survival of SKCM.
Little is known about LINC00943. According to the LINC00943-miRNA-mRNA subnetwork, miRNA-99a-5p, miRNA-100-5p, miRNA-23b-3p, miRNA-204-5p, miRNA-224-5p, miRNA-149-5p and miRNA-125b-5p closely interacted with LINC00943. No connection between LINC00943 and these miRNAs has been discovered yet; however, these miRNAs were also demonstrated to be associated with melanoma, except miRNA-99a-5p. The links between miRNA-204-5p, miRNA-224-5p, miRNA-149-5p and melanoma are discussed above. In addition, miRNA-23b was suggested as a tumour suppressor gene.54 miRNA-100-5p and miRNA-125b-5p are associated with resistance to treatment with immune checkpoint inhibitors in melanoma [65]. Additionally, we confirmed that LINC00943 is an independent risk factor for the prognosis of SKCM. Therefore, understanding the relationships among LINC00943, miRNAs and malignancies may provide further information for future research on melanoma and other malignancies.
Seven KEGG pathways were enriched based on the LINC00261 subnetwork. One of these pathways, the PI3K/Akt signalling pathway, has been proven to play a critical role in tumorigenesis [66], especially in melanoma [67]. Additionally, a study has demonstrated that LINC00261 promotes cancer cell proliferation and metastasis in human choriocarcinoma [68]. However, LINC00261 has shown a strong capacity in improving the chemotherapeutic response and survival of patients with oesophageal cancer [69]. In gastric cancer, LINC00261 can suppress tumour metastasis by regulating epithelial-mesenchymal transition [70]. Moreover, LINC00261 can block cellular proliferation by activating the DNA damage response [71]. LINC00261 may affect the biological behaviour of different tumours in different ways. Therefore, it is essential to further explore the role of LINC00261 in different tumours. However, five miRNAs, miRNA-23b-3p, miRNA-211-5p, miRNA-205-5p, miRNA-140-3p and miRNA-125b-5p, interacted with LINC00261 according to the LINC00261-miRNA-mRNA subnetwork. Similarly, no connection between LINC00261 and these miRNAs has been discovered yet. The roles of miRNA-23b-3p, miRNA-211-5p, miRNA-205-5p, and miRNA-125b-5p in melanoma are discussed above. miRNA-140-3p was reported to be regulated by MALAT1 in uveal melanoma cells [72]. The multivariate Cox regression model for survival suggested that LINC00261 was not a risk factor for the prognosis of SKCM, however, the median overall survival and disease-free survival time for patients with LINC00261 CNV deficiency were significantly lower than those without LINC00261 CNV deficiency (17.03 m vs 61.05 m, 13.50 vs 25.02).
Three of the 16 predicted miRNAs were not associated with MALAT1, LINC00943 and LINC00261: miRNA-21-5p, miRNA-20b-5p and miRNA-424-5p. They are closely related to SGMS1.AS1, EPB41L4A.AS1 and SNHG1 according to the ceRNA network. Little is known about miRNA-424-5p in melanoma, while studies have suggested that miRNA-20b-5p may inhibit tumour metastasis via regulation of the PAR-1 receptor in melanoma cells [73], and miRNA-21 may regulate melanoma cell proliferation, migration, and apoptosis through the ERK/NF-κB signalling pathway by targeting SPRY1, PDCD4 and PTEN [74, 75].
Conclusions
This study advances our understanding of tumorigenesis and development in cutaneous melanoma from the perspective of the ceRNA theory. In addition, MALAT1 and LINC00943 may be independent risk factors for the prognosis of patients with cutaneous melanoma and might become predictive molecules for the long-term treatment of melanoma and potential therapeutic targets. Further studies are required to validate the role of MALAT1, LINC00943 and LINC00261 in cutaneous melanoma.
This manuscript is approved by all authors for publication. And we sincerely thank those who help finishing this article.
Ethics approval and consent to participate
The study protocol was approved by the Ethics Committee of The First Affiliated Hospital, Sun Yat-sen University. All patients provided written informed consent in compliance with the code of ethics of World Medical Association (Declaration of Helsinki). All the data used in this article were from open assess databases, and no permission was required.
Consent for publication
Written informed consent for publication of this article was obtained from patients themselves.
Competing interests
No potential conflict of interest was declared by the authors.
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Auch myeloide Immunzellen lassen sich mit chimären Antigenrezeptoren gegen Tumoren ausstatten. Solche CAR-Fresszell-Therapien werden jetzt für solide Tumoren entwickelt. Künftig soll dieser Prozess nicht mehr ex vivo, sondern per mRNA im Körper der Betroffenen erfolgen.
Frauen mit unbehandelter oder neu auftretender Hypertonie haben ein deutlich erhöhtes Risiko für Uterusmyome. Eine Therapie mit Antihypertensiva geht hingegen mit einer verringerten Inzidenz der gutartigen Tumoren einher.
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