Cutaneous melanoma (CM) is a malignant neoplasia characterized by rapid progression, metastasis to regional lymph nodes as well as distant organs, and limited responsiveness to therapeutics (MacKie et al., 2009). It contributes to more than 80% death of skin cancer patients (Miller and Mihm, 2006), and its incidence is one of the most rapidly increasing cancers in the United States where it is estimated that there will be 91,270 new cases and 9,320 deaths due to this disease in 2018 (Siegel et al., 2018). Although significant progress has been made in both understanding CM biology and genetics, and in therapeutic approaches, the prognosis remains poor due to the high potential for CM invasion and metastasis. This malignancy still represents a major public health problem worldwide. Primary localized melanoma has a relatively high survival rate. The 5- year survival rate prognosis of patients with lymph node or distant metastases was only 15–20% (Siegel et al., 2018; Weiss et al., 2015). Assessment of patients prior to therapy may aid in the identification of individuals at high risk for recurrence and may guide the development of future targeted treatment strategies. For example, for patients who are at high operative risk, conservative therapy may be helpful in the operative decision-making process. Molecular biomarkers could provide additional prognostic information and insight into the mechanisms of melanoma progression, as well as guide treatment selection. Consequently, new strategies for the identification of effective prognostic biomarkers may improve the clinical management of melanoma by providing more accurate prognostic information.

Aberrant DNA methylation is an epigenetic hallmark of cancer and actively contributes to cancer development and progression by inactivating tumor suppressor genes (Egger et al., 2004). Some characteristics of methylation markers render them particularly attractive for development of clinically applicable biomarkers, including high stability in biologic samples, limited susceptibility to tumor environmental factors, and ease of detection (Keeley et al., 2013). A growing number of studies have demonstrated that aberrant DNA methylation plays important roles in tumorigenesis and progression, and DNA methylation has great potential to act as a biomarker for predicting the prognosis of patients with a variety of malignancies (Egger et al., 2004; Guo et al., 2004; Roh et al., 2016). For instance, GATA4 is epigenetically silenced in gastrointestinal cancers (Akiyama et al., 2003) and lung cancer (Guo et al., 2004); OPCML promoter methylation has been identified as a biomarker for predicting ovarian cancer prognosis (Zhou et al., 2014); PCDH19 methylation is associated with poor hepatocellular carcinoma prognosis (Zhang et al., 2018) and Sigalotti et al. identified a 17-gene methylation signature as a molecular marker of survival in stage IIIC melanoma (Sigalotti et al., 2012). Unfortunately, many recent melanoma studies have several limitations including relatively small sample cohorts, lack of subsequent biomarker validation, narrow focus on patient specimens with specific clinical features, or investigation of only one or a few genes. These studies lack the comprehensive and systematic approach of genome-wide methylation analysis. Because of this, the identified methylation signatures do not have universal prognostic power, and their capability is limited by the specimen type. The Cancer Genome Atlas (TCGA) database (Hudson et al., 2010), a large well-annotated database with nearly 500 CM samples collected worldwide is a helpful resource for developing promising biomarkers with prospective studies into a methylation signature which can be of clinical utility.

Consequently, the purpose of this study was to identify DNA methylation biomarkers so as to explore the utility of DNA methylation analysis for cancer prognosis. The whole genome methylation profiles of tumor tissues from patients with CM in the TCGA database were analyzed, and the potential clinical significance of methylation biomarkers serving as molecular prognostic predictors was examined using the Kaplan–Meier method and receiver operating characteristic (ROC) analyses. Furthermore, the prognostic capacity of the identified methylation biomarker was evaluated with an independent cohort of patients in the Gene Expression Omnibus (GEO) database. Also, we investigated the independence and reproducibility in various clinical groups, as well as the possible role of the methylation biomarker in immune-checkpoint blockade (ICB) immunotherapy.

CM is the deadliest form of skin cancer and lead to 60,712 deaths in 2018 (Miller and Mihm, 2006). In recent years, the importance of DNA methylation in the biology of CM has been increasingly acknowledged. For instance, hypermethylated estrogen receptor alpha (ER-α) is a significant factor in melanoma progression (Mori et al., 2006); methylation-dependent SOX9 expression mediates invasion in human melanoma cells and is a negative prognostic factor in advanced melanoma (Cheng et al., 2015), and MGMT gene promoter methylation in metastatic CM is associated with longer survival (Cesinaro et al., 2012). However, these studies usually concentrated on single gene methylation or patient samples with specific clinical characteristics, and combinations of DNA methylation as biomarkers could achieve higher sensitivity and specificity than individual DNA methylation (Dai et al., 2011). Moreover, a limited overlap between signatures published by various studies can be observed, possibly due to variation in disease causes, tissue heterogeneity, or stage of disease at the point of analysis (Tremante et al., 2012). The TCGA database provides a large number of samples with a variety of clinical characteristics. Based on a TCGA dataset that included 461 CM samples, the current study identified a prognostic DNA methylation signature with potential clinical applicability, validated it in an independent cohort, and investigated its high reproducibility and utility in various clinical groups.

CM has a high degree of heterogeneity in terms of clinical, dermatological, and histopathological presentation (Coricovac et al., 2018). Several parameters, such as age, sex, stage of disease, Breslow thickness, and ulceration status have significant influence on CM patient prognosis, in which Breslow thickness has been demonstrated as the most important clinicopathological characteristic for predicting prognosis. In order to be clinically useful, a DNA methylation signature must be independent of clinical factors. Here we adopted a grouping method not influenced by our subjective, that is based on the TCGA series number of patients, without adjusting for clinical parameters. If detection, treatment and surgical excision occur when the tumor burden is restricted to a primary site, a patient’s prognostic survival is enhanced, but once the disease has metastasized to distant organs such as the brain and liver, prognosis is poor (Balch et al., 2009). Since patients with primary tumors had shorter follow-ups, none more than 5 years, we analyzed the independence and applicability of our four-DNA methylation signature in samples obtained from distant metastasis, subcutaneous tissue, and regional lymph node metastasis. The results showed that our signature was independent of tumor metastatic sites. Moreover, as patients suffering from early stages of the disease exhibit higher potential for healing, a prognostic signature that can also efficiently risk-stratify these patients would have higher clinical application value (Segura et al., 2010). Our signature has been demonstrated to be not only independent of all clinical factors, but also to have higher predictive performance for patients with tumor thickness of less than 2 mm and patients in early stages (AUCs were 0.830 and 0.814, respectively). Therefore, our signature was an independent applicable prognostic biomarker, which may be of high clinical value.

Considering that an ideal prognostic marker is one that can also efficiently risk-stratify in other independent cohorts, we employed GEO dataset (GSE51547) to further evaluate the practicality of our four-DNA methylation signature. Although the predictive accuracy in the GEO dataset is not as high as in the validation dataset due to the low number of samples (N = 47), the four-DNA methylation signature performed well in distinguishing low- and high-risk groups (AUC = 0.708, p<0.05). Furthermore, it was demonstrated that in both the validation and independent cohorts, our signature outperformed other known prognostic biomarkers, including mRNA, lncRNA, and DNA methylation, and statistical comparison using Z-test revealed that it has significantly higher (p<0.05) predictive performance than almost all the other known biomarkers. When further samples become available it will be important to analyze this methylation signature in another validation dataset.

Targeting immune checkpoints such as PD-1, PD-L1, and CTLA-4 have achieved noteworthy benefit in multiple cancers by blocking immunoinhibitory signals and enabling patients to produce an effective antitumor response, especially in patients with CM (Riaz et al., 2017). However, a significant limitation of ICB is that less than one-third of patients respond to ICB treatment, and identification of ICB response biomarkers and resistance regulators is a critical challenge (Sharma et al., 2017). DNA methylation plays a critical role in cell lineage specification and may serve as a specific molecular marker for measurement of immune responses. Recently, Jeschke et al highlighted the power of MeTIL to evaluate local and functional TIL-based tumor immune responses and the ability of this approach to improve prognosis (Jeschke et al., 2017). However, the identification of MeTIL was focused on CpGs that are highly differentially methylated between T lymphocytes and epithelial cells. Lymphocytes only account for a small fraction of TME (Pretscher et al., 2009); thus, there may be bias when using MeTIL as a prognostic marker to predict survival outcomes. Intriguingly, the correlation analyses and the observed predictive performance suggested that our four-DNA methylation signature was significantly correlated with the ICB immunotherapy-related signature. Additionally, our signature displayed higher predictive performance than other known signatures, including PD-1, PD-L1, PD-L2, CTLA-4, and MeTIL. These results demonstrate that our four-DNA methylation signature, although developed for accurate prognosis, may also have potential as a guide for precision cancer ICB immunotherapy.

Furthermore, epigenetic changes have been shown to alter gene expression, and epigenetic inactivation of tumor suppressor genes has been implicated in tumorigenesis of various malignancies, including CM (Herman and Baylin, 2003). Here, the expression of GBP5 and KLHL21 were significantly (p<0.001) negatively correlated with their methylation levels, and the other two genes show significant positive correlation (p<0.001) between the expression and their methylation levels (Figure 1—figure supplement 3). We also found that expression of this four-gene can also be used as a prognostic biomarker (Figure 2—figure supplement 1), but the four-DNA methylation biomarker offer a better potential to fulfill much more sensitive and specific prognostic test. For our four-DNA methylation sites, researchers have revealed that their corresponding genes may be crucial in immunity and cancer development, including CM. For instance, GBP5 promotes NLRP3 inflammasome assembly and immunity in mammals (Shenoy et al., 2012). GBP5 was induced by IFN-γ, could serve as a marker of IFN-γ-induced classically activated macrophages and the substitute indicator of IFN-γ, which can directly suppress tumorigenesis and infection and/or can modulate the immunological status in cancer cells (Chang et al., 2015; Yamamoto et al., 2012). Meanwhile, GBP5 expression in CM is associated with favorable prognosis (Wang et al., 2018). RAB37, as a tumor suppressor gene, promotes M1-like macrophage infiltration and suppresses tumor growth (Tzeng et al., 2018), and it was frequently down-regulated due to promoter hypermethylation in metastatic lung cancer, can serve as a potential predictive biomarker (Wu et al., 2009). RAB37-mediated SFRP1 secretion suppresses cancer stemness, and dysregulated RAB37-SFRP1 pathway confers cancer stemness via the activation of Wnt signaling (Cho et al., 2018). OCA2 is involved in the melanin biosynthetic process and mammalian pigmentation (Crawford et al., 2017), and the DNA variant in intron of OCA2 (rs4778138) has been found associated with CM risk (Law et al., 2015). The hypomethylation levels of cg18456782 (OCA2) was associated with lower expression of OCA2 and a lower risk. Meanwhile separating CM patients by median expression of OCA2, there is a significant differential survival (p<0.0001) with low expression favoring better survival. All these results suggest a risk pattern for OCA2 gene in CM. KLHL21 could affect cell migration and invasion, play an essential role in tumorigenesis and progression, and it might serve as a potential therapeutic target for cholangiocarcinoma (Chen et al., 2018) and hepatocellular carcinoma (Shi et al., 2016). Although the functional mechanism of these four genes in CM still needs further study, significant correlation between these four genes and OS or response to therapy of patients with CM, and DNA methylation might also be suitable as biomarkers for response to ICB therapy.

In addition, the results of the univariate Cox regression, Kaplan–Meier and ROC analyses for the four individual methylation sites show that each of the DNA methylation sites also could distinguish high- and low-risk patients, but the predictive performances were lower than the combination of these four DNA methylation sites in both the training and validation cohorts (Figure 2—figure supplements 2–3), indicating that single methylation sites are likely to play a role in the prognostic prediction, and a combination of methylation sites might offer better potential to fulfill much more sensitive and specific prognostic tests for patients with CM. To the best of our knowledge, the prognostic value of this multi-marker signature in melanoma has not been previously reported. Therefore, the current study provides new insight that a combination of epigenetic biomarkers could help to improve risk-stratification and prediction of survival in patients with melanoma.

In conclusion, we identified and verified a four-DNA methylation signature that was significantly associated with the OS of patients in TCGA and an independent cohort. The four-DNA methylation signature was not only independent of clinical factors including patient sex, age, stage, tumor location, and Breslow thickness, but also exhibited superior ability in predicting OS compared with known biomarkers. The four-DNA methylation signature was able to stratify patients with startling accuracy in survival differences, suggesting that it may be used to select patients for therapies, and help to determine whether patients may require more or less aggressive treatment. Furthermore, the four-DNA methylation signature was significantly correlated with the ICB immunotherapy-related signature. Therefore, though these exploratory findings are warranted to validate the potential role of this prognostic signature in clinical application and the functional characterization in CM development, these four-DNA methylation sites, or some of them, may participate in the progress of the cancer, and have great potential implications for both risk-stratification, adjuvant management and measures of response to ICB immunotherapy of patients with CM.

We downloaded the data from publicly available databases: The Cancer Genome Atlas database (https://cancergenome.nih.gov/) and GEO database (under accession code GSE51547).

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Author details

1. Wenna Guo

   State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China

   Contribution

   Data curation, Software, Formal analysis, Investigation, Methodology, Writing—original draft, Writing—review and editing

   Contributed equally with

   Liucun Zhu

   Competing interests

   No competing interests declared

2. Liucun Zhu

   School of Life Sciences, Shanghai University, Shanghai, China

   Contribution

   Software, Formal analysis, Validation, Investigation, Methodology, Writing—review and editing

   Contributed equally with

   Wenna Guo

   Competing interests

   No competing interests declared

3. Rui Zhu

   School of Life Sciences, Shanghai University, Shanghai, China

   Contribution

   Validation, Investigation, Writing—review and editing

   Competing interests

   No competing interests declared

4. Qihan Chen

   State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China

   Contribution

   Funding acquisition, Validation, Writing—review and editing

   Competing interests

   No competing interests declared

5. Qiang Wang

   State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China

   Contribution

   Conceptualization, Software, Supervision, Funding acquisition, Validation, Project administration, Writing—review and editing

   For correspondence

   wangq@nju.edu.cn

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-2907-9851

6. Jian-Qun Chen

   State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China

   Contribution

   Conceptualization, Supervision, Validation, Project administration, Writing—review and editing

   For correspondence

   chenjq@nju.edu.cn

   Competing interests

   No competing interests declared

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