The melanoma proteome


Malignant melanoma is the leading cause of skin-related death in Caucasians, but rare in populations with darker pigmented skin color. The incidence has increased dramatically during the last decades, with an almost four-fold increase in the Nordic countries in the time period 1964-2003. The increased incidence reflects in part different UV exposure behaviour in the population, but hereditary risk factors including skin type are also important. Short intermittent exposure with sunburns appears to be the main risk factor. Other important risk factors include the number of melanocytic nevi and the number of dysplastic melanocytic nevi.

Primary cutaneous malignant melanoma is thought to develop in a multi-step process. Precursor lesions, such as dysplastic melanocytic nevi develop into a melanoma in situ stage and further into invasive melanoma and eventually metastatic melanoma. Invasive malignant melanoma is traditionally divided into four principal histopathological subgroups based on the microscopical appearance: superficial spreading melanoma (SSM), nodular malignant melanoma (NMM), lentigo maligna melanoma (LMM) and acral lentiginous melanoma (ALM).

Here, we explore the melanoma proteome using TCGA transcriptomics data and antibody based protein data. 205 genes are suggested as prognostic based on transcriptomics data from 102 patients; 163 genes associated with unfavourable prognosis and 42 genes associated with favourable prognosis.

TCGA data analysis


In this metadata study we used data from TCGA where transcriptomics data was available from 102 patients with skin cutaneous melanoma in total. The total dataset included 42 females and 60 males. Most of the patients (73 patients) were still alive at the time of data collection. The stage distribution was stage i) 2 patients, stage i/ii NOS) 1 patient, stage ii) 65 patients, stage iii) 27 patients, stage iv) 32 patients, and 4 patients with missing stage information.

Unfavourable prognostic genes in melanoma


For unfavourable genes, higher relative expression levels at diagnosis gives significantly lower overall survival for the patients. There are 163 genes associated with unfavourable prognosis in melanoma. In Table 1, the top 20 most significant genes related to unfavourable prognosis are listed.

MCM6 is a gene associated with unfavourable prognosis in melanoma. The best separation is achieved by an expression cutoff at 16.5 fpkm which divides the patients into two groups with 0% 3-year survival for patients with high expression versus 62% for patients with low expression, p-value: 1.09e-5. Immunohistochemical staining using an antibody targeting MCM6 (HPA004818) shows differential expression pattern in melanoma samples.

MCM6 - survival analysis p<0.001
MCM6 - high expression
MCM6 - low expression

TIMELESS is another gene associated with unfavourable prognosis in melanoma. The best separation is achieved by an expression cutoff at 10.0 fpkm which divides the patients into two groups with 0% 3-year survival for patients with high expression versus 48% for patients with low expression, p-value: 1.06e-5. Immunohistochemical staining using an antibody targeting TIMELESS (HPA060655) shows differential expression pattern in melanoma samples.

TIMELESS - survival analysis p<0.001
TIMELESS - high expression
TIMELESS - low expression

Table 1. The 20 genes with highest significance associated with unfavourable prognosis in melanoma.

Gene Description Predicted localization mRNA (cancer) p-value
SKP2 S-phase kinase associated protein 2 Intracellular 4.3 3.72e-7
PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 Intracellular 4.2 1.33e-6
TICRR TOPBP1 interacting checkpoint and replication regulator Intracellular 1.2 2.87e-6
TIMELESS timeless circadian clock Intracellular 8.7 1.06e-5
MCM6 minichromosome maintenance complex component 6 Intracellular 14.2 1.09e-5
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Favourable prognostic genes in melanoma


For favourable genes, higher relative expression levels at diagnosis gives significantly higher overall survival for the patients. There are 42 genes associated with favourable prognosis in melanoma. In Table 2, the top 20 most significant genes related to favourable prognosis are listed.

WIPI1 is a gene associated with favourable prognosis in melanoma. The best separation is achieved by an expression cutoff at 14.0 fpkm which divides the patients into two groups with 52% 3-year survival for patients with high expression versus 0% for patients with low expression, p-value: 3.11e-4. Immunohistochemical staining using an antibody targeting WIPI1 (HPA007493) shows differential expression pattern in melanoma samples.

WIPI1 - survival analysis p<0.001
WIPI1 - high expression
WIPI1 - low expression

Table 2. The 20 genes with highest significance associated with favourable prognosis in melanoma.

Gene Description Predicted localization mRNA (cancer) p-value
SIRPG signal regulatory protein gamma Membrane 1.3 7.36e-7
HLA-G major histocompatibility complex, class I, G Membrane 10.7 3.91e-5
CD2 CD2 molecule Membrane,Secreted 6.4 3.97e-5
OTUD7B OTU deubiquitinase 7B Intracellular 8.6 5.09e-5
LCK LCK proto-oncogene, Src family tyrosine kinase Intracellular 2.2 5.65e-5
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The melanoma transcriptome


The transcriptome analysis shows that 68% (n=13290) of all human genes (n=19479) are expressed in melanoma. All genes were classified according to the melanoma-specific expression into one of five different categories, based on the ratio between mRNA levels in melanoma compared to the mRNA levels in the other 16 analyzed cancer tissues. 236 genes show some level of elevated expression in melanoma compared to other cancers (Figure 1). The elevated category is further subdivided into three categories as shown in Table 3.

Figure 1. The distribution of all genes across the five categories based on transcript abundance in melanoma as well as in all other cancer tissues.

Table 3. Number of genes in the subdivided categories of elevated expression in melanoma.

Category Number of genes Description
Tissue enriched 72 At least five-fold higher mRNA levels in a particular cancer as compared to all other cancers
Group enriched 107 At least five-fold higher mRNA levels in a group of 2-7 cancers
Tissue enhanced 57 At least five-fold higher mRNA levels in a particular cancer as compared to average levels in all cancers
Total 236 Total number of elevated genes in melanoma

Additional information


The histopathological features of malignant melanomas vary widely. A typical feature, often facilitating the diagnosis of melanoma, is the occurrence of a pagetoid growth pattern, characterized by growth of melanoma cells in the upper layers of the epidermis from below, as opposed to the localization of normal melanocytes in basal layers of epidermis. Melanoma cells can be large and rich in cytoplasm, small or even spindly. In a subset of melanomas, there are areas with abundant melanin and in other melanomas melanin pigment is scarce or absent. Tumor cell nuclei are enlarged, often with a prominent nucleolus and mitoses are present at a variable degree.

Patients that present with an advanced tumor stage at time for diagnosis and patients with relapse of melanoma after surgical removal generally have a poor prognosis. In patients diagnosed with localized disease, the most important prognostic indicator is tumor thickness at the time of diagnosis. The tumor thickness is measured in mm, according to a system initially described by Breslow, and is the dominating parameter for determining the tumor stage (T-stage) of melanoma. Other prognostic factors include mitotic rate and ulceration, as well as clinical factors such as age, gender and the anatomic site of the primary tumor. In Sweden, the 5-year melanoma specific survival rate is 98% for patients in stage IA (tumor thickness <1mm without ulceration, and 49% for patients in stage IVB (tumor thickness >4 mm with ulceration).

Immunohistochemistry is often used to distinguish malignant melanoma from other tumor types. Traditionally, antibodies towards different S-100 proteins have been used as markers of melanocytes, however, these antibodies also stain in e.g. Langerhans cells and nerve fibers. Other markers, such as Melan-A (MART-1) and tyrosinase (TYR), stain melanocytes more specifically and are useful to determine if a tumor is of melanocytic origin. Proliferation markers are also widely used in the differential diagnostics of melanocytic lesions with uncertain malignant potential. The most accepted marker for determining mitotic cells is Ki-67 (MKI67). The presence of Ki-67 positive melanocytic cells is often used in routine pathology to distinguish malignant melanoma from benign melanocytic tumors.

Relevant links and publications


Uhlen M et al, 2017. A pathology atlas of the human cancer transcriptome. Science.
PubMed: 28818916 DOI: 10.1126/science.aan2507

Cancer Genome Atlas Research Network et al, 2013. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet.
PubMed: 24071849 DOI: 10.1038/ng.2764

UhlĂ©n M et al, 2015. Tissue-based map of the human proteome. Science
PubMed: 25613900 DOI: 10.1126/science.1260419

Edqvist PH et al, 2015. Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling. J Histochem Cytochem.
PubMed: 25411189 DOI: 10.1369/0022155414562646

Ossio R et al, 2017. Melanoma: a global perspective. Nat Rev Cancer.
PubMed: 28450704 DOI: 10.1038/nrc.2017.43

Dermnet - Skin Disease Atlas

Histology dictionary - Melanoma