An Observational Study on the Molecular Profiling of Primary Melanomas Reveals a Progression Dependence on Mitochondrial Activation

Melanoma in advanced stages is one of the most aggressive tumors and the deadliest of skin cancers. To date, the histopathological staging focuses on tumor thickness, and clinical staging is a major estimate of the clinical behavior of primary melanoma. Here we report on an observational study with in-depth molecular profiling at the protein level including post-translational modifications (PTMs) on eleven primary tumors from melanoma patients. Global proteomics, phosphoproteomics, and acetylomics were performed on each sample. We observed an up-regulation of key mitochondrial functions, including the mitochondrial translation machinery and the down-regulation of structural proteins involved in cell adhesion, the cytoskeleton organization, and epidermis development, which dictates the progression of the disease. Additionally, the PTM level pathways related to RNA processing and transport, as well as chromatin organization, were dysregulated in relation to the progression of melanoma. Most of the pathways dysregulated in this cohort were enriched in genes differentially expressed at the transcript level when similar groups are compared or metastasis to primary melanomas. At the genome level, we found significant differences in the mutation profiles between metastatic and primary melanomas. Our findings also highlighted sex-related differences in the molecular profiles. Remarkably, primary melanomas in women showed higher levels of antigen processing and presentation, and activation of the immune system response. Our results provide novel insights, relevant for developing personalized precision treatments for melanoma patients.

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Identification of Germline Mutations in Melanoma Patients with Early Onset, Double Primary Tumors, or Family Cancer History by NGS Analysis of 217 Genes

Biomedicines ◽

10.3390/biomedicines8100404 ◽

2020 ◽

Vol 8 (10) ◽

pp. 404

Author(s):

Lenka Stolarova ◽

Sandra Jelinkova ◽

Radka Storchova ◽

Eva Machackova ◽

Petra Zemankova ◽

...

Keyword(s):

Age At Onset ◽

Primary Melanoma ◽

Germline Mutations ◽

Cancer Syndrome ◽

Melanoma Risk ◽

Cancer History ◽

Primary Tumors ◽

Risk Genes ◽

Increased Risk ◽

Melanoma Patients

Cutaneous melanoma is the deadliest skin malignity with a rising prevalence worldwide. Patients carrying germline mutations in melanoma-susceptibility genes face an increased risk of melanoma and other cancers. To assess the spectrum of germline variants, we analyzed 264 Czech melanoma patients indicated for testing due to early melanoma (at <25 years) or the presence of multiple primary melanoma/melanoma and other cancer in their personal and/or family history. All patients were analyzed by panel next-generation sequencing targeting 217 genes in four groups: high-to-moderate melanoma risk genes, low melanoma risk genes, cancer syndrome genes, and other genes with an uncertain melanoma risk. Population frequencies were assessed in 1479 population-matched controls. Selected POT1 and CHEK2 variants were characterized by functional assays. Mutations in clinically relevant genes were significantly more frequent in melanoma patients than in controls (31/264; 11.7% vs. 58/1479; 3.9%; p = 2.0 × 10−6). A total of 9 patients (3.4%) carried mutations in high-to-moderate melanoma risk genes (CDKN2A, POT1, ACD) and 22 (8.3%) patients in other cancer syndrome genes (NBN, BRCA1/2, CHEK2, ATM, WRN, RB1). Mutations in high-to-moderate melanoma risk genes (OR = 52.2; 95%CI 6.6–413.1; p = 3.2 × 10−7) and in other cancer syndrome genes (OR = 2.3; 95%CI 1.4–3.8; p = 0.003) were significantly associated with melanoma risk. We found an increased potential to carry these mutations (OR = 2.9; 95%CI 1.2–6.8) in patients with double primary melanoma, melanoma and other primary cancer, but not in patients with early age at onset. The analysis revealed affected genes in Czech melanoma patients and identified individuals who may benefit from genetic testing and future surveillance management of mutation carriers.

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Exploring the Ability of LARS2 Carboxy-Terminal Domain in Rescuing the MELAS Phenotype

Life ◽

10.3390/life11070674 ◽

2021 ◽

Vol 11 (7) ◽

pp. 674

Author(s):

Francesco Capriglia ◽

Francesca Rizzo ◽

Giuseppe Petrosillo ◽

Veronica Morea ◽

Giulia d’Amati ◽

...

Keyword(s):

Protein Synthesis ◽

Molecular Mechanisms ◽

Mitochondrial Protein ◽

Trna Synthetase ◽

Mitochondrial Protein Synthesis ◽

Mitochondrial Translation ◽

Terminal Domain ◽

Carboxy Terminal Domain ◽

Mitochondrial Functions ◽

Carboxy Terminal

The m.3243A>G mutation within the mitochondrial mt-tRNALeu(UUR) gene is the most prevalent variant linked to mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome. This pathogenic mutation causes severe impairment of mitochondrial protein synthesis due to alterations of the mutated tRNA, such as reduced aminoacylation and a lack of post-transcriptional modification. In transmitochondrial cybrids, overexpression of human mitochondrial leucyl-tRNA synthetase (LARS2) has proven effective in rescuing the phenotype associated with m.3243A>G substitution. The rescuing activity resides in the carboxy-terminal domain (Cterm) of the enzyme; however, the precise molecular mechanisms underlying this process have not been fully elucidated. To deepen our knowledge on the rescuing mechanisms, we demonstrated the interactions of the Cterm with mutated mt-tRNALeu(UUR) and its precursor in MELAS cybrids. Further, the effect of Cterm expression on mitochondrial functions was evaluated. We found that Cterm ameliorates de novo mitochondrial protein synthesis, whilst it has no effect on mt-tRNALeu(UUR) steady-state levels and aminoacylation. Despite the complete recovery of cell viability and the increase in mitochondrial translation, Cterm-overexpressing cybrids were not able to recover bioenergetic competence. These data suggest that, in our MELAS cell model, the beneficial effect of Cterm may be mediated by factors that are independent of the mitochondrial bioenergetics.

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BRAF/NRAS Mutation Frequencies Among Primary Tumors and Metastases in Patients With Melanoma

Journal of Clinical Oncology ◽

10.1200/jco.2011.41.2452 ◽

2012 ◽

Vol 30 (20) ◽

pp. 2522-2529 ◽

Cited By ~ 295

Author(s):

Maria Colombino ◽

Mariaelena Capone ◽

Amelia Lissia ◽

Antonio Cossu ◽

Corrado Rubino ◽

...

Keyword(s):

Lymph Nodes ◽

Primary Melanoma ◽

Similar Distribution ◽

Nras Mutation ◽

Tissue Samples ◽

Primary Tumors ◽

Paired Samples ◽

Automated Dna Sequencing ◽

Tumor Tissues ◽

Visceral Metastases

Purpose The prevalence of BRAF, NRAS, and p16CDKN2A mutations during melanoma progression remains inconclusive. We investigated the prevalence and distribution of mutations in these genes in different melanoma tissues. Patients and Methods In all, 291 tumor tissues from 132 patients with melanoma were screened. Paired samples of primary melanomas (n = 102) and synchronous or asynchronous metastases from the same patients (n = 165) were included. Tissue samples underwent mutation analysis (automated DNA sequencing). Secondary lesions included lymph nodes (n = 84), and skin (n = 36), visceral (n = 25), and brain (n = 44) sites. Results BRAF/NRAS mutations were identified in 58% of primary melanomas (43% BRAF; 15% NRAS); 62% in lymph nodes, 61% subcutaneous, 56% visceral, and 70% in brain sites. Mutations were observed in 63% of metastases (48% BRAF; 15% NRAS), a nonsignificant increase in mutation frequency after progression from primary melanoma. Of the paired samples, lymph nodes (93% consistency) and visceral metastases (96% consistency) presented a highly similar distribution of BRAF/NRAS mutations versus primary melanomas, with a significantly less consistent pattern in brain (80%) and skin metastases (75%). This suggests that independent subclones are generated in some patients. p16CDKN2A mutations were identified in 7% and 14% of primary melanomas and metastases, with a low consistency (31%) between secondary and primary tumor samples. Conclusion In the era of targeted therapies, assessment of the spectrum and distribution of alterations in molecular targets among patients with melanoma is needed. Our findings about the prevalence of BRAF/NRAS/p16CDKN2A mutations in paired tumor lesions from patients with melanoma may be useful in the management of this disease.

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Lack of tumor recognition by hTERT peptide 540-548-specific CD8+ T cells from melanoma patients reveals inefficient antigen processing

European Journal of Immunology ◽

10.1002/1521-4141(200109)31:9<2642::aid-immu2642>3.0.co;2-6 ◽

2001 ◽

Vol 31 (9) ◽

pp. 2642-2651 ◽

Cited By ~ 54

Author(s):

Maha Ayyoub ◽

Marco Migliaccio ◽

Philippe Guillaume ◽

Danielle Liénard ◽

Jean-Charles Cerottini ◽

...

Keyword(s):

T Cells ◽

Cd8 T Cells ◽

Antigen Processing ◽

Tumor Recognition ◽

Melanoma Patients

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Prospective, Multicenter Clinical Impact Evaluation of a 31-Gene Expression Profile Test for Management of Melanoma Patients

SKIN The Journal of Cutaneous Medicine ◽

10.25251/skin.2.2.3 ◽

2018 ◽

Vol 2 (2) ◽

pp. 111-121 ◽

Cited By ~ 13

Author(s):

Larry D Dillon ◽

Joseph E Gadzia ◽

Robert S Davidson ◽

Michael McPhee ◽

Kyle R Covington ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profile ◽

Expression Profile ◽

Tumor Biology ◽

Primary Melanoma ◽

Risk Class ◽

Class 1 ◽

Post Test ◽

Melanoma Patients ◽

And Performance

Objective: A 31-gene expression profile (GEP) test that has been clinically validated identifies melanoma patients with low (Class 1) or high (Class 2) risk of metastasis based on primary tumor biology. This study aimed to prospectively evaluate the test impact on clinical management of melanoma patients.Methods: Physicians at 16 dermatology, surgical or medical oncology centers examined patients to assess clinical features of the primary melanoma. Recommendations for clinical follow-up and surveillance were collected. Following consent of the patient and performance of the GEP test, recommendations for management were again collected, and pre- and post-test recommendations were assessed to determine changes in management resulting from the addition of GEP testing to traditional clinicopathologic risk factors. Results: Post-test management plans changed for 49% (122 of 247) of cases in the study when compared to pre-test plans. Thirty-six percent (66 of 181) of Class 1 cases had a management change, compared to 85% (56 of 66) of Class 2 cases. GEP class was a significant factor for change in care during the study (p<0.001), with Class 1 accounting for 91% (39 of 43) of cases with decreased management intensity, and Class 2 accounting for 72% (49 of 68) of cases with increases.Conclusions: The reported study show that the 31-gene GEP test improves net health outcomes in the management of cutaneous melanoma. Physicians used test results to guide risk-appropriate changes that match the biological risk of the tumor, including directing more frequent and intense surveillance to high-risk, Class 2 patients.

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Genetic Alterations among Korean Melanoma Patients Showing Tumor Heterogeneity: A Comparison between Primary Tumors and Corresponding Metastatic Lesions

Cancer Research and Treatment ◽

10.4143/crt.2017.535 ◽

2018 ◽

Vol 50 (4) ◽

pp. 1378-1387 ◽

Cited By ~ 5

Author(s):

Si-Hyung Lee ◽

Jee Eun Kim ◽

Hong Sun Jang ◽

Kyu Hyun Park ◽

Byung Ho Oh ◽

...

Keyword(s):

Tumor Heterogeneity ◽

Genetic Alterations ◽

Primary Tumors ◽

Metastatic Lesions ◽

Melanoma Patients

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494 Heterogeneous mutational status of melanomas in multiple primary melanoma patients

Journal of Investigative Dermatology ◽

10.1016/j.jid.2016.06.516 ◽

2016 ◽

Vol 136 (9) ◽

pp. S244

Author(s):

C. Pellegrini ◽

C. Martorelli ◽

G. Cipolloni ◽

L. Di Nardo ◽

A. Antonini ◽

...

Keyword(s):

Primary Melanoma ◽

Mutational Status ◽

Multiple Primary ◽

Melanoma Patients

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Do Oncologic Outcomes From Head and Neck Versus Truncal and Extremity Melanoma Differ? A Single-Institution Single-Subspecialty Experience

The American Surgeon ◽

10.1177/00031348211050813 ◽

2021 ◽

pp. 000313482110508

Author(s):

Kirsten M Baecher ◽

Michael K Turgeon ◽

Caroline R Medin ◽

Geetha Mahendran ◽

Terrill M Flakes ◽

...

Keyword(s):

Head And Neck ◽

Primary Melanoma ◽

High Volume ◽

Oncologic Outcomes ◽

Single Institution ◽

Tertiary Referral Center ◽

Definitive Evidence ◽

Multivariable Analyses ◽

Melanoma Patients ◽

Eighth Edition

Background Outcomes are thought to be worse in head and neck (H&N) melanoma patients. However, definitive evidence of inferior outcomes in H&N melanoma in the modern era is lacking. We sought to ascertain whether H&N melanomas carry a worse prognosis than melanomas of other sites. Methods All patients who underwent excision for primary melanoma by fellowship-trained surgical oncologists at a single institution from 2014 to 2020 were queried from the electronic medical record. Patients who had AJCC eighth edition stage I-III disease were included. Results Of 1127 patients, 28.7% had primary H&N melanoma. H&N patients were more likely to be male, older, and present with more advanced AJCC stage. Median follow-up was 20.0 months (IQR 26.4). On multivariable analyses controlling for other variables, H&N melanoma was associated with worse RFS. Notably, H&N melanoma was not associated with worse MSS, DMFS, or OS on univariate or multivariable analyses. Among patients who recurred, H&N patients were significantly more likely to recur locally compared to non-H&N patients. On subgroup analysis, scalp melanoma was also associated with worse RFS compared to patients with melanoma in locations other than the scalp. When patients with scalp melanoma were excluded from analysis, non-scalp H&N RFS was not significantly different from the non-H&N group on univariate or multivariable analyses. Discussion In this series from a high-volume tertiary referral center, the differences in rates and sites of recurrence between H&N and non-H&N melanoma do not impact melanoma-specific or overall survival, suggesting that H&N melanoma patients should be treated similarly with respect to regional and systemic therapies.

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Can the plasma PD-1 levels predict the presence and efficiency of tumor-infiltrating lymphocytes in patients with metastatic melanoma?

Therapeutic Advances in Medical Oncology ◽

10.1177/1758835919848872 ◽

2019 ◽

Vol 11 ◽

pp. 175883591984887 ◽

Cited By ~ 5

Author(s):

Lorena Incorvaia ◽

Giuseppe Badalamenti ◽

Gaetana Rinaldi ◽

Juan Lucio Iovanna ◽

Daniel Olive ◽

...

Keyword(s):

Immune Response ◽

Overall Survival ◽

Survival Rate ◽

Metastatic Melanoma ◽

Braf Mutation ◽

Primary Melanoma ◽

Tumor Infiltrating Lymphocytes ◽

Enzyme Linked Immunosorbent Assay ◽

Melanoma Patients ◽

Infiltrating Lymphocytes

Background: The immune response in melanoma patients is locally affected by presence of tumor-infiltrating lymphocytes (TILs), generally divided into brisk, nonbrisk, and absent. Several studies have shown that a greater presence of TILs, especially brisk, in primary melanoma is associated with a better prognosis and higher survival rate. Patients and Methods: We investigated by enzyme-linked immunosorbent assay (ELISA) the correlation between PD-1 levels in plasma and the presence/absence of TILs in 28 patients with metastatic melanoma. Results: Low plasma PD-1 levels were correlated with brisk TILs in primary melanoma, whereas intermediate values correlated with the nonbrisk TILs, and high PD-1 levels with absent TILs. Although the low number of samples did not allow us to obtain a statistically significant correlation between the plasma PD-1 levels and the patients’ overall survival depending on the absence/presence of TILs, the median survival of patients having brisk type TILs was 5 months higher than that of patients with absent and nonbrisk TILs. Conclusions: This work highlights the ability of measuring the plasma PD-1 levels in order to predict the prognosis of patients with untreated metastatic melanoma without a BRAF mutation at the time of diagnosis.

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Multi-Omics and Informatics Analysis of FFPE Tissues Derived from Melanoma Patients with Long/Short Responses to Anti-PD1 Therapy Reveals Pathways of Response

Cancers ◽

10.3390/cancers12123515 ◽

2020 ◽

Vol 12 (12) ◽

pp. 3515

Author(s):

Saurabh K. Garg ◽

Eric A. Welsh ◽

Bin Fang ◽

Yuliana I. Hernandez ◽

Trevor Rose ◽

...

Keyword(s):

Antigen Processing ◽

Expression Profiles ◽

Stage Iii ◽

Poor Responders ◽

Tissue Samples ◽

Immune Therapies ◽

Formalin Fixed Paraffin Embedded ◽

Ffpe Tissues ◽

Melanoma Patients ◽

Pathway Analyses

Anti-PD-1 based immune therapies are thought to be dependent on antigen processing and presentation mechanisms. To characterize the immune-dependent mechanisms that predispose stage III/IV melanoma patients to respond to anti-PD-1 therapies, we performed a multi-omics study consisting of expression proteomics and targeted immune-oncology-based mRNA sequencing. Formalin-fixed paraffin-embedded tissue samples were obtained from stage III/IV patients with melanoma prior to anti-PD-1 therapy. The patients were first stratified into poor and good responders based on whether their tumors had or had not progressed while on anti-PD-1 therapy for 1 year. We identified 263 protein/gene candidates that displayed differential expression, of which 223 were identified via proteomics and 40 via targeted-mRNA analyses. The downstream analyses of expression profiles using MetaCore software demonstrated an enrichment of immune system pathways involved in antigen processing/presentation and cytokine production/signaling. Pathway analyses showed interferon (IFN)-γ-mediated signaling via NF-κB and JAK/STAT pathways to affect immune processes in a cell-specific manner and to interact with the inducible nitric oxide synthase. We review these findings within the context of available literature on the efficacy of anti-PD-1 therapy. The comparison of good and poor responders, using efficacy of PD-1-based therapy at 1 year, elucidated the role of antigen presentation in mediating response or resistance to anti-PD-1 blockade.

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