Next-Generation Sequencing in the Identification of Biomarkers in Cutaneous Melanoma According to the Etiopathogenic Development Pathway and their Potential Clinical Relevance

Tesis por compendio[ES] El melanoma es el tipo de cáncer de piel más mortífero y peligroso, ya que tumores de pequeño tamaño pueden generar metástasis. Hasta la fecha, se ha tratado de clasificar desde el punto de vista clínico, epidemiológico y molecular, empleándose actualmente el nivel de exposición solar y la localización del tumor como criterios principales para dividir en distintos grupos a los pacientes de melanoma. En 1998, David Whiteman y colaboradores propusieron un "modelo de vías divergentes" para el desarrollo del melanoma. Este presentaba dos vías: una vinculada a la proliferación melanocítica (nevogénica) y otra relacionada con la exposición solar crónica (CSD). Corroborado desde el punto de vista clínico y epidemiológico, todavía no se ha aportado una caracterización molecular en profundidad. A nivel general se habían identificado genes cuyas mutaciones eran relevantes para el desarrollo del melanoma, como por ejemplo KIT. Sin embargo, todavía se había de estudiar con más detalle la distribución de estas mutaciones entre los distintos subgrupos de melanoma, así como su posible valor pronóstico. En esta tesis se han empleado técnicas de secuenciación - masiva y tradicional - para caracterizar los perfiles mutacionales de las poblaciones del modelo de vías divergentes. Encontramos diferencias tanto en el número de mutaciones como en los genes afectados. También hemos visto cómo los melanomas con mutaciones en KIT parecen desarrollarse por una vía independiente de la etiopatogenia conocida, careciendo el estatus mutacional de este gen de valor pronóstico para la supervivencia de los pacientes.[CA] El melanoma és el tipus de càncer de pell més mortífer i perillós, ja que fins els tumors de menor mida poden acabar generant metàstasi. Al llarg dels anys, s'ha tractat de classificar des del punt de vista clínic, epidemiològic i molecular. Les classificacions actuals utilitzen el nivell d'exposició solar i la localització tumoral per dividir en diferents grups als pacients de melanoma. Al 1998, David Whiteman i col·laboradors proposaren un model de desenvolupament del melanoma que anomenaren "model de vies divergents". Aquest presentava dos vies per la melanomagènesi: una vinculada a la proliferació melanocítica (nevogènica) i l'altra relacionada amb l'exposició solar crònica (CSD). Malgrat aquest model fou corroborat des del punt de vista clínic i epidemiològic, encara no s'ha aportat una caracterització molecular en profunditat. A nivell general s'havien identificat gens les mutacions dels quals eren rellevants per al desenvolupament del melanoma, com el gen KIT. Però, encara s'havia d'estudiar amb més cura la distribució d'estes mutacions entre els distints subgrups de melanoma, així com el seu possible valor pronòstic. En aquesta tesi s'han emprat tècniques de seqüenciació -massiva i tradicional- per caracteritzar els perfils mutacionals de les dues poblacions proposades pel model de vies divergents, trobant diferències tant al nombre de mutacions com als gens afectats. També hem vist com els melanomes mutats en KIT semblen desenvolupar-se per una via independent de l'etiopatogènia coneguda, mancant l'estatus mutacional d'aquest gen de valor pronòstic per la supervivència dels pacients.[EN] Melanoma is the deadliest and most dangerous type of skin cancer, given that a small tumor can spread and result in metastasis. Over the years, classifications have been made either from a clinical, epidemiological or molecular point of view. Current classifications use the degree of solar exposure and tumoral location to divide into different melanoma groups. In 1998, David Whiteman and collaborators proposed the divergent pathway model for melanoma development. This presented two pathways to melanomagenesis: one related to melanocytic proliferation (nevogenic) and the other related to chronic sun exposure (CSD). Despite corroborations of this model from the clinic and epidemiology, it is yet to be molecularly characterized in depth. At a general level, different genes had been identified with relevant mutations for the development of melanoma, as is the gene KIT. However, there was a lack of knowledge on how these mutations were distributed among different melanoma subgroups, as well as the potential prognostic value. In this thesis we have implemented sequencing techniques - both massive and traditional - to characterize the mutational profile of the two populations proposed by the divergent pathways model. We found differences both in the number of mutations and in the genes carrying the mutations. We have also seen how melanomas harboring KIT mutations seem to develop in a way which is independent from the known etiology, and how the mutational status of this gene lacks prognostic value on the outcome of the patients.Millán Esteban, D. (2022). Next-Generation Sequencing in the Identification of Biomarkers in Cutaneous Melanoma According to the Etiopathogenic Development Pathway and their Potential Clinical Relevance [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/182977Compendi

Histologic and phenotypic factors and MC1R status associated with BRAF(V600E), BRAF(V600K), and NRAS mutations in a community-based sample of 414 cutaneous melanomas

Cutaneous melanomas arise through causal pathways involving interplay between exposure to UV radiation and host factors, resulting in characteristic patterns of driver mutations in BRAF, NRAS, and other genes. To gain clearer insights into the factors contributing to somatic mutation genotypes in melanoma, we collected clinical and epidemiologic data, performed skin examinations, and collected saliva and tumor samples from a community-based series of 414 patients aged 18 to 79, newly diagnosed with cutaneous melanoma. We assessed constitutional DNA for nine common polymorphisms in melanocortin-1 receptor gene (MC1R). Tumor DNA was assessed for somatic mutations in 25 different genes. We observed mutually exclusive mutations in BRAF (26%), BRAF (8%), BRAF (5%), and NRAS (9%). Compared to patients with BRAF wild-type melanomas, those with BRAF mutants were significantly younger, had more nevi but fewer actinic keratoses, were more likely to report a family history of melanoma, and had tumors that were more likely to harbor neval remnants. BRAF mutations were also associated with high nevus counts. Both BRAF and NRAS mutants were associated with older age but not with high sun exposure. We also found no association between MC1R status and any somatic mutations in this community sample of cutaneous melanomas, contrary to earlier reports

Malignant melanoma and other malignancies of the nasal cavity and the paranasal sinuses in Sweden

Background: Malignancies emerging in the nasal cavity and the paranasal sinuses are rare and accounts for 5% of all head and neck malignancies and 0.1% of all malignancies in Sweden. The incidence of sinonasal malignancy (SNM), except sinonasal malignant melanoma (SNMM), has been reported to decrease since 1960 in Sweden. Despite similar improvement in the prognosis of other malignancies, treatment of SNM still yields a poor survival outcome. About 1–2% of all malignant melanomas originate from mucosal membranes in the genitourinary, digestive and the respiratory regions, whereas mucosal melanomas are most frequently located in the nasal cavity, followed by sites in paranasal sinuses in the head and neck region. The incidence of cutaneous malignant melanoma (CMM) continues to increase in many parts of the world, possibly due mainly to the effects of sun-related behaviour; however, the incidence of mucosal melanomas such as vulvar and ano-rectal melanoma display a more complicated pattern with a stable or decreasing incidence rate. We now know that the incidence of SNMM is increasing in Sweden, as we have documented one of the largest consecutively studied SNMM groups in the world. Nevertheless, the underlying mechanism remains unclear. The treatment options for these patients have remained the same over the years; mainly radical surgery followed by radiotherapy. Alternatively, recent molecular-targeted therapy has become available for sub-groups of patients with malignant melanomas. Such therapeutic advances stress the importance of investigating the aetiology and molecular characteristics of SNMM, which are not yet well. Aims: Given the rarity of SNM and SNMM, relevant knowledge is limited. Therefore, the overall aim of this thesis was to examine the clinical characteristics and features of SNMM and SNM and to determine the occurrence of molecular alterations. They include KIT, NRAS and BRAF mutation frequencies and mutation frequency of the TERT (Telomerase Reverse Transcriptase) promotor gene in SNMM. Results: In the first project, we identified 3221 patients from the Swedish National Cancer Registry diagnosed with primary malignancies arising from the nasal cavity, paranasal sinuses, or both, during the period 1960 through 2011. The anatomical site, gender and age, incidence and survival were scrutinized. We found that the incidence of sinonasal malignancies decreased except for SNMM and adenoid cystic cancer during the study period. More than 50% of these malignancies involved the nasal cavity. The five-year relative survival was highest for patients with adenoid cystic cancer followed by adenocarcinoma. Those with SNMM and undifferentiated carcinoma had the poorest prognosis. In the second project we identified 186 SNMM patients during the period 1960 through 2000 in Sweden from the National Swedish Cancer Registry (SCR). We investigated the incidence, gender, age, primary anatomical sites, geographic distribution, treatment and survival. In this population the incidence of SNMM increased during the study period. The incidence for females was higher than for males, and the incidence increased with age for both genders. We found that about 70% of the tumours were clinically described as amelanotic. Surgery was the most common primary treatment. The five-year disease- specific survival rates were poor for both genders, but females had a better survival than males. The survival rate improved for both genders during the study period, regardless of therapeutic strategy. We conclude that the incidence of SNMM in Sweden increased significantly from 1960 through 2000 but not as rapidly as that of CMM. In the third project, we analysed 56 primary SNMMs, the largest number, as far as we know, for mutations in KIT (exons 11, 13 and 17), NRAS (exons 1 and 2) and BRAF (exon 15) identified by using direct sequencing. Twelve of the 56 (21%) tumours contained mutations in these oncogenes, 2 tumours harboured KIT mutations, another 2 harboured BRAF mutation and 8 had NRAS mutations. We found a higher frequency of mutations in tumours originating from the paranasal sinuses compared to tumours from the nasal cavity (p=0.027). In the fourth project we analysed 49 SNMM tumours for TERT promotor gene mutations, since former investigators found only a few driver mutations for these patients, who were never previously examined for this mutation. Recent studies of CMM have shown a high frequency (>70%) of driver mutations in this gene. TERT promoter mutations occur at a moderate frequency in SNMM. We suggest that SNMM tumours should be included in molecular characterization, since these alterations probably will be therapeutic targets in the near future

Cutaneous Melanoma Classification: The Importance of High-Throughput Genomic Technologies

Cutaneous melanoma is an aggressive tumor responsible for 90% of mortality related to skin cancer. In the recent years, the discovery of driving mutations in melanoma has led to better treatment approaches. The last decade has seen a genomic revolution in the field of cancer. Such genomic revolution has led to the production of an unprecedented mole of data. High-throughput genomic technologies have facilitated the genomic, transcriptomic and epigenomic profiling of several cancers, including melanoma. Nevertheless, there are a number of newer genomic technologies that have not yet been employed in large studies. In this article we describe the current classification of cutaneous melanoma, we review the current knowledge of the main genetic alterations of cutaneous melanoma and their related impact on targeted therapies, and we describe the most recent high-throughput genomic technologies, highlighting their advantages and disadvantages. We hope that the current review will also help scientists to identify the most suitable technology to address melanoma-related relevant questions. The translation of this knowledge and all actual advancements into the clinical practice will be helpful in better defining the different molecular subsets of melanoma patients and provide new tools to address relevant questions on disease management. Genomic technologies might indeed allow to better predict the biological - and, subsequently, clinical - behavior for each subset of melanoma patients as well as to even identify all molecular changes in tumor cell populations during disease evolution toward a real achievement of a personalized medicine

Molecular Subtypes of Melanoma. Biological and Clinical Significance.

Cutaneous malignant melanoma (CMM) is the most lethal form of skin cancer and its incidence has increased faster than that of any other cancer, rendering it a major public health problem worldwide. High-throughput screenings have opened the door to a new scientific world, which enables molecular-based characterization of large cancer cohort collections. The aim of the research presented in this thesis was to explore the molecular landscapes of melanoma tumors on a genomic and transcriptomic level and subsequently correlate certain molecular features with patient survival, treatment response and tumor evolutionary patterns. In Paper I, it was concluded that metastatic melanoma could be divided into transcriptomic subtypes (gene expression (GEX) phenotypes) possessing diverse biological and clinical features. Patients harboring melanomas infiltrated by immune cells, i.e. the high-immune subtype, showed a superior survival, whereas highly proliferative melanomas, i.e. the proliferative subtype, was correlated to a poor survival outcome and resistance to targeted therapies. Moreover, it was also shown that, irrespectively of the GEX phenotypes, melanomas could be divided into genomic subtypes based on genetic aberrations in the mitogen-activated protein kinase (MAPK) signaling pathway. In Paper II, it was found that mutations in the tumor suppressor gene neurofibromin 1 (NF1), was linked to inferior survival. Today, it is well accepted that most tumors possess some level of intratumor heterogeneity (ITH), i.e. subclonality, influencing disease progression. In Papers III and IV, the evolutionary aspects of melanoma were considered by analyzing ITH, as well as disease progression on a molecular basis. When analyzing multiple metastatic lesions from individual patients, we found that most tumors were genetically different, with a common stem of genetic aberrations and the addition of new “private” ones, thus pointing to continued evolution during progression. Moreover, the GEX proliferative phenotype appeared to be correlated to a later disease course. From multiregional biopsies from single tumors, it was found that mutations in the MAPK signaling pathway appeared to be early events in tumorigenesis. Heterogeneous somatic mutations were found in the range of 3-38%, thus highlighting different levels of subclonality in melanoma. A high degree of mutational heterogeneity was associated with a more aggressive disease progression. In conclusion, melanoma is a complex molecular disease that can be characterized by genomic and transcriptomic signatures with clinical implications. However, a single biopsy might not reflect the true tumor complexity, and subclonality may be one reason behind resistance development

Molecular Characterization and Patient Outcome of Melanoma Nodal Metastases and an Unknown Primary Site

Background Melanoma of unknown primary site (MUP) is not a completely understood entity with nodal metastases as the most common first clinical manifestation. The aim of this multicentric study was to assess frequency and type of oncogenic BRAF/NRAS/KIT mutations in MUP with clinically detected nodal metastases in relation to clinicopathologic features and outcome. Materials and Methods We analyzed series of 103 MUP patients (period: 1992-2010) after therapeutic lymphadenectomy (LND): 40 axillary, 47 groin, 16 cervical, none treated with BRAF inhibitors. We performed molecular characterization of BRAF/NRAS/KIT mutational status in nodal metastases using direct sequencing of respective coding sequences. Median follow-up time was 53 months. Results BRAF mutations were detected in 55 cases (53 %) (51 V600E, 93 %; 4 others, 7 %), and mutually exclusive NRAS mutations were found in 14 cases (14 %) (7 p.Q61R, 4 p.Q61K, 2 p.Q61H, 1 p.Q13R). We have not detected any mutations in KIT. The 5-year overall survival (OS) was 34 %; median was 24 months. We have not found significant correlation between mutational status (BRAF/NRAS) and OS; however, for BRAF or NRAS mutated melanomas we observed significantly shorter disease-free survival (DFS) when compared with wild-type melanoma patients (p = .04; 5-year DFS, 18 vs 19 vs 31 %, respectively). The most important factor influencing OS was number of metastatic lymph nodes >1 (p = .03). Conclusions Our large study on molecular characterization of MUP with nodal metastases showed that MUPs had molecular features similar to sporadic non-chronic-sun-damaged melanomas. BRAF/NRAS mutational status had negative impact on DFS in this group of patients. These observations might have potential implication for molecular-targeted therapy in MUPs

Molecular Markers of Tumor Progression in Melanoma

Malignant melanoma represents one of the most aggressive malignancies but outcome is highly variable with early tumor lesions having an excellent prognosis following resection. We review here the data on identification of genes involved in the progression of melanoma as a result of expression array studies, genomic profiling, and genetic models. We focus on the role of tumor suppressors involved in cell cycle function, DNA repair, and genome maintenance. Highlighted are the roles of loss of p16 in promoting neoplasia in cooperation with deregulated MAPK signaling, and the role of loss of the RASSF1A protein in promoting chromosomal instability. The interactions between point mutation in growth signaling molecules and epigenetic changes in genes involved in DNA repair and cell division are discussed