Characterization of genetic factors associated with melanoma susceptibility and prognosis

Abstract

Melanoma is the malignant tumor arising from melanocytes and is the most aggressive of the common skin cancers. Melanoma is the tumor with the highest heritability (58%) and around 10% of cases occur in a familial context. Genetic susceptibility can be explained due to the inheritance of low, medium or high-risk variants, or a combination of them. To date, germline mutations in high-risk genes have been detected in 20-30% of melanoma-prone families. Interestingly, there is an important relationship between genetic factors associated with the risk to develop melanoma and genetic factors modulating melanoma outcome.

The thesis hypotheses were: a) The proper characterization of known melanoma risk genes in a specific population context will facilitate genetic counseling in melanoma b) The use of genome-wide linkage can allow the identification of new melanoma susceptibility loci in our population. c) Melanoma susceptibility and nevus-related genes can play a role in melanoma prognosis. d) Variants in immune checkpoints genes can play a role in melanoma prognosis.

Based on those hypotheses, the aims of this thesis were: 1) To characterize known risk genes in patients at high-risk to develop melanoma in Spain to refine genetic counseling. 2) To identify new familial melanoma loci using genome-wide linkage analysis. 3) To study the role of candidate genes in melanoma prognosis.

To answer those aims we designed six studies. In the first study, we evaluated the prevalence of CDKN2A germline mutations in patients at high risk to develop melanoma in our population and characterize families with mutation. We identified a higher prevalence of lung, breast and pancreatic cancer cases in families with mutation. Based on the study results, CDKN2A mutation carriers, besides sun protection advice and dermatologic surveillance, should receive recommendations on avoiding smoking and can be included in early detection programs for pancreatic, lung and breast cancers. In the second study, we evaluated the prevalence of MITF p.Glu318Lys carriers and assessed their characteristics detecting fast-growing melanoma among carriers. Thus, MITF p.Glu318Lys should be given fast-track visits to dermatology as they may be at risk to develop fast-growing melanomas and can be included in early detection programs for renal cancer. In the third study we identified that POT1 is mutated in a subset of melanoma families in Spain, thus genetic testing in melanoma should include the analysis of this gene. In the fourth study we identified a new melanoma locus at 11q associated with familial melanoma. Next-generation sequencing studies focused on the analysis of this region may allow the identification of new melanoma susceptibility genes or variants. Finally, in the last two studies, we focused on melanoma prognosis. We determined that IRF4 rs12203592 T functional variant, associated with a low melanogenesis (and low nevus count) and immune tolerance, correlates with a worse melanoma survival. Moreover, inherited functional variants of the lymphocyte receptor CD5, associated with more immune reactivity, correlated with better melanoma outcome. To conclude, we have established the genetic bases of melanoma susceptibility in our population and refined genetic counseling, knowing the mutation prevalence of each gene and adapting secondary prevention measures in melanoma and other tumors according to the genetic testing results. Genome-wide linkage analysis in melanoma-prone families from Spain has allowed the identification of a new locus at 11q involved in familial melanoma. We have identified new genes modulating melanoma outcome based on the study of candidate genes involved in melanoma susceptibility, nevi count, and immune regulation.

El melanoma és el més agressiu dels càncers de pell comuns. És el tumor amb una major heretabilitat. La susceptibilitat genètica depèn de variants d’alt, mig o baix risc, o la seva combinació. Hi ha una gran correlació entre factors genètics associats al risc i al pronòstic del melanoma. Els objectius d’aquesta tesi han estat: 1. Caracteritzar gens coneguts en pacients amb alt risc a desenvolupar melanoma per millorar el consell genètic. 2. Identificar nous loci implicats en la susceptibilitat a melanoma mitjançant anàlisi de lligament massiu. 3. Estudiar el paper de gens candidats en el pronòstic del melanoma En els primers tres estudis, es va avaluar la prevalença de mutacions a CDKN2A, POT1, promotor de TERT i la variant p.Glu318Lys a MITF en pacients amb alt risc a desenvolupar melanoma. També es van estudiar les característiques de les famílies i portadors d’aquestes variants. Els resultats observats mostren que els portadors de mutació a CDKN2A, a banda de les mesures de fotoprotecció i seguiment dermatològic, haurien d’evitar el tabac i es poden incloure en programes de detecció precoç de càncer de pàncrees, pulmó o mama. Els portadors de la variant p.Glu318Lys a MITF haurien de tenir accés ràpid a la consulta dermatològica pel risc a desenvolupar melanoma de ràpid creixement. POT1 s’hauria d’incloure en el test genètic. En el quart, hem identificat un nou locus a 11q associat a la susceptibilitat del melanoma familiar. Finalment, en els dos últims treballs, hem observat que la variant funcional d’IRF4 rs12203592 T, associada a un recompte de nevus baix i immunotolerància, correlaciona amb un pitjor pronòstic. A més, variants funcionals de CD5 associades amb una major reactivitat immunològica correlacionen amb un millor pronòstic. En conclusió, hem establert les bases genètiques de la susceptibilitat del melanoma en la nostra població i millorat el consell genètic. Estudis de lligament massiu han permès la identificació d’un nou locus associat al melanoma familiar. Per acabar, hem identificat nous gens que modulen el pronòstic del melanoma basant-nos en l’estudi de candidats relacionats amb la susceptibilitat a melanoma, el recompte de nevus i la regulació del sistema immune.