Genetic dependencies in hereditary and sporadic melanoma

Christodoulou, E.

The studies in this thesis explored several aspects of genetic dependencies in the development of familial and sporadic melanoma. CDKN2A is the most common high-penetrance susceptibility gene responsible for up to 40% of melanoma families worldwide. Interestingly, more than half of germline variation in familial predisposition to melanoma remains to be determined. To identify novel high-penetrance melanoma susceptibility genes we applied Whole Exome Sequencing (WES) and co-segregation analysis in a Dutch melanoma family. We identified NEK11 as a candidate high-penetrance melanoma susceptibility gene and performed functional characterization in cancer cell lines to show loss-of-function (chapter 2). Our additional focus of investigation was a specific cohort of familial melanoma patients carrying a CDKN2A founder mutation, a 19-bp deletion known as the p16-Leiden mutation. Due to the variability in occurrence of pancreatic cancer (PC) and melanoma within familial melanoma families...Show moreThe studies in this thesis explored several aspects of genetic dependencies in the development of familial and sporadic melanoma. CDKN2A is the most common high-penetrance susceptibility gene responsible for up to 40% of melanoma families worldwide. Interestingly, more than half of germline variation in familial predisposition to melanoma remains to be determined. To identify novel high-penetrance melanoma susceptibility genes we applied Whole Exome Sequencing (WES) and co-segregation analysis in a Dutch melanoma family. We identified NEK11 as a candidate high-penetrance melanoma susceptibility gene and performed functional characterization in cancer cell lines to show loss-of-function (chapter 2). Our additional focus of investigation was a specific cohort of familial melanoma patients carrying a CDKN2A founder mutation, a 19-bp deletion known as the p16-Leiden mutation. Due to the variability in occurrence of pancreatic cancer (PC) and melanoma within familial melanoma families, we sought to examine genetic modifiers predicting the risk of PC and melanoma (chapter 3). In this specific cohort of familial melanoma patients, the timing of CDKN2A wild-type allele loss in melanoma development is unknown. We have applied a customized SNP-based digital PCR (dPCR) methodology to precisely quantify CDKN2A allelic imbalance depicting loss-of-heterozygosity (LOH) and attempted to deduce the order of genetic events based on absolute quantification of mutations and losses (CDKN2A LOH, BRAFV600E, TERT promoter, chromosome 9q LOH) (chapter 4). Finally, in addition to high-penetrance genes in familial melanoma, there are genes that are important fitness factors for cancer cell growth and may provide insight into the biology and progression of sporadic melanoma. The application of screening technologies has been successful in identifying genetic dependencies that could possibly be implemented as therapeutic targets in cancer. We have therefore analyzed Clustered Regular Interspaced Short Palindromic Repeats (CRISPR-Cas9) screening data to identify fitness genes in melanoma and used in-vitro systems to validate our findings (chapter 5). Combined, we hope to have uncovered novel genetic dependencies that could be used in the targeted treatment of sporadic as well as familial melanoma.
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Genetic dependencies in hereditary and sporadic melanoma

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