Publications by authors named "William Bruno"

69 Publications

Birth cohort-specific trends of sun-related behaviors among individuals from an international consortium of melanoma-prone families.

BMC Public Health 2021 04 23;21(1):692. Epub 2021 Apr 23.

Department of Dermatology, Leiden University Medical Centre, Leiden, The Netherlands.

Background: Individuals from melanoma-prone families have similar or reduced sun-protective behaviors compared to the general population. Studies on trends in sun-related behaviors have been temporally and geographically limited.

Methods: Individuals from an international consortium of melanoma-prone families (GenoMEL) were retrospectively asked about sunscreen use, sun exposure (time spent outside), sunburns, and sunbed use at several timepoints over their lifetime. Generalized linear mixed models were used to examine the association between these outcomes and birth cohort defined by decade spans, after adjusting for covariates.

Results: A total of 2407 participants from 547 families across 17 centers were analyzed. Sunscreen use increased across subsequent birth cohorts, and although the likelihood of sunburns increased until the 1950s birth cohort, it decreased thereafter. Average sun exposure did not change across the birth cohorts, and the likelihood of sunbed use increased in more recent birth cohorts. We generally did not find any differences in sun-related behavior when comparing melanoma cases to non-cases. Melanoma cases had increased sunscreen use, decreased sun exposure, and decreased odds of sunburn and sunbed use after melanoma diagnosis compared to before diagnosis.

Conclusions: Although sunscreen use has increased and the likelihood of sunburns has decreased in more recent birth cohorts, individuals in melanoma-prone families have not reduced their overall sun exposure and had an increased likelihood of sunbed use in more recent birth cohorts. These observations demonstrate partial improvements in melanoma prevention and suggest that additional intervention strategies may be needed to achieve optimal sun-protective behavior in melanoma-prone families.
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http://dx.doi.org/10.1186/s12889-021-10424-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8063451PMC
April 2021

Seven Synchronous Primary Melanomas on the Back.

Dermatol Pract Concept 2021 Jan 29;11(1):e2021104. Epub 2020 Jan 29.

Dermatology Unit, Galliera Hospital, Genoa, Italy.

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http://dx.doi.org/10.5826/dpc.1101a104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875657PMC
January 2021

Preferences of Italian patients for return of secondary findings from clinical genome/exome sequencing.

J Genet Couns 2021 Jun 3;30(3):665-675. Epub 2020 Nov 3.

Division of Medical Genetics, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.

Exome/genome sequencing (ES/GS) is increasingly becoming routine in clinical genetic diagnosis, yet issues regarding how to disclose and manage secondary findings (SFs) remain to be addressed, and limited evidence is available on patients' preferences. We carried out semi-structured interviews with 307 individuals undergoing clinical genetic testing to explore their preferences for return of SFs in the hypothetical scenario that their test would be performed using ES/GS. Participants were 254 females (82.7%) and 53 males (17.3%), aged 18-86 years; 73.9% (81.1% of those with lower education levels) reported no prior knowledge of ES/GS. Prior knowledge of ES/GS was more common among patients tested for Mendelian conditions (34.5%), compared to those undergoing cancer genetic testing (22.3%) or carrier screening (7.4%). Despite this reported lack of knowledge, most participants (213, 69.6%) stated they would prefer to be informed of all possible results. Reasons in favor of disclosure included wanting to be aware of any risks (168; 83.6%) and to help relatives (23; 11.4%), but also hope that preventive measures might become available in the future (10, 5%). Conversely, potential negative impact on quality of life was the commonest motivation against disclosure. Among 179 participants seen for cancer genetic counseling who were interviewed again after test disclosure, 81.9% had not heard about ES/GS in the meantime; however, the proportion of participants opting for disclosure of any variants was lower (116; 64.8%), with 36 (20.1%) changing opinion compared to the first interview. Based on these findings, we conclude that genetic counseling for ES/GS should involve enhanced education and decision-making support to enable informed consent to SFs disclosure.
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http://dx.doi.org/10.1002/jgc4.1350DOI Listing
June 2021

Non-BRAF Mutant Melanoma: Molecular Features and Therapeutical Implications.

Front Mol Biosci 2020 24;7:172. Epub 2020 Jul 24.

Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy.

Melanoma is one of the most aggressive tumors of the skin, and its incidence is growing worldwide. Historically considered a drug resistant disease, since 2011 the therapeutic landscape of melanoma has radically changed. Indeed, the improved knowledge of the immune system and its interactions with the tumor, and the ever more thorough molecular characterization of the disease, has allowed the development of immunotherapy on the one hand, and molecular target therapies on the other. The increased availability of more performing technologies like Next-Generation Sequencing (NGS), and the availability of increasingly large genetic panels, allows the identification of several potential therapeutic targets. In light of this, numerous clinical and preclinical trials are ongoing, to identify new molecular targets. Here, we review the landscape of mutated non- skin melanoma, in light of recent data deriving from Whole-Exome Sequencing (WES) or Whole-Genome Sequencing (WGS) studies on melanoma cohorts for which information on the mutation rate of each gene was available, for a total of 10 NGS studies and 992 samples, focusing on available, or in experimentation, targeted therapies beyond those targeting mutated BRAF. Namely, we describe 33 established and candidate driver genes altered with frequency greater than 1.5%, and the current status of targeted therapy for each gene. Only 1.1% of the samples showed no coding mutations, whereas 30% showed at least one mutation in the genes (mostly ) and 70% showed mutations outside of the genes, suggesting potential new roads for targeted therapy. Ongoing clinical trials are available for 33.3% of the most frequently altered genes.
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http://dx.doi.org/10.3389/fmolb.2020.00172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7396525PMC
July 2020

Current State of Target Treatment in BRAF Mutated Melanoma.

Front Mol Biosci 2020 14;7:154. Epub 2020 Jul 14.

Medical Oncology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.

Incidence of melanoma has been constantly growing during the last decades. Although most of the new diagnoses are represented by thin melanomas, the number of melanoma-related deaths in 2018 was 60,712 worldwide (Global Cancer Observatory, 2019). Until 2011, no systemic therapy showed to improve survival in patients with advanced or metastatic melanoma. At that time, standard of care was chemotherapy, with very limited results. The identification of V600 mutation, and the subsequent introduction of targeting drugs, radically changed the clinical practice and dramatically improved outcomes. In this review, we will retrace the development of molecular-target drugs and the current therapeutic scenario for patients with mutated melanoma, from the introduction of inhibitors as single agents to modern clinical practice. We will also discuss the resistance mechanisms identified so far, and the future therapeutic perspectives in mutated melanoma.
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http://dx.doi.org/10.3389/fmolb.2020.00154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371970PMC
July 2020

The Current State of Molecular Testing in the BRAF-Mutated Melanoma Landscape.

Front Mol Biosci 2020 30;7:113. Epub 2020 Jun 30.

Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.

The incidence of melanoma, among the most lethal cancers, is widespread and increasing. Metastatic melanoma has a poor prognosis, representing about 90% of skin cancer mortality. The increased knowledge of tumor biology and the greater understanding of the immune system role in the anti-tumor response has allowed us to develop a more rational approach to systemic therapies. The discovery of activating mutations in half of all melanomas has led to the development of molecularly targeted therapy with BRAF and MEK inhibitors, which dramatically improved outcomes of patients with stage IV BRAF-mutant melanoma. More recently, the results of clinical phase III studies conducted in the adjuvant setting led to the combined administration of BRAF and MEK inhibitors also in patients with resected high-risk melanoma (stage III). Therefore, mutation testing has become a priority to determine the oncologist's choice and course of therapy. In this review, we will report the molecular biology-based strategies used for mutation detection with the main advantages and disadvantages of the most commonly used diagnostic strategies. The timing of such molecular assessment in patients with cutaneous melanoma will be discussed, and we will also examine considerations and approaches for accurate and effective testing.
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http://dx.doi.org/10.3389/fmolb.2020.00113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338720PMC
June 2020

A systematic literature review of the ethics of conducting research in the humanitarian setting.

Confl Health 2020 24;14:27. Epub 2020 May 24.

Division of Epidemiology and Biostatistics, School of Public Health, Research Fellow, Human Rights Center, School of Law, University of California at Berkeley, Berkeley, USA.

Background: Research around humanitarian crises, aid delivery, and the impact of these crises on health and well-being has expanded dramatically. Ethical issues around these topics have recently received more attention. We conducted a systematic literature review to synthesize the lessons learned regarding the ethics of research in humanitarian crises.

Methods: We conducted a systematic review using the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines to identify articles regarding the ethics of research in humanitarian contexts between January 1, 1997 and September 1, 2019. We analyzed the articles to extract key themes and develop an agenda for future research.

Results: We identified 52 articles that matched our inclusion criteria. We categorized the article data into five categories of analysis: 32 were expert statements, 18 were case studies, 11 contained original research, eight were literature reviews and three were book chapters. All included articles were published in English. Using a step-wise qualitative analysis, we identified 10 major themes that encompassed these concepts and points. These major themes were: (21 articles, [40.38%]); (15 articles [28.85%]); , or necessity that research be both academically sound and policy driven, (13 articles for each, [25.0%)]; (10 articles [19.23%]); (6 articles, [11.54%]); (5 articles, [9.62%]); (4 articles [7.69%]); and finally , and (2 articles for each [3.85%]).

Conclusions: Interest in the ethics of studying humanitarian crises has been dramatically increasing in recent years. While key concepts within all research settings such as beneficence, justice and respect for persons are crucially relevant, there are considerations unique to the humanitarian context. The particular vulnerabilities of conflict-affected populations, the contextual challenges of working in humanitarian settings, and the need for ensuring strong community engagement at all levels make this area of research particularly challenging. Humanitarian crises are prevalent throughout the globe, and studying them with the utmost ethical forethought is critical to maintaining sound research principles and ethical standards.
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http://dx.doi.org/10.1186/s13031-020-00282-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245798PMC
May 2020

Insights into Genetic Susceptibility to Melanoma by Gene Panel Testing: Potential Pathogenic Variants in ACD, and .

Cancers (Basel) 2020 04 19;12(4). Epub 2020 Apr 19.

Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, MD 20892, USA.

The contribution of recently established or candidate susceptibility genes to melanoma missing heritability has yet to be determined. Multigene panel testing could increase diagnostic yield and better define the role of candidate genes. We characterized 273 and negative probands through a custom-designed targeted gene panel that included and Co-segregation, loss of heterozygosity (LOH)/protein expression analysis, and splicing characterization were performed to improve variant classification. We identified 16 (5.9%) pathogenic and likely pathogenic variants in established high/medium penetrance cutaneous melanoma susceptibility genes ( and ), including two novel variants in and 4 in . We also found four deleterious and five likely deleterious variants in (3.3%). Thus, including potentially deleterious variants in increased the diagnostic yield to about 9%. Inclusion of rare variants of uncertain significance would increase the overall detection yield to 14%. At least 10% of melanoma missing heritability may be explained through panel testing in our population. To our knowledge, this is the highest frequency of putative deleterious variants reported in melanoma families, suggesting a possible role in melanoma susceptibility, which needs further investigation.
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http://dx.doi.org/10.3390/cancers12041007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7226507PMC
April 2020

Clinical, pathological and dermoscopic phenotype of MITF p.E318K carrier cutaneous melanoma patients.

J Transl Med 2020 02 13;18(1):78. Epub 2020 Feb 13.

IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy.

Background: The p.E318K variant of the Melanocyte Inducing Transcription Factor (MITF) has been implicated in genetic predisposition to melanoma as an intermediate penetrance allele. However, the impact of this variant on clinico-phenotypic, as well as on dermoscopic patterns features of affected patients is not entirely defined. The purpose of our study was to assess the association between the p.E318K germline variant and clinic-phenotypical features of MITF+ compared to non-carriers (MITF-), including dermoscopic findings of melanomas and dysplastic nevi.

Methods: we retrospectively analyzed a consecutive series of 1386 patients recruited between 2000 and 2017 who underwent genetic testing for CDKN2A, CDK4, MC1R and MITF germline variants in our laboratory for diagnostic/research purposes. The patients were probands of melanoma-prone families and apparently sporadic single or multiple primary melanoma patients. For all, we collected clinical, pathological information and dermoscopic images of the histopathologically diagnosed melanomas and dysplastic nevi, when available.

Results: After excluding patients positive for CDKN2A/CDK4 pathogenic variants and those affected by non-cutaneous melanomas, our study cohort comprised 984 cutaneous melanoma patients, 22 MITF+ and 962 MITF-. MITF+ were more likely to develop dysplastic nevi and multiple primary melanomas. Nodular melanoma was more common in MITF+ patients (32% compared to 19% in MITF-). MITF+ patients showed more frequently dysplastic nevi and melanomas with uncommon dermoscopic patterns (unspecific), as opposed to MITF- patients, whose most prevalent pattern was the multicomponent.

Conclusions: MITF+ patients tend to develop melanomas and dysplastic nevi with histopathological features, frequency and dermoscopic patterns often different from those prevalent in MITF- patients. Our results emphasize the importance of melanoma prevention programs for MITF+ patients, including dermatologic surveillance with digital follow-up.
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http://dx.doi.org/10.1186/s12967-020-02253-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017513PMC
February 2020

A Case of Four Synchronous Cutaneous Melanomas: Melanocortin 1 Receptor Polymorphisms and Excessive Sun Exposure.

Acta Derm Venereol 2020 Jan 7;100(1):adv00016. Epub 2020 Jan 7.

Section of Dermatology, Department of Health Sciences (Di.S.Sal.), University of Genoa and Ospedale Policlinico San Martino Largo Rosanna Benzi 10, IT-16132 Genoa, Italy.

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http://dx.doi.org/10.2340/00015555-3371DOI Listing
January 2020

Assessment of mental health and psycho-social support pilot program's effect on intended stigmatizing behavior at the Saftawi Health Center, Gaza: a cross-sectional study.

J Ment Health 2019 Aug 20;28(4):436-442. Epub 2019 May 20.

b Department of Family Medicine and Public Health, School of Medicine , University of California at San Diego , La Jolla , CA , USA.

In the midst of a global refugee crisis, addressing mental health is critical for refugee health care delivery. Understanding efficacy of mental health interventions is more important than ever. In this study, we aim to assess the efficacy of comprehensive mental health and psychosocial support services for refugees in Gaza by comparing intended stigmatizing behavior toward mental health disorders between two health centers (HCs)(Saftawi and Nasser). One year after these services by the United Nations Relief and Works Agency (UNRWA) for Palestine Refugees in the Near East were implemented at Saftawi HC, a randomly selected sample of HC patrons ( = 205) from Saftawi, and a comparable number from a control HC ( = 203 at Nasser) completed the Reported and Intended Behavior Scale (RIBS) regarding stigma towards mental illnesses. Multivariable linear regressions were used to determine the impact of these services in the HC on attitudes against mental health. Saftawi respondents endorsed significantly less intended stigmatizing behavior compared to Nasser respondents ( < 0.001). Multivariable analysis demonstrated significantly less intended stigmatizing behavior at Saftawi compared to Nasser ( < 0.01) while controlling for demographic covariables. UNRWA primary care services and education implemented for refugees in Gaza was associated with reduced stigmatizing behavior toward mental health, which can help guide efficacious mental health care interventions within the Palestine refugee community and in other simiilar communities.
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http://dx.doi.org/10.1080/09638237.2019.1608936DOI Listing
August 2019

Estimating CDKN2A mutation carrier probability among global familial melanoma cases using GenoMELPREDICT.

J Am Acad Dermatol 2019 Aug 5;81(2):386-394. Epub 2019 Feb 5.

Department of Clinical Sciences, Lund University Hospital Lund, Sweden; Department of Surgery, Lund University Hospital, Lund, Sweden.

Background: Although rare in the general population, highly penetrant germline mutations in CDKN2A are responsible for 5%-40% of melanoma cases reported in melanoma-prone families. We sought to determine whether MELPREDICT was generalizable to a global series of families with melanoma and whether performance improvements can be achieved.

Methods: In total, 2116 familial melanoma cases were ascertained by the international GenoMEL Consortium. We recapitulated the MELPREDICT model within our data (GenoMELPREDICT) to assess performance improvements by adding phenotypic risk factors and history of pancreatic cancer. We report areas under the curve (AUC) with 95% confidence intervals (CIs) along with net reclassification indices (NRIs) as performance metrics.

Results: MELPREDICT performed well (AUC 0.752, 95% CI 0.730-0.775), and GenoMELPREDICT performance was similar (AUC 0.748, 95% CI 0.726-0.771). Adding a reported history of pancreatic cancer yielded discriminatory improvement (P < .0001) in GenoMELPREDICT (AUC 0.772, 95% CI 0.750-0.793, NRI 0.40). Including phenotypic risk factors did not improve performance.

Conclusion: The MELPREDICT model functioned well in a global data set of familial melanoma cases. Adding pancreatic cancer history improved model prediction. GenoMELPREDICT is a simple tool for predicting CDKN2A mutational status among melanoma patients from melanoma-prone families and can aid in directing these patients to receive genetic testing or cancer risk counseling.
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http://dx.doi.org/10.1016/j.jaad.2019.01.079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6634996PMC
August 2019

Comprehensive Study of the Clinical Phenotype of Germline BAP1 Variant-Carrying Families Worldwide.

J Natl Cancer Inst 2018 12;110(12):1328-1341

Medical Oncology Unit, Ospedale Policlinico San Martino, Genoa, Italy.

Background: The BRCA1-associated protein-1 (BAP1) tumor predisposition syndrome (BAP1-TPDS) is a hereditary tumor syndrome caused by germline pathogenic variants in BAP1 encoding a tumor suppressor associated with uveal melanoma, mesothelioma, cutaneous melanoma, renal cell carcinoma, and cutaneous BAP1-inactivated melanocytic tumors. However, the full spectrum of tumors associated with the syndrome is yet to be determined. Improved understanding of the BAP1-TPDS is crucial for appropriate clinical management of BAP1 germline variant carriers and their families, including genetic counseling and surveillance for new tumors.

Methods: We collated germline variant status, tumor diagnoses, and information on BAP1 immunohistochemistry or loss of somatic heterozygosity on 106 published and 75 unpublished BAP1 germline variant-positive families worldwide to better characterize the genotypes and phenotypes associated with the BAP1-TPDS. Tumor spectrum and ages of onset were compared between missense and null variants. All statistical tests were two-sided.

Results: The 181 families carried 140 unique BAP1 germline variants. The collated data confirmed the core tumor spectrum associated with the BAP1-TPDS and showed that some families carrying missense variants can exhibit this phenotype. A variety of noncore BAP1-TPDS -associated tumors were found in families of variant carriers. Median ages of onset of core tumor types were lower in null than missense variant carriers for all tumors combined (P < .001), mesothelioma (P < .001), cutaneous melanoma (P < .001), and nonmelanoma skin cancer (P < .001).

Conclusions: This analysis substantially increases the number of pathogenic BAP1 germline variants and refines the phenotype. It highlights the need for a curated registry of germline variant carriers for proper assessment of the clinical phenotype of the BAP1-TPDS and pathogenicity of new variants, thus guiding management of patients and informing areas requiring further research.
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http://dx.doi.org/10.1093/jnci/djy171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292796PMC
December 2018

CDKN2A germline mutations are not associated with poor survival in an Italian cohort of melanoma patients.

J Am Acad Dermatol 2019 May 28;80(5):1263-1271. Epub 2018 Sep 28.

Department of Internal Medicine and Medical Specialties, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy.

Background: Cyclin dependent kinase inhibitor 2A gene (CDKN2A) germline mutations have recently been associated with poor survival in patients with melanoma. Despite the high mutation rate in our cohort (up to 10% in patients with apparently sporadic melanoma), information on the impact of CDKN2A on survival in this cohort is lacking.

Objective: To investigate whether poor survival associated with CDKN2A germline mutations was confirmed in a high mutation-prevalence cohort of Italian patients with melanoma undergoing a mutation-based follow-up.

Methods: A total of 1239 patients with cutaneous melanoma were tested for CDKN2A mutational status and then assigned to a follow-up scheme according not only to family history but also to CDKN2A mutational status, as follow-up intervals were more frequent for CDKN2A germline mutation-positive (MUT) patients. From this cohort, we selected 106 MUT patients (with familial melanoma or apparently sporadic melanoma) and 199 CDKN2A germline mutation-negative (MUT) patients with sporadic melanoma who were matched by age and sex and had a similar tumor stage distribution.

Results: We found no difference in overall survival (hazard ratio, 0.85; 95% confidence interval, 0.48-1.52; P = .592,) or melanoma-specific survival (hazard ratio, 0.86; 95% confidence interval, 0.38-1.95; P = .718,) between MUT and MUT patients. MUT patients were more likely to develop multiple melanomas and to undergo surgical excision of dysplastic nevi than were MUT patients.

Limitations: Retrospective study.

Conclusion: CDKN2A mutations were not associated with survival in our cohort.
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http://dx.doi.org/10.1016/j.jaad.2018.07.060DOI Listing
May 2019

Correction: Combining molecular and immunohistochemical analyses of key drivers in primary melanomas: interplay between germline and somatic variations.

Oncotarget 2018 06 19;9(47):28798. Epub 2018 Jun 19.

Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy.

[This corrects the article DOI: 10.18632/oncotarget.23204.].
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http://dx.doi.org/10.18632/oncotarget.25684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6033371PMC
June 2018

Combining molecular and immunohistochemical analyses of key drivers in primary melanomas: interplay between germline and somatic variations.

Oncotarget 2018 01 14;9(5):5691-5702. Epub 2017 Dec 14.

Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy.

Due to the high mutational somatic burden of Cutaneous Malignant Melanoma (CMM) a thorough profiling of the driver mutations and their interplay is necessary to explain the timing of tumorigenesis or for the identification of actionable genetic events. The aim of this study was to establish the mutation rate of some of the key drivers in melanoma tumorigenesis combining molecular analyses and/or immunohistochemistry in 93 primary CMMs from an Italian cohort also characterized for germline status, and to investigate an interplay between germline and somatic variants. mutations were present in 68% of cases, while germline mutations were found in 16 % and p16 loss in tissue was found in 63%. promoter somatic mutations were detected in 38% of cases while the -245T>C polymorphism was found in 51% of cases. mutations were found in 39% of negative or undetermined cases. NF1 was expressed in all cases analysed. MC1R variations were both considered as a dichotomous variable or scored. While a positive, although not significant association between germline mutations, but not variants, and somatic mutation was found, we did not observe other associations between germline and somatic events. A yet undescribed inverse correlation between -245T>C polymorphism and the presence of mutation was found. It is possible to hypothesize that -245T>C polymorphism could be included in those genotypes which may influence the occurrence of BRAF mutations. Further studies are needed to investigate the role of -245T>C polymorphism as a germline predictor of somatic mutation status.
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http://dx.doi.org/10.18632/oncotarget.23204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814167PMC
January 2018

Functional analysis of a CDKN2A 5'UTR germline variant associated with pancreatic cancer development.

PLoS One 2017 7;12(12):e0189123. Epub 2017 Dec 7.

Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and Ospedale Policlinico San Martino, Genoa, Italy.

CDKN2A coding region germline variants are associated with pancreatic adenocarcinoma (PC) susceptibility. Recently, we described functional germline 5'UTR CDKN2A variants from melanoma patients affecting the post-transcriptional regulation of p16INK4a mRNA that is dependent, at least in part, on an Internal Ribosome Entry Site (IRES) in the 5'UTR region. Here we describe a 5'UTR c.-201_-198delinsCTTT CDKN2A variant (frequency 0.0028 based on 350 PC patients), which seems to be private to PC, since it has never been found in public databases nor in thousands of melanoma patients tested. Functional analyses confirmed IRES activity of the 5'UTR in BX-PC3 PC cells and revealed a functional impact of the identified variant. Using gene reporter assays we observed reduced translation potential in cells treated with the mTOR inhibitor Torin1, a condition that favors the assessment of IRES activity. At the endogenous gene level we quantified allelic imbalance among polysome-associated mRNAs using a patient-derived cell line heterozygous for the c.-201_-198delinsCTTT. Overall, we conclude that this very rare private variant can be considered a potential mutation, specifically associated with PC. Our data indicate that sequencing of the entire 5'UTR of CDKN2A should be included in routine screening of PC cases with suspected inherited susceptibility.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189123PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5720692PMC
December 2017

Germline Variation at CDKN2A and Associations with Nevus Phenotypes among Members of Melanoma Families.

J Invest Dermatol 2017 12 19;137(12):2606-2612. Epub 2017 Aug 19.

Melanoma Institute Australia, Westmead, New South Wales, Australia; Westmead Institute for Cancer Research, University of Sydney at Westmead Millennium Institute, New South Wales, Australia.

Germline mutations in CDKN2A are frequently identified among melanoma kindreds and are associated with increased atypical nevus counts. However, a clear relationship between pathogenic CDKN2A mutation carriage and other nevus phenotypes including counts of common acquired nevi has not yet been established. Using data from GenoMEL, we investigated the relationships between CDKN2A mutation carriage and 2-mm, 5-mm, and atypical nevus counts among blood-related members of melanoma families. Compared with individuals without a pathogenic mutation, those who carried one had an overall higher prevalence of atypical (odds ratio = 1.64; 95% confidence interval = 1.18-2.28) nevi but not 2-mm nevi (odds ratio = 1.06; 95% confidence interval = 0.92-1.21) or 5-mm nevi (odds ratio = 1.26; 95% confidence interval = 0.94-1.70). Stratification by case status showed more pronounced positive associations among non-case family members, who were nearly three times (odds ratio = 2.91; 95% confidence interval = 1.75-4.82) as likely to exhibit nevus counts at or above the median in all three nevus categories simultaneously when harboring a pathogenic mutation (vs. not harboring one). Our results support the hypothesis that unidentified nevogenic genes are co-inherited with CDKN2A and may influence carcinogenesis.
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http://dx.doi.org/10.1016/j.jid.2017.07.829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701856PMC
December 2017

Identification, genetic testing, and management of hereditary melanoma.

Cancer Metastasis Rev 2017 03;36(1):77-90

Department of Internal Medicine and Medical Specialties, University of Genoa and Genetics of Rare Cancers, IRCCS AOU San Martino-IST, Genoa, Italy.

Several distinct melanoma syndromes have been defined, and genetic tests are available for the associated causative genes. Guidelines for melanoma genetic testing have been published as an informal "rule of twos and threes," but these guidelines apply to CDKN2A testing and are not intended for the more recently described non-CDKN2A melanoma syndromes. In order to develop an approach for the full spectrum of hereditary melanoma patients, we have separated melanoma syndromes into two types: "melanoma dominant" and "melanoma subordinate." Syndromes in which melanoma is a predominant cancer type are considered melanoma dominant, although other cancers, such as mesothelioma or pancreatic cancers, may also be observed. These syndromes are associated with defects in CDKN2A, CDK4, BAP1, MITF, and POT1. Melanoma-subordinate syndromes have an increased but lower risk of melanoma than that of other cancer(s) seen in the syndrome, such as breast and ovarian cancer or Cowden syndrome. Many of these melanoma-subordinate syndromes are associated with well-established predisposition genes (e.g., BRCA1/2, PTEN). It is likely that these predisposition genes are responsible for the increased susceptibility to melanoma as well but with lower penetrance than that observed for the dominant cancer(s) in those syndromes. In this review, we describe our extension of the "rule of twos and threes" for melanoma genetic testing. This algorithm incorporates an understanding of the spectrum of cancers and genes seen in association with melanoma to create a more comprehensive and tailored approach to genetic testing.
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http://dx.doi.org/10.1007/s10555-017-9661-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385190PMC
March 2017

Heterogeneity and frequency of BRAF mutations in primary melanoma: Comparison between molecular methods and immunohistochemistry.

Oncotarget 2017 Jan;8(5):8069-8082

Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy.

Finding the best technique to identify BRAF mutations with a high sensitivity and specificity is mandatory for accurate patient selection for target therapy. BRAF mutation frequency ranges from 40 to 60% depending on melanoma clinical characteristics and detection technique used.Intertumoral heterogeneity could lead to misinterpretation of BRAF mutational status; this is especially important if testing is performed on primary specimens, when metastatic lesions are unavailable.Aim of this study was to identify the best combination of methods for detecting BRAF mutations (among peptide nucleic acid - PNA-clamping real-time PCR, immunohistochemistry and capillary sequencing) and investigate BRAF mutation heterogeneity in a series of 100 primary melanomas and a subset of 25 matched metastatic samples.Overall, we obtained a BRAF mutation frequency of 62%, based on the combination of at least two techniques. Concordance between mutation status in primary and metastatic tumor was good but not complete (67%), when agreement of at least two techniques were considered. Next generation sequencing was used to quantify the threshold of detected mutant alleles in discordant samples. Combining different methods excludes that the observed heterogeneity is technique-based. We propose an algorithm for BRAF mutation testing based on agreement between immunohistochemistry and PNA; a third molecular method could be added in case of discordance of the results. Testing the primary tumor when the metastatic sample is unavailable is a good option if at least two methods of detection are used, however the presence of intertumoral heterogeneity or the occurrence of additional primaries should be carefully considered.
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http://dx.doi.org/10.18632/oncotarget.14094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5352383PMC
January 2017

Multiple rare variants in high-risk pancreatic cancer-related genes may increase risk for pancreatic cancer in a subset of patients with and without germline CDKN2A mutations.

Hum Genet 2016 Nov 23;135(11):1241-1249. Epub 2016 Jul 23.

Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.

The risk of pancreatic cancer (PC) is increased in melanoma-prone families but the causal relationship between germline CDKN2A mutations and PC risk is uncertain, suggesting the existence of non-CDKN2A factors. One genetic possibility involves patients having mutations in multiple high-risk PC-related genes; however, no systematic examination has yet been conducted. We used next-generation sequencing data to examine 24 putative PC-related genes in 43 PC patients with and 23 PC patients without germline CDKN2A mutations and 1001 controls. For each gene and the four pathways in which they occurred, we tested whether PC patients (overall or CDKN2A+ and CDKN2A- cases separately) had an increased number of rare nonsynonymous variants. Overall, we identified 35 missense variants in PC patients, 14 in CDKN2A+ and 21 in CDKN2A- PC cases. We found nominally significant associations for mismatch repair genes (MLH1, MSH2, MSH6, PMS2) in all PC patients and for ATM, CPA1, and PMS2 in CDKN2A- PC patients. Further, nine CDKN2A+ and four CDKN2A- PC patients had rare potentially deleterious variants in multiple PC-related genes. Loss-of-function variants were only observed in CDKN2A- PC patients, with ATM having the most pathogenic variants. Also, ATM variants (n = 5) were only observed in CDKN2A- PC patients with a family history that included digestive system tumors. Our results suggest that a subset of PC patients may have increased risk because of germline mutations in multiple PC-related genes.
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http://dx.doi.org/10.1007/s00439-016-1715-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5152573PMC
November 2016

Multiple primary melanomas (MPMs) and criteria for genetic assessment: MultiMEL, a multicenter study of the Italian Melanoma Intergroup.

J Am Acad Dermatol 2016 Feb;74(2):325-32

Dermatology Unit, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy.

Background: Multiple primary melanoma (MPM), in concert with a positive family history, is a predictor of cyclin-dependent kinase (CDK) inhibitor 2A (CDKN2A) germline mutations. A rule regarding the presence of either 2 or 3 or more cancer events (melanoma and pancreatic cancer) in low or high melanoma incidence populations, respectively, has been established to select patients for genetic referral.

Objective: We sought to determine the CDKN2A/CDK4/microphthalmia-associated transcription factor mutation rate among Italian patients with MPM to appropriately direct genetic counseling regardless of family history.

Methods: In all, 587 patients with MPM and an equal number with single primary melanomas and control subjects were consecutively enrolled at the participating centers and tested for CDKN2A, CDK4, and microphthalmia-associated transcription factor.

Results: CDKN2A germline mutations were found in 19% of patients with MPM versus 4.4% of patients with single primary melanoma. In familial MPM cases the mutation rate varied from 36.6% to 58.8%, whereas in sporadic MPM cases it varied from 8.2% to 17.6% in patients with 2 and 3 or more melanomas, respectively. The microphthalmia-associated transcription factor E318K mutation accounted for 3% of MPM cases altogether.

Limitations: The study was hospital based, not population based. Rare novel susceptibility genes were not tested.

Conclusion: Italian patients who developed 2 melanomas, even in situ, should be referred for genetic counseling even in the absence of family history.
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http://dx.doi.org/10.1016/j.jaad.2015.09.053DOI Listing
February 2016

Physical and Chemical Interactions with Conspecifics Mediate Sex Change in a Protandrous Gastropod Crepidula fornicata.

Biol Bull 2015 Dec;229(3):276-81

Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245.

The protandrous marine snail Crepidula fornicata has been a theoretical and empirical model for studies of sex change for many decades. We investigated the social conditions under which sex change occurs in this species by manipulating physical and chemical contact with conspecifics. Male snails were either in physical and chemical contact with females or in chemical contact with, but physically isolated from, females. Males were tested both with living females and with empty, sterilized shells. Males that were physically touching a living female were less likely to change sex than the isolated controls, while males in chemical (but not physical) contact with females changed sex no slower than the isolated controls. These results provide experimental evidence that the factor controlling sex change in C. fornicata is due to a contact-borne inhibitor associated with female conspecifics. These findings serve as a basis for future studies of sex change in this model system.
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http://dx.doi.org/10.1086/BBLv229n3p276DOI Listing
December 2015

The CDKN2A/p16(INK) (4a) 5'UTR sequence and translational regulation: impact of novel variants predisposing to melanoma.

Pigment Cell Melanoma Res 2016 Mar 17;29(2):210-21. Epub 2015 Dec 17.

Department of Internal Medicine and Medical Specialties, DiMI, University of Genoa, Genoa, Italy.

Many variants of uncertain functional significance in cancer susceptibility genes lie in regulatory regions, and clarifying their association with disease risk poses significant challenges. We studied 17 germline variants (nine of which were novel) in the CDKN2A 5'UTR with independent approaches, which included mono and bicistronic reporter assays, Western blot of endogenous protein, and allelic representation after polysomal profiling to investigate their impact on CDKN2A mRNA translation regulation. Two of the novel variants (c.-27del23, c.-93-91delAGG) were classified as causal mutations (score ≥3), along with the c.-21C>T, c.-34G>T, and c.-56G>T, which had already been studied by a subset of assays. The novel c.-42T>A as well as the previously described c.-67G>C were classified as potential mutations (score 1 or 2). The remaining variants (c.-14C>T, c.-20A>G, c.-25C>T+c.-180G>A, c.-30G>A, c.-40C>T, c.-45G>A, c.-59C>G, c.-87T>A, c.-252A>T) were classified as neutral (score 0). In conclusion, we found evidence that nearly half of the variants found in this region had a negative impact on CDKN2A mRNA translation, supporting the hypothesis that 5'UTR can act as a cellular Internal Ribosome Entry Site (IRES) to modulate p16(INK) (4a) translation.
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http://dx.doi.org/10.1111/pcmr.12444DOI Listing
March 2016

Signs and genetics of rare cancer syndromes with gastroenterological features.

World J Gastroenterol 2015 Aug;21(30):8985-93

William Bruno, Paola Ghiorzo, Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, IRCCS AOU San Martino-IST, 16132 Genoa, Italy.

Although the genetic bases of most hereditary cancer syndromes are known, and genetic tests are available for them, the incidence of the most rare of these syndromes is likely underestimated, partially because the clinical expression is neither fully understood nor easily diagnosed due to the variable and complex expressivity. The clinical features of a small pool of rare cancer syndromes include gastroenterological signs, though not necessarily tumors, that could require the intervention of a gastroenterologist during any of the phases of the clinical management. Herein we will attempt to spread the knowledge on these rare syndromes by summarizing the phenotype and genetic basis, and revising the peculiar gastroenterological signs whose underlying role in these rare hereditary cancer syndromes is often neglected. Close collaboration between geneticists and gastroenterologists could facilitate both the early identification of patients or relatives at-risk and the planning of multidisciplinary and tailored management of these subjects.
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http://dx.doi.org/10.3748/wjg.v21.i30.8985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4533032PMC
August 2015

Development of forensic assay signatures for ebolaviruses.

J Forensic Sci 2015 Mar 10;60(2):315-25. Epub 2015 Feb 10.

Bioenergy and Biome Sciences (B-11), Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545.

Ebolaviruses are a diverse group of RNA viruses comprising five different species, four of which cause fatal hemorrhagic fever in humans. Because of their high infectivity and lethality, ebolaviruses are considered major biothreat agents. Although detection assays exist, no forensic assays are currently available. Here, we report the development of forensic assays that differentiate ebolaviruses. We performed phylogenetic analyses and identified canonical SNPs for all species, major clades and isolates. TaqMan-MGB allelic discrimination assays based on these SNPs were designed, screened against synthetic RNA templates, and validated against ebolavirus genomic RNAs. A total of 45 assays were validated to provide 100% coverage of the species and variants with additional resolution at the isolate level. These assays enabled accurate forensic analysis on 4 "unknown" ebolaviruses. Unknowns were correctly classified to species and variant. A goal of providing resolution below the isolate level was not successful. These high-resolution forensic assays allow rapid and accurate genotyping of ebolaviruses for forensic investigations.
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http://dx.doi.org/10.1111/1556-4029.12655DOI Listing
March 2015

Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma.

Nat Genet 2014 May 30;46(5):482-6. Epub 2014 Mar 30.

Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, USA.

Although CDKN2A is the most frequent high-risk melanoma susceptibility gene, the underlying genetic factors for most melanoma-prone families remain unknown. Using whole-exome sequencing, we identified a rare variant that arose as a founder mutation in the telomere shelterin gene POT1 (chromosome 7, g.124493086C>T; p.Ser270Asn) in five unrelated melanoma-prone families from Romagna, Italy. Carriers of this variant had increased telomere lengths and numbers of fragile telomeres, suggesting that this variant perturbs telomere maintenance. Two additional rare POT1 variants were identified in all cases sequenced in two separate Italian families, one variant per family, yielding a frequency for POT1 variants comparable to that for CDKN2A mutations in this population. These variants were not found in public databases or in 2,038 genotyped Italian controls. We also identified two rare recurrent POT1 variants in US and French familial melanoma cases. Our findings suggest that POT1 is a major susceptibility gene for familial melanoma in several populations.
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http://dx.doi.org/10.1038/ng.2941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4056593PMC
May 2014

Automated maximum likelihood separation of signal from baseline in noisy quantal data.

Biophys J 2013 Jul;105(1):68-79

Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

Data recordings often include high-frequency noise and baseline fluctuations that are not generated by the system under investigation, which need to be removed before analyzing the signal for the system's behavior. In the absence of an automated method, experimentalists fall back on manual procedures for removing these fluctuations, which can be laborious and prone to subjective bias. We introduce a maximum likelihood formalism for separating signal from a drifting baseline plus noise, when the signal takes on integer multiples of some value, as in ion channel patch-clamp current traces. Parameters such as the quantal step size (e.g., current passing through a single channel), noise amplitude, and baseline drift rate can all be optimized automatically using the expectation-maximization algorithm, taking the number of open channels (or molecules in the on-state) at each time point as a hidden variable. Our goal here is to reconstruct the signal, not model the (possibly highly complex) underlying system dynamics. Thus, our likelihood function is independent of those dynamics. This may be thought of as restricting to the simplest possible hidden Markov model for the underlying channel current, in which successive measurements of the state of the channel(s) are independent. The resulting method is comparable to an experienced human in terms of results, but much faster. FORTRAN 90, C, R, and JAVA codes that implement the algorithm are available for download from our website.
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http://dx.doi.org/10.1016/j.bpj.2013.02.060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699741PMC
July 2013

Definitions of genetic testing in Italian legal documents.

J Community Genet 2013 Apr 18;4(2):289-91. Epub 2012 Dec 18.

Section of Forensic Medicine and Bioethics, Department of Health Sciences, University of Genova, Via A. De Toni, 12 16132, Genova, Italy,

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http://dx.doi.org/10.1007/s12687-012-0129-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3666840PMC
April 2013
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