Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests

The use of NGS in clinical practice for precision diagnosis requires a quality starting material. Despite the broadly established use of formalin-fixed paraffin-embedded (FFPE) samples in molecular testing, these usually have low-quality DNA. We established a method to determine the suitability of melanoma FFPE samples for an amplicon-based NGS custom panel analysis. DNA was extracted from unstained melanoma samples and wide local excision samples. Amplicon-based libraries were constructed and tested using time and quality parameters as variables. Time elapsed from sample retrieval >7 years, a quality control value > 5.63 and a DNA integrity value < 2.05 indicated samples were not suitable. A decision tree is provided with rate of samples suitable for analysis according to the combination of these parametersThis study has been funded by the Instituto de Salud Carlos III grant number PI15/01860, the Junta Provincial de Valencia de la Asociación Española contra el Cancer through a PhD grant, and by the Universidad Católica de Valencia San Vicente Mártir. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscrip

Mutational Characterization of Cutaneous Melanoma Supports Divergent Pathways Model for Melanoma Development

This article belongs to the Special Issue Melanoma: Prevention and Molecular Epidemiology.[Simple Summary] The divergent pathway model established at least two approaches for melanoma development. One was related to a propensity to melanocytic proliferation (nevogenic), and the other was associated with an accumulation of solar damage (CSD). We conducted a retrospective study to examine whether this model had a molecular support using sequencing and bioinformatic tools on a set of cutaneous melanomas corresponding to these two groups. We found that the nevogenic melanomas were associated with mutations in BRAF, while the CSD melanomas were associated with mutations in NF1, ROS1, GNA11, and RAC1. We concluded that nevogenic and CSD melanomas constitute two different biological entities.[Abstract] According to the divergent pathway model, cutaneous melanoma comprises a nevogenic group with a propensity to melanocyte proliferation and another one associated with cumulative solar damage (CSD). While characterized clinically and epidemiologically, the differences in the molecular profiles between the groups have remained primarily uninvestigated. This study has used a custom gene panel and bioinformatics tools to investigate the potential molecular differences in a thoroughly characterized cohort of 119 melanoma patients belonging to nevogenic and CSD groups. We found that the nevogenic melanomas had a restricted set of mutations, with the prominently mutated gene being BRAF. The CSD melanomas, in contrast, showed mutations in a diverse group of genes that included NF1, ROS1, GNA11, and RAC1. We thus provide evidence that nevogenic and CSD melanomas constitute different biological entities and highlight the need to explore new targeted therapies.This study was supported by the Ministerio de Ciencia e Innovación-Instituto de Salud Carlos III (PI15/01860; PI19/00667), the Asociación Española Contra el Cáncer-Valencia through “Ayudas predoctorales en Oncología” grant, and the European Academy of Dermatology and Venereology (PPRC-2018-36)

Mutational Characterization of Cutaneous Melanoma Supports Divergent Pathways Model for Melanoma Development

From MDPI via Jisc Publications RouterHistory: accepted 2021-10-14, pub-electronic 2021-10-18Publication status: PublishedFunder: Instituto de Salud Carlos III; Grant(s): PI15/01860; PI19/00667Funder: EADV; Grant(s): PPRC-2018-36, Ayuda predoctoral en OncologíaAccording to the divergent pathway model, cutaneous melanoma comprises a nevogenic group with a propensity to melanocyte proliferation and another one associated with cumulative solar damage (CSD). While characterized clinically and epidemiologically, the differences in the molecular profiles between the groups have remained primarily uninvestigated. This study has used a custom gene panel and bioinformatics tools to investigate the potential molecular differences in a thoroughly characterized cohort of 119 melanoma patients belonging to nevogenic and CSD groups. We found that the nevogenic melanomas had a restricted set of mutations, with the prominently mutated gene being BRAF. The CSD melanomas, in contrast, showed mutations in a diverse group of genes that included NF1, ROS1, GNA11, and RAC1. We thus provide evidence that nevogenic and CSD melanomas constitute different biological entities and highlight the need to explore new targeted therapies

Ultraviolet light-induced collagen degradation inhibits melanoma invasion

From Springer Nature via Jisc Publications RouterHistory: received 2020-08-31, accepted 2021-04-08, registration 2021-04-11, online 2021-05-12, pub-electronic 2021-05-12, collection 2021-12Publication status: PublishedAbstract: Ultraviolet radiation (UVR) damages the dermis and fibroblasts; and increases melanoma incidence. Fibroblasts and their matrix contribute to cancer, so we studied how UVR modifies dermal fibroblast function, the extracellular matrix (ECM) and melanoma invasion. We confirmed UVR-damaged fibroblasts persistently upregulate collagen-cleaving matrix metalloprotein-1 (MMP1) expression, reducing local collagen (COL1A1), and COL1A1 degradation by MMP1 decreased melanoma invasion. Conversely, inhibiting ECM degradation and MMP1 expression restored melanoma invasion. Primary cutaneous melanomas of aged humans show more cancer cells invade as single cells at the invasive front of melanomas expressing and depositing more collagen, and collagen and single melanoma cell invasion are robust predictors of poor melanoma-specific survival. Thus, primary melanomas arising over collagen-degraded skin are less invasive, and reduced invasion improves survival. However, melanoma-associated fibroblasts can restore invasion by increasing collagen synthesis. Finally, high COL1A1 gene expression is a biomarker of poor outcome across a range of primary cancers

Effect of time to sentinel-node biopsy on the prognosis of cutaneous melanoma

Introduction: In patients with primary cutaneous melanoma, there is generally a delay between excisional biopsy of the primary tumour and sentinel-node biopsy. The objective of this study is to analyse the prognostic implications of this delay. Patients and method: This was an observational, retrospective, cohort study in four tertiary referral hospitals. A total of 1963 patients were included. The factor of interest was the interval between the date of the excisional biopsy of the primary melanoma and the date of the sentinel-node biopsy (delay time) in the prognosis. The primary outcome was melanoma-specific survival and disease-free survival. Results: A delay time of 40 days or less (hazard ratio (HR), 1.7; confidence interval (CI), 1.2-2.5) increased Breslow thickness (Breslow ⩾2 mm, HR, >3.7; CI, 1.4-10.7), ulceration (HR, 1.6; CI, 1.1-2.3), sentinel-node metastasis (HR, 2.9; CI, 1.9-4.2), and primary melanoma localised in the head or neck were independently associated with worse melanoma-specific survival (all P < 0.03). The stratified analysis showed that the effect of delay time was at the expense of the patients with a negative sentinel-node biopsy and without regression. Conclusion: Early sentinel-node biopsy is associated with worse survival in patients with cutaneous melanoma

Estudio de los modos propios de una barra de xilófono mediante el Método de Elementos Finitos

El objetivo de este Trabajo Final de Carrera es estudiar un instrumento musical de percusión desde una perspectiva diferente a la que tienen los músicos, compositores e instrumentistas: desde una perspectiva física, cercana a la del constructor de instrumentos musicales o luthier, que es quien debe relacionar directamente la ciencia con el arte de la música. En este trabajo se va ha hacer una descripción general de las principales características físicas de los instrumentos de percusión para después pasar a una descripción más detallada del sistema de elementos que componen un instrumento musical de percusión: el xilófonoTraves Domingo, V. (2006). Estudio de los modos propios de una barra de xilófono mediante el Método de Elementos Finitos. Universitat Politècnica de València. http://hdl.handle.net/10251/34531Archivo delegad

Germline cancer-related mutations detected by routine targeted NGS for tumour analysis: A series of 357 melanoma patients

Screening for somatic mutations using next-generation sequencing (NGS) is the standard of care for many cancers to select the most appropriate tratment. Ideally, matched tumour-normal (T/N) sequencing allows the identification of true somatic mutations. This approach may also identify incidental germline pathogenic variants associated with inherited syndromesThis study was supported in part by Project PROMETEO21/067, Generalitat ValencianaMedicin

Clinical, histological, and molecular differences in melanoma due to different TERT promoter mutations subtypes. A retrospective cross‐sectional study in 684 melanoma patients

Differences in survival according to the pTERT mutation subtypes (−124C > T, −146C > T, and tandem −138_139CC > TT) have been observed. The present study aimed to describe the clinical as the histopathological and molecular cutaneous melanoma features according to the presence of the three most prevalent pTERT mutation subtypes (−124C > T, −146C > T, and tandem −138_139CC > TT). A retrospective cross‐sectional study including 684 patients was designed, and a Partial Least‐Squares Discriminant Analysis (PLS‐DA) was performed. After the PSL‐DA, it was observed that the tandem −138_139CC > TT subtype differs from the other subtypes. The model demonstrated that the −124C > T and the −138_139 CC > TT subtypes were associated with fast‐growing melanomas (OR 0.5, CI 0.29–0.86, p = .012) and with Breslow >2 mm (OR 0.6, CI 0.37–0.97, p = .037), compared to the −146C > T mutation. Finally, the −124C > T appeared to be more associated with the presence of TILs (non‐brisk) than the −146C > T (OR 0.6, CI 0.40–1.01, p = .05). These findings confirmed that the −124C > T and the tandem −138_139 CC > TT subtypes are both highly associated with the presence of features of aggressiveness; however, only the −124C > T was highly associated with TILs. This difference could explain the worse survival rate associated with the tandem −138_139CC > TT mutations.Medicin

Clinical, environmental and histological distribution of BRAF, NRAS and TERT promoter mutations among patients with cutaneous melanoma: a retrospective study of 563 patients

Background The distinct somatic mutations that define clinical and histopathological heterogeneity in cutaneous melanoma could be dependent on host susceptibility to exogenous factors like ultraviolet radiation. Objectives Firstly, to characterize patients with cutaneous melanoma clinically and pathologically based on the mutational status of BRAF, NRAS and TERT promoter. Secondly, to elucidate the modified features due to the presence of TERT promoter mutations over the background of either BRAF or NRAS mutations. Methods We performed a retrospective study on 563 patients with melanoma by investigating somatic mutations in BRAF, NRAS and TERT promoter. Results We observed co‐occurrence of TERT promoter mutations with BRAF and NRAS mutations in 26.3% and 6.9% of melanomas, respectively. Multivariate analysis showed an independent association between BRAF mutations and a decreased presence of cutaneous lentigines at the melanoma site, and an increased association with the presence of any MC1R polymorphism. We also observed an independent association between TERT promoter mutations and increased tumour mitotic rate. Co‐occurrence of BRAF and TERT promoter mutations was independently associated with occurrence of primary tumours at usually sun‐exposed sites, lack of histological chronic sun damage in surrounding unaffected skin at the melanoma site, and increased tumour mitotic rate. Co‐occurrence of NRAS and TERT promoter mutations was independently associated with increased tumour mitotic rate. The presence of TERT promoter together with BRAF or NRAS mutations was associated with statistically significantly worse survival. Conclusions The presence of TERT promoter mutations discriminates BRAF‐ and NRAS‐mutated tumours and indicates a higher involvement of ultraviolet‐induced damage and tumours with worse melanoma‐specific survival than those without any mutation. These observations refine classification of patients with melanoma based on mutational status.Medicin

Angiosarcomas: histology, immunohistochemistry and molecular insights with implications for differential diagnosis

Angiosarcomas (AS) represent a heterogenous group of tumors with variable clinical presentation. AS share an important morphologic and immunohistochemical overlap with other sarcomas, hence the differential diagnosis is challenging, especially in poorly-differentiated tumors. Although molecular studies provide significant clues, especially in the differential diagnosis with other vascular neoplasms, a thorough hematoxylin and eosin analysis remains an essential tool in AS diagnosis. In this review, we discuss pathological and molecular insights with emphasis on implications for differential diagnosis in cutaneous, breast, soft tissue and visceral AS