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

Immunophenotype and Transcriptome Profile of Patients With Multiple Sclerosis Treated With Fingolimod: Setting Up a Model for Prediction of Response in a 2-Year Translational Study

BackgroundFingolimod is a functional sphingosine-1-phosphate antagonist approved for the treatment of multiple sclerosis (MS). Fingolimod affects lymphocyte subpopulations and regulates gene expression in the lymphocyte transcriptome. Translational studies are necessary to identify cellular and molecular biomarkers that might be used to predict the clinical response to the drug. In MS patients, we aimed to clarify the differential effects of fingolimod on T, B, and natural killer (NK) cell subsets and to identify differentially expressed genes in responders and non-responders (NRs) to treatment.Materials and methodsSamples were obtained from relapsing–remitting multiple sclerosis patients before and 6 months after starting fingolimod. Forty-eight lymphocyte subpopulations were measured by flow cytometry based on surface and intracellular marker analysis. Transcriptome sequencing by next-generation technologies was used to define the gene expression profiling in lymphocytes at the same time points. NEDA-3 (no evidence of disease activity) and NEDA-4 scores were measured for all patients at 1 and 2 years after beginning fingolimod treatment to investigate an association with cellular and molecular characteristics.ResultsFingolimod affects practically all lymphocyte subpopulations and exerts a strong effect on genetic transcription switching toward an anti-inflammatory and antioxidant response. Fingolimod induces a differential effect in lymphocyte subpopulations after 6 months of treatment in responder and NR patients. Patients who achieved a good response to the drug compared to NR patients exhibited higher percentages of NK bright cells and plasmablasts, higher levels of FOXP3, glucose phosphate isomerase, lower levels of FCRL1, and lower Expanded Disability Status Scale at baseline. The combination of these possible markers enabled us to build a probabilistic linear model to predict the clinical response to fingolimod.ConclusionMS patients responsive to fingolimod exhibit a recognizable distribution of lymphocyte subpopulations and a different pretreatment gene expression signature that might be useful as a biomarker

Infequus: plataforma de enfermedades infecciosas equinas

Desarrollo de la herramienta de formación online Infequus, que ofrecerá a los alumnos y profesionales información actualizada sobre el diagnóstico y control de las enfermedades infecciosas en la especie equina

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Variables psicológicas implicadas en la actitud e iniciativa emprendedora (II): personalidad, cognición y emoción

El proyecto titulado: Variables implicadas en la actitud e iniciativa emprendedora (II): personalidad, cognición y emoción, es la continuidad de otro presentado en la convocatoria anterior (2016-2017) cuyo objetivo era evaluar variables psicológicas en la actitud emprendedora de los estudiantes universitarios de la Universidad Complutense de Madrid (UCM). Este segundo proyecto ha tenido por objetivo principal ampliar la evaluación a otras facultades y áreas de conocimiento de nuestra universidad a fin de obtener el mapa y perfil de la iniciativa emprendedora del universitario UCM

Adelante / Endavant

Séptimo desafío por la erradicación de la violencia contra las mujeres del Institut Universitari d’Estudis Feministes i de Gènere "Purificación Escribano" de la Universitat Jaume

La Moderación y la Gestión del Proceso Tutorial en un Entorno Virtual

Décimo Congreso Internaciona

Posverdad humanismos e imaginarios: cinco ensayos filosóficos: cinco ensayos filosóficos

El Semillero Ethos pertenece al grupo de investigación Cibercultura y Territorio de la Escuela de Ciencias Sociales Artes y Humanidades (ECSAH) de la Universidad Nacional Abierta y a Distancia. Este semillero tiene como bandera incentivar la reflexión filosófica para la construcción de un pensamiento crítico que conduzca a conocimientos epistémicos en torno a la realidad, la actualidad, la política y la ética. Bajo este derrotero, el trabajo que aquí se presenta es producto de lecturas, disertaciones, discusiones y socialización de textos que cada uno de los integrantes realizó, teniendo en cuenta que la escritura es un ejercicio fundamental para el desarrollo intelectual de la persona que se ejercita mediante la comprensión, interpretación, reflexión y proposición, que le permite al individuo consolidar conocimientos epistémicos. De esta forma, se discuten temas como la estética y su configuración local para una experiencia sublime dentro de la filosofía del arte; el tratamiento de la verdad en la posverdad, la cual no solo debe verse desde su construcción como término, sino directamente desde la experiencia, como sucede con las víctimas del conflicto armado colombiano; la voluntad, el vitalismo y la negación del cuerpo como entidad enajenada del bien, visto desde la perspectiva de Nietzsche; la necesidad en tanto a género humano de consolidar el humanismo para su construcción ontológica, axiológica y epistémica. Lo anterior, en el marco de su evolución histórica que se consolida en la actualidad, pero que no conforme con ello, debe verse desde la dimensión local, puesto que es imperativo que se observe desde las subjetividades que nacen en cada territorio, desde el individuo mismo, de forma que pueda ampliarse la comprensión que brinde los elementos de un trabajo propositivo