Puesta a punto de un algoritmo molecular diagnóstico en pacientes con ELA y/o DFT

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 17-01-2020El diagnóstico genético de la esclerosis lateral amiotrófica y la demencia frontotemporal han quedado ligados a partir de dos principales eventos. En 2006, se identificó TDP-43 como el componente principal de las inclusiones citoplasmáticas ubiquitinadas en la ELA y como la característica neuropatológica más importante de la enfermedad (Neumann et al., 2006); y en 2011, el descubrimiento de la expansión de la repetición GGGGCC en el intrón 1 de C9orf72 en pacientes con ELA y en pacientes con DFT (Alan E Renton et al., 2011; Dejesus-Hernandez et al., 2011). Desde entonces, la unión clínica, neuropatológica y genética se ha ido estrechando hasta el punto de considerarse un espectro sindrómico (Robberecht and Philips, 2013). Al menos en algunos casos, la ELA y la DFT son diferentes manifestaciones del mismo proceso patológico subyacente, por lo que hay individuos con ELA, otros con DFT y otros con ambas patologías tanto en casos aislados como en linajes con varios miembros (Mackenzie, Rademakers and Neumann, 2010). El cambio en el escenario del diagnóstico molecular gracias a la inclusión de las nuevas tecnologías de secuenciación masiva han provocado un enorme aumento de conocimiento en la genética de ambas patologías (Marangi and Bryan J Traynor, 2015; Lamp et al., 2018a) provocando a su vez una mayor dificultad en el procesamiento de los datos y especialmente en la interpretación de los resultados, haciendo más necesario el asesoramiento al paciente a través de la formación de equipos especializados en consejo genético. Uno de los objetivos más ambiciosos de este trabajo es intentar demostrar la existencia de un origen somático a través de la secuenciación del exoma completo. Además, a través de la utilización de distintas técnicas de secuenciación, se intenta analizar la oligogenia y la eficiencia de la NGS para el diagnóstico molecular y su utilización como herramienta rutinaria. También, gracias a la NGS se busca encontrar el mejor algoritmo diagnóstico molecular que permita realizar un óptimo análisis genético a todos los pacientes con ELA y DFT. A su vez, con el fin de encontrar posibles factores de riesgo de estas patologías se han analizado las longitudes intermedias de la expansión causante de la enfermedad de Kennedy. Nuestros resultados no encuentran diferencias en la presencia de variantes puntuales ni de pequeñas deleciones en los genes asociados al espectro ELA-DFT ni tampoco la presencia o acumulación de variantes raras (MAF < 0,01) puntuales en la parte codificante del genoma en diferentes tejidos de pacientes con ELA para el hallazgo de mutaciones de origen somático. Los resultados de esta tesis apoyan la necesidad de incluir WES en el diagnóstico genético de los casos ELAf y DFTf, e incluye el grupo de comorbilidad de ambas patologías (ELA-DFT) independientemente de la existencia de antecedentes familiares. La presencia de la oligogenia es un proceso más frecuente de lo esperado en la población española, teniendo especial relevancia los factores de riesgo en genes ampliamente conocidos. De igual manera, se establece un algoritmo molecular diagnóstico que incluye las prioridades en el análisis genético ante la llegada de nuevos pacientes, así como las técnicas necesarias para llevar a cabo un diagnóstico costo-eficienteEsta tesis doctoral ha sido realizada gracias a las subvenciones concedidas al Dr. Alberto García Redondo como IP por el ISCIII, para el desarrollo de los proyectos PI14/00088 y PI17/00491

A neural network for semantic labelling of structured information

Intelligent systems rely on rich sources of information to make informed decisions. Using information from external sources requires establishing correspondences between the information and known information classes. This can be achieved with semantic labelling, which assigns known labels to structured information by classifying it according to computed features. The existing proposals have explored different sets of features, without focusing on what classification techniques are used. In this paper we present three contributions: first, insights on architectural issues that arise when using neural networks for semantic labelling; second, a novel implementation of semantic labelling that uses a state-of-the-art neural network classifier which achieves significantly better results than other four traditional classifiers; third, a comparison of the results obtained by the former network when using different subsets of features, comparing textual features to structural ones, and domain-dependent features to domain-independent ones. The experiments were carried away with datasets from three real world sources. Our results show that there is a need to develop more semantic labelling proposals with sophisticated classification techniques and large features catalogues.Ministerio de Economía y Competitividad TIN2016-75394-

AYNEC: All you need for evaluating completion techniques in knowledge graphs

The popularity of knowledge graphs has led to the development of techniques to refine them and increase their quality. One of the main refinement tasks is completion (also known as link prediction for knowledge graphs), which seeks to add missing triples to the graph, usually by classifying potential ones as true or false. While there is a wide variety of graph completion techniques, there is no standard evaluation setup, so each proposal is evaluated using different datasets and metrics. In this paper we present AYNEC, a suite for the evaluation of knowledge graph completion techniques that covers the entire evaluation workflow. It includes a customisable tool for the generation of datasets with multiple variation points related to the preprocessing of graphs, the splitting into training and testing examples, and the generation of negative examples. AYNEC also provides a visual summary of the graph and the optional exportation of the datasets in an open format for their visualisation. We use AYNEC to generate a library of datasets ready to use for evaluation purposes based on several popular knowledge graphs. Finally, it includes a tool that computes relevant metrics and uses significance tests to compare each pair of techniques. These open source tools, along with the datasets, are freely available to the research community and will be maintained.Ministerio de Economía y Competitividad TIN2016-75394-

Silence: un framework de apoyo a la docencia de desarrollo web

La programación web es, actualmente, una de las vertientes más importantes de la informática en la industria nacional e internacional. Un aspecto muy relacionado, aunque en muchas ocasiones impartido de manera separada, es la enseñanza sobre bases de datos y el acceso a los datos contenidos en las mismas. Con objeto de unir más estrechamente la enseñanza de estas dos ramas, en el presente trabajo presentamos Silence, un framework que provee un entorno unificado para el desarrollo de bases de datos relacionales que den soporte a una aplicación, y de aplicaciones web que consuman los servicios provistos por la base de datos a través de una API RESTful moderna. Silence permite simplificar en gran medida el despliegue de endpoints RESTful sobre una base de datos relacional, posibilitando un aprendizaje del desarrollo web más ágil y una diferenciación clara entre back-end y front-end. Además, da soporte al aprendizaje basado en proyectos, siendo éstos autocontenidos y facilitando su despliegue, desarrollo y evaluación. El framework se encuentra actualmente en uso por más de 500 alumnos en tres titulaciones de grado, y está disponible libremente como código abierto.Web development is currently one of the most prominent fields in the computing industry, both local and international. Database management and usage stands out as a highly related field, though it is often taught independently. In this work we introduce Silence, a framework whose goal is to allow for a joint teaching of databases and web development. Silence provides a unified environment for developing relational databases to store an application’s data, and web applications that use such databases through a modern RESTful API. Silence greatly simplifies the process of deploying RESTful endpoints to interact with a database, resulting in a more agile web development learning process and in a very clear distinction between back-end and front-end. Furthermore, Silence is oriented towards project-based learning, offering self-contained projects that are easy to develop, deploy and evaluate. Our framework is currently actively used by more than 500 students in three different degrees, and it is freely available as open source software

Molecular alterations in sporadic and sod1-als immortalized lymphocytes: Towards a personalized therapy

Amyotrophic lateral sclerosis (ALS) is a fatal neurological condition where motor neurons (MNs) degenerate. Most of the ALS cases are sporadic (sALS), whereas 10% are hereditarily trans-mitted (fALS), among which mutations are found in the gene that codes for the enzyme superoxide dismutase 1 (SOD1). A central question in ALS field is whether causative mutations display selective alterations not found in sALS patients, or they converge on shared molecular pathways. To identify specific and common mechanisms for designing appropriate therapeutic interventions, we focused on the SOD1-mutated (SOD1-ALS) versus sALS patients. Since ALS pathology involves different cell types other than MNs, we generated lymphoblastoid cell lines (LCLs) from sALS and SOD1-ALS patients and healthy donors and investigated whether they show changes in oxidative stress, mito-chondrial dysfunction, metabolic disturbances, the antioxidant NRF2 pathway, inflammatory profile, and autophagic flux. Both oxidative phosphorylation and glycolysis appear to be upregulated in lymphoblasts from sALS and SOD1-ALS. Our results indicate significant differences in NRF2/ARE pathway between sALS and SOD1-ALS lymphoblasts. Furthermore, levels of inflammatory cytokines and autophagic flux discriminate between sALS and SOD1-ALS lymphoblasts. Overall, different molecular mechanisms are involved in sALS and SOD1-ALS patients and thus, personalized medicine should be developed for each case.This research was funded by Comunidad de Madrid (grant ELA_Madrid B2017/BMD-3813 and S2017/BMD-3688), European Commission MSCA-ITN-ETN (grant DRIVE GA: 765912), ISCiii (CIBERNED CB18/05/000 and CB06/05/0089), Fundela (2019/00325/001) for I.L.-B. and AEI (grant PID2019-105600RB-I00) for, A.M. and I.L.-B

Intermediate Repeat Expansion in the ATXN2 Gene as a Risk Factor in the ALS and FTD Spanish Population

Intermediate CAG expansions in the gene ataxin-2 (ATXN2) are a known risk factor for ALS, but little is known about their role in FTD risk. Moreover, their contribution to the risk and phenotype of patients might vary in populations with different genetic backgrounds. The aim of this study was to assess the relationship of intermediate CAG expansions in ATXN2 with the risk and phenotype of ALS and FTD in the Spanish population. Repeat-primed PCR was performed in 620 ALS and 137 FTD patients in three referral centers in Spain to determine the exact number of CAG repeats. In our cohort, >= 27 CAG repeats in ATXN2 were associated with a higher risk of developing ALS (odds ratio [OR] = 2.666 [1.471-4.882]; p = 0.0013) but not FTD (odds ratio [OR] = 1.446 [0.558-3.574]; p = 0.44). Moreover, ALS patients with >= 27 CAG repeats in ATXN2 showed a shorter survival rate compared to those with = 27 repeats in ATXN2 are associated with ALS risk but not with FTD in the Spanish population. ALS patients carrying an intermediate expansion in ATXN2 show more frequent limb onset but a worse prognosis than those without expansions. In patients carrying C9orf72 expansions, the intermediate ATXN2 expansion might increase the penetrance and modify the phenotype

Characterizing SOD1 mutations in Spain. The impact of genotype, age, and sex in the natural history of the disease

11 páginas, 3 figuras, 2 tablasIntroduction: The aim of this study is to describe the frequency and distribution of SOD1 mutations in Spain, and to explore those factors contributing to their phenotype and prognosis. Methods: Seventeen centres shared data on amyotrophic lateral sclerosis (ALS) patients carrying pathogenic or likely pathogenic SOD1 variants. Multivariable models were used to explore prognostic modifiers. Results: In 144 patients (from 88 families), 29 mutations (26 missense, 2 deletion/insertion and 1 frameshift) were found in all 5 exons of SOD1, including 7 novel mutations. 2.6% of ALS patients (including 17.7% familial and 1.3% sporadic) were estimated to carry SOD1 mutations. Its frequency varied considerably between regions, due to founder events. The most frequent mutation was p.Gly38Arg (n = 58), followed by p.Glu22Gly (n = 11), p.Asn140His (n = 10), and the novel p.Leu120Val (n = 10). Most mutations were characterized by a protracted course, and some of them by atypical phenotypes. Older age of onset was independently associated with faster disease progression (exp(Estimate) = 1.03 [0.01, 0.05], p = 0.001) and poorer survival (HR = 1.05 [1.01, 1.08], p = 0.007), regardless of the underlying mutation. Female sex was independently associated to faster disease progression (exp(Estimate) = 2.1 [1.23, 3.65], p = 0.012) in patients carrying the p.Gly38Arg mutation, resulting in shorter survival compared with male carriers (236 vs 301 months). Conclusions: These data may help to evaluate the efficacy of SOD1 targeted treatments, and to expand the number of patients that might benefit from these treatments.This study has received funding from: Instituto de Salud Carlos III (21/00737 PI J.F.V.C., 19/01178 PI T.S., PI 19/01543 to R.R.), cofunded by European Regional Development Fund (‘A way to make Europe’); STOPELA (2017/0653); I + D biomedicina 2017 from Comunidad de Madrid ‘ELA-Madrid’ (B2017/BMD-3813 to A.G.-R.); estrategias frente a Enfermedades Neurodegenerativas Ministerio de Sanidad – Comunidad de Madrid B.O.C.M. Num. 142 - Lunes 17 de junio de 2019 - Pág. 10 ‘Estudio genético de la población con ELA de la Comunidad de Madrid’ to A.G.-R. The Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) and the Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) are initiatives from the ISCIII. J.F.V.C., T.S., C.P., M.P., R.R.-G., J.T.S. and R.J.M. are members of the European Reference Network for Rare Neuromuscular Diseases (ERN EURO-NMD). The funders had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.Peer reviewe

Eligibility criteria for Menopausal Hormone Therapy (MHT): a position statement from a consortium of scientific societies for the use of MHT in women with medical conditions. MHT Eligibility Criteria Group

This project aims to develop eligibility criteria for menopausal hormone therapy (MHT). The tool should be similar to those already established for contraception A consortium of scientific societies coordinated by the Spanish Menopause Society met to formulate recommendations for the use of MHT by women with medical conditions based on the best available evidence. The project was developed in two phases. As a first step, we conducted 14 systematic reviews and 32 metanalyses on the safety of MHT (in nine areas: age, time of menopause onset, treatment duration, women with thrombotic risk, women with a personal history of cardiovascular disease, women with metabolic syndrome, women with gastrointestinal diseases, survivors of breast cancer or of other cancers, and women who smoke) and on the most relevant pharmacological interactions with MHT. These systematic reviews and metanalyses helped inform a structured process in which a panel of experts defined the eligibility criteria according to a specific framework, which facilitated the discussion and development process. To unify the proposal, the following eligibility criteria have been defined in accordance with the WHO international nomenclature for the different alternatives for MHT (category 1, no restriction on the use of MHT; category 2, the benefits outweigh the risks; category 3, the risks generally outweigh the benefits; category 4, MHT should not be used). Quality was classified as high, moderate, low or very low, based on several factors (including risk of bias, inaccuracy, inconsistency, lack of directionality and publication bias). When no direct evidence was identified, but plausibility, clinical experience or indirect evidence were available, "Expert opinion" was categorized. For the first time, a set of eligibility criteria, based on clinical evidence and developed according to the most rigorous methodological tools, has been defined. This will provide health professionals with a powerful decision-making tool that can be used to manage menopausal symptoms

Cumulative Genetic Score and C9orf72 Repeat Status Independently Contribute to Amyotrophic Lateral Sclerosis Risk in 2 Case-Control Studies

[Background and Objectives] Most patients with amyotrophic lateral sclerosis (ALS) lack a monogenic mutation. This study evaluates ALS cumulative genetic risk in an independent Michigan and Spanish replication cohort using polygenic scores.[Methods] Participant samples from University of Michigan were genotyped and assayed for the chromosome 9 open reading frame 72 hexanucleotide expansion. Final cohort size was 219 ALS and 223 healthy controls after genotyping and participant filtering. Polygenic scores excluding the C9 region were generated using an independent ALS genome-wide association study (20,806 cases, 59,804 controls). Adjusted logistic regression and receiver operating characteristic curves evaluated the association and classification between polygenic scores and ALS status, respectively. Population attributable fractions and pathway analyses were conducted. An independent Spanish study sample (548 cases, 2,756 controls) was used for replication.[Results] Polygenic scores constructed from 275 single-nucleotide variation (SNV) had the best model fit in the Michigan cohort. An SD increase in ALS polygenic score associated with 1.28 (95% CI 1.04–1.57) times higher odds of ALS with area under the curve of 0.663 vs a model without the ALS polygenic score (p value = 1 × 10−6). The population attributable fraction of the highest 20th percentile of ALS polygenic scores, relative to the lowest 80th percentile, was 4.1% of ALS cases. Genes annotated to this polygenic score enriched for important ALS pathomechanisms. Meta-analysis with the Spanish study, using a harmonized 132 single nucleotide variation polygenic score, yielded similar logistic regression findings (odds ratio: 1.13, 95% CI 1.04–1.23).[Discussion] ALS polygenic scores can account for cumulative genetic risk in populations and reflect disease-relevant pathways. If further validated, this polygenic score will inform future ALS risk models.National ALS Registry/CDC/ATSDR (1R01TS000289); National ALS Registry/CDC/ATSDR CDCP-DHHS-US (CDC/ATSDR 200-2013-56856); NIEHS K23ES027221; NIEHS R01ES030049; NINDS R01NS127188, ALS Association (20-IIA-532), the Dr. Randall W. Whitcomb Fund for ALS Genetics, the Peter R. Clark Fund for ALS Research, the Scott L. Pranger ALS Clinic Fund, and the NeuroNetwork for Emerging Therapies at the University of Michigan. This work was supported in part by the Intramural Research Program of the NIH, National Institute on Aging (Z01-AG000949-02). Project “ALS Genetic study in Madrid Autonomous Community” funded by “ESTRATEGIAS FRENTE A ENFERMEDADES NEURODEGENERATIVAS” from Spanish Ministry of Health.Peer reviewe

Geodivulgar: Geología y Sociedad 2018

Depto. de Geodinámica, Estratigrafía y PaleontologíaFac. de Ciencias GeológicasFALSEsubmitte