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Instituto de Medicina Molecular
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A systematic pan-cancer analysis of genetic heterogeneity reveals associations with epigenetic modifiers
Publication . Ramos De Matos, Mafalda; Posa, Ioana; Carvalho, Filipa; Morais, Vanessa A.; Grosso, Ana Rita; de Almeida, Sérgio F.
Intratumor genetic heterogeneity (ITH) is the main obstacle to effective cancer treatment and a major mechanism of drug resistance. It results from the continuous evolution of different clones of a tumor over time. However, the molecular features underlying the emergence of genetically-distinct subclonal cell populations remain elusive. Here, we conducted an exhaustive characterization of ITH across 2807 tumor samples from 16 cancer types. Integration of ITH scores and somatic variants detected in each tumor sample revealed that mutations in epigenetic modifier genes are associated with higher ITH levels. In particular, genes that regulate genome-wide histone and DNA methylation emerged as being determinant of high ITH. Indeed, the knockout of histone methyltransferase SETD2 or DNA methyltransferase DNMT3A using the CRISPR/Cas9 system on cancer cells led to significant expansion of genetically-distinct clones and culminated in highly heterogeneous cell populations. The ITH scores observed in knockout cells recapitulated the heterogeneity levels observed in patient tumor samples and correlated with a better mitochondrial bioenergetic performance under stress conditions. Our work provides new insights into tumor development, and discloses new drivers of ITH, which may be useful as either predictive biomarkers or therapeutic targets to improve cancer treatment.
West Nile virus capsid protein interacts with biologically relevant host lipid systems
Publication . Martins, Ana S.; Carvalho, Filomena Almeida; Faustino, André F.; Martins, Ivo C.; Santos, Nuno C.
West Nile and dengue viruses are closely related flaviviruses, originating mosquito-borne viral infections for which there are no effective and specific treatments. Their capsid proteins sequence and structure are particularly similar, forming highly superimposable α-helical homodimers. Measuring protein-ligand interactions at the single-molecule level yields detailed information of biological and biomedical relevance. In this work, such an approach was successfully applied on the characterization of the West Nile virus capsid protein interaction with host lipid systems, namely intracellular lipid droplets (an essential step for dengue virus replication) and blood plasma lipoproteins. Dynamic light scattering measurements show that West Nile virus capsid protein binds very low-density lipoproteins, but not low-density lipoproteins, and this interaction is dependent of potassium ions. Zeta potential experiments show that the interaction with lipid droplets is also dependent of potassium ions as well as surface proteins. The forces involved on the binding of the capsid protein with lipid droplets and lipoproteins were determined using atomic force microscopy-based force spectroscopy, proving that these interactions are K+-dependent rather than a general dependence of ionic strength. The capsid protein interaction with host lipid systems may be targeted in future therapeutic strategies against different flaviviruses. The biophysical and nanotechnology approaches employed in this study may be applied to characterize the interactions of other important proteins from different viruses, in order to understand their life cycles, as well as to find new strategies to inhibit them.
SVC Is a marker of respiratory decline function, similar to FVC, in patients with ALS
Publication . Pinto, Susana; Carvalho, Mamede
Introduction: Respiratory function is a critical predictor of survival in amyotrophic lateral sclerosis (ALS). We aimed to determine if slow vital capacity (SVC) is a predictor of functional loss in ALS as compared to forced vital capacity (FVC). Methods: Consecutive ALS patients in whom respiratory tests were performed at baseline and 6 months later were included. All patients were evaluated with revised ALS functional rating scale (ALSFRS-R) and the respiratory tests, SVC, and FVC. Significant independent variables of functional decay were assessed by univariate Kaplan-Meier log-rank test and multivariate Cox proportional hazards model. A monthly decay not exceeding 0.92 in ALSFRS was considered as the time event. Results: We included 232 patients (134 men; mean onset-age 59.1 ± 11.23 years; mean disease duration from first symptoms to first visit: 14.5 ± 12.9 months; 166 spinal and 66 bulbar onset). All variables studied declined significantly between the two evaluations (p < 0.001). FVC and SVC were strongly correlated at study entry (r 2 = 0.98, p < 0.001) and FVC and SVC decays between first evaluation and 6 months after were the only significant prognostic variables of functional decay (p < 0.001). Conclusion: FVC and SVC decay are inter-changeable in predicting functional decay in ALS. Pharmacological interventions reducing the decline rate of FVC and SVC can have a positive impact on the global functional impairment, with relevant implications for clinical trials' design and interpretation.
DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
Publication . Mendes, Catarina Inês; Lizarazo, Erley; Machado, Miguel P.; Silva, Diogo N.; Tami, Adriana; Ramirez, Mário; Couto, Natacha; Rossen, John W. A.; Carrico, Joao Andre
Dengue virus (DENV) represents a public health threat and economic burden in affected countries. The availability of genomic data is key to understanding viral evolution and dynamics, supporting improved control strategies. Currently, the use of high-throughput sequencing (HTS) technologies, which can be applied both directly to patient samples (shotgun metagenomics) and to PCR-amplified viral sequences (amplicon sequencing), is potentially the most informative approach to monitor viral dissemination and genetic diversity by providing, in a single methodological step, identification and characterization of the whole viral genome at the nucleotide level. Despite many advantages, these technologies require bioinformatics expertise and appropriate infrastructure for the analysis and interpretation of the resulting data. In addition, the many software solutions available can hamper the reproducibility and comparison of results. Here we present DEN-IM, a one-stop, user-friendly, containerized and reproducible workflow for the analysis of DENV short-read sequencing data from both amplicon and shotgun metagenomics approaches. It is able to infer the DENV coding sequence (CDS), identify the serotype and genotype, and generate a phylogenetic tree. It can easily be run on any UNIX-like system, from local machines to high-performance computing clusters, performing a comprehensive analysis without the requirement for extensive bioinformatics expertise. Using DEN-IM, we successfully analysed two types of DENV datasets. The first comprised 25 shotgun metagenomic sequencing samples from patients with variable serotypes and genotypes, including an in vitro spiked sample containing the four known serotypes. The second consisted of 106 paired-end and 76 single-end amplicon sequences of DENV 3 genotype III and DENV 1 genotype I, respectively, where DEN-IM allowed detection of the intra-genotype diversity. The DEN-IM workflow, parameters and execution configuration files, and documentation are freely available at https://github.com/B-UMMI/DEN-IM).
Challenges of BDNF-based therapies : from common to rare diseases
Publication . Miranda-Lourenço, Catarina; Ribeiro Rodrigues, Leonor; Fonseca-Gomes, João; Tanqueiro, Sara; Belo, Rita F.; Ferreira, Catarina B.; Rei, Nádia; Ferreira-Manso, Mafalda; de Almeida-Borlido, Carolina; Costa-Coelho, Tiago; Freitas, Céline; Zavalko, Svitlana; Mouro, Francisco; Sebastião, Ana M; Xapelli, Sara; Rodrigues, Tiago M.; Diógenes, Maria José
Neurotrophins are a well-known family of neurotrophic factors that play an important role both in the central and peripheral nervous systems, where they modulate neuronal survival, development, function and plasticity. Brain-derived neurotrophic factor (BDNF) possesses diverse biological functions which are mediated by the activation of two main classes of receptors, the tropomyosin-related kinase (Trk) B and the p75 neurotrophin receptor (p75NTR). The therapeutic potential of BDNF has drawn attention since dysregulation of its signalling cascades has been suggested to underlie the pathogenesis of both common and rare diseases. Multiple strategies targeting this neurotrophin have been tested; most have found obstacles that ultimately hampered their effectiveness. This review focuses on the involvement of BDNF and its receptors in the pathophysiology of Alzheimer's disease (AD), Amyotrophic Lateral Sclerosis (ALS) and Rett Syndrome (RTT). We describe the known mechanisms leading to the impairment of BDNF/TrkB signalling in these disorders. Such mechanistic insight highlights how BDNF signalling compromise can take various shapes, nearly disease-specific. Therefore, BDNF-based therapeutic strategies must be specifically tailored and are more likely to succeed if a combination of resources is employed.
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Entidade financiadora
Fundação para a Ciência e a Tecnologia
Programa de financiamento
6817 - DCRRNI ID
Número da atribuição
UID/BIM/50005/2019