Browsing by Author "Magno, Ramiro"
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- Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer riskPublication . Jacinta-Fernandes, Ana; Xavier, Joana M.; Magno, Ramiro; Lage, Joel; Maia, Ana-TeresaMost breast cancer (BC) risk-associated single-nucleotide polymorphisms (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting microRNA (miRNA) genes and/or miRNA binding. To test this, we adapted two miRNA-binding prediction algorithms-TargetScan and miRanda-to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant ( P≤5×10-8 ) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3'-untranslated regions of putative miRNA target genes were predicted to alter miRNA::mRNA (messenger RNA) pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and reinforce the role of miRNA-mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.
- Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significantPublication . Correia, Lizelle; Magno, Ramiro; Xavier, JM; Almeida, Bernardo; Duarte, Isabel; Esteves, Filipa; Ghezzo, Marinella; Eldridge, Matthew; Sun, Chong; Bosma, Astrid; Mittempergher, Lorenza; Marreiros, Ana; Bernards, Rene; Caldas, Carlos; Chin, Suet-Feung; Maia, Ana-TeresaPIK3CA mutations are the most common in breast cancer, particularly in the estrogen receptor-positive cohort, but the benefit of PI3K inhibitors has had limited success compared with approaches targeting other less common mutations. We found a frequent allelic expression imbalance between the missense mutant and wild-type PIK3CA alleles in breast tumors from the METABRIC (70.2%) and the TCGA (60.1%) projects. When considering the mechanisms controlling allelic expression, 27.7% and 11.8% of tumors showed imbalance due to regulatory variants in cis, in the two studies respectively. Furthermore, preferential expression of the mutant allele due to cis-regulatory variation is associated with poor prognosis in the METABRIC tumors (P = 0.031). Interestingly, ER-, PR-, and HER2+ tumors showed significant preferential expression of the mutated allele in both datasets. Our work provides compelling evidence to support the clinical utility of PIK3CA allelic expression in breast cancer in identifying patients of poorer prognosis, and those with low expression of the mutated allele, who will unlikely benefit from PI3K inhibitors. Furthermore, our work proposes a model of differential regulation of a critical cancer-promoting gene in breast cancer.
- An approach to map and quantify the fishing effort of polyvalent passive gear fishing fleets using geospatial dataPublication . Sales Henriques, Nuno; Russo, Tommaso; Bentes, Luis; Monteiro, Pedro; Parisi, Antonio; Magno, Ramiro; Oliveira, Frederico; Erzini, Karim; Gonçalves, Jorge Manuel SantosThe use of tracking devices, such as vessel monitoring systems or automatic identification system, enabled us to expand our knowledge on the distribution and quantification of fishing activities. However, methods and models based on vessel tracking data are mostly devised to be applied to towed gears, whereas applications to multi-gear and passive fisheries have been underrepresented. Here, we propose a methodology to deal with geospatial data to map and quantify the fishing effort, as soak time, of passive fishing gears used by a multi-gear fishing fleet. This approach can be adapted to other passive multi-or single-gear fisheries, since it requires only three variables that can be extracted from a pre-classified dataset, to identify the beginning (gear deployment) and the end (hauling) of passive fishing events. As far as we are aware, this is the first time a methodology that allows quantifying the soak time of static passive fishing events, within a polyvalent fishery context, is presented. We argue that the information that can be extracted from such approaches could contribute to improved management of multi-gear and static-gear fisheries and the ecosystem-based approach.
- Coding and non-coding RNA expression in NSC34 cells following TDP-43 depletion and mutant TDP-43 M337V expressionPublication . Gbadamosi, Ismail; Binias, Sandra; Gielniewski, Bartłomiej; Magno, Ramiro; dos Santos Duarte, Guilhermina Isabel; Jawaid, AliSeveral neurodegenerative disorders (NDDs), notably amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are characterized by pathological cytoplasmic aggregation of TAR DNA-binding protein 43 (TDP-43) in neurons and glia. Primarily localized in the nucleus under physiological conditions, TDP-43 is a critical regulator of RNA processing and metabolism. Therefore, RNA changes induced by TDP-43 depletion or mutation could play an important role in the pathogenesis of ALS and other TDP-43 related NDDs.To investigate these effects in NSC34 motor neuron-like cells, a commonly used cellular model of ALS, we used RNA interference to knock down TDP-43 and overexpressed the ALS-associated TDP-43 M337V mutation. RNA from both these experiments was enriched for small and large transcripts and subsequently analyzed via next-generation sequencing. The resulting transcriptomics datasets offer a valuable resource for studying the impact of TDP-43 depletion and mutant over-expression in motor neurons. These data enable comprehensive differential expression analyses and functional enrichment studies, identifying cellular pathways affected by TDP43 depletion or mutation. Additionally, the inclusion of non-coding RNAs facilitates the construction of gene regulatory networks, providing insights into the interplay between coding and non-coding RNAs in gene expression regulation under TDP-43 loss-of-function or pathogenic mutation conditions.
- Gwasrapidd: an R package to query, download and wrangle GWAS catalog dataPublication . Magno, Ramiro; Maia, Ana-TeresaThe National Human Genome Research Institute Catalog of Published Genome-Wide Association Studies (GWAS) Catalog has collected, curated and made available data from over 7100 studies. The recently developed GWAS Catalog representational state transfer (REST) application programming interface (API) is the only method allowing programmatic access to this resource.
- Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysisPublication . Gonçalves de Gouveia Maia Xavier, Joana; Magno, Ramiro; Russell, Roslin; Almeida, Bernardo P. de; Jacinta-Fernandes, Ana; Duarte, André; Besouro-Duarte, André; Dunning, Mark; Samarajiwa, Shamith; O’Reilly, Martin; Marques Maia de Almeida, José António; Rocha, Cátia L.; Rosli, Nordiana; Ponder, Bruce A. J.; Maia, Ana-TeresaUnderstanding breast cancer genetic risk relies on identifying causal variants and candidate target genes in risk loci identified by genome-wide association studies (GWAS), which remains challenging. Since most loci fall in active gene regulatory regions, we developed a novel approach facilitated by pinpointing the variants with greater regulatory potential in the disease’s tissue of origin. Through genome-wide differential allelic expression (DAE) analysis, using microarray data from 64 normal breast tissue samples, we mapped the variants associated with DAE (daeQTLs). Then, we intersected these with GWAS data to reveal candidate risk regulatory variants and analysed their cis-acting regulatory potential. Finally, we validated our approach by extensive functional analysis of the 5q14.1 breast cancer risk locus. We observed widespread gene expression regulation by cis-acting variants in breast tissue, with 65% of coding and noncoding expressed genes displaying DAE (daeGenes). We identified over 54 K daeQTLs for 6761 (26%) daeGenes, including 385 daeGenes harbouring variants previously associated with BC risk. We found 1431 daeQTLs mapped to 93 different loci in strong linkage disequilibrium with risk-associated variants (risk-daeQTLs), suggesting a link between risk-causing variants and cis-regulation. There were 122 risk-daeQTL with stronger cis-acting potential in active regulatory regions with protein binding evidence. These variants mapped to 41 risk loci, of which 29 had no previous report of target genes and were candidates for regulating the expression levels of 65 genes. As validation, we identified and functionally characterised five candidate causal variants at the 5q14.1 risk locus targeting the ATG10 and ATP6AP1L genes, likely acting via modulation of alternative transcription and transcription factor binding. Our study demonstrates the power of DAE analysis and daeQTL mapping to identify causal regulatory variants and target genes at breast cancer risk loci, including those with complex regulatory landscapes. It additionally provides a genome-wide resource of variants associated with DAE for future functional studies.
- Quincunx: an R package to query, download and wrangle PGS catalog dataPublication . Magno, Ramiro; Duarte, Isabel; Maia, Ana-TeresaFor two decades, GWAS identified individual variants associated with risk for complex diseases. These associations can be combined into polygenic scores (PGS) aiming at quantifying an individual’s risk to disease, inform on prognosis and even treatment response (Lambert et al., 2019). Broadly, PGS use summary statistics produced by GWAS to calculate a weighted sum of trait-associated alleles carried by each individual, in which the weights correspond to the per-allele size effects. Initially used to validate associations with disease and uncover interactions between variants, PGS have been more challenging to implement in the clinic. In 2020, over 1400 publications on PGS appeared in PubMed, raising the need for a standardized distribution of studies’ key data, assuring their wide evaluation and accurate use. The Polygenic Score (PGS) Catalog, created in 2019, is a publicly available, manually curated database of PGS and relevant metadata, that responds to this need (Lambert et al., 2020). Its current release [date 2021-02-03] includes data from 133 publications and 721 PGS associated with 194 traits. Currently, data is accessed via three ways: (i) the web graphical user interface (GUI); (ii) by downloading database dumps; and (iii) the recent PGS Catalog representational state transfer (REST) application programming interface (API), the preferred method for batch analyses.
- rdml: A Mathematica package for parsing and importing Real-Time qPCR dataPublication . Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.; Palmeirim, IsabelObjective The purpose and objective of the research presented is to provide a package for easy importing of Real-Time PCR data markup language (RDML) data to Mathematica. Results Real-Time qPCR is the most widely used experimental method for the accurate quantification of gene expression. To enable the straightforward archiving and sharing of qPCR data and its associated experimental information, an XML-based data standard was developed—the Real-Time PCR data markup language (RDML)—devised by the RDML consortium. Here, we present rdml, a package to parse and import RDML data into Mathematica, allowing the quick loading and extraction of relevant data, thus promoting the re-analysis, meta-analysis or experimental re-validation of gene expression data deposited in RDML format.
- Spatio-temporal dynamics of early somite segmentation in the chicken embryoPublication . Maia-Fernandes, Ana C; Martins, Ana; Martins, Nísia Borralho; Pais de Azevedo, Tomás; Magno, Ramiro; dos Santos Duarte, Guilhermina Isabel; Andrade, Raquel; MDuring vertebrate embryo development, the body is progressively segmented along the anterior-posterior (A-P) axis early in development. The rate of somite formation is controlled by the somitogenesis embryo clock (EC), which was first described as gene expression oscillations of hairy1 (hes4) in the presomitic mesoderm of chick embryos with 15-20 somites. Here, the EC displays the same periodicity as somite formation, 90 min, whereas the posterior-most somites (44-52) only arise every 150 minutes, matched by a corresponding slower pace of the EC. Evidence suggests that the rostral-most somites are formed faster, however, their periodicity and the EC expression dynamics in these early stages are unknown. In this study, we used time-lapse imaging of chicken embryos from primitive streak to somitogenesis stages with high temporal resolution (3-minute intervals). We measured the length between the anterior-most and the last formed somitic clefts in each captured frame and developed a simple algorithm to automatically infer both the length and time of formation of each somite. We found that the occipital somites (up to somite 5) form at an average rate of 75 minutes, while somites 6 onwards are formed approximately every 90 minutes. We also assessed the expression dynamics of hairy1 using half-embryo explants cultured for different periods of time. This showed that EC hairy1 expression is highly dynamic prior to somitogenesis and assumes a clear oscillatory behaviour as the first somites are formed. Importantly, using ex ovo culture and live-imaging techniques, we showed that the hairy1 expression pattern recapitulates with the formation of each new pair of somites, indicating that somite segmentation is coupled with EC oscillations since the onset of somitogenesis.
- Spatio-temporal dynamics of early somite segmentation in the chicken embryoPublication . Ana Martins-Jesus; Borralho-Martins, Nísia; Tomás Pais-de-Azevedo; Magno, Ramiro; Maia-Fernandes, Ana C; Martins, Nísia Borralho; Pais de Azevedo, Tomás; dos Santos Duarte, Guilhermina Isabel; Andrade, Raquel Gláucia Varzielas Pego deDuring vertebrate embryo development, the body is progressively segmented along the anterior-posterior (A-P) axis early in development. The rate of somite formation is controlled by the somitogenesis embryo clock (EC), which was first described as gene expression oscillations of hairy1 (hes4) in the presomitic mesoderm of chick embryos with 15–20 somites. Here, the EC displays the same periodicity as somite formation, 90 min, whereas the posterior-most somites (44–52) only arise every 150 minutes, matched by a corresponding slower pace of the EC. Evidence suggests that the rostral-most somites are formed faster, however, their periodicity and the EC expression dynamics in these early stages are unknown. In this study, we used time-lapse imaging of chicken embryos from primitive streak to somitogenesis stages with high temporal resolution (3-minute intervals). We measured the length between the anterior-most and the last formed somitic clefts in each captured frame and developed a simple algorithm to automatically infer both the length and time of formation of each somite. We found that the occipital somites (up to somite 5) form at an average rate of 75 minutes, while somites 6 onwards are formed approximately every 90 minutes. We also assessed the expression dynamics of hairy1 using half-embryo explants cultured for different periods of time. This showed that EC hairy1 expression is highly dynamic prior to somitogenesis and assumes a clear oscillatory behaviour as the first somites are formed. Importantly, using ex ovo culture and live-imaging techniques, we showed that the hairy1 expression pattern recapitulates with the formation of each new pair of somites, indicating that somite segmentation is coupled with EC oscillations since the onset of somitogenesis.