Nuestros investigadores

Fernando Carazo Melo

Publicaciones científicas más recientes (desde 2010)

Autores: Ferrer-Bonsoms, J. A.; Cassol, I. ; Fernandez-Acin, P. ; et al.
Revista: SCIENTIFIC REPORTS
ISSN 2045-2322  Vol. 10  Nº 1  2020 
The advent of RNA-seq technologies has switched the paradigm of genetic analysis from a genome to a transcriptome-based perspective. Alternative splicing generates functional diversity in genes, but the precise functions of many individual isoforms are yet to be elucidated. Gene Ontology was developed to annotate gene products according to their biological processes, molecular functions and cellular components. Despite a single gene may have several gene products, most annotations are not isoform-specific and do not distinguish the functions of the different proteins originated from a single gene. Several approaches have tried to automatically annotate ontologies at the isoform level, but this has shown to be a daunting task. We have developed ISOGO (ISOform + GO function imputation), a novel algorithm to predict the function of coding isoforms based on their protein domains and their correlation of expression along 11,373 cancer patients. Combining these two sources of information outperforms previous approaches: it provides an area under precision-recall curve (AUPRC) five times larger than previous attempts and the median AUROC of assigned functions to genes is 0.82. We tested ISOGO predictions on some genes with isoform-specific functions (BRCA1, MADD,VAMP7 and ITSN1) and they were coherent with the literature. Besides, we examined whether the main isoform of each gene -as predicted by APPRIS- was the most likely to have the annotated gene functions and it occurs in 99.4% of the genes. We also evaluated the predictions for isoform-specific functions provided by the CAFA3 challenge and results were also convincing. To make these results available to the scientific community, we have deployed a web application to consult ISOGO predictions (https://biotecnun.unav.es/app/isogo). Initial data, website link, isoform-specific GO function predictions and R code is available at https://gitlab.com/icassol/isogo.
Autores: Carazo Melo, Fernando; Bértolo Martín de Rosales, Cristina María; Castilla Ruíz, Carlos; et al.
Revista: CANCERS
ISSN 2072-6694  Vol. 12  Nº 7  2020 
The development of predictive biomarkers of response to targeted therapies is an unmet clinical need for many antitumoral agents. Recent genome-wide loss-of-function screens, such as RNA interference (RNAi) and CRISPR-Cas9 libraries, are an unprecedented resource to identify novel drug targets, reposition drugs and associate predictive biomarkers in the context of precision oncology. In this work, we have developed and validated a large-scale bioinformatics tool named DrugSniper, which exploits loss-of-function experiments to model the sensitivity of 6237 inhibitors and predict their corresponding biomarkers of sensitivity in 30 tumor types. Applying DrugSniper to small cell lung cancer (SCLC), we identified genes extensively explored in SCLC, such as Aurora kinases or epigenetic agents. Interestingly, the analysis suggested a remarkable vulnerability to polo-like kinase 1 (PLK1) inhibition inCREBBP-mutant SCLC cells. We validated this association in vitro using four mutated and four wild-type SCLC cell lines and twoPLK1inhibitors (Volasertib and BI2536), confirming that the effect ofPLK1inhibitors depended on the mutational status ofCREBBP. Besides, DrugSniper was validated in-silico with several known clinically-used treatments, including the sensitivity of Tyrosine Kinase Inhibitors (TKIs) and Vemurafenib toFLT3andBRAFmutant cells, respectively. These findings show the potential of genome-wide loss-of-function screens to identify new personalized therapeutic hypotheses in SCLC and potentially in other tumors, which is a valuable starting point for further drug development and drug repositioning projects.
Autores: Carazo Melo, Fernando; Romero Riojas, Juan Pablo; Rubio Díaz-Cordoves, Ángel (Autor de correspondencia)
Revista: BRIEFINGS IN BIOINFORMATICS
ISSN 1467-5463  Vol. 20  Nº 4  2019  págs. 1358 - 1375
Alternative splicing (AS) has shown to play a pivotal role in the development of diseases, including cancer. Specifically, all the hallmarks of cancer (angiogenesis, cell immortality, avoiding immune system response, etc.) are found to have a counterpart in aberrant splicing of key genes. Identifying the context-specific regulators of splicing provides valuable information to find new biomarkers, as well as to define alternative therapeutic strategies. The computational models to identify these regulators are not trivial and require three conceptual steps: the detection of AS events, the identification of splicing factors that potentially regulate these events and the contextualization of these pieces of information for a specific experiment. In this work, we review the different algorithmic methodologies developed for each of these tasks. Main weaknesses and strengths of the different steps of the pipeline are discussed. Finally, a case study is detailed to help the reader be aware of the potential and limitations of this computational approach.
Autores: Carazo Melo, Fernando; Gimeno, M.; Ferrer-Bonsoms, J. A.; et al.
Revista: BMC GENOMICS
ISSN 1471-2164  Vol. 20  Nº Art. 521  2019 
BackgroundSplicing is a genetic process that has important implications in several diseases including cancer. Deciphering the complex rules of splicing regulation is crucial to understand and treat splicing-related diseases. Splicing factors and other RNA-binding proteins (RBPs) play a key role in the regulation of splicing. The specific binding sites of an RBP can be measured using CLIP experiments. However, to unveil which RBPs regulate a condition, it is necessary to have a priori hypotheses, as a single CLIP experiment targets a single protein.ResultsIn this work, we present a novel methodology to predict context-specific splicing factors from transcriptomic data. For this, we systematically collect, integrate and analyze more than 900 CLIP experiments stored in four CLIP databases: POSTAR2, CLIPdb, DoRiNA and StarBase. The analysis of these experiments shows the strong coherence between the binding sites of RBPs of similar families. Augmenting this information with expression changes, we are able to correctly predict the splicing factors that regulate splicing in two gold-standard experiments in which specific splicing factors are knocked-down.ConclusionsThe methodology presented in this study allows the prediction of active splicing factors in either cancer or any other condition by only using the information of transcript expression. This approach opens a wide range of possible studies to understand the splicing regulation of different conditions. A tutorial with the source code and databases is available at https://gitlab.com/fcarazo.m/sfprediction.
Autores: Carazo Melo, Fernando; Campuzano, L.; Cendoya Garmendia, Xabier; et al.
Revista: GIGASCIENCE
ISSN 2047-217X  Vol. 8  Nº 4  2019 
BACKGROUND: Aberrant alternative splicing plays a key role in cancer development. In recent years, alternative splicing has been used as a prognosis biomarker, a therapy response biomarker, and even as a therapeutic target. Next-generation RNA sequencing has an unprecedented potential to measure the transcriptome. However, due to the complexity of dealing with isoforms, the scientific community has not sufficiently exploited this valuable resource in precision medicine. FINDINGS: We present TranscriptAchilles, the first large-scale tool to predict transcript biomarkers associated with gene essentiality in cancer. This application integrates 412 loss-of-function RNA interference screens of >17,000 genes, together with their corresponding whole-transcriptome expression profiling. Using this tool, we have studied which are the cancer subtypes for which alternative splicing plays a significant role to state gene essentiality. In addition, we include a case study of renal cell carcinoma that shows the biological soundness of the results. The databases, the source code, and a guide to build the platform within a Docker container are available at GitLab. The application is also available online. CONCLUSIONS: TranscriptAchilles provides a user-friendly web interface to identify transcript or gene biomarkers of gene essentiality, which could be used as a starting point for a drug development project. This approach opens a wide range of translational applications in cancer.
Autores: Carazo Melo, Fernando; San José Enériz, Edurne; Garate, L.; et al.
Revista: HAEMATOLOGICA
ISSN 0390-6078  Vol. 104  2019  págs. 49 - 49
Autores: Carazo Melo, Fernando; San José Enériz, Edurne; Garate Iturriagagoitia, Leire; et al.
Revista: BLOOD
ISSN 0006-4971  Vol. 134  Nº supl.1  2019 
Autores: Romero Riojas, Juan Pablo; Ortiz-Estevez, M.; Muniategui Merino, Ander; et al.
Revista: BMC GENOMICS
ISSN 1471-2164  Vol. 19  Nº 703  2018 
Background: RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to splicing events. Commercial arrays that include probes within exon junctions have been developed in order to overcome this problem. We compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of transcript splicing events. Three different breast cancer cell lines were treated with CX-4945, a drug that severely affects splicing. To enable a direct comparison of the two platforms, we adapted EventPointer, an algorithm that detects and labels alternative splicing events using junction arrays, to work also on RNA-seq data. Common results and discrepancies between the technologies were validated and/or resolved by over 200 PCR experiments. Results: As might be expected, RNA-seq appears superior in cases where the technologies disagree and is able to discover novel splicing events beyond the limitations of physical probe-sets. We observe a high degree of coherence between the two technologies, however, with correlation of EventPointer results over 0.90. Through decimation, the detection power of the junction arrays is equivalent to RNA-seq with up to 60 million reads. Conclusions: Our results suggest, therefore, that exon-junction arrays are a viable alternative to RNA-seq for detection of alternative splicing events when focusing on well-described transcriptional regions.
Autores: Carazo Melo, Fernando; Romero Riojas, Juan Pablo; Rubio Díaz-Cordoves, Ángel (Autor de correspondencia)
Revista: BRIEFINGS IN BIOINFORMATICS
ISSN 1477-4054  2018 
Alternative splicing (AS) has shown to play a pivotal role in the development of diseases, including cancer. Specifically, all the hallmarks of cancer (angiogenesis, cell immortality, avoiding immune system response, etc.) are found to have a counterpart in aberrant splicing of key genes. Identifying the context-specific regulators of splicing provides valuable information to find new biomarkers, as well as to define alternative therapeutic strategies. The computational models to identify these regulators are not trivial and require three conceptual steps: the detection of AS events, the identification of splicing factors that potentially regulate these events and the contextualization of these pieces of information for a specific experiment. In this work, we review the different algorithmic methodologies developed for each of these tasks. Main weaknesses and strengths of the different steps of the pipeline are discussed. Finally, a case study is detailed to help the reader be aware of the potential and limitations of this computational approach.
Autores: Tubia Antillera, Imanol (Autor de correspondencia); Carazo Melo, Fernando; Apezteguia, A.; et al.
Revista: SENSORS AND ACTUATORS A-PHYSICAL
ISSN 0924-4247  Vol. 277  2018  págs. 1 - 7
Impedance spectroscopy analysis (IS) has awakened a great interest for many industrial applications and sectors for the implementation of novel monitoring capabilities. More specifically, microelectrode-based sensors are increasingly being used to analyze electrical or electrochemical changes in liquid samples, as well as other effects such as biofouling, particle adhesion, etc. However, real environmental conditions are usually subjected physiochemical changes that affect the impedance measurement. In this context, it is difficult to isolate the effect of only one parameter (Le., conductivity of the medium) from the other ones. This work is focused specifically on the analysis of the influence of temperature and pH on the impedance measurements. Different experiments were carried out using interdigitated microelectrodes (IDE) sensors for a geometry range in wine samples to adjust a proposed mathematical model of the impedance behavior. In the case of fermentation processes of alcoholic beverages, this methodology will help to isolate the chemical changes measured by impedance from temperature or pH variation. This model also provides the significance of the effect of each parameter on the impedance values. After the experimental validation, the model was used to correct the impedance values accordingly to the variation of each parameter showing its applicability to the real field. Finally, the proposed methodology can be easily applied and extended to other environments and sensors types. (C) 2018 Elsevier B.V. All rights reserved.