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Background: Precision medicine is a promising strategy to identify biomarkers, stratify asthmatic patients according to different endotypes, and match them with the appropriate therapy. This proof-of-concept study aimed to investigate whether gene expression in peripheral blood could provide a valuable noninvasive approach for the molecular phenotyping of asthma. Methods: We performed whole-transcriptome RNA sequencing on peripheral blood of 30 non-atopic non-asthmatic controls and 30 asthmatic patients. A quantitative PCR (qPCR) validation study of PTGDR2 that encodes for CRTH2 receptor, expressed in cells involved in T2 inflammation, was developed in a cohort of 361 independent subjects: 94 non-asthmatic non-atopic controls, 187 asthmatic patients [including 82 with chronic rhinosinusitis with nasal polyposis (CRSwNP) and 24 with aspirin-exacerbated respiratory disease (AERD)], 52 with allergic rhinitis, and 28 with CRSwNP without asthma. Results: PTGDR2 was one of the most differentially overexpressed genes in asthmatic patients’ peripheral blood (p-value 2.64 × 106). These results were confirmed by qPCR in the validation study, where PTGDR2 transcripts were significantly upregulated in asthmatic patients (p< 0.001). This upregulation was mainly detected in some subgroups such as allergic asthma, asthma with CRSwNP, AERD, eosinophilic asthma, and severe persistent asthma. PTGDR2 expression was detected in different blood cell types, and its correlation with eosinophil counts showed differences in some groups of asthmatic patients. Conclusions: We found that PTGDR2 expression levels could identify asthma patients, introduce a minimally invasive biomarker for adult asthma molecular phenotyping, and add additional information to blood eosinophils. Although further studies are required, analyzing PTGDR2 expression levels in peripheral blood of asthmatics might assist in selecting patients for treatment with specific antagonists.
Asunción García-Sánchez; Miguel Estravís; Maria J. Martin; Jacqueline Pérez-Pazos; Cristina Martín-García; María Gil-Melcón; Jacinto Ramos-González; Ibon Eguiluz-Gracia; Juan Carlos Triviño; María Isidoro-García; Ignacio Dávila; Catalina Sanz. PTGDR2 Expression in Peripheral Blood as a Potential Biomarker in Adult Patients with Asthma. Journal of Personalized Medicine 2021, 11, 827 .
AMA StyleAsunción García-Sánchez, Miguel Estravís, Maria J. Martin, Jacqueline Pérez-Pazos, Cristina Martín-García, María Gil-Melcón, Jacinto Ramos-González, Ibon Eguiluz-Gracia, Juan Carlos Triviño, María Isidoro-García, Ignacio Dávila, Catalina Sanz. PTGDR2 Expression in Peripheral Blood as a Potential Biomarker in Adult Patients with Asthma. Journal of Personalized Medicine. 2021; 11 (9):827.
Chicago/Turabian StyleAsunción García-Sánchez; Miguel Estravís; Maria J. Martin; Jacqueline Pérez-Pazos; Cristina Martín-García; María Gil-Melcón; Jacinto Ramos-González; Ibon Eguiluz-Gracia; Juan Carlos Triviño; María Isidoro-García; Ignacio Dávila; Catalina Sanz. 2021. "PTGDR2 Expression in Peripheral Blood as a Potential Biomarker in Adult Patients with Asthma." Journal of Personalized Medicine 11, no. 9: 827.
Some diatom species of the genus Pseudo-nitzschia produce the toxin domoic acid. The depuration rate of domoic acid in Pecten maximus is very low; for this reason, king scallops generally contain high levels of domoic acid in their tissues. A transcriptomic approach was used to identify the genes differentially expressed in the P. maximus digestive gland after the injection of domoic acid. The differential expression analysis found 535 differentially expressed genes (226 up-regulated and 309 down-regulated). Protein–protein interaction networks obtained with the up-regulated genes were enriched in gene ontology terms, such as vesicle-mediated transport, response to stress, signal transduction, immune system process, RNA metabolic process, and autophagy, while networks obtained with the down-regulated genes were enriched in gene ontology terms, such as response to stress, immune system process, ribosome biogenesis, signal transduction, and mRNA processing. Genes that code for cytochrome P450 enzymes, glutathione S-transferase theta-1, glutamine synthase, pyrroline-5-carboxylate reductase 2, and sodium- and chloride-dependent glycine transporter 1 were among the up-regulated genes. Therefore, a stress response at the level of gene expression, that could be caused by the domoic acid injection, was evidenced by the alteration of several biological, cellular, and molecular processes.
Pablo Ventoso; Antonio Pazos; Juan Blanco; M. Pérez-Parallé; Juan Triviño; José Sánchez. Transcriptional Response in the Digestive Gland of the King Scallop (Pecten maximus) After the Injection of Domoic Acid. Toxins 2021, 13, 339 .
AMA StylePablo Ventoso, Antonio Pazos, Juan Blanco, M. Pérez-Parallé, Juan Triviño, José Sánchez. Transcriptional Response in the Digestive Gland of the King Scallop (Pecten maximus) After the Injection of Domoic Acid. Toxins. 2021; 13 (5):339.
Chicago/Turabian StylePablo Ventoso; Antonio Pazos; Juan Blanco; M. Pérez-Parallé; Juan Triviño; José Sánchez. 2021. "Transcriptional Response in the Digestive Gland of the King Scallop (Pecten maximus) After the Injection of Domoic Acid." Toxins 13, no. 5: 339.
Overfishing of sea cucumber Isostichopus badionotus from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed I. badionotus has now been studied for the first time by an RNA-Seq approach. The functional profile of wild I. badionotus was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed I. badionotus was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild I. badionotus is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed I. badionotus is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.
Roberto Martín-Hernández; Rossanna Rodríguez-Canul; Nuvia Kantún-Moreno; Miguel Olvera-Novoa; Oscar Medina-Contreras; Cristobal Garikoitz-Legarda; Juan Triviño; Jesús Zamora-Briseño; Víctor May-Solis; Alicia Poot-Salazar; Juan Pérez-Vega; Judit Gil-Zamorano; George Grant; Alberto Dávalos; Leticia Olivera-Castillo. Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus. International Journal of Molecular Sciences 2021, 22, 3882 .
AMA StyleRoberto Martín-Hernández, Rossanna Rodríguez-Canul, Nuvia Kantún-Moreno, Miguel Olvera-Novoa, Oscar Medina-Contreras, Cristobal Garikoitz-Legarda, Juan Triviño, Jesús Zamora-Briseño, Víctor May-Solis, Alicia Poot-Salazar, Juan Pérez-Vega, Judit Gil-Zamorano, George Grant, Alberto Dávalos, Leticia Olivera-Castillo. Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus. International Journal of Molecular Sciences. 2021; 22 (8):3882.
Chicago/Turabian StyleRoberto Martín-Hernández; Rossanna Rodríguez-Canul; Nuvia Kantún-Moreno; Miguel Olvera-Novoa; Oscar Medina-Contreras; Cristobal Garikoitz-Legarda; Juan Triviño; Jesús Zamora-Briseño; Víctor May-Solis; Alicia Poot-Salazar; Juan Pérez-Vega; Judit Gil-Zamorano; George Grant; Alberto Dávalos; Leticia Olivera-Castillo. 2021. "Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus." International Journal of Molecular Sciences 22, no. 8: 3882.
Carotid atherosclerotic plaque rupture can lead to cerebrovascular accident (CVA). By comparing RNA-Seq data from vascular smooth muscle cells (VSMC) extracted from carotid atheroma surgically excised from a group of asymptomatic and symptomatic subjects, we identified more than 700 genomic variants associated with symptomatology (p < 0.05). From these, twelve single nucleotide polymorphisms (SNPs) were selected for further validation. Comparing genotypes of a hospital-based cohort of asymptomatic with symptomatic patients, an exonic SNP in the BIRC6 (BRUCE/Apollon) gene, rs35286811, emerged as significantly associated with CVA symptomatology (p = 0.002; OR = 2.24). Moreover, BIRC6 mRNA levels were significantly higher in symptomatic than asymptomatic subjects upon measurement by qPCR in excised carotid atherosclerotic tissue (p < 0.0001), and significantly higher in carriers of the rs35286811 risk allele (p < 0.0001). rs35286811 is a proxy of a GWAS SNP reported to be associated with red cell distribution width (RDW); RDW was increased in symptomatic patients (p < 0.03), but was not influenced by the rs35286811 genotype in our cohort. BIRC6 is a negative regulator of both apoptosis and autophagy. This work introduces BIRC6 as a novel genetic risk factor for stroke, and identifies autophagy as a genetically regulated mechanism of carotid plaque vulnerability.
Iraide Alloza; Andrea Salegi; Jorge Mena; Raquel Tulloch Navarro; César Martin; Patricia Aspichueta; Lucía Martínez Salazar; Jon Uriarte Carpio; Patricia De-La-Hera Cagigal; Reyes Vega; Juan Carlos Triviño; Maria Del Mar Freijo; Koen Vandenbroeck. BIRC6 Is Associated with Vulnerability of Carotid Atherosclerotic Plaque. International Journal of Molecular Sciences 2020, 21, 9387 .
AMA StyleIraide Alloza, Andrea Salegi, Jorge Mena, Raquel Tulloch Navarro, César Martin, Patricia Aspichueta, Lucía Martínez Salazar, Jon Uriarte Carpio, Patricia De-La-Hera Cagigal, Reyes Vega, Juan Carlos Triviño, Maria Del Mar Freijo, Koen Vandenbroeck. BIRC6 Is Associated with Vulnerability of Carotid Atherosclerotic Plaque. International Journal of Molecular Sciences. 2020; 21 (24):9387.
Chicago/Turabian StyleIraide Alloza; Andrea Salegi; Jorge Mena; Raquel Tulloch Navarro; César Martin; Patricia Aspichueta; Lucía Martínez Salazar; Jon Uriarte Carpio; Patricia De-La-Hera Cagigal; Reyes Vega; Juan Carlos Triviño; Maria Del Mar Freijo; Koen Vandenbroeck. 2020. "BIRC6 Is Associated with Vulnerability of Carotid Atherosclerotic Plaque." International Journal of Molecular Sciences 21, no. 24: 9387.
Substantial natural variation in color have been observed in fruits of diploid and octoploid strawberry (Fragaria spp.), resulting from distinct accumulation and distribution of anthocyanins. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 has been shown as the main activator in strawberry fruit. Here, we show that MYB10 mutations cause most of the anthocyanin variation observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F. ×ananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function MYB10 mutations were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses in octoploid Fragaria spp. revealed that FaMYB10-2, one of three MYB10 homoeologs identified, regulates the biosynthesis of anthocyanins in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression. Our findings suggest that cis-regulatory elements in FaEnSpm-2 are required for ectopic MYB10-2 expression and anthocyanin biosynthesis in fruit flesh.
Cristina Castillejo; Veronika Waurich; Henning Wagner; Rubén Ramos; Nicolás Oiza; Pilar Muñoz; Juan Carlos Triviño; Julie Caruana; Zhongchi Liu; Nicolás Cobo; Michael A. Hardigan; Steven J. Knapp; José G. Vallarino; Sonia Osorio; Carmen Martín-Pizarro; David Posé; Tuomas Toivainen; Timo Hytönen; Youngjae Oh; Christopher R. Barbey; Vance M. Whitaker; Seonghee Lee; Klaus Olbricht; José F. Sánchez-Sevilla; Iraida Amaya. Allelic Variation of MYB10 Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry (Fragaria spp.) Fruit. The Plant Cell 2020, 32, 3723 -3749.
AMA StyleCristina Castillejo, Veronika Waurich, Henning Wagner, Rubén Ramos, Nicolás Oiza, Pilar Muñoz, Juan Carlos Triviño, Julie Caruana, Zhongchi Liu, Nicolás Cobo, Michael A. Hardigan, Steven J. Knapp, José G. Vallarino, Sonia Osorio, Carmen Martín-Pizarro, David Posé, Tuomas Toivainen, Timo Hytönen, Youngjae Oh, Christopher R. Barbey, Vance M. Whitaker, Seonghee Lee, Klaus Olbricht, José F. Sánchez-Sevilla, Iraida Amaya. Allelic Variation of MYB10 Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry (Fragaria spp.) Fruit. The Plant Cell. 2020; 32 (12):3723-3749.
Chicago/Turabian StyleCristina Castillejo; Veronika Waurich; Henning Wagner; Rubén Ramos; Nicolás Oiza; Pilar Muñoz; Juan Carlos Triviño; Julie Caruana; Zhongchi Liu; Nicolás Cobo; Michael A. Hardigan; Steven J. Knapp; José G. Vallarino; Sonia Osorio; Carmen Martín-Pizarro; David Posé; Tuomas Toivainen; Timo Hytönen; Youngjae Oh; Christopher R. Barbey; Vance M. Whitaker; Seonghee Lee; Klaus Olbricht; José F. Sánchez-Sevilla; Iraida Amaya. 2020. "Allelic Variation of MYB10 Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry (Fragaria spp.) Fruit." The Plant Cell 32, no. 12: 3723-3749.
MiRNAs have been associated with psoriasis since just over a decade. However, we are far from a complete understanding of their role during the development of this disease. Our objective was to characterize the cutaneous expression of miRNAs not previously described in psoriasis, the changes induced following the treatment with biologicals and their association with disease improvement. Next generation sequencing was performed from five skin samples from psoriasis patients (lesional and non-lesional skin) and five controls, and from this cohort, 12 microRNAs were selected to be analyzed in skin samples from 44 patients with plaque psoriasis. In 15 patients, an additional sample was obtained after three months of biological treatment. MiR-9-5p, miR-133a-3p and miR-375 were downregulated in the lesional skin of psoriasis patients. After treatment, expression of miR-133a-3p, miR-375, miR-378a and miR-135b in residual lesions returned towards the levels observed in non-lesional skin. The decrease in miR-135b levels after treatment with biologics was associated with both the improvement of patients evaluated through Psoriasis Area and Severity Index score and the decrease in local inflammatory response. Moreover, basal expression of miR-135b along with age was associated with the improvement of psoriasis, suggesting its possible usefulness as a prognostic biomarker.
Pablo Chicharro; Pedro Rodríguez-Jiménez; Mar Llamas-Velasco; Nuria Montes; Ancor Sanz-García; Danay Cibrian; Alicia Vara; Manuel J Gómez; María Jiménez-Fernández; Pedro Martínez-Fleta; Inés Sánchez-García; Marta Lozano-Prieto; Juan C Triviño; Rebeca Miñambres; Francisco Sánchez-Madrid; Hortensia De La Fuente; Esteban Dauden. Expression of miR-135b in Psoriatic Skin and Its Association with Disease Improvement. Cells 2020, 9, 1603 .
AMA StylePablo Chicharro, Pedro Rodríguez-Jiménez, Mar Llamas-Velasco, Nuria Montes, Ancor Sanz-García, Danay Cibrian, Alicia Vara, Manuel J Gómez, María Jiménez-Fernández, Pedro Martínez-Fleta, Inés Sánchez-García, Marta Lozano-Prieto, Juan C Triviño, Rebeca Miñambres, Francisco Sánchez-Madrid, Hortensia De La Fuente, Esteban Dauden. Expression of miR-135b in Psoriatic Skin and Its Association with Disease Improvement. Cells. 2020; 9 (7):1603.
Chicago/Turabian StylePablo Chicharro; Pedro Rodríguez-Jiménez; Mar Llamas-Velasco; Nuria Montes; Ancor Sanz-García; Danay Cibrian; Alicia Vara; Manuel J Gómez; María Jiménez-Fernández; Pedro Martínez-Fleta; Inés Sánchez-García; Marta Lozano-Prieto; Juan C Triviño; Rebeca Miñambres; Francisco Sánchez-Madrid; Hortensia De La Fuente; Esteban Dauden. 2020. "Expression of miR-135b in Psoriatic Skin and Its Association with Disease Improvement." Cells 9, no. 7: 1603.
Anthocyanins are the principal color-producing compounds synthesized in developing fruits of strawberry (Fragaria spp.). Substantial natural variation in color have been observed in fruits of diploid and octoploid accessions, resulting from distinct accumulation and distribution of anthocyanins in fruits. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 has been shown as the main activator in strawberry fruit. Here, we show that MYB10 mutations cause most of the anthocyanin variation observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F. ×ananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon insertion in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function MYB10 mutations were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses in octoploid Fragaria spp. revealed that FaMYB10-2, one of three MYB10 homoeologs identified, residing in the F. iinumae-derived subgenome, regulates the biosynthesis of anthocyanins in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression and anthocyanin accumulation. Our findings suggest that putative cis regulatory elements provided by FaEnSpm-2 are required for high and ectopic MYB10-2 expression and induction of anthocyanin biosynthesis in fruit flesh. We developed MYB10-2 (sub-genome) specific DNA markers for marker-assisted selection that accurately predicted anthocyanin phenotypes in octoploid segregating populations.
Cristina Castillejo; Veronika Waurich; Henning Wagner; Ruben Ramos; Nicolas Oiza; Pilar Muñoz; Juan C. Triviño; Julie Caruana; Zhongchi Liu; Nicolas Cobo; Michael A. Hardigan; Steven J. Knapp; José G. Vallarino; Sonia Osorio; Carmen Martin-Pizarro; David Pose; Tuomas Toivainen; Timo Hytonen; Youngjae Oh; Christopher R. Barbey; Vance M. Whitaker; Seonghee Lee; Klaus Olbricht; José F. Sánchez-Sevilla; Iraida Amaya. Allelic Variation of MYB10 is the Major Force Controlling Natural Variation of Skin and Flesh Color in Strawberry (Fragaria spp.) fruit. bioRxiv 2020, 1 .
AMA StyleCristina Castillejo, Veronika Waurich, Henning Wagner, Ruben Ramos, Nicolas Oiza, Pilar Muñoz, Juan C. Triviño, Julie Caruana, Zhongchi Liu, Nicolas Cobo, Michael A. Hardigan, Steven J. Knapp, José G. Vallarino, Sonia Osorio, Carmen Martin-Pizarro, David Pose, Tuomas Toivainen, Timo Hytonen, Youngjae Oh, Christopher R. Barbey, Vance M. Whitaker, Seonghee Lee, Klaus Olbricht, José F. Sánchez-Sevilla, Iraida Amaya. Allelic Variation of MYB10 is the Major Force Controlling Natural Variation of Skin and Flesh Color in Strawberry (Fragaria spp.) fruit. bioRxiv. 2020; ():1.
Chicago/Turabian StyleCristina Castillejo; Veronika Waurich; Henning Wagner; Ruben Ramos; Nicolas Oiza; Pilar Muñoz; Juan C. Triviño; Julie Caruana; Zhongchi Liu; Nicolas Cobo; Michael A. Hardigan; Steven J. Knapp; José G. Vallarino; Sonia Osorio; Carmen Martin-Pizarro; David Pose; Tuomas Toivainen; Timo Hytonen; Youngjae Oh; Christopher R. Barbey; Vance M. Whitaker; Seonghee Lee; Klaus Olbricht; José F. Sánchez-Sevilla; Iraida Amaya. 2020. "Allelic Variation of MYB10 is the Major Force Controlling Natural Variation of Skin and Flesh Color in Strawberry (Fragaria spp.) fruit." bioRxiv , no. : 1.
In recent years, high-throughput next-generation sequencing technology has allowed a rapid increase in diagnostic capacity and precision through different bioinformatics processing algorithms, tools, and pipelines. The identification, annotation, and classification of sequence variants within different target regions are now considered a gold standard in clinical genetic diagnosis. However, this procedure lacks the ability to link regulatory events such as differential splicing to diseases. RNA-seq is necessary in clinical routine in order to interpret and detect among others splicing events and splicing variants, as it would increase the diagnostic rate by up to 10–35%. The transcriptome has a very dynamic nature, varying according to tissue type, cellular conditions, and environmental factors that may affect regulatory events such as splicing and the expression of genes or their isoforms. RNA-seq offers a robust technical analysis of this complexity, but it requires a profound knowledge of computational/statistical tools that may need to be adjusted depending on the disease under study. In this article we will cover RNA-seq analyses best practices applied to clinical routine, bioinformatics procedures, and present challenges of this approach.
Guillermo Marco-Puche; Sergio Lois; Javier Benítez; Juan Carlos Trivino. RNA-Seq Perspectives to Improve Clinical Diagnosis. Frontiers in Genetics 2019, 10, 1152 .
AMA StyleGuillermo Marco-Puche, Sergio Lois, Javier Benítez, Juan Carlos Trivino. RNA-Seq Perspectives to Improve Clinical Diagnosis. Frontiers in Genetics. 2019; 10 ():1152.
Chicago/Turabian StyleGuillermo Marco-Puche; Sergio Lois; Javier Benítez; Juan Carlos Trivino. 2019. "RNA-Seq Perspectives to Improve Clinical Diagnosis." Frontiers in Genetics 10, no. : 1152.
Molecular diagnosis of myeloid neoplasms (MN) is based on the detection of multiple genetic alterations using various techniques. Next-generation sequencing (NGS) has been proved as a useful method for analyzing many genes simultaneously. In this context, we analyzed diagnostic samples from 121 patients affected by MN and ten relapse samples from a subset of acute myeloid leukemia patients using two enrichment-capture NGS gene panels. Pathogenicity classification of variants was enhanced by the development and application of a custom onco-hematology score. A total of 278 pathogenic variants were detected in 84% of patients. For structural alterations, 82% of those identified by cytogenetics were detected by NGS, 25 of 31 copy number variants and three out of three translocations. The detection of variants using NGS changed the diagnosis of seven patients and the prognosis of 15 patients and enabled us to identify 44 suitable candidates for clinical trials. Regarding AML, six of the ten relapsed patients lost or gained variants, comparing with diagnostic samples. In conclusion, the use of NGS panels in MN improves genetic characterization of the disease compared with conventional methods, thus demonstrating its potential clinical utility in routine clinical testing. This approach leads to better-adjusted treatments for each patient.
Diego Carbonell; Julia Suárez-González; María Chicano; Cristina Andrés Zayas; Juan Carlos Triviño; Gabriela Rodríguez-Macías; Mariana Bastos-Oreiro; Patricia Font; Mónica Ballesteros; Paula Muñiz; Pascual Balsalobre; Mi Kwon; Javier Anguita; José Luis Díez-Martín; Ismael Buño; Carolina Martínez-Laperche. Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms. Cancers 2019, 11, 1364 .
AMA StyleDiego Carbonell, Julia Suárez-González, María Chicano, Cristina Andrés Zayas, Juan Carlos Triviño, Gabriela Rodríguez-Macías, Mariana Bastos-Oreiro, Patricia Font, Mónica Ballesteros, Paula Muñiz, Pascual Balsalobre, Mi Kwon, Javier Anguita, José Luis Díez-Martín, Ismael Buño, Carolina Martínez-Laperche. Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms. Cancers. 2019; 11 (9):1364.
Chicago/Turabian StyleDiego Carbonell; Julia Suárez-González; María Chicano; Cristina Andrés Zayas; Juan Carlos Triviño; Gabriela Rodríguez-Macías; Mariana Bastos-Oreiro; Patricia Font; Mónica Ballesteros; Paula Muñiz; Pascual Balsalobre; Mi Kwon; Javier Anguita; José Luis Díez-Martín; Ismael Buño; Carolina Martínez-Laperche. 2019. "Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms." Cancers 11, no. 9: 1364.
Disintegrin and metalloproteinase domain-containing protein 33
María Isidoro-García; Asunción García-Sánchez; Catalina Sanz; Miguel Estravís; Elena Marcos-Vadillo; Marien Pascual; Sergio Roa; Fernando Marques-García; Juan Carlos Triviño; Ignacio Dávila. YRNAs overexpression and potential implications in allergy. World Allergy Organization Journal 2019, 12, 100047 .
AMA StyleMaría Isidoro-García, Asunción García-Sánchez, Catalina Sanz, Miguel Estravís, Elena Marcos-Vadillo, Marien Pascual, Sergio Roa, Fernando Marques-García, Juan Carlos Triviño, Ignacio Dávila. YRNAs overexpression and potential implications in allergy. World Allergy Organization Journal. 2019; 12 (8):100047.
Chicago/Turabian StyleMaría Isidoro-García; Asunción García-Sánchez; Catalina Sanz; Miguel Estravís; Elena Marcos-Vadillo; Marien Pascual; Sergio Roa; Fernando Marques-García; Juan Carlos Triviño; Ignacio Dávila. 2019. "YRNAs overexpression and potential implications in allergy." World Allergy Organization Journal 12, no. 8: 100047.
Some species of the genus Pseudo-nitzschia produce the toxin domoic acid, which causes amnesic shellfish poisoning (ASP). Given that bivalve mollusks are filter feeders, they can accumulate these toxins in their tissues. To elucidate the transcriptional response of the queen scallop Aequipecten opercularis after exposure to domoic acid-producing Pseudo-nitzschia, the digestive gland transcriptome was de novo assembled using an Illumina HiSeq 2000 platform. Then, a differential gene expression analysis was performed. After the assembly, 142,137 unigenes were obtained, and a total of 10,144 genes were differentially expressed in the groups exposed to the toxin. Functional enrichment analysis found that 374 Pfam (protein families database) domains were significantly enriched. The C1q domain, the C-type lectin, the major facilitator superfamily, the immunoglobulin domain, and the cytochrome P450 were among the most enriched Pfam domains. Protein network analysis showed a small number of highly connected nodes involved in specific functions: proteasome components, mitochondrial ribosomal proteins, protein translocases of mitochondrial membranes, cytochromes P450, and glutathione S-transferases. The results suggest that exposure to domoic acid-producing organisms causes oxidative stress and mitochondrial dysfunction. The transcriptional response counteracts these effects with the up-regulation of genes coding for some mitochondrial proteins, proteasome components, and antioxidant enzymes (glutathione S-transferases, thioredoxins, glutaredoxins, and copper/zinc superoxide dismutases).
Pablo Ventoso; Antonio J. Pazos; M. Luz Pérez-Parallé; Juan Blanco; Juan C. Triviño; José L. Sánchez. Aequipecten opercularis) Digestive Gland after Exposure to Domoic Acid-Producing Pseudo-nitzschia. Toxins 2019, 11, 97 .
AMA StylePablo Ventoso, Antonio J. Pazos, M. Luz Pérez-Parallé, Juan Blanco, Juan C. Triviño, José L. Sánchez. Aequipecten opercularis) Digestive Gland after Exposure to Domoic Acid-Producing Pseudo-nitzschia. Toxins. 2019; 11 (2):97.
Chicago/Turabian StylePablo Ventoso; Antonio J. Pazos; M. Luz Pérez-Parallé; Juan Blanco; Juan C. Triviño; José L. Sánchez. 2019. "Aequipecten opercularis) Digestive Gland after Exposure to Domoic Acid-Producing Pseudo-nitzschia." Toxins 11, no. 2: 97.
It remains unclear whether disease course in multiple sclerosis (MS) is influenced by genetic polymorphisms. Here, we aimed to identify genetic variants associated with benign and aggressive disease courses in MS patients. MS patients were classified into benign and aggressive phenotypes according to clinical criteria. We performed exome sequencing in a discovery cohort, which included 20 MS patients, 10 with benign and 10 with aggressive disease course, and genotyping in 2 independent validation cohorts. The first validation cohort encompassed 194 MS patients, 107 with benign and 87 with aggressive phenotypes. The second validation cohort comprised 257 patients, of whom 224 patients had benign phenotypes and 33 aggressive disease courses. Brain immunohistochemistries were performed using disease course associated genes antibodies. By means of single-nucleotide polymorphism (SNP) detection and comparison of allele frequencies between patients with benign and aggressive phenotypes, a total of 16 SNPs were selected for validation from the exome sequencing data in the discovery cohort. Meta-analysis of genotyping results in two validation cohorts revealed two polymorphisms, rs28469012 and rs10894768, significantly associated with disease course. SNP rs28469012 is located in CPXM2 (carboxypeptidase X, M14 family, member 2) and was associated with aggressive disease course (uncorrected p value < 0.05). SNP rs10894768, which is positioned in IGSF9B (immunoglobulin superfamily member 9B) was associated with benign phenotype (uncorrected p value < 0.05). In addition, a trend for association with benign phenotype was observed for a third SNP, rs10423927, in NLRP9 (NLR family pyrin domain containing 9). Brain immunohistochemistries in chronic active lesions from MS patients revealed expression of IGSF9B in astrocytes and macrophages/microglial cells, and expression of CPXM2 and NLRP9 restricted to brain macrophages/microglia. Genetic variants located in CPXM2, IGSF9B, and NLRP9 have the potential to modulate disease course in MS patients and may be used as disease activity biomarkers to identify patients with divergent disease courses. Altogether, the reported results from this study support the influence of genetic factors in MS disease course and may help to better understand the complex molecular mechanisms underlying disease pathogenesis.
Elia Gil-Varea; Elena Urcelay; Carles Vilariño-Güell; Carme Costa; Luciana Midaglia; Fuencisla Matesanz; Alfredo Rodríguez-Antigüedad; Jorge Oksenberg; Laura Espino-Paisan; A. Dessa Sadovnick; Albert Saiz; Luisa M. Villar; Juan Antonio García-Merino; Lluís Ramió-Torrentà; Juan Carlos Triviño; Ester Quintana; René Robles; Antonio Sánchez-López; Rafael Arroyo; Jose C. Alvarez-Cermeño; Angela Vidal-Jordana; Sunny Malhotra; Nicolas Fissolo; Xavier Montalban; Manuel Comabella. Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course. Journal of Neuroinflammation 2018, 15, 1 -10.
AMA StyleElia Gil-Varea, Elena Urcelay, Carles Vilariño-Güell, Carme Costa, Luciana Midaglia, Fuencisla Matesanz, Alfredo Rodríguez-Antigüedad, Jorge Oksenberg, Laura Espino-Paisan, A. Dessa Sadovnick, Albert Saiz, Luisa M. Villar, Juan Antonio García-Merino, Lluís Ramió-Torrentà, Juan Carlos Triviño, Ester Quintana, René Robles, Antonio Sánchez-López, Rafael Arroyo, Jose C. Alvarez-Cermeño, Angela Vidal-Jordana, Sunny Malhotra, Nicolas Fissolo, Xavier Montalban, Manuel Comabella. Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course. Journal of Neuroinflammation. 2018; 15 (1):1-10.
Chicago/Turabian StyleElia Gil-Varea; Elena Urcelay; Carles Vilariño-Güell; Carme Costa; Luciana Midaglia; Fuencisla Matesanz; Alfredo Rodríguez-Antigüedad; Jorge Oksenberg; Laura Espino-Paisan; A. Dessa Sadovnick; Albert Saiz; Luisa M. Villar; Juan Antonio García-Merino; Lluís Ramió-Torrentà; Juan Carlos Triviño; Ester Quintana; René Robles; Antonio Sánchez-López; Rafael Arroyo; Jose C. Alvarez-Cermeño; Angela Vidal-Jordana; Sunny Malhotra; Nicolas Fissolo; Xavier Montalban; Manuel Comabella. 2018. "Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course." Journal of Neuroinflammation 15, no. 1: 1-10.
The use of biological control agents (BCAs) is of interest within an integrated management strategy of Verticillium wilt of olive (VWO) caused by the soil-borne fungus Verticillium dahliae Kleb. Previous studies have shown that the root/rhizosphere of healthy olive plants is an important reservoir of microorganisms displaying biocontrol activity against VWO (i.e., Pseudomonas strains PICF7 and PIC141). Moreover, these BCAs are already adapted to the ecological niche where they are deployed. Three novel bacteria (strains PIC28, PIC73 and PIC167) from nursery-produced olive plants were in-depth characterized using a previously implemented approach consisting of in situ isolation, in vitro antagonism tests, in planta bioassays, phenotypic and metabolic characterization, genome analyses and in silico identification of traits involved in plant-bacteria interactions, and multi-locus sequence analyses. All strains displayed in vitro growth inhibition of different olive pathogens and biocontrol effectiveness against Verticillium dahliae, with strain PIC73 being the most effective BCA. Strains PIC73 and PIC167 were identified as Paenibacillus polymyxa (Prazmowski) Ash et al. and Paenibacillus terrae Yoon et al., respectively. Strain PIC28 belongs to the Bacillus genus. Some of these Bacillales members showed in vitro compatibility with previously characterized BCAs (Pseudomonas spp. strains) also originating from the olive rhizosphere, paving the way for the future development of tailored bacterial consortia effective against VWO.
Carmen Gómez-Lama Cabanás; David Ruano-Rosa; Garikoitz Legarda; Paloma Pizarro-Tobías; Antonio Valverde-Corredor; Juan Carlos Triviño; Amalia Roca; Jesús Mercado-Blanco. Bacillales Members from the Olive Rhizosphere Are Effective Biological Control Agents against the Defoliating Pathotype of Verticillium dahliae. Agriculture 2018, 8, 90 .
AMA StyleCarmen Gómez-Lama Cabanás, David Ruano-Rosa, Garikoitz Legarda, Paloma Pizarro-Tobías, Antonio Valverde-Corredor, Juan Carlos Triviño, Amalia Roca, Jesús Mercado-Blanco. Bacillales Members from the Olive Rhizosphere Are Effective Biological Control Agents against the Defoliating Pathotype of Verticillium dahliae. Agriculture. 2018; 8 (7):90.
Chicago/Turabian StyleCarmen Gómez-Lama Cabanás; David Ruano-Rosa; Garikoitz Legarda; Paloma Pizarro-Tobías; Antonio Valverde-Corredor; Juan Carlos Triviño; Amalia Roca; Jesús Mercado-Blanco. 2018. "Bacillales Members from the Olive Rhizosphere Are Effective Biological Control Agents against the Defoliating Pathotype of Verticillium dahliae." Agriculture 8, no. 7: 90.
The B-class of MADS-box transcription factors has been studied in many plant species, but remain functionally uncharacterized in the Rosaceae family. APETALA3 (AP3), a member of this class, controls the identity of petals and stamens in Arabidopsis thaliana. In this work, we identified two members of the AP3 lineage in the cultivated strawberry (Fragaria × ananassa): FaAP3 and FaTM6. Interestingly, FaTM6, and not FaAP3, shows an expression pattern equivalent to that of AP3 in Arabidopsis. Genome editing using Cluster Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system is becoming a robust tool for targeted and stable mutagenesis of DNA. However, whether it can be efficiently used in an octoploid species such as F. × ananassa is not known. Here we report for the first time the application of CRISPR/Cas9 in F. × ananassa to characterize the function of FaTM6 in flower development. An exhaustive analysis by high-throughput sequencing of the FaTM6 locus spanning the target sites showed a high efficiency genome editing already in the T0 generation. The phenotypic characterization of the mutant lines indicates that FaTM6 plays a key role in petal and especially in anther development in strawberry. in an octoploid species such as F. × ananassa, and offer new opportunities for engineering strawberry to improve traits of interest in breeding programs.
Carmen Martín-Pizarro; Juan Carlos Triviño; David Posé. Functional Analysis of TM6 MADS-box gene in the Octoploid Strawberry by CRISPR/Cas9 directed mutagenesis. 2018, 351296 .
AMA StyleCarmen Martín-Pizarro, Juan Carlos Triviño, David Posé. Functional Analysis of TM6 MADS-box gene in the Octoploid Strawberry by CRISPR/Cas9 directed mutagenesis. . 2018; ():351296.
Chicago/Turabian StyleCarmen Martín-Pizarro; Juan Carlos Triviño; David Posé. 2018. "Functional Analysis of TM6 MADS-box gene in the Octoploid Strawberry by CRISPR/Cas9 directed mutagenesis." , no. : 351296.
High grade serous ovarian cancer is characterised by high initial response to chemotherapy but poor outcome in the long term due to acquired resistance. One of the main genetic features of this disease is TP53 mutation. The majority of TP53 mutated tumors harbor missense mutations in this gene, correlated with p53 accumulation. TP53 null tumors constitute a specific subgroup characterised by nonsense, frameshift or splice-site mutations associated to complete absence of p53 expression. Different studies show that this kind of tumors may have a worse prognosis than other TP53 mutated HGSC. In this study, we sought to characterise the intra-tumor heterogeneity of a TP53 null HGSC consisting of six primary tumor samples, two intra-pelvic and four extra-pelvic recurrences using exome sequencing and comparative genome hybridisation. Significant heterogeneity was found among the different tumor samples, both at the mutational and copy number levels. Exome sequencing identified 102 variants, of which only 42 were common to all three samples; whereas 7 of the 18 copy number changes found by CGH analysis were presented in all samples. Sanger validation of 20 variants found by exome sequencing in additional regions of the primary tumor and the recurrence allowed us to establish a sequence of the tumor clonal evolution, identifying those populations that most likely gave rise to recurrences and genes potentially involved in this process, like GPNMB and TFDP1. Using functional annotation and network analysis, we identified those biological functions most significantly altered in this tumor. Remarkably, unexpected functions such as microtubule-based movement and lipid metabolism emerged as important for tumor development and progression, suggesting its potential interest as therapeutic targets. Altogether, our results shed light on the clonal evolution of the distinct tumor regions identifying the most aggressive subpopulations and at least some of the genes that may be implicated in its progression and recurrence, and highlights the importance of considering intra-tumor heterogeneity when carrying out genetic and genomic studies, especially when these are aimed to diagnostic procedures or to uncover possible therapeutic strategies.
Alba Mota; Juan Carlos Triviño; Alejandro Rojo-Sebastian; Ángel Martínez-Ramírez; Luis Chiva; Antonio González-Martín; Juan F. Garcia; Pablo Garcia-Sanz; Gema Moreno-Bueno. Intra-tumor heterogeneity in TP53 null High Grade Serous Ovarian Carcinoma progression. BMC Cancer 2015, 15, 1 -11.
AMA StyleAlba Mota, Juan Carlos Triviño, Alejandro Rojo-Sebastian, Ángel Martínez-Ramírez, Luis Chiva, Antonio González-Martín, Juan F. Garcia, Pablo Garcia-Sanz, Gema Moreno-Bueno. Intra-tumor heterogeneity in TP53 null High Grade Serous Ovarian Carcinoma progression. BMC Cancer. 2015; 15 (1):1-11.
Chicago/Turabian StyleAlba Mota; Juan Carlos Triviño; Alejandro Rojo-Sebastian; Ángel Martínez-Ramírez; Luis Chiva; Antonio González-Martín; Juan F. Garcia; Pablo Garcia-Sanz; Gema Moreno-Bueno. 2015. "Intra-tumor heterogeneity in TP53 null High Grade Serous Ovarian Carcinoma progression." BMC Cancer 15, no. 1: 1-11.
Ischemic cardiomyopathy (ICM) is characterized by transcriptomic changes that alter cellular processes leading to decreased cardiac output. Because the molecular network of ICM is largely unknown, the aim of this study was to characterize the role of new transcriptional regulators in the molecular mechanisms underlying the responses to ischemia. Myocardial tissue explants from ICM patients and control (CNT) subjects were analyzed by RNA-Sequencing (RNA-Seq) and quantitative Real-Time PCR. Enrichment analysis of the ICM transcriptomic profile allowed the characterization of novel master regulators. We found that the expression of the transcriptional regulators SP100 (−1.5-fold, p < 0.05), CITED2 (−3.8-fold, p < 0.05), CEBPD (−4.9-fold, p < 0.05) and BCL3 (−3.3-fold, p < 0.05) were lower in ICM than in CNT. To gain insights into the molecular network defined by the transcription factors, we identified CEBPD, BCL3, and HIF1A target genes in the RNA-Seq datasets. We further characterized the biological processes of the target genes by gene ontology annotation. Our results suggest that CEBPD-inducible genes with roles in the inhibition of apoptosis are downregulated and that BCL3-repressible genes are involved in the regulation of cellular metabolism in ICM. Moreover, our results suggest that CITED2 downregulation causes increased expression of HIF1A target genes. Functional analysis of HIF1A target genes revealed that hypoxic and stress response genes are activated in ICM. Finally, we found a significant correlation between the mRNA levels of BCL3 and the mRNA levels of both CEBPD (r = 0.73, p < 0.001) and CITED2 (r = 0.56, p < 0.05). Interestingly, CITED2 mRNA levels are directly related to ejection fraction (EF) (r = 0.54, p < 0.05). Our data indicate that changes in the expression of SP100, CITED2, CEBPD, and BCL3 affect their transcription regulatory networks, which subsequently alter a number of biological processes in ICM patients. The relationship between CITED2 mRNA levels and EF emphasizes the importance of this transcription factor in ICM. Moreover, our findings identify new mechanisms used to interpret gene expression changes in ICM and provide valuable resources for further investigation of the molecular basis of human cardiac ischemic response. The online version of this article (doi:10.1186/s12920-015-0088-y) contains supplementary material, which is available to authorized users.
Isabel Herrer; Esther Roselló-Lletí; Ana Ortega; Estefanía Tarazón; María Micaela Molina-Navarro; Juan Carlos Triviño; Luis Martínez-Dolz; Luis Almenar; Francisca Lago; Ignacio Sánchez-Lázaro; José Ramón González-Juanatey; Antonio Salvador; Manuel Portolés; Miguel Rivera. Gene expression network analysis reveals new transcriptional regulators as novel factors in human ischemic cardiomyopathy. BMC Medical Genomics 2015, 8, 14 .
AMA StyleIsabel Herrer, Esther Roselló-Lletí, Ana Ortega, Estefanía Tarazón, María Micaela Molina-Navarro, Juan Carlos Triviño, Luis Martínez-Dolz, Luis Almenar, Francisca Lago, Ignacio Sánchez-Lázaro, José Ramón González-Juanatey, Antonio Salvador, Manuel Portolés, Miguel Rivera. Gene expression network analysis reveals new transcriptional regulators as novel factors in human ischemic cardiomyopathy. BMC Medical Genomics. 2015; 8 (1):14.
Chicago/Turabian StyleIsabel Herrer; Esther Roselló-Lletí; Ana Ortega; Estefanía Tarazón; María Micaela Molina-Navarro; Juan Carlos Triviño; Luis Martínez-Dolz; Luis Almenar; Francisca Lago; Ignacio Sánchez-Lázaro; José Ramón González-Juanatey; Antonio Salvador; Manuel Portolés; Miguel Rivera. 2015. "Gene expression network analysis reveals new transcriptional regulators as novel factors in human ischemic cardiomyopathy." BMC Medical Genomics 8, no. 1: 14.
Carolina Gil-Cayuela; Miguel Rivera; Ana Ortega; Estefanía Tarazón; Juan Carlos Triviño; Francisca Lago; José Ramón González-Juanatey; Luis Almenar; Luis Martínez-Dolz; Manuel Portoles. RNA Sequencing Analysis Identifies New Human Collagen Genes Involved in Cardiac Remodeling. Journal of the American College of Cardiology 2015, 65, 1265 -1267.
AMA StyleCarolina Gil-Cayuela, Miguel Rivera, Ana Ortega, Estefanía Tarazón, Juan Carlos Triviño, Francisca Lago, José Ramón González-Juanatey, Luis Almenar, Luis Martínez-Dolz, Manuel Portoles. RNA Sequencing Analysis Identifies New Human Collagen Genes Involved in Cardiac Remodeling. Journal of the American College of Cardiology. 2015; 65 (12):1265-1267.
Chicago/Turabian StyleCarolina Gil-Cayuela; Miguel Rivera; Ana Ortega; Estefanía Tarazón; Juan Carlos Triviño; Francisca Lago; José Ramón González-Juanatey; Luis Almenar; Luis Martínez-Dolz; Manuel Portoles. 2015. "RNA Sequencing Analysis Identifies New Human Collagen Genes Involved in Cardiac Remodeling." Journal of the American College of Cardiology 65, no. 12: 1265-1267.