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485 results on '"Sabidó, Eduard"'

1. Machine learning-based health environmental-clinical risk scores in European children

Author

Guimbaud, Jean-Baptiste, Siskos, Alexandros P., Sakhi, Amrit Kaur, Heude, Barbara, Sabidó, Eduard, Borràs, Eva, Keun, Hector, Wright, John, Julvez, Jordi, Urquiza, Jose, Gützkow, Kristine Bjerve, Chatzi, Leda, Casas, Maribel, Bustamante, Mariona, Nieuwenhuijsen, Mark, Vrijheid, Martine, López-Vicente, Mónica, de Castro Pascual, Montserrat, Stratakis, Nikos, Robinson, Oliver, Grazuleviciene, Regina, Slama, Remy, Alemany, Silvia, Basagaña, Xavier, Plantevit, Marc, Cazabet, Rémy, and Maitre, Léa

Published
2024
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6. Childhood exposure to non-persistent endocrine disrupting chemicals and multi-omic profiles: A panel study

Author

Fabbri, Lorenzo, Garlantézec, Ronan, Audouze, Karine, Bustamante, Mariona, Carracedo, Ángel, Chatzi, Leda, Ramón González, Juan, Gražulevičienė, Regina, Keun, Hector, Lau, Chung-Ho E, Sabidó, Eduard, Siskos, Alexandros P, Slama, Rémy, Thomsen, Cathrine, Wright, John, Lun Yuan, Wen, Casas, Maribel, Vrijheid, Martine, and Maitre, Léa

Published
2023
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8. Mass Spectrometry Identification of Biomarkers in Extracellular Vesicles From Plasmodium vivax Liver Hypnozoite Infections

Author

Gualdrón-López, Melisa, Díaz-Varela, Miriam, Zanghi, Gigliola, Aparici-Herraiz, Iris, Steel, Ryan W.J., Schäfer, Carola, Cuscó, Pol, Chuenchob, Vorada, Kangwangransan, Niwat, Billman, Zachary P., Olsen, Tayla M., González, Juan R., Roobsoong, Wanlapa, Sattabongkot, Jetsumon, Murphy, Sean C., Mikolajczak, Sebastian A., Borràs, Eva, Sabidó, Eduard, Fernandez-Becerra, Carmen, Flannery, Erika L., Kappe, Stefan H.I., and del Portillo, Hernando A.

Published
2022
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10. Short- and medium-term air pollution exposure, plasmatic protein levels and blood pressure in children

Author

de Prado-Bert, Paula, Warembourg, Charline, Dedele, Audrius, Heude, Barbara, Borràs, Eva, Sabidó, Eduard, Aasvang, Gunn Marit, Lepeule, Johanna, Wright, John, Urquiza, Jose, Gützkow, Kristine B., Maitre, Léa, Chatzi, Leda, Casas, Maribel, Vafeiadi, Marina, Nieuwenhuijsen, Mark J., de Castro, Montserrat, Grazuleviciene, Regina, McEachan, Rosemary R.C., Basagaña, Xavier, Vrijheid, Martine, Sunyer, Jordi, and Bustamante, Mariona

Published
2022
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11. The multi-omics signatures of telomere length in childhood.

Author

Wang, Congrong, Martens, Dries S., Bustamante, Mariona, Alfano, Rossella, Plusquin, Michelle, Maitre, Lea, Wright, John, McEachan, Rosemary R. C., Lepeule, Johanna, Slama, Remy, Vafeiadi, Marina, Chatzi, Leda, Grazuleviciene, Regina, Gutzkow, Kristine B., Keun, Hector, Borràs, Eva, Sabidó, Eduard, Carracedo, Angel, Escarami, Georgia, and Anguita-Ruiz, Augusto

Subjects
GENE expression, LIFE sciences, BLOOD proteins, MULTIOMICS, DNA methylation, TELOMERES
Abstract

Background: Telomere length is an important indicator of biological age and a complex multi-factor trait. To date, the telomere interactome for comprehending the high-dimensional biological aspects linked to telomere regulation during childhood remains unexplored. Here we describe the multi-omics signatures associated with childhood telomere length. Methods: This study included 1001 children aged 6 to 11 years from the Human Early-life Exposome (HELIX) project. Telomere length was quantified via qPCR in peripheral blood of the children. Blood DNA methylation, gene expression, miRNA expression, plasma proteins and serum and urinary metabolites were measured through microarrays or (semi-) targeted assays. The association between each individual omics feature and telomere length was assessed in omics-wide association analyses. In addition, a literature-guided, sparse supervised integration method was applied to multiple omics, and latent components were extracted as predictors of child telomere length. The association of these latent components with early-life aging risk factors (child lifestyle, body mass index (BMI), exposure to smoking, etc.), were interrogated. Results: After multiple-testing correction, only two CpGs (cg23686403 and cg16238918 at PARD6G gene) out of all the omics features were significantly associated with child telomere length. The supervised multi-omics integration approach revealed robust associations between latent components and child BMI, with metabolites and proteins emerging as the primary contributing features. In these latent components, the contributing molecular features were known as involved in metabolism and immune regulation-related pathways. Conclusions: Findings of this multi-omics study suggested an intricate interplay between telomere length, metabolism and immune responses, providing valuable insights into the molecular underpinnings of the early-life biological aging. [ABSTRACT FROM AUTHOR]

Published
2025
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12. Multi-omics architecture of childhood obesity and metabolic dysfunction uncovers biological pathways and prenatal determinants.

Author

Stratakis, Nikos, Anguita-Ruiz, Augusto, Fabbri, Lorenzo, Maitre, Léa, González, Juan R., Andrusaityte, Sandra, Basagaña, Xavier, Borràs, Eva, Keun, Hector C., Chatzi, Lida, Conti, David V., Goodrich, Jesse, Grazuleviciene, Regina, Haug, Line Småstuen, Heude, Barbara, Yuan, Wen Lun, McEachan, Rosemary, Nieuwenhuijsen, Mark, Sabidó, Eduard, and Slama, Rémy

Subjects
METABOLIC disorders, POLLUTANTS, PUBLIC health, ENVIRONMENTAL indicators, MEDICAL sciences, CHILDHOOD obesity
Abstract

Childhood obesity poses a significant public health challenge, yet the molecular intricacies underlying its pathobiology remain elusive. Leveraging extensive multi-omics profiling (methylome, miRNome, transcriptome, proteins and metabolites) and a rich phenotypic characterization across two parts of Europe within the population-based Human Early Life Exposome project, we unravel the molecular landscape of childhood obesity and associated metabolic dysfunction. Our integrative analysis uncovers three clusters of children defined by specific multi-omics profiles, one of which characterized not only by higher adiposity but also by a high degree of metabolic complications. This high-risk cluster exhibits a complex interplay across many biological pathways, predominantly underscored by inflammation-related cascades. Further, by incorporating comprehensive information from the environmental risk-scape of the critical pregnancy period, we identify pre-pregnancy body mass index and environmental pollutants like perfluorooctanoate and mercury as important determinants of the high-risk cluster. Overall, our work helps to identify potential risk factors for prevention and intervention strategies early in the life course aimed at mitigating obesity and its long-term health consequences. Obesity encompasses numerous interconnected pathological mechanisms. Here, the authors show that integrating multi-omics data uncovers distinct molecular profiles and prenatal factors linked to childhood obesity and metabolic dysfunction, providing insights for early prevention and intervention strategies. [ABSTRACT FROM AUTHOR]

Published
2025
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13. LAP1 Interactome Profiling Provides New Insights into LAP1's Physiological Functions.

Author

Pereira, Cátia D., Espadas, Guadalupe, Martins, Filipa, Bertrand, Anne T., Servais, Laurent, Sabidó, Eduard, Chevalier, Philippe, da Cruz e Silva, Odete A. B., and Rebelo, Sandra

Abstract

The nuclear envelope (NE), a protective membrane bordering the nucleus, is composed of highly specialized proteins that are indispensable for normal cellular activity. Lamina-associated polypeptide 1 (LAP1) is a NE protein whose functions are just beginning to be unveiled. The fact that mutations causing LAP1 deficiency are extremely rare and pathogenic is indicative of its paramount importance to preserving human health, anticipating that LAP1 might have a multifaceted role in the cell. Mapping the LAP1 protein interactome is, thus, imperative to achieve an integrated view of its potential biological properties. To this end, we employed in silico- and mass spectrometry-based approaches to identify candidate LAP1-interacting proteins, whose functional attributes were subsequently characterized using bioinformatics tools. Our results reveal the complex and multifunctional network of protein–protein interactions associated to LAP1, evidencing a strong interconnection between LAP1 and cellular processes as diverse as chromatin and cytoskeleton organization, DNA repair, RNA processing and translation, as well as protein biogenesis and turnover, among others. Novel interactions between LAP1 and DNA repair proteins were additionally validated, strengthening the previously proposed involvement of LAP1 in the maintenance of genomic stability. Overall, this study reaffirms the biological relevance of LAP1 and the need to deepen our knowledge about this NE protein, providing new insights about its potential functional partners that will help guiding future research towards a mechanistic understanding of LAP1's functioning. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Proteomic study of the membrane components of signalling cascades of Botrytis cinerea controlled by phosphorylation

Author

Escobar-Niño, Almudena, Liñeiro, Eva, Amil, Francisco, Carrasco, Rafael, Chiva, Cristina, Fuentes, Carlos, Blanco-Ulate, Barbara, Cantoral Fernández, Jesús M, Sabidó, Eduard, and Fernández-Acero, Francisco Javier

Subjects
Biotechnology, Infection, Generic health relevance, Botrytis, Cell Wall, Chromatography, Liquid, Fungal Proteins, Solanum lycopersicum, Phosphoproteins, Phosphorylation, Plant Diseases, Proteome, Proteomics, Signal Transduction, Tandem Mass Spectrometry
Abstract

Protein phosphorylation and membrane proteins play an important role in the infection of plants by phytopathogenic fungi, given their involvement in signal transduction cascades. Botrytis cinerea is a well-studied necrotrophic fungus taken as a model organism in fungal plant pathology, given its broad host range and adverse economic impact. To elucidate relevant events during infection, several proteomics analyses have been performed in B. cinerea, but they cover only 10% of the total proteins predicted in the genome database of this fungus. To increase coverage, we analysed by LC-MS/MS the first-reported overlapped proteome in phytopathogenic fungi, the "phosphomembranome" of B. cinerea, combining the two most important signal transduction subproteomes. Of the 1112 membrane-associated phosphoproteins identified, 64 and 243 were classified as exclusively identified or overexpressed under glucose and deproteinized tomato cell wall conditions, respectively. Seven proteins were found under both conditions, but these presented a specific phosphorylation pattern, so they were considered as exclusively identified or overexpressed proteins. From bioinformatics analysis, those differences in the membrane-associated phosphoproteins composition were associated with various processes, including pyruvate metabolism, unfolded protein response, oxidative stress response, autophagy and cell death. Our results suggest these proteins play a significant role in the B. cinerea pathogenic cycle.

Published
2019

16. Multi-omics signatures of the human early life exposome

Author

Maitre, Léa, Bustamante, Mariona, Hernández-Ferrer, Carles, Thiel, Denise, Lau, Chung-Ho E., Siskos, Alexandros P., Vives-Usano, Marta, Ruiz-Arenas, Carlos, Pelegrí-Sisó, Dolors, Robinson, Oliver, Mason, Dan, Wright, John, Cadiou, Solène, Slama, Rémy, Heude, Barbara, Casas, Maribel, Sunyer, Jordi, Papadopoulou, Eleni Z., Gutzkow, Kristine B., Andrusaityte, Sandra, Grazuleviciene, Regina, Vafeiadi, Marina, Chatzi, Leda, Sakhi, Amrit K., Thomsen, Cathrine, Tamayo, Ibon, Nieuwenhuijsen, Mark, Urquiza, Jose, Borràs, Eva, Sabidó, Eduard, Quintela, Inés, Carracedo, Ángel, Estivill, Xavier, Coen, Muireann, González, Juan R., Keun, Hector C., and Vrijheid, Martine

Published
2022
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19. Prenatal and postnatal exposure to PFAS and cardiometabolic factors and inflammation status in children from six European cohorts

Author

Papadopoulou, Eleni, Stratakis, Nikos, Basagaña, Xavier, Brantsæter, Anne Lise, Casas, Maribel, Fossati, Serena, Gražulevičienė, Regina, Småstuen Haug, Line, Heude, Barbara, Maitre, Léa, McEachan, Rosemary R.C., Robinson, Oliver, Roumeliotaki, Theano, Sabidó, Eduard, Borràs, Eva, Urquiza, Jose, Vafeiadi, Marina, Zhao, Yinqi, Slama, Rémy, Wright, John, Conti, David V., Vrijheid, Martine, and Chatzi, Lida

Published
2021
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20. Origins of de novo genes in human and chimpanzee

Author

Ruiz-Orera, Jorge, Hernandez-Rodriguez, Jessica, Chiva, Cristina, Sabidó, Eduard, Kondova, Ivanela, Bontrop, Ronald, Marqués-Bonet, Tomàs, and Albà, M. Mar

Subjects
Quantitative Biology - Genomics
Abstract

The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process we have performed in-depth sequencing of the transcriptomes of four mammalian species, human, chimpanzee, macaque and mouse, and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new transcriptional multiexonic events in human and/or chimpanzee that are not observed in the rest of species. By comparative genomics we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. We also find that the coding potential of the new genes is higher than expected by chance, consistent with the presence of protein-coding genes in the dataset. Using available human tissue proteomics and ribosome profiling data we identify several de novo genes with translation evidence. These genes show significant purifying selection signatures, indicating that they are probably functional. Taken together, the data supports a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins., Comment: 25 pages, 4 figures, 2 tables

Published
2015

22. MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets

Author

Choi, Meena, Carver, Jeremy, Chiva, Cristina, Tzouros, Manuel, Huang, Ting, Tsai, Tsung-Heng, Pullman, Benjamin, Bernhardt, Oliver M., Hüttenhain, Ruth, Teo, Guo Ci, Perez-Riverol, Yasset, Muntel, Jan, Müller, Maik, Goetze, Sandra, Pavlou, Maria, Verschueren, Erik, Wollscheid, Bernd, Nesvizhskii, Alexey I., Reiter, Lukas, Dunkley, Tom, Sabidó, Eduard, Bandeira, Nuno, and Vitek, Olga

Published
2020
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23. The dental proteome of Homo antecessor

Author

Welker, Frido, Ramos-Madrigal, Jazmín, Gutenbrunner, Petra, Mackie, Meaghan, Tiwary, Shivani, Rakownikow Jersie-Christensen, Rosa, Chiva, Cristina, Dickinson, Marc R., Kuhlwilm, Martin, de Manuel, Marc, Gelabert, Pere, Martinón-Torres, María, Margvelashvili, Ann, Arsuaga, Juan Luis, Carbonell, Eudald, Marques-Bonet, Tomas, Penkman, Kirsty, Sabidó, Eduard, Cox, Jürgen, Olsen, Jesper V., Lordkipanidze, David, Racimo, Fernando, Lalueza-Fox, Carles, Bermúdez de Castro, José María, Willerslev, Eske, and Cappellini, Enrico

Published
2020
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24. The loss of DHX15 impairs endothelial energy metabolism, lymphatic drainage and tumor metastasis in mice

Author

Ribera, Jordi, Portolés, Irene, Córdoba-Jover, Bernat, Rodríguez-Vita, Juan, Casals, Gregori, González-de la Presa, Bernardino, Graupera, Mariona, Solsona-Vilarrasa, Estel, Garcia-Ruiz, Carmen, Fernández-Checa, José C., Soria, Guadalupe, Tudela, Raúl, Esteve-Codina, Anna, Espadas, Guadalupe, Sabidó, Eduard, Jiménez, Wladimiro, Sessa, William C., and Morales-Ruiz, Manuel

Published
2021
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26. Variability of multi-omics profiles in a population-based child cohort

Author

Gallego-Paüls, Marta, Hernández-Ferrer, Carles, Bustamante, Mariona, Basagaña, Xavier, Barrera-Gómez, Jose, Lau, Chung-Ho E., Siskos, Alexandros P., Vives-Usano, Marta, Ruiz-Arenas, Carlos, Wright, John, Slama, Remy, Heude, Barbara, Casas, Maribel, Grazuleviciene, Regina, Chatzi, Leda, Borràs, Eva, Sabidó, Eduard, Carracedo, Ángel, Estivill, Xavier, Urquiza, Jose, Coen, Muireann, Keun, Hector C., González, Juan R., Vrijheid, Martine, and Maitre, Léa

Published
2021
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28. Molecular basis for the protective effects of low-density lipoprotein receptor-related protein 1 (LRP1)-derived peptides against LDL aggregation

Author

Benitez-Amaro, Aleyda, Pallara, Chiara, Nasarre, Laura, Rivas-Urbina, Andrea, Benitez, Sonia, Vea, Angela, Bornachea, Olga, de Gonzalo-Calvo, David, Serra-Mir, Gabriel, Villegas, Sandra, Prades, Roger, Sanchez-Quesada, José Luís, Chiva, Cristina, Sabido, Eduard, Tarragó, Teresa, and Llorente-Cortés, Vicenta

Published
2019
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29. Changes in Synaptic Proteins Precede Neurodegeneration Markers in Preclinical Alzheimer's Disease Cerebrospinal Fluid

Author

Lleó, Alberto, Núñez-Llaves, Raúl, Alcolea, Daniel, Chiva, Cristina, Balateu-Paños, Daniel, Colom-Cadena, Martí, Gomez-Giro, Gemma, Muñoz, Laia, Querol-Vilaseca, Marta, Pegueroles, Jordi, Rami, Lorena, Lladó, Albert, Molinuevo, José L., Tainta, Mikel, Clarimón, Jordi, Spires-Jones, Tara, Blesa, Rafael, Fortea, Juan, Martínez-Lage, Pablo, Sánchez-Valle, Raquel, Sabidó, Eduard, Bayés, Àlex, and Belbin, Olivia

Published
2019
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30. CSF Chitinase 3–Like 2 Is Associated With Long-term Disability Progression in Patients With Progressive Multiple Sclerosis

Author

Comabella, Manuel, Sastre-Garriga, Jaume, Borras, Eva, Villar, Luisa M., Saiz, Albert, Martínez-Yélamos, Sergio, García-Merino, Juan Antonio, Pinteac, Rucsanda, Fissolo, Nicolas, Sánchez López, Antonio J., Costa-Frossard, Lucienne, Blanco, Yolanda, Llufriu, Sara, Vidal-Jordana, Angela, Sabidó, Eduard, and Montalban, Xavier

Published
2021
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33. Targeted Proteomics of the Eicosanoid Biosynthetic Pathway Completes an Integrated Genomics-Proteomics-Metabolomics Picture of Cellular Metabolism*

Author

Sabidó, Eduard, Quehenberger, Oswald, Shen, Qin, Chang, Ching-Yun, Shah, Ishita, Armando, Aaron M, Andreyev, Alexander, Vitek, Olga, Dennis, Edward A, and Aebersold, Ruedi

Subjects
Analytical Chemistry, Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Chemical Sciences, Medical Biochemistry and Metabolomics, Human Genome, Biotechnology, Genetics, 2.1 Biological and endogenous factors, Aetiology, Adenosine Triphosphate, Animals, Arachidonic Acid, Biosynthetic Pathways, Cell Line, Eicosanoids, Inflammation, Lipid Metabolism, Lipopolysaccharides, Macrophages, Mass Spectrometry, Metabolomics, Mice, Proteomics, Signal Transduction, Biochemistry & Molecular Biology
Abstract

Eicosanoids constitute a diverse class of bioactive lipid mediators that are produced from arachidonic acid and play critical roles in cell signaling and inflammatory aspects of numerous diseases. We have previously quantified eicosanoid metabolite production in RAW264.7 macrophage cells in response to Toll-like receptor 4 signaling and analyzed the levels of transcripts coding for the enzymes involved in the eicosanoid metabolite biosynthetic pathways. We now report the quantification of changes in protein levels under similar experimental conditions in RAW264.7 macrophages by multiple reaction monitoring mass spectrometry, an accurate targeted protein quantification method. The data complete the first fully integrated genomic, proteomic, and metabolomic analysis of the eicosanoid biochemical pathway.

Published
2012

34. In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in children

Author

Vives-Usano, Marta, Hernandez-Ferrer, Carles, Maitre, Léa, Ruiz-Arenas, Carlos, Andrusaityte, Sandra, Borràs, Eva, Carracedo, Ángel, Casas, Maribel, Chatzi, Leda, Coen, Muireann, Estivill, Xavier, González, Juan R., Grazuleviciene, Regina, Gutzkow, Kristine B., Keun, Hector C., Lau, Chung-Ho E., Cadiou, Solène, Lepeule, Johanna, Mason, Dan, Quintela, Inés, Robinson, Oliver, Sabidó, Eduard, Santorelli, Gillian, Schwarze, Per E., Siskos, Alexandros P., Slama, Rémy, Vafeiadi, Marina, Martí, Eulàlia, Vrijheid, Martine, and Bustamante, Mariona

Published
2020
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35. Plasma-derived extracellular vesicles from Plasmodium vivax patients signal spleen fibroblasts via NF-kB facilitating parasite cytoadherence

Author

Toda, Haruka, Diaz-Varela, Miriam, Segui-Barber, Joan, Roobsoong, Wanlapa, Baro, Barbara, Garcia-Silva, Susana, Galiano, Alicia, Gualdrón-López, Melisa, Almeida, Anne C. G., Brito, Marcelo A. M., de Melo, Gisely Cardoso, Aparici-Herraiz, Iris, Castro-Cavadía, Carlos, Monteiro, Wuelton Marcelo, Borràs, Eva, Sabidó, Eduard, Almeida, Igor C., Chojnacki, Jakub, Martinez-Picado, Javier, Calvo, Maria, Armengol, Pilar, Carmona-Fonseca, Jaime, Yasnot, Maria Fernanda, Lauzurica, Ricardo, Marcilla, Antonio, Peinado, Hector, Galinski, Mary R., Lacerda, Marcus V. G., Sattabongkot, Jetsumon, Fernandez-Becerra, Carmen, and del Portillo, Hernando A.

Published
2020
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36. A multicentric study to evaluate the use of relative retention times in targeted proteomics

Author

Vialas, Vital, Colomé-Calls, Núria, Abian, Joaquín, Aloria, Kerman, Alvarez-Llamas, Gloria, Antúnez, Oreto, Arizmendi, Jesus M., Azkargorta, Mikel, Barceló-Batllori, Silvia, Barderas, María G., Blanco, Francisco, Casal, J. Ignacio, Casas, Vanessa, de la Torre, Carolina, Chicano-Gálvez, Eduardo, Elortza, Felix, Espadas, Guadalupe, Estanyol, Josep M., Fernandez-Irigoyen, Joaquín, Fernandez-Puente, Patricia, Fidalgo, María José, Fuentes, Manuel, Gay, Marina, Gil, Concha, Hainard, Alexandre, Hernaez, Maria Luisa, Ibarrola, Nieves, Kopylov, Arthur T., Lario, Antonio, Lopez, Juan Antonio, López-Lucendo, María, Marcilla, Miguel, Marina-Ramírez, Anabel, Marko-Varga, Gyorgy, Martín, Luna, Mora, Maria I., Morato-López, Esperanza, Muñoz, Javier, Odena, Maria Antonia, de Oliveira, Eliandre, Orera, Irene, Ortea, Ignacio, Pasquarello, Carla, Ray, Kevin B., Rezeli, Melinda, Ruppen, Isabel, Sabidó, Eduard, del Pino, Manuel M. Sanchez, Sancho, Jaime, Santamaría, Enrique, Vazquez, Jesus, Vilaseca, Marta, Vivanco, Fernando, Walters, James J., Zgoda, Victor G., Corrales, Fernando J., Canals, Francesc, and Paradela, Alberto

Published
2017
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37. Molecular signature associated with cladribine treatment in patients with multiple sclerosis

Author

Fissolo, Nicolas, primary, Calvo-Barreiro, Laura, additional, Eixarch, Herena, additional, Boschert, Ursula, additional, Villar, Luisa M., additional, Costa-Frossard, Lucienne, additional, Ferrer, Mireia, additional, Sanchez, Alex, additional, Borràs, Eva, additional, Sabidó, Eduard, additional, Espejo, Carmen, additional, Montalban, Xavier, additional, and Comabella, Manuel, additional

Published
2023
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39. SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state

Author

Sebastian-Perez, Ruben, primary, Nakagawa, Shoma, additional, Tu, Xiaochuan, additional, Aranda, Sergi, additional, Pesaresi, Martina, additional, Gomez-Garcia, Pablo Aurelio, additional, Alcoverro-Bertran, Marc, additional, Gomez-Vazquez, Jose Luis, additional, Carnevali, Davide, additional, Borràs, Eva, additional, Sabidó, Eduard, additional, Martin, Laura, additional, Nissim-Rafinia, Malka, additional, Meshorer, Eran, additional, Neguembor, Maria Victoria, additional, Di Croce, Luciano, additional, and Cosma, Maria Pia, additional

Published
2023
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43. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

Author

Instituto de Salud Carlos III, Abián, Joaquín [0000-0003-2823-5429], Aloria, Kerman [0000-0001-7268-7700], Arizmendi, Jesús M. [0000-0002-1412-4042], Barceló-Batllori, Silvia [0000-0002-5352-9747], Burlet-Schiltz, Odile [0000-0002-3606-2356], Carrascal, Montserrat [0000-0002-0205-2176], Casal, J. Ignacio [0000-0003-1085-2840], Chicano-Gálvez, Eduardo [0000-0002-9481-9628], Chiva, Cristina [0000-0001-8150-6203], Elortza, Felix [0000-0001-8839-5438], Estanyol, Josep M. [0000-0001-8621-0057], Fernández-Irigoyen, Joaquín [0000-0001-5072-4099], Fernandez-Puente, Patricia [0000-0001-9968-1034], Froment, Carine [0000-0003-3688-5560], Fuentes-Almagro, Carlos [0000-0001-9940-9065], Gay, Marina [0000-0002-8827-7092], Heller, Manfred [0000-0002-6364-7325], Ibarrola, Nieves [0000-0002-9259-5739], Iloro, Ibon [0000-0002-9537-1714], Kieselbach, Thomas [0000-0001-5577-2938], Lario, Antonio [0000-0002-7457-2402], Locard-Paulet, Marie [0000-0003-2879-9224], Morato-López, Esperanza [0000-0003-4768-895X], Muñoz, Javier [0000-0003-3288-3496], Navajas, Rosana [0000-0002-4481-0553], Odena, Maria Antonia [0000-0002-4530-7829], Oliveira, Eliandre [0000-0003-4771-5719], Paradela, Alberto [0000-0001-6837-7056], Ríos, Vivian de los [0000-0001-5582-6879], Ruiz-Romero, Cristina [0000-0001-7649-9803], Sabidó, Eduard 0000-0001-6506-7714], Sánchez del Pino, Manuel M. [0000-0001-9696-7600], Sancho, Jaime [0000-0003-3852-7951], Santamaría, Enrique [0000-0001-8046-8102], Schaeffer-Reiss, Christine [0000-0003-0672-1979], Valero, M. Luz [0000-0002-2082-4600], Vilaseca, Marta [0000-0002-1666-1300], Canals, Francesc [0000-0002-0650-1135], Colomé, Nuria, Abián, Joaquín, Aloria, Kerman, Arizmendi, Jesús M., Barceló-Batllori, Silvia, Braga-Lagache, Sophie, Burlet-Schiltz, Odile, Carrascal, Montserrat, Casal, J. Ignacio, Chicano-Gálvez, Eduardo, Chiva, Cristina, Clemente, Luis Felipe, Elortza, Felix, Estanyol, Josep M., Fernández-Irigoyen, Joaquín, Fernandez-Puente, Patricia, Fidalgo, María José, Froment, Carine, Fuentes, Manuel, Fuentes-Almagro, Carlos, Gay, Marina, Hainard, Alexandre, Heller, Manfred, Hernández, María Luisa, Ibarrola, Nieves, Iloro, Ibon, Kieselbach, Thomas, Lario, Antonio, Locard-Paulet, Marie, Marina, Anabel, Martín, Luna, Morato-López, Esperanza, Muñoz, Javier, Navajas, Rosana, Odena, Maria Antonia, Odriozola, Leticia, Oliveira, Eliandre, Paradela, Alberto, Pasquarello, Carla, Ríos, Vivian de los, Ruiz-Romero, Cristina, Sabidó, Eduard, Sánchez del Pino, Manuel M., Sancho, Jaime, Santamaría, Enrique, Schaeffer-Reiss, Christine, Schneider, Justine, De la Torre, Carolina, Valero, M. Luz, Vilaseca, Marta, Wu, Shuai, Wu, Linfeng, Ximénez de Embún, Pilar, Canals, Francesc, Corrales, Fernando J., ProteoRed-ISCIII, EuPA, Instituto de Salud Carlos III, Abián, Joaquín [0000-0003-2823-5429], Aloria, Kerman [0000-0001-7268-7700], Arizmendi, Jesús M. [0000-0002-1412-4042], Barceló-Batllori, Silvia [0000-0002-5352-9747], Burlet-Schiltz, Odile [0000-0002-3606-2356], Carrascal, Montserrat [0000-0002-0205-2176], Casal, J. Ignacio [0000-0003-1085-2840], Chicano-Gálvez, Eduardo [0000-0002-9481-9628], Chiva, Cristina [0000-0001-8150-6203], Elortza, Felix [0000-0001-8839-5438], Estanyol, Josep M. [0000-0001-8621-0057], Fernández-Irigoyen, Joaquín [0000-0001-5072-4099], Fernandez-Puente, Patricia [0000-0001-9968-1034], Froment, Carine [0000-0003-3688-5560], Fuentes-Almagro, Carlos [0000-0001-9940-9065], Gay, Marina [0000-0002-8827-7092], Heller, Manfred [0000-0002-6364-7325], Ibarrola, Nieves [0000-0002-9259-5739], Iloro, Ibon [0000-0002-9537-1714], Kieselbach, Thomas [0000-0001-5577-2938], Lario, Antonio [0000-0002-7457-2402], Locard-Paulet, Marie [0000-0003-2879-9224], Morato-López, Esperanza [0000-0003-4768-895X], Muñoz, Javier [0000-0003-3288-3496], Navajas, Rosana [0000-0002-4481-0553], Odena, Maria Antonia [0000-0002-4530-7829], Oliveira, Eliandre [0000-0003-4771-5719], Paradela, Alberto [0000-0001-6837-7056], Ríos, Vivian de los [0000-0001-5582-6879], Ruiz-Romero, Cristina [0000-0001-7649-9803], Sabidó, Eduard 0000-0001-6506-7714], Sánchez del Pino, Manuel M. [0000-0001-9696-7600], Sancho, Jaime [0000-0003-3852-7951], Santamaría, Enrique [0000-0001-8046-8102], Schaeffer-Reiss, Christine [0000-0003-0672-1979], Valero, M. Luz [0000-0002-2082-4600], Vilaseca, Marta [0000-0002-1666-1300], Canals, Francesc [0000-0002-0650-1135], Colomé, Nuria, Abián, Joaquín, Aloria, Kerman, Arizmendi, Jesús M., Barceló-Batllori, Silvia, Braga-Lagache, Sophie, Burlet-Schiltz, Odile, Carrascal, Montserrat, Casal, J. Ignacio, Chicano-Gálvez, Eduardo, Chiva, Cristina, Clemente, Luis Felipe, Elortza, Felix, Estanyol, Josep M., Fernández-Irigoyen, Joaquín, Fernandez-Puente, Patricia, Fidalgo, María José, Froment, Carine, Fuentes, Manuel, Fuentes-Almagro, Carlos, Gay, Marina, Hainard, Alexandre, Heller, Manfred, Hernández, María Luisa, Ibarrola, Nieves, Iloro, Ibon, Kieselbach, Thomas, Lario, Antonio, Locard-Paulet, Marie, Marina, Anabel, Martín, Luna, Morato-López, Esperanza, Muñoz, Javier, Navajas, Rosana, Odena, Maria Antonia, Odriozola, Leticia, Oliveira, Eliandre, Paradela, Alberto, Pasquarello, Carla, Ríos, Vivian de los, Ruiz-Romero, Cristina, Sabidó, Eduard, Sánchez del Pino, Manuel M., Sancho, Jaime, Santamaría, Enrique, Schaeffer-Reiss, Christine, Schneider, Justine, De la Torre, Carolina, Valero, M. Luz, Vilaseca, Marta, Wu, Shuai, Wu, Linfeng, Ximénez de Embún, Pilar, Canals, Francesc, Corrales, Fernando J., ProteoRed-ISCIII, and EuPA

Abstract

Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.

Published
2022

47. Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato

Author

Proietti, Silvia, Falconieri, Gaia Salvatore, Laura, BERTINI, Pascale, Alberto, Bizzarri, Elisabetta, Morales-Sanfrutos, Julia, Sabidó, Eduard, Ruocco, Michelina, MAURILIA, MARIA MONTI, Russo, Assunta, Dziurka, Kinga, Ceci, Marcello, Loreto, Francesco, Caruso, Carla, Proietti, Silvia, Falconieri, Gaia Salvatore, Laura, BERTINI, Pascale, Alberto, Bizzarri, Elisabetta, Morales-Sanfrutos, Julia, Sabidó, Eduard, Ruocco, Michelina, MAURILIA, MARIA MONTI, Russo, Assunta, Dziurka, Kinga, Ceci, Marcello, Loreto, Francesco, and Caruso, Carla

Abstract

Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring in tomato interacting with the beneficial fungus Beauveria bassiana. The tomato leaf proteome revealed perturbed molecular pathways during the establishment of the plant–fungus relationship. In the early stages of colonization (5–7 d), proteins related to defense responses to the fungus were down-regulated and proteins related to calcium transport were up-regulated. At later time points (12–19 d after colonization), up-regulation of molecular pathways linked to protein/amino acid turnover and to biosynthesis of energy compounds suggests beneficial interaction enhancing plant growth and development. At the later stage, the profile of leaf hormones and related compounds was also investigated, highlighting up-regulation of those related to plant growth and defense. Finally, B. bassiana colonization was found to improve plant resistance to Botrytis cinerea, impacting plant oxidative damage. Overall, our findings further expand current knowledge on the possible mechanisms underlying the beneficial role of B. bassiana in tomato plants.

Published
2023

48. Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato

Author

Plant Microbe Interactions, Sub Plant-Microbe Interactions, Proietti, Silvia, Falconieri, Gaia Salvatore, Laura, BERTINI, Pascale, Alberto, Bizzarri, Elisabetta, Morales-Sanfrutos, Julia, Sabidó, Eduard, Ruocco, Michelina, MAURILIA, MARIA MONTI, Russo, Assunta, Dziurka, Kinga, Ceci, Marcello, Loreto, Francesco, Caruso, Carla, Plant Microbe Interactions, Sub Plant-Microbe Interactions, Proietti, Silvia, Falconieri, Gaia Salvatore, Laura, BERTINI, Pascale, Alberto, Bizzarri, Elisabetta, Morales-Sanfrutos, Julia, Sabidó, Eduard, Ruocco, Michelina, MAURILIA, MARIA MONTI, Russo, Assunta, Dziurka, Kinga, Ceci, Marcello, Loreto, Francesco, and Caruso, Carla

Published
2023

49. Peptidomics Methods Applied to the Study of Flower Development

Author

Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), European Commission, Agència de Gestió d'Ajuts Universitaris i de Recerca, Generalitat de Catalunya, Álvarez Urdiola, Raquel, Borràs, Eva, Valverde, Federico, Matus, José Tomás, Sabidó, Eduard, Riechmann, José Luis, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), European Commission, Agència de Gestió d'Ajuts Universitaris i de Recerca, Generalitat de Catalunya, Álvarez Urdiola, Raquel, Borràs, Eva, Valverde, Federico, Matus, José Tomás, Sabidó, Eduard, and Riechmann, José Luis

Abstract

Understanding the global and dynamic nature of plant developmental processes requires not only the study of the transcriptome, but also of the proteome, including its largely uncharacterized peptidome fraction. Recent advances in proteomics and high-throughput analyses of translating RNAs (ribosome profiling) have begun to address this issue, evidencing the existence of novel, uncharacterized, and possibly functional peptides. To validate the accumulation in tissues of sORF-encoded polypeptides (SEPs), the basic setup of proteomic analyses (i.e., LC-MS/MS) can be followed. However, the detection of peptides that are small (up to ~100 aa, 6–7 kDa) and novel (i.e., not annotated in reference databases) presents specific challenges that need to be addressed both experimentally and with computational biology resources. Several methods have been developed in recent years to isolate and identify peptides from plant tissues. In this chapter, we outline two different peptide extraction protocols and the subsequent peptide identification by mass spectrometry using the database search or the de novo identification methods.

Published
2023

50. IKKα kinase coordinates BRD4 and STAT3 signaling to subvert DNA damage-based anticancer therapy

Author

Pecharroman, Irene, primary, Sole, Laura, additional, Villanueva, Daniel Alvarez, additional, Bertran, Joan, additional, Guillén, Yolanda, additional, Lobo, Teresa, additional, Alonso-Marañon, Josune, additional, Martínez, Maria, additional, García-Hernández, Violeta, additional, Gimenez, Gemma, additional, Colomer, Carlota, additional, Mulero, María Carmen, additional, Gonzales, Jessica, additional, Salazar, Ramon, additional, Santos, Cristina, additional, Garrido, Marta, additional, Villanueva, Alberto, additional, Borràs, Eva, additional, Sabidó, Eduard, additional, Bonfill-Teixidor, Ester, additional, Iurlaro, Raffaella, additional, Montoto, Angela, additional, Seoane, Joan, additional, Iglesias, Mar, additional, Bigas, Anna, additional, and Espinosa, Lluis, additional

Published
2023
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