• The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development

  Nakagawa, Shoma; Carnevali, Davide; Tan, Xiangtian; Alvarez, Mariano J.; Parfitt, David-Emlyn; Di Vicino, Umberto; Arumugam, Karthik; Shin, William; Aranda, Sergi; Normanno, Davide; Sebastián Pérez, Rubén; Cannatá, Chiara; Cortes, Paola; Neguembor, Maria Victoria; Shen, Michael M.; Califano, Andrea; Cosma, Maria Pia (Elsevier, 2024)

  Embryo size, specification, and homeostasis are regulated by a complex gene regulatory and signaling network. Here we used gene expression signatures of Wnt-activated mouse embryonic stem cell (mESC) clones to reverse ...
• TANGO1 inhibitors reduce collagen secretion and limit tissue scarring

  Raote, Ishier; Häkkinen, Hanna-Maria; Vibe, Carine; Broadbent, Katrina; Carolis, Carlo; Ruprecht, Verena; Malhotra, Vivek (Nature Research, 2024)

  Uncontrolled secretion of ECM proteins, such as collagen, can lead to excessive scarring and fibrosis and compromise tissue function. Despite the widespread occurrence of fibrotic diseases and scarring, effective therapies ...
• Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization

  Kant, Aayush; Guo, Zixian; Vinayak, Vinayak; Neguembor, Maria Victoria; Li, Wing Shun; Agrawal, Vasundhara; Pujadas, Emily; Almassalha, Luay; Backman, Vadim; Lakadamyali, Melike; Cosma, Maria Pia; Shenoy, Vivek B. (Nature Research, 2024)

  In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this ...
• Developing a platform for secretion of biomolecules in Mycoplasma feriruminatoris

  Gonzalez de Miguel, Javier; Montero-Blay, Ariadna, 1994-; Ciampi, Ludovica; Rodriguez-Arce, Irene; Serrano Pubull, Luis, 1982- (BioMed Central, 2024)

  Background: Having a simple and fast dividing organism capable of producing and exposing at its surface or secreting functional complex biomolecules with disulphide bridges is of great interest. The mycoplasma bacterial ...
• Non-canonical role for the BAF complex subunit DPF3 in mitosis and ciliogenesis

  Verrillo, Giulia; Obeid, Anna Maria; Genco, Alexia; Scrofani, Jacopo, 1984-; Orange, François; Hanache, Sarah; Mignon, Julien; Leyder, Tanguy; Michaux, Catherine; Kempeneers, Céline; Bricmont, Noëmie; Herkenne, Stephanie; Vernos, Isabelle, 1959-; Martin, Maud; Mottet, Denis (Company of Biologists, 2024)

  DPF3, along with other subunits, is a well-known component of the BAF chromatin remodeling complex, which plays a key role in regulating chromatin remodeling activity and gene expression. Here, we elucidated a non-canonical ...
• Characterization of the common genetic variation in the spanish population of Navarre

  Maillo, Alberto; Beltran, Sergi; Gómez Cabrero, David (MDPI, 2024)

  Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. ...
• Association between radiation dose, thyroid hormone, and IQ levels in children exposed to radiation in utero after the Chernobyl accident

  Liutsko, Liudmila; Igumnov, Sergey; Drozdovitch, Vladimir; Cardis, Elisabeth (Taylor & Francis, 2024)

  Few studies have explored the effects of n utero radiation exposure on human health and cognition and none have taken into account thyroid hormone levels (T3), which have shown to affect cognitive performance. We investigated ...
• Cohort Profile: Barcelona Life Study Cohort (BiSC)

  Dadvand, Payam; Gascon Merlos, Mireia, 1984-; Bustamante Pineda, Mariona; Rivas, Ioar; Foraster Pulido, Maria, 1984-; Basagaña Flores, Xavier; Cosín Tomàs, Marta; Ferrer Vergés, Muriel; Gómez Herrera, Laura C.; Jiménez Arenas, Pol; Júlvez Calvo, Jordi; Morillas, Àlex; Nieuwenhuijsen, Mark J.; Persavento, Cecilia; Pujol, Jesús; Vrijheid, Martine; Sunyer Deu, Jordi; BiSC Group (Oxford University Press, 2024)
• Short-term exposure to air pollution and hospital admission after COVID-19 in Catalonia: the COVAIR-CAT study

  Alari, Anna; Ranzani, Otavio; Olmos, Sergio; Milà, Carles; Rico, Alex; Ballester, Joan; Basagaña Flores, Xavier; Dadvand, Payam; Duarte Salles, Talita, 1985-; Nieuwenhuijsen, Mark J.; Vivanco Hidalgo, Rosa María; Tonne, Cathryn (Oxford University Press, 2024)

  Background: A growing body of evidence has reported positive associations between long-term exposure to air pollution and poor COVID-19 outcomes. Inconsistent findings have been reported for short-term air pollution, mostly ...
• Physical activity and body mass related to catch-up lung function growth in childhood: a population-based accelerated cohort study

  Koch, Sarah; Prado Peralta, María Gabriela; Carsin, Anne-Elie; Abellan, Alicia; Roda, Célina; Torrent, Maties; Iñiguez, Carmen; Ballester Díez, Ferran; Ferrero, Amparo; Zabaleta, Carlos; Lertxundi, Aitana; Guxens Junyent, Mònica; Vrijheid, Martine; Sunyer Deu, Jordi; Casas Sanahuja, Maribel; García Aymerich, Judith (BMJ Publishing Group, 2024)

  Objective: The existence of catch-up lung function growth and its predictors is uncertain. We aimed to identify lung function trajectories and their predictors in a population-based birth cohort. Methods: We applied ...
• Metabolomic signatures of exposure to nitrate and trihalomethanes in drinking water and colorectal cancer risk in a Spanish Multicentric Study (MCC-Spain)

  Alcolea, Jose A.; Donat-Vargas, Carolina; Chatziioannou, Anastasia Chrysovalantou; Keski-Rahkonen, Pekka; Robinot, Nivonirina; Molina, Antonio J.; Amiano, Pilar; Gómez-Acebo, Inés; Castaño Vinyals, Gemma; Maitre, Léa; Chadeau-Hyam, Marc; Dagnino, Sonia; Cheng, Sibo Lucas; Scalbert, Augustin; Vineis, Paolo; Kogevinas, Manolis; Villanueva Belmonte, Cristina (American Chemical Society (ACS), 2023)

  We investigated the metabolomic profile associated with exposure to trihalomethanes (THMs) and nitrate in drinking water and with colorectal cancer risk in 296 cases and 295 controls from the Multi Case-Control Spain ...
• Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster

  Sklias, Athena; Cruciani, Sonia; Marchand, Virginie; Spagnuolo, Mariangela; Lavergne, Guillaume; Bourguignon, Valérie; Brambilla, Alessandro; Dreos, René; Marygold, Steven J.; Novoa Pardo, Ana María; Motorin, Yuri; Roignant, Jean-Yves (Oxford University Press, 2024)

  During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding of rRNA secondary structures and therefore in ribosomal function. Along with pseudouridine, ...
• Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells

  Conti, Sefora; Venturini, Valeria; Cañellas Socias, Adrià; Cortina Duran, Carme; Abenza, Juan F.; Stephan-Otto Attolini, Camille; Middendorp Guerra, Emily; Xu, Catherine K.; Li, Jia Hui; Rossetti, Leone; Stassi, Giorgio; Roca-Cusachs, Pere; Diz-Muñoz, Alba; Ruprecht, Verena; Guck, Jochen; Batlle Gómez, Eduard; Labernadie, Anna; Trepat, Xavier (Nature Research, 2024)

  Colorectal cancer (CRC) tumors are composed of heterogeneous and plastic cell populations, including a pool of cancer stem cells that express LGR5. Whether these distinct cell populations display different mechanical ...
• Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche

  González Iglesias, Ainara; Arcas Mantas, Aida; Domingo Muelas, Ana; Mancini, Estefanía; Galcerán, Joan; Valcárcel, J. (Juan); Fariñas, Isabel; Nieto, M. Ángela (Nature Research, 2024)

  The adult mammalian brain retains some capacity to replenish neurons and glia, holding promise for brain regeneration. Thus, understanding the mechanisms controlling adult neural stem cell (NSC) differentiation is crucial. ...
• CSDE1: a versatile regulator of gene expression in cancer

  Ciocia, Annagiulia; Mestre Farràs, Neus; Vicent Nacht, Ignacio; Guitart, Tanit; Gebauer, Fátima (Oxford University Press, 2024)

  RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug ...
• Beyond quiescent and active: Intermediate microglial transcriptomic states in a mouse model of down syndrome

  Fernández Blanco, Álvaro; Sierra, Cesar; Tejido, Clara; Dierssen, Mara (MDPI, 2024)

  Research on microglia in Down syndrome (DS) has shown that microglial activation, increased inflammatory gene expression, and oxidative stress occur at different ages in DS brains. However, most studies resulted in simplistic ...
• LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells

  Ramírez Cuéllar, Angélica Julieta; Ferrari, Roberto; Sanz, Rosario T.; Valverde Santiago, Marta; García García, Judith; Nacht, A. Silvina; Castillo, David; Le Dily, François; Neguembor, Maria Victoria; Malatesta, Marco; Bonnin, Sarah; Martí Renom, Marc A.; Beato, Miguel; Vicent, Guillermo Pablo (Nature Research, 2024)

  The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular ...
• Integrating physics in deep learning algorithms: a force field as a PyTorch module

  Orlando, Gabriele; Serrano Pubull, Luis, 1982-; Schymkowitz, Joost; Rousseau, Frédéric (Oxford University Press, 2024)

  Motivation: Deep learning algorithms applied to structural biology often struggle to converge to meaningful solutions when limited data is available, since they are required to learn complex physical rules from examples. ...
• Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung

  Martins, Leila R.; Sieverling, Lina; Michelhans, Michelle; Schiller, Chiara; Erkut, Cihan; Grünewald, Thomas G. P.; Triana, Sergio; Fröhling, Stefan; Velten, Lars; Glimm, Hanno; Scholl, Claudia (Nature Research, 2024)

  Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of therapeutic approaches for lung diseases. We combine mouse models allowing diphtheria toxin-mediated ...
• Single cell atlas of Xenoturbella bocki highlights limited cell-type complexity

  Robertson, Helen E.; Sebé-Pedrós, Arnau; Saudemont, Baptiste; Loe-Mie, Yann; Zakrzewski, Anne-C.; Grau Bové, Xavier; Mailhe, Marie-Pierre; Schiffer, Philipp H.; Telford, Maximilian J.; Marlow, Heather (Nature Research, 2024)

  Phylogenetic analyses over the last two decades have united a few small, and previously orphan clades, the nematodermatids, acoels and xenoturbelids, into the phylum Xenacoelomorpha. Some phylogenetic analyses support a ...

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