Articles publicats en revistes (Ciències Fisiològiques)

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Characterization of ClC-1 chloride channels in zebrafish: a new model to study myotonia
(The Physiological Society, 2024-07-19) Gaitán-Peñas, Héctor; Perez-Rius, Carla; Muhaisen, Ashraf; Castellanos, Aida; Errasti-Murugarren, Ekaitz; Barrallo-Gimeno, Alejandro; Alcaraz-Perez, Francisca; Estévez Povedano, Raúl
The function of the chloride channel ClC-1 is crucial for the control of muscle excitability. Thus, reduction of ClC-1 functions by CLCN1 mutations leads to myotonia congenita. Many different animal models have contributed to understanding the myotonia pathophysiology. However, these models do not allow in vivo screening of potentially therapeutic drugs, as the zebrafish model does. In this work, we identified and characterized the two zebrafish orthologues (clc-1a and clc-1b) of the ClC-1 channel. Both channels are mostly expressed in the skeletal muscle as revealed by RT-PCR, western blot, and electrophysiological recordings of myotubes, and clc-1a is predominantly expressed in adult stages. Characterization in Xenopus oocytes shows that the zebrafish channels display similar anion selectivity and voltage dependence to their human counterparts. However, they show reduced sensitivity to the inhibitor 9-anthracenecarboxylic acid (9-AC), and acidic pH inverts the voltage dependence of activation. Reduction of clc-1a/b expression hampers spontaneous and mechanically stimulated movement, which could be reverted by expression of human ClC-1 but not by some ClC-1 containing myotonia mutations. Treatment of clc-1-depleted zebrafish with mexiletine, a typical drug used in human myotonia, improves the motor behaviour. Our work extends the repertoire of ClC channels to evolutionary structure–function studies and proposes the zebrafish clcn1 crispant model as a simple tool to find novel therapies for myotonia.
Deletion of Mfn2 in endothelial cells triggers a mitohormetic response that improves systemic metabolism and healthspan in mice
(Cell Press, 2026-03-03) Chivite, Iñigo; Monelli, Erika; Munar Gelabert, Margalida; Gómez Valadés, Alicia G.; Alvarado Díaz, Abdiel; Pozo, Macarena; Varela, Luis; Ramírez, Samuel; Haddad Tovolli, Roberta; Toledo, Miriam; Fos Domènech, Júlia; Díaz-Castro, Francisco; Tahiri, Iasim; García Ramón, Pau; Ferreira, Mariana; van Gelder, Chloe; Abot, Anne; Osorio Conles, Óscar; Valer, José Antonio; Obri, Arnaud; Milà Guasch, Maria; Alvarez-Luis, J.; Villacampa, Pilar; Eyre, Elena; Altirriba Gutiérrez, Jordi; Genbler Sabrina; Haake, Markus; Schuberth Wagner, Christine; Remesar Betlloch, Xavier; Zorzano Olarte, Antonio; Garcia Roves Gonzalez, Pablo Miguel; Ventura Pujol, Francesc; Vidal i Cortada, Josep; Knauf, Claude; Nogueiras, Rubén; Horvath, Tamas L.; de Bock, Katrien; Graupera i Garcia-Milà, Mariona; Claret i Carles, Marc
Endothelial cells (ECs) are key metabolic gatekeepers, yet their role in metabolic health remains unclear. Given their central involvement in energy metabolism, mitochondria are ideally positioned to enable ECs to adapt to ever-changing metabolic requirements. Here, we explore the hypothesis that mitochondrial dynamics proteins in ECs influence whole-body metabolic status. Genetic deficiency of Mfn2 in ECs (Mfn2iΔEC), but not of Mfn1iΔEC, induces a mitohormetic response in the adipose vasculature, enhancing antioxidant defenses, mitochondrial fitness, and lipid oxidation, ultimately improving metabolic outcomes. Cultured ECs secrete the mitokine growth differentiation factor 15 (GDF15) via a forkhead box O1 (FOXO1)-dependent axis, a response also observed under stress conditions in vivo. Notably, Mfn2iΔEC mice exhibited elevated endothelial and circulating GDF15 levels, and neutralization of GDF15 partly attenuated their metabolic benefits. Consistent with mitohormetic activation, Mfn2iΔEC mice showed protection against diet-induced obesity and delayed age-related decline. Hence, vascular mitohormetic adaptations emerge as a novel mechanism promoting systemic metabolic health.
New Values, New Lives, and Emerging Dating Violence: Insights on Detection and Intervention from Health Sciences Students
(MDPI, 2026-04-23) Sánchez Balcells, Sara; Sanchez-Ortega, M. Aurelia; Prats Arimon, Marta; Giménez Bonafé, Pepita; Vergés Bosch, Núria; Puig Llobet, Montserrat
Gender-based violence in dating relationships is a multifaceted issue that encompasses diverse forms. In university settings, high prevalence rates have been reported, with psychological violence being the most common. New forms of digital violence, such as cyberbullying, control through social media, and digital aesthetic pressure, further complicate the phenomenon. Purpose: This study aimed to explore Health Sciences students’ perceptions of gender-based violence in dating relationships to identify key dimensions for understanding and intervention. Methods: A qualitative design was employed using focus groups with ten participants, analyzed through Interpretative Phenomenological Analysis (IPA). Results: Four main themes emerged: characteristics of gender-based violence in dating relationships, types of violence identified, aesthetic pressure within affective relationships, and strategies for detecting and responding to violence. Conclusions: Findings emphasize the importance of incorporating students’ voices into prevention strategies and propose educational interventions that address both offline and online dynamics of gender-based violence in dating relationships.
Sensory-cell population integrity required to preserve minimal and normal vestibulo-ocular reflexes reveals the critical role of type I hair cells in canal- and otolith-specific functions
(The Society for Neuroscience, 2026-02-09) Schenberg, Louise; Simon, François; Palou Miranda, Aida; Dijan, Cassandre; Tagliabue, Michele; Llorens i Baucells, Jordi; Beraneck, Mathieu
Vestibular dysfunction constitutes a major medical concern, and regeneration of hair cells (HC) is a primary target of gene therapy aimed at restoring vestibular functions. Thus far, therapeutic trials in animal models targeting vestibular loss associated with genetic diseases have yielded variable and partial results, and the functional identity and quantity of HCs required to restore minimal or normal vestibular function remain undefined. Indeed, direct comparisons between structural pathology and quantitative assessments of vestibular dysfunctions are lacking in humans and are rather limited in animal models, representing a significant gap in current knowledge. Here, we present an innovative methodology to bridge the gap between HC integrity and functional vestibular loss in individual mice of either sex. Gradual vestibular deficits were induced through a dose-dependent ototoxic lesion, quantified with canal or utricular-specific vestibulo-ocular reflex tests, and were then correlated in all individuals with the loss of type I and type II HCs in different regions of ampulla and macula. Our findings reveal that the structure-function relationship is nonlinear, with lower bound of approximately 50% of HCs necessary to retain minimal vestibular function, and threshold exceeding 80% to preserve normal function, thus shedding light on population coding mechanisms for vestibular response. Our data further support the decisive role of type I, rather than type II, HC in the tested VOR functions.
Identifying chronotype for the preservation of muscle mass, quality and strength
(MDPI, 2026-01-10) Barrientos-Salinas, R.; Dahdah, N.; Alvarez-Luis, J.; Vilarrasa, Nuria; García-Roves, Pablo M. (Pablo Miguel)
Chronotype, an individual’s preferred timing of sleep and activity within a 24 h cycle, significantly influences metabolic health, muscle function, and body composition. This review explores the interplay between circadian rhythms, hormonal fluctuations, and behavioral patterns—such as nutrition timing, physical activity and sleep quality—and their impact on muscle mass, strength, and quality. Evening chronotypes (ETs) are consistently associated with poorer sleep, irregular eating habits, reduced physical activity, and increased risk of obesity, sarcopenia and metabolic disorders compared to morning types (MTs). At the molecular level, disruptions in circadian clock gene expression (e.g., BMAL1, PER2, CRY1) affect protein synthesis, insulin sensitivity, and energy metabolism, contributing to muscle degradation and impaired recovery. The review highlights critical components—targeting chrono-nutrition, sleep quality, and exercise timing—to align lifestyle behaviors with circadian biology, thereby preserving muscle health and improving overall metabolic outcomes.
Hyperdiploidy impairs fetal hematopoietic progenitor fitness and differentiation enabling persistence of rare preleukemic aneuploid clones
(Elsevier, 2026-03-27) Thampi, Namitha; Calvo, Cristina; Rodríguez Cortez, Virginia Carolina; Martínez-Moreno, Alba; Roca-Ho, Heleia; Vinyoles, Meritxell; Bueno, Clara; Espinosa-Aroca, Lady; Pablo-Fontecha, Verónica; Camps, Jordi; Fuente-González, A. de la; Puente, Xose S; Solé, Francesc; Foijer, Floris; Menéndez Buján, Pablo; Molina, Òscar
Aneuploidy is a hallmark of cancer but often reduces cellular fitness. In childhood B cell acute lymphoblastic leukemia (cB-ALL), hyperdiploidy is the most common cytogenetic abnormality and arises in utero from early hematopoietic stem/progenitor cells (HSPCs), yet its impact on early hematopoiesis remains unclear. We model two proposed routes to hyperdiploidy, chromosome mis-segregation and cytokinesis failure, by transiently exposing human fetal liver-derived HSPCs to reversine or cytochalasin D. Induced hyperdiploidy impaired fitness and delayed differentiation in vitro, causing hyperdiploid cells to be rapidly outcompeted by euploid counterparts. Nonetheless, hyperdiploid cells engrafted immunodeficient mice, where rare clones persisted long term and acquired non-random chromosomal gains frequently observed in cB-ALL. Despite this persistence, they did not initiate leukemia. These findings support a two-step model in which hyperdiploid fetal clones require additional perinatal/postnatal events for malignant transformation. Our work establishes a valuable human model for studying early aneuploidy-driven events in childhood leukemia.
Ca2+-phospholipid–dependent regulation of Munc13-1 is essential for post-tetanic potentiation at mossy fiber synapses and supports working memory.
(Elsevier, 2026-02-19) López Murcia, Francisco José; Krueger-Burg, Dilja; Wenger, Sally; López Hernández, Tania; Lipstein, Noa; Taschenberger, Holger; Brose, Nils
Hippocampal mossy fiber (hMF) to CA3 pyramidal cell synapses are thought to support the formation of working memory through presynaptic short-term facilitation (STF) and post-tetanic potentiation (PTP). However, the molecular mechanisms underlying these transient forms of synaptic enhancement are unclear. We show here that Munc13-1-mediated priming of synaptic vesicles (SVs) at active zones controls hMF STF and PTP in response to Ca2+-phospholipid and Ca2+-calmodulin (CaM) signaling. Knock-in mice expressing Munc13-1 variants insensitive to either signaling pathway exhibit pronounced deficits in STF and PTP, and the PTP-induction threshold is markedly increased upon block of Ca2+-phospholipid-Munc13-1 signaling. Since these synaptic defects are accompanied by working memory deficits, especially in mice expressing the Ca2+-phospholipid-insensitive Munc13-1 variant, we conclude that the Ca2+-dependent regulation of Munc13-1-mediated SV priming co-determines hMF short-term plasticity and working memory formation.
Echinocandins Pharmacokinetics: A Comprehensive Review of Micafungin, Caspofungin, Anidulafungin, and Rezafungin Population Pharmacokinetic Models and Dose Optimization in Special Populations
(Springer Nature Switzerland, 2025-01-01) Albanell Fernández, Marta
In recent years, many population pharmacokinetic (popPK) models have been developed for echinocandins to better understand the pharmacokinetics (PK) of these antifungals. This comprehensive review aimed to summarize popPK models of echinocandins (micafungin, caspofungin, anidulafungin, and rezafungin), by focusing on dosage optimization to maximize the probability of attaining the PK/PD target proposed in special populations. A search in PubMed, Embase, Web of Science, and Scopus, supplemented by the bibliography of relevant articles, was conducted from inception to March 2024, including both observational and prospective trials. A total of 1126 articles were identified, 47 of them were included in the review (22 for micafungin, 13 for caspofungin, 9 for anidulafungin, and 3 for rezafungin). A two-compartment model was more frequently used to describe the PK parameters of echinocandin (78.7% of developed models), although more complex structural models with three and four compartments have also been developed. The covariates to estimate the PK parameters such as clearance (CL) and volume of distribution (Vd) differed between models. Weight total (WT) was the most frequently reported to be a significant predictor for both parameters, especially for estimating the CL in pediatrics. The PD parameter most widely reported assessing the drug exposure–efficacy relationship was the area under the concentration–time curve to minimum inhibitory concentration (MIC) ratio (AUC0–24/MIC) with different targets proposed for each echinocandin. In certain populations such as patients that are critically ill, obese, receiving extracorporeal membrane oxygenation (ECMO) and/or continuous renal replacement therapy (CRRT), or pediatric patients and/or patients with cancer or that are immunocompromised, the fixed dosing strategies recommended in the drug prescribing information may not reach the PK/PD target. For these populations, different strategies have been proposed, such as a dosing regimen based on body weight or increasing the loading and/or maintenance dose. Despite echinocandins’ favorable safety profile and predictable PK, certain groups at risk of suboptimal drug exposure can benefit from therapeutic drug monitoring (TDM) to prevent clinical failures. Numerous popPK models of echinocandins have been developed. However, an external validation of the suggested dosing regimens in conjunction with an analysis of population subgroups should be conducted before implementing a popPK model in clinical practice.
Identification of a crosstalk between ClC-1 C-terminal CBS domains and the transmembrane region
(The Physiological Society, 2025-02-07) Gaitán-Peñas, Héctor; Pérez González, Anna Priscil·la; González Subías, Marc; Zdebik, Anselm A.; Gasull Casanova, Xavier; Buey, Ruben M.; Errasti-Murugarren, Ekaitz; Estévez Povedano, Raúl
CLC channels and transporters have large C-terminal regions which contain two cystathionine β-synthetase (CBS) domains. It has been hypothesized that conformational changes in these domains upon nucleotide binding modulate the gating of the CLC dimer. It is not clear how rearrangements that occur in the CBS domains are transmitted to the ion pathway, as CBS domains interact with the rest of the channel at multiple locations and some of these sites are not visible in recent solved cryogenic electron microscopy structures or are difficult to model using the AlphaFold server. Using ClC-1 as a model, we started working with a described ClC-1 mutation (H835R) located in the first alpha helix of the CBS2 domain which changes the voltage dependence of gating. We then identified several residues located in the disorganized loop after helix R (R-linker) that revert the phenotype of this mutation. We additionally proved that R-linker's function is connected to the CBS2 domain as current intensity, plasma membrane levels and gating defects of several R-linker variants were corrected by adding the mutation H835R. Furthermore, cross-linking studies using newly developed split-cysless ClC-1 channels containing specific cysteine mutants in the R-linker and the CBS2 domain indicate that these two regions are in close contact. Considering these new results, we propose that conformational changes occurring in the CBS domains could be transmitted to the CLC intracellular chloride binding site by means of its interaction with the R-linker.
The multiomics blueprint of the individual with the most extreme lifespan
(Cell Press, 2025-10-21) Torrubiano, Marta; Massip Salcedo, Marta; Khidir, Kamal A.; Cao, Thong Huy; Quinn, Paulene A.; Jones, Donald J. L.; Macip, Salvador; Brigos Barril, Eva; Moldes, Mauricio; Barteri, Fabio; Ferrer, Gerardo; Muntané, Gerard; Davalos, Veronica; Laayouni, Hafid; Mereu, Elisabetta; Navarro, Arcadi; Pluvinet, Raquel; Esteller, Manel; Arribas, Carles; Torre, Carolina de la; Villavicencio Goula, Francisco; Sumoy, Lauro; Granada, Isabel; Coles, Natalie S.; Santos Pujol, Eloy; Noguera Castells, Aleix; Casado Pelaez, Marta; García Prieto, Carlos A.; Vasallo, Claudia; Campillo Marcos, Ignacio; Quero Dotor, Carlos; Crespo García, Eva; Bueno Costa, Alberto; Setién, Fernando; Acha, Pamela; Solé, Francesc; Mallo, Mar; Mata, Caterina; Peregrina, Sara; Gabaldón, Toni; Llirós, Marc; Pujolassos, Meritxell; Carrera Torres, Robert; Lluansí, Aleix; García Gil, Librado Jesús; Aldeguer, Xavier; Samino, Sara; Torné, Pol; Ribalta, Josep; Guardiola, Montse; Amigó, Núria; Yanes, Oscar; Martínez, Paula; Sánchez Vázquez, Raúl; Blasco, Maria A.; Oviedo, Jose; Lemos, Bernardo; Rius Bonet, Julia
Extreme human lifespan, exemplified by supercentenarians, presents a paradox in understanding aging: despite advanced age, they maintain relatively good health. To investigate this duality, we have performed a high-throughput multiomics study of the world's oldest living person, interrogating her genome, transcriptome, metabolome, proteome, microbiome, and epigenome, comparing the results with larger matched cohorts. The emerging picture highlights different pathways attributed to each process: the record-breaking advanced age is manifested by telomere attrition, abnormal B cell population, and clonal hematopoiesis, whereas absence of typical age-associated diseases is associated with rare European-population genetic variants, low inflammation levels, a rejuvenated bacteriome, and a younger epigenome. These findings provide a fresh look at human aging biology, suggesting biomarkers for healthy aging, and potential strategies to increase life expectancy. The extrapolation of our results to the general population will require larger cohorts and longitudinal prospective studies to design potential anti-aging interventions.
Human microglia-like cells differentiated from monocytes with GM-CSF and IL-34 show phagocytosis of α-synuclein aggregates and C/EBPβ-dependent proinflammatory activation
(Springer Nature, 2025-02) Llaves López, Andrea; Micoli, Elia; Belmonte Mateos, Carla; Aguilar, Gerard; Alba, Clara; Marsal, Anais; Pulido Salgado, Marta; Rabaneda Lombarte, Neus; Solà i Subirana, Carme; Serratosa i Serdà, Joan; Vidal Taboada, José Manuel; Saura Martí, Josep
Microglia, the main resident immune cells in the central nervous system, are implicated in the pathogenesis of various neurological disorders. Much of our knowledge on microglial biology was obtained using rodent microglial cultures. To understand the role of microglia in human disease, reliable in vitro models of human microglia are necessary. Monocyte-derived microglia-like cells (MDMi) are a promising approach. This study aimed to characterize MDMi cells generated from adult human monocytes using granulocyte–macrophage colony-stimulating factor and interleukin-34. To this end, 49 independent cultures of MDMI were prepared, and various methodological and functional studies were performed. We show that with this protocol, adult human monocytes develop into microglia-like cells, a coating is unnecessary, and high cell density seeding is preferable. When compared to monocytes, MDMi upregulate the expression of many, but not all, microglial markers, indicating that, although these cells display a microglia-like phenotype, they cannot be considered bona fide human microglia. At the functional level, MDMi phagocytose α-synuclein aggregates and responds to lipopolysaccharide (LPS) by nuclear translocation of the transcription factor nuclear factor-kappaB (NFkappaB) and the upregulation of proinflammatory genes. Finally, a long-lasting silencing of the transcription factor CCAAT/enhancer protein β (C/EBPβ) was achieved by small interfering RNA, resulting in the subsequent downregulation of proinflammatory genes. This supports the hypothesis that C/EBPβ plays a key role in proinflammatory gene program activation in human microglia. Altogether, this study sheds new light on the properties of MDMi cells and supports these cells as a promising in vitro model for studying adult human microglia–like cells.
SIRT7 and p53 interaction in embryonic development and tumorigenesis
(Frontiers Media, 2023-12) Vazquez, Berta N.; Fernández Duran, Irene; Hernandez, Yuridana; Tarighi, Shahriar; Thackray, Joshua K.; Espinosa Alcantud, Maria; Kumari, Poonam; Ianni, Alessandro; Cesaire, Lionel; Braun, Thomas; Esteller, Manel, 1968-; Tischfield, Jay A.; Vaquero, Alejandro; Serrano, Lourdes
p53 is a hallmark tumor suppressor due in part to its role in cell cycle progression, DNA damage repair, and cellular apoptosis; its protein activity interrelates with the Sirtuin family of proteins, major regulators of the cellular response to metabolic, oxidative, and genotoxic stress. In the recent years, mammalian Sirtuin 7 (SIRT7) has emerged as a pivotal regulator of p53, fine-tuning its activity in a context dependent manner. SIRT7 is frequently overexpressed in human cancer, yet its precise role in tumorigenesis and whether it involves p53 regulation is insufficiently understood. Depletion of SIRT7 in mice results in impaired embryo development and premature aging. While p53 activity has been suggested to contribute to tissue specific dysfunction in adult Sirt7−/− mice, whether this also applies during development is currently unknown. By generating SIRT7 and p53 double-knockout mice, here we show that the demise of SIRT7-deficient embryos is not the result of p53 activity. Notably, although SIRT7 is commonly considered an oncogene, SIRT7 haploinsufficiency increases tumorigenesis in p53 knockout mice. Remarkably, in specific human tumors harboring p53 mutation, we identified that SIRT7 low expression correlates with poor patient prognosis. Transcriptomic analysis unveils a previously unrecognized interplay between SIRT7 and p53 in epithelial-to-mesenchymal transition (EMT) and extracellular matrix regulation with major implications for our understanding of embryonic development and tumor progression.
PVR (CD155) epigenetic status mediates immunotherapy response in multiple myeloma
(Springer Nature, 2024-09-24) Vaqué Salsench, Sergi; Ferrer, Gerardo; Garcia Ortiz, Almudena; Esteller, Manel, 1968-; Valeri, Antonio; Rojas, Elizabeta A.; Barrena, Naroa; Gutiérrez, Norma C.; Prosper, Felipe; Agirre, Xabier; Fernández de Larrea Rodríguez, Carlos José ; Martínez-Verbo, Laura; Veselinova, Yoana; Llinàs Arias, Pere; García-Prieto, Carlos A.; Noguera Castells, Aleix; López Pato, Miguel; Bueno Costa, Alberto; Campillo Marcos, Ignacio; Villanueva, Lorea; Oliver Caldés, Aina; Cardús Granell, Oriol ; Martínez López, Joaquín
he immune system is tightly regulated but plastic in humans. It has several lines of control, and its imbalance has severe consequences for our health. Epigenetics encompasses heritable biochemical changes of the chromatin that do not affect the DNA sequence.
Age-driven genetic and epigenetic heterogeneity in B-ALL
(MDPI, 2025-09-09) Veselinova, Yoana; Esteller, Manel, 1968-; Ferrer, Gerardo
B-cell acute lymphoblastic leukemia (B-ALL) remains a major clinical challenge in hematologic oncology, characterized by a continuous evolution of molecular drivers that shape its heterogeneity across the age spectrum. Pediatric B-ALL is generally associated with high cure rates, while adult forms of the disease are often more aggressive and less responsive to treatment. This review examines the age-specific genetic and epigenetic landscapes that contribute to this disparity, revealing how the nature and timing of molecular alterations point to fundamentally different leukemogenic processes. Favorable genetic aberrations, such as ETV6::RUNX1 and hyperdiploidy, are predominant in children, whereas adults more frequently present with high-risk features, including BCR::ABL1 fusions and IKZF1 deletions. Epigenetic distinctions are similarly age-dependent, involving divergent patterns of DNA methylation, histone modifications, and non-coding RNA expression. For example, pediatric B-ALL frequently harbors mutations in epigenetic regulators like SETD2 and CREBBP, while adult B-ALL is more commonly affected by alterations in TET2 and IDH1/2. These molecular differences are not only prognostic but also mechanistic, reflecting distinct developmental trajectories and vulnerabilities. Understanding these age-driven transitions is essential for improving risk stratification and developing precision therapies tailored to the unique biology of B-ALL across the lifespan.
Development of a microRNA-based prognostic model for accurate prediction of distant metastasis in breast cancer patients
(BioMed Central, 2025-09-29) Fontana, Andrea; Barbano, Raffaela; Pasculli, Barbara; Mazza, Tommaso; Palumbo, Orazio; Binda, Elena; Trivieri, Nadia; Mencarelli, Gandino; Laurenzana, Ilaria; Lamorte, Daniela; De Luca, Luciana; Caivano, Antonella; Biagini, Tommaso; Rendina, Michelina; Lo Mele, Antonio; Prencipe, Giuseppene; Bravaccini, Sara; Murgo, Roberto; Ciuffreda, Luigi; Morritti, Maria; Valori, Vanna Maria; Di Lisa, Francesca Sofia; Vici, Patrizia; Castelvetere, Marina; Carella, Massimo; Graziano, Paolo; Maiello, Evaristo; Copetti, Massimiliano; Esteller, Manel, 1968-; Parrella, Paolo
Background: The attempt to exploit molecular subtyping for risk stratification in breast cancer patients has been only partially successful with a limited application in the clinical practice. In the BREMIR study, we aimed to identify a panel of miRNAs as prognostic biomarkers for breast cancer. We first confirmed the association of previously linked miRNAs with critical clinical parameters, then adopted a discovery-driven approach to identify novel biomarkers. Methods: miRNA expression was analyzed using the Affymetrix Gene Chip 4.0 array in a discovery cohort of 34 patients (3 with synchronous metastases, 14 who developed metastases after 10 years, and 17 who remained metastasis-free) and 6 controls. RT-qPCR validated selected miRNAs in an extended cohort (n = 223) with a median follow up of 6.6 years. A stepwise logistic regression model incorporating miRNA levels and clinicopathological features was developed to predict metastasis risk. Additionally, miRNA expression was assessed in plasma extracellular vesicles (EVs) using digital PCR in an independent cohort (n = 39). In silico enrichment analyses explored the functional role of relevant miRNAs in metastasis development. Results: Eight differentially expressed miRNAs were identified in the discovery cohort. In the extended cohort, miR-3916 and miR-3613-5p were the most effective in distinguishing patients who developed metastases. Higher miR-3916 expression was associated with reduced metastasis risk (OR = 0.42, 95%CI 0.23-0.70, p = 0.002), while higher miR-3613-5p expression was linked to increased risk (OR = 2.06, 95%CI 1.27-3.50, p = 0.005). Adding these miRNAs to a model with clinicopathological features improved discrimination (AUC = 0.85 vs. AUC = 0.76, p = 0.001). The model was effective across all breast cancer subtypes. In extracellular vesicles, miR-3613-5p was more abundant in tumors than benign lesions (p = 0.039), while miR-3916 was lower in metastatic samples than in non-metastatic tumors (p = 0.020). In-silico pathway enrichment analyses indicates their involvement in critical steps of the metastatic process including EMT plasticity, DNA damage response and metastatic niche formation. Conclusions: This is the first study integrating miRNA expression with clinicopathological features in a logistic model for breast cancer prognosis. While further validation is needed, our model shows promise as a prognostic tool across all breast cancer subtypes. In silico pathway enrichment analysis highlights miR-3613-5p and miR-3916 as critical regulators of metastasis development, underscoring the need for further investigation.
Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
(Oxford University Press, 2025-10-21) Lin, Yu-Yu; Breuer, Kersten; Weichenhan, Dieter; Lafrenz, Pascal; Sarnataro, Antonella; Wilk, Agata; Chepeleva, Maryna; Mücke, Oliver; Schönung, Maximilian; Petermann, Franziska; Kensche, Philip Reiner; Weiser, Lena; Thommen, Frank; Giacomelli, Gideon; Nordstroem, Karl; Gonzalez-Avalos, Edahi; Merkel, Angelika; Kretzmer, Helene; Fischer, Jonas; Krämer, Stephen; Iskar, Murat; Wolf, Stephan; Buchhalter, Ivo; Esteller, Manel, 1968-; Lawerenz, Christian; Twardziok, Sven; Zapatka, Marc; Hovestadt, Volker; Schlesner, Matthias; Schulz, Marcel H.; Hoffmann, Steve; Gerhauser, Clarissa; Walter, Jörn; Hartmann, Mark; Lipka, Daniel B.; Assenov, Yassen; Bock, Christoph; Plass, Christoph; Toth, Reka; Lutsik, Pavlo
DNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulfite treatment or enzymatic methods remains the reference method for DNA methylation profiling genome-wide. While numerous software tools facilitate processing of DNA methylation sequencing reads, a comprehensive benchmarking study has been lacking. In this study, we systematically compared complete computational workflows for processing DNA methylation sequencing data using a dedicated benchmarking dataset generated with five whole-genome profiling protocols. As an evaluation reference, we employed accurate locus-specific measurements from our previous benchmark of targeted DNA methylation assays. Based on this experimental gold-standard assessment and multiple performance metrics, we identified workflows that consistently demonstrated superior performance and revealed major workflow development trends. To ensure the long-term utility of our benchmark, we implemented an interactive workflow execution and data presentation platform, adaptable to user-defined criteria and readily expandable to future software.
Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer
(BioMed Central, 2023-05-12) Ortiz Barahona, Vanessa; Soler, Marta; Davalos, Veronica; García-Prieto, Carlos A.; Janin, Maxime; Setién, Fernando; Fernández-Rebollo, Irene; Bech-Serra, Joan J.; De La Torre, Carolina; Guil, Sonia; Villanueva Garatachea, Alberto; Zhang, Pei-Hong; Yang, Li; Guarnacci, Marco; Schumann, Ulrike; Preiss, Thomas; Balaseviciute, Ugne; Montal, Robert; Llovet i Bayer, Josep Maria; Esteller, Manel, 1968-
Background: RNA modifications are important regulators of transcript activity and an increasingly emerging body of data suggests that the epitranscriptome and its associated enzymes are altered in human tumors. Methods: Combining data mining and conventional experimental procedures, NSUN7 methylation and expression status was assessed in liver cancer cell lines and primary tumors. Loss-of-function and transfection-mediated recovery experiments coupled with RNA bisulfite sequencing and proteomics determined the activity of NSUN7 in downstream targets and drug sensitivity. Results: In this study, the initial screening for genetic and epigenetic defects of 5-methylcytosine RNA methyltransferases in transformed cell lines, identified that the NOL1/NOP2/Sun domain family member 7 (NSUN7) undergoes promoter CpG island hypermethylation-associated with transcriptional silencing in a cancer-specific manner. NSUN7 epigenetic inactivation was common in liver malignant cells and we coupled bisulfite conversion of cellular RNA with next-generation sequencing (bsRNA-seq) to find the RNA targets of this poorly characterized putative RNA methyltransferase. Using knock-out and restoration-of-function models, we observed that the mRNA of the coiled-coil domain containing 9B (CCDC9B) gene required NSUN7-mediated methylation for transcript stability. Most importantly, proteomic analyses determined that CCDC9B loss impaired protein levels of its partner, the MYC-regulator Influenza Virus NS1A Binding Protein (IVNS1ABP), creating sensitivity to bromodomain inhibitors in liver cancer cells exhibiting NSUN7 epigenetic silencing. The DNA methylation-associated loss of NSUN7 was also observed in primary liver tumors where it was associated with poor overall survival. Interestingly, NSUN7 unmethylated status was enriched in the immune active subclass of liver tumors. Conclusion: The 5-methylcytosine RNA methyltransferase NSUN7 undergoes epigenetic inactivation in liver cancer that prevents correct mRNA methylation. Furthermore, NSUN7 DNA methylation-associated silencing is associated with clinical outcome and distinct therapeutic vulnerability.
Interrelation of adipose tissue macrophages and fibrosis in obesity.
(Elsevier B.V., 2024-05-28) Dahdah, N.; Tercero Alcázar, Carmen; Malagón, María M.; García-Roves, Pablo M. (Pablo Miguel); Guzmán Ruiz, Rocío
Obesity is characterized by adipose tissue expansion, extracellular matrix remodelling and unresolved inflammation that contribute to insulin resistance and fibrosis. Adipose tissue macrophages represent the most abundant class of immune cells in adipose tissue inflammation and could be key mediators of adipocyte dysfunction and fibrosis in obesity. Although macrophage activation states are classically defined by the M1/M2 polarization nomenclature, novel studies have revealed a more complex range of macrophage phenotypes in response to external condition or the surrounding microenvironment. Here, we discuss the plasticity of adipose tissue macrophages (ATMs) in response to their microenvironment in obesity, with special focus on macrophage infiltration and polarization, and their contribution to adipose tissue fibrosis. A better understanding of the role of ATMs as regulators of adipose tissue remodelling may provide novel therapeutic strategies against obesity and associated metabolic diseases.
Neural cell diversity in the light of single-cell transcriptomics
(CRC Press, Taylor and Francis Group, 2024-01-17) Fernandez Moya, Sandra M.; Jaya Ganesh, Akshay; Plass, Mireya
The development of highly parallel and affordable high-throughput single-cell transcriptomics technologies has revolutionized our understanding of brain complexity. These methods have been used to build cellular maps of the brain, its different regions, and catalog the diversity of cells in each of them during development, aging and even in disease. Now we know that cellular diversity is way beyond what was previously thought. Single-cell transcriptomics analyses have revealed that cell types previously considered homogeneous based on imaging techniques differ depending on several factors including sex, age and location within the brain. The expression profiles of these cells have also been exploited to understand which are the regulatory programs behind cellular diversity and decipher the transcriptional pathways driving them. In this review, we summarize how single-cell transcriptomics have changed our view on the cellular diversity in the human brain, and how it could impact the way we study neurodegenerative diseases. Moreover, we describe the new computational approaches that can be used to study cellular differentiation and gain insight into the functions of individual cell populations under different conditions and their alterations in disease.
Energy substrate metabolism, mitochondrial structure and oxidative stress after cardiac ischemia-reperfusion in mice lacking UCP3.
(Elsevier B.V., 2023-08-20) Sánchez-Pérez, Patricia; Mata, Ana; Torp, May-Kristin; López Bernardo, Elia; Heiestad, Christina M.; Aronsen, Jan Magnus; Molina-Iracheta, Antonio; Jiménez-Borreguero, Luis J.; García-Roves, Pablo M. (Pablo Miguel); Costa, Ana S.H.; Frezza, Christian; Murphy, Michael P.; Stenslokken, Kåre-Olav; Cadenas, Susana
Myocardial ischemia-reperfusion (IR) injury may result in cardiomyocyte dysfunction. Mitochondria play a critical role in cardiomyocyte recovery after IR injury. The mitochondrial uncoupling protein 3 (UCP3) has been proposed to reduce mitochondrial reactive oxygen species (ROS) production and to facilitate fatty acid oxidation. As both mechanisms might be protective following IR injury, we investigated functional, mitochondrial structural, and metabolic cardiac remodeling in wild-type mice and in mice lacking UCP3 (UCP3-KO) after IR. Results showed that infarct size in isolated perfused hearts subjected to IR ex vivo was larger in adult and old UCP3-KO mice than in equivalent wild-type mice, and was accompanied by higher levels of creatine kinase in the effluent and by more pronounced mitochondrial structural changes. The greater myocardial damage in UCP3-KO hearts was confirmed in vivo after coronary artery occlusion followed by reperfusion. S1QEL, a suppressor of superoxide generation from site IQ in complex I, limited infarct size in UCP3-KO hearts, pointing to exacerbated superoxide production as a possible cause of the damage. Metabolomics analysis of isolated perfused hearts confirmed the reported accumulation of succinate, xanthine and hypoxanthine during ischemia, and a shift to anaerobic glucose utilization, which all recovered upon reoxygenation. The metabolic response to ischemia and IR was similar in UCP3-KO and wild-type hearts, being lipid and energy metabolism the most affected pathways. Fatty acid oxidation and complex I (but not complex II) activity were equally impaired after IR. Overall, our results indicate that UCP3 deficiency promotes enhanced superoxide generation and mitochondrial structural changes that increase the vulnerability of the myocardium to IR injury.

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