Institute for Research in Biomedicine

We aim to inform the design of new diffusion MRI (dMRI) approaches for microvasculature quantification that enhance the biological specificity of imaging towards cancer. We adopted simulation-informed modelling of the vascular dMRI signal. We synthesised signals from 1500 synthetic vascular networks, for a variety of protocols (flow-compensated [FC], non-compensated [NC], hybrid), featuring different samplings and diffusion times. We estimated the number of independent, recoverable signal degrees of freedom in presence of noise (signal-to-noise ratio of 5), and ranked 12 microvascular metrics depending on the quality of their estimation. Lastly, we demonstrated the feasibility of estimating the top-ranking metrics on 3T dMRI of a healthy volunteer and of a metastatic colorectal cancer (CRC) patient. Both NC and FC synthetic vascular signals exhibited complex behaviour as, for example, non-zero kurtosis and diffusion time dependence. Two independent degrees of freedom appeared recoverable from directionally-averaged vascular signals (SNR of 5). Mean volumetric flow rate and an Apparent Network Branching (ANB) index maximised correlations between ground truth and estimated values in silico. In the patient, both and detected re-vascularisation after 3 months of targeted therapy against liver metastases, consistently with Intra-Voxel Incoherent Motion (IVIM) metrics. Simulation-based modelling of the vascular dMRI signal suggests and as the most promising metrics for tissue microvasculature characterisation. Their estimation in vivo appears feasible to capture general trends, and demonstrates contrasts that are biologically plausible, encouraging their usage in future studies.

Mutant phenotypes often vary across genetically distinct individuals. To identify the causes of such genetic background effects, we studied differences in gene essentiality across 18 genetically diverse natural yeast strains. We identified 39 genes that were essential in the laboratory reference strain but not in at least one other genetic background, and we mapped and validated the genetic variants that were responsible for the differences in gene essentiality. These variants typically occurred in single modifier genes that tended to differ between genetic backgrounds. The affected genes often indirectly compensated for the loss of the essential gene and identified naturally occurring evolutionary trajectories. Overall, our results highlight the prevalence of changes in gene essentiality in natural populations, as well as the underlying mechanisms. A thorough understanding of the causes of genetic background effects is crucial for the interpretation of genotype-to-phenotype relationships, including those associated with human disease.

Psychedelics have garnered significant interest for their therapeutic potential in mental health conditions such as depression, anxiety, and post-traumatic stress disorder. While research has primarily focused on well-studied psychedelics, phenethylamine derivatives have also gathered interest for their potential therapeutic applications. Thus, this study aims to investigate the pharmacological profile, safety and therapeutic potential of novel N-(2-fluorobenzyl) phenethylamine analogs (NBFs) of the 2C-X series-25C-NBF, 25B-NBF, and 25I-NBF. NBFs displayed high affinity and selectivity for the 5-HT2A receptor and demonstrated bias factors (defined in our study as the preference for Gq over β-arrestin pathways at 5-HT2A receptor) similar to that of 5-HT. Acute administration induced moderate head-twitch responses without affecting locomotion or pre-pulse inhibition. Our studies revealed no rewarding effects in mice nor reinforcing effects or changes in accumbal dopamine levels in rats after NBFs administration. Further characterization of 25C-NBF revealed psychoplastogenic effects (dendritogenesis, spinogenesis and increased Bdnf mRNA levels) both in vitro and in vivo. In addition, 25C-NBF reduced despair-like behavior in response to acute stress and exerted rapid antidepressant effects in a model of anhedonia-like behavior induced by chronic corticosterone administration. Taken together, these findings suggest that 25C-NBF, and further analogs, may hold potential as novel antidepressants with a rapid onset of action and a favorable safety profile in terms of no abuse potential or sensorimotor gating deficits.

Mosaic variegated aneuploidy (MVA), a rare human congenital disorder that causes microcephaly, is characterized by extensive abnormalities in chromosome number and results from mutations in genes involved in accurate mitotic chromosome segregation. To characterize the cellular mechanisms underlying this disease, here we generated a Drosophila model of microcephaly caused by the depletion of a single spindle assembly checkpoint (SAC) gene in the neural stem cell (NSC) compartment. We present evidence that loss of stemness - compromised identity and proliferative capacity of NSCs- plays an important role in MVA and results in a reduced number of neurons and glial cells. We show that loss of stemness arises from the accumulation over time of an unbalanced number of gains and losses of more than one chromosome, rather than a direct consequence of chromosomal instability-induced DNA damage or the production of simple aneuploidies. We unravel a contribution of proteostasis failure and mitochondrial dysfunction to the negative impact of complex aneuploidies on stemness, a highly energy demanding cellular state. We identify overexpression of Radical Oxygen Species scavengers, mitochondria chaperones and apoptosis inhibition as genetic interventions capable of dampening the deleterious effects of aneuploidy on brain size.

Nephrolithiasis is a major global health challenge, with oxidative stress and mitochondrial dysfunction emerging as key drivers of renal injury and stone formation. l-ergothioneine (l-Erg), a naturally occurring antioxidant transported by OCTN1, has shown promising effects in cystinuria models, preventing stone formation. Despite evidence supporting an indirect mechanism of action, key mechanistic aspects have yet to be fully clarified. This study aimed to evaluate whether l-Erg can prevent stone progression in cystinuria and in other types of lithiasis, such as calcium oxalate nephrolithiasis, and to further elucidate its mechanistic basis. Using mouse models, l-Erg significantly reduced cystine stone growth and renal inflammation, and its combination with d-penicillamine enhanced stone dissolution and mitigated drug-related toxicity. In calcium oxalate nephrolithiasis, l-Erg decreased crystal deposition, preserved renal architecture, normalized glutathione levels, and restored mitochondrial respiration. Transcriptomic analysis revealed downregulation of immune pathways and activation of cell cycle genes, suggesting attenuation of inflammation and promotion of tubular repair. This study is the first to demonstrate that l-Erg exerts renoprotective effects through combined antioxidant and mitochondrial mechanisms in two major forms of nephrolithiasis and introduces a dual therapeutic approach combining an antioxidant with a cystine-solubilizing agent. By targeting oxidative stress and mitochondrial dysfunction, l-Erg represents a promising therapeutic strategy for nephrolithiasis, either alone or as an adjunct to current treatments. Antioxid. Redox Signal. 44, 878-891.

Across our lifespan, cells divide and differentiate to create the functional units of all organs, yet with age and cancer a small number of cellular families (clones) will rule the fate of the organism. Advances in synthetic and natural barcoding methods now enable cellular ancestries to be reconstructed with unprecedented single-cell resolution. These single-cell lineage-tracing studies are leading to a re-evaluation of long-standing paradigms in development, ageing and cancer biology and are revealing the underpinnings of phenotypic heterogeneity for various cellular functions, including regeneration and stress responses. Despite remaining methodological challenges, progress continues towards multimodal tracing methods that combine spatial, genetic, epigenetic and transcriptomic information. The future transition of clonal analysis into the clinic may eventually help detect, predict and prevent disease progression.

Abstract Background: Resistance to endocrine therapy (ET) and CDK4/6 inhibitors (CDK4/6i) is a major challenge in HR+/HER2- breast cancer (BC). The HER2-enriched (HER2-E) intrinsic subtype represents an aggressive molecular form of HR+/HER2- disease and is associated with significantly worse progression-free survival (PFS) and overall survival (OS) under ET+CDK4/6i treatment compared to luminal subtypes (Prat et al. JCO 2021; CCR 2024). HER2-E is present in up to 10-20% of tumors prior to ET+CDK4/6i and accounts for 50-60% of tumors at progression, reflecting both pre-existing and acquired HER2-E through molecular subtype switching. These findings underscore the need to better understand its underlying biology and the mechanisms driving resistance in order to develop new therapies. Methods: A genome-wide CRISPR/Cas9 loss-of-function screen was conducted in 2 HER2-E and palbociclib-resistant BC cell lines. Findings were integrated with gene expression data of tumor samples of patients (pts) treated with CDK4/6i in both early (CORALLEEN trial [n=49 pts]) and metastatic (CDK cohort [n=375 pts]) settings. FGFR4 immunohistochemistry was performed in BC and healthy tissues. FGFR4 was functionally validated via knockdown and overexpression in vitro and in cell line-derived (CDX) and pt-derived xenograft (PDX) models. An antibody-drug conjugate (ADC) targeting FGFR4, composed of a humanized IgG1 antibody linked to the cytotoxic payload monomethyl auristatin E (MMAE) at a drug-to-antibody ratio of 4, was developed and tested preclinically. We employed descriptive statistics and Cox and logistic regression models. Results: Among 11 candidate resistance genes, including known mediators such as CCNE1, FGFR4 emerged as a novel and key driver of resistance. FGFR4 expression was significantly higher in HER2-E tumors, increased in progressive disease (PD) samples following CDK4/6i+ET, and was significantly associated with worse PFS (HR=1.49, 95% CI: 1.19-1.78, p<0.001) and OS (HR=2.01, 95% CI: 1.49-2.72, p<0.001). FGFR4 protein levels correlated strongly with mRNA expression (r=0.66, p<0.001), were elevated in PD samples, and were absent in healthy tissues. Functionally, FGFR4 knockdown restored palbociclib sensitivity, reduced tumor growth, and suppressed CCNE1 expression and RB phosphorylation. Conversely, FGFR4 overexpression induced resistance and HER2-E features. A selective tyrosine kinase inhibitor targeting FGFR4 and a naked monoclonal antibody showed limited in vitro activity. In contrast, a FGFR4-directed ADC exhibited high specificity, rapid internalization, and potent cytotoxicity in FGFR4-high cells, sparing FGFR4-low/negative cells. The ADC also demonstrated a bystander effect in co-culture experiments and significantly inhibited tumor growth in FGFR4-high CDXs and PDXs without detectable toxicities. Conclusions: FGFR4 is as a clinically actionable driver of resistance to CDK4/6i+ET in HR+/HER2- breast cancer. A FGFR4-directed ADC shows strong preclinical efficacy and represents a novel strategy to overcome resistance. These findings pave the way for clinical translation, with a first-in-human phase I trial launching in Q4 2025 in Spain. Citation Format: F. Braso-Maristany, N. Lorman-Carbó, S. Gregorio, T. Blasco, B. Morancho, A. Martínez-Romero, E. Sanfeliu, N. Chic, I. Fonseca, P. Galván, M. Guiu, V. Sirenko, A. Aguirre, A. Morales, S. Guardiola, R. Gómez-Bravo, B. Adamo, M. Bergamino, I. Garcia-Fructuoso, F. Schettini, H. Sun, D. M. González-Gironès, M. de Frias, M. Muñoz, M. Vidal, O. Martínez-Sáez, T. Pascual, V. Vanhooren, A. Prat, R. Gomis. Targeting FGFR4 with an antibody-drug conjugate in hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer progressing to CDK4/6 inhibitors and endocrine therapy [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PD3-05.

Following their success in natural language processing and protein biology, pretrained largelanguage models have started appearing in genomics in large numbers. These genomic language models (gLMs), trained on diverse DNA and RNA sequences, promise improved performance on a variety of downstream prediction and understanding tasks. In this review, we trace the rapid evolution of gLMs, analyze current trends, and offer an overview of their application in genomic research. We investigate each gLM component in detail, from trainingdatacuration to the architecture, and highlight the present trends of increasing model complexity. We review major benchmarking efforts, suggesting that no single model dominates, and that task-specific design and pretraining dataoften outweigh general model scale or architecture. In addition, we discuss requirements for making gLMs practically useful for genomic research. While several applications, ranging from genome annotation to DNAsequence generation, showcase the potential of gLMs, their use highlights gaps and pitfalls that remain unresolved. This guide aims to equip researchers with a grounded understanding of gLM capabilities, limitations, and best practices for their effective use in genomics.

Metformin, the most prescribed drug for the treatment of type 2 diabetes mellitus, increases the circulating levels of the metabolic regulator growth differentiation factor 15 (GDF15) via transcriptional regulation, with the kidneys being responsible for this increase. Since peroxisome proliferator-activated receptor (PPAR)β/δ agonists mimic many of the effects of metformin, including the rise in circulating GDF15 levels, we herein investigated whether the metformin-mediated antidiabetic effects and GDF15 upregulation were dependent on this nuclear receptor. Male Ppard-/- and wild-type (WT) mice received a western-type high-fat diet (HFD) for 12 weeks and were treated with metformin (200 mg ·kg-1 ·d-1, i.g.) in the last 3 weeks. At the end of the treatment, the mice were sacrificed, and the skeletal muscle, kidney, and liver samples were collected for analyses. We showed that metformin treatment ameliorated glucose intolerance and increased hepatic and circulating GDF15 levels in WT mice, but not in Ppard-/- mice fed aHFD. In the kidneys, metformin treatment increased the expression levels of phosphorylated AMPK and GDF15 in the WT mice, which was abolished in the Ppard-/- mice. Both β-arrestin 1 and proprotein convertase subtilisin/kexin type 6 (PCSK6) are involved in the posttranslational maturation of GDF15. Likewise, metformin treatment increased the levels of β-arrestin 1 and PCSK6 in the kidneys of WT mice, but not Ppard-/- mice. Furthermore, treatment of mice with a PPARβ/δ activator, GW501516 (3 mg· kg-1 ·d-1, i.g., for 7 days), increased the levels of these proteins in the kidneys and liver. In contrast, a PPARβ/δ antagonist GSK0660 (50 µM) prevented the increase in GDF15, β-arrestin 1, and PCSK6 levels caused by metformin in cultured podocytes. Collectively, these data uncover a regulatory axis wherein metformin, via PPARβ/δ, orchestrates glucose tolerance, AMPK activity, and GDF15 maturation.