Biology subjects

Moreno, L.

Publications and source records attributed to Moreno, L..

10 recordsLinked to original sources

bioRxiv2026

A Cross-Study Multi-Organ Cell Atlas ofMacaca fascicularis Informed by Human Foundation Model Annotation: A Resource for Translational Target Assessment

Non-human primates (NHPs), particularly Macaca fascicularis (cynomolgus macaque), represent an essential model for preclinical assessment of biologics due to their high genetic and physiological similarity to humans. However, mounting regulatory pressure to reduce NHP use and the lack of a unified, well-annotated single-cell atlas currently limits both target qualification and mechanistic interpretation of toxicity in this species. To address this gap, we assembled and harmonized the largest single-cell transcriptomic atlas of M. fascicularis to date, integrating 30 publicly available studies spanning 57 anatomical regions, 43 organs and 14 physiological systems. We implemented a scalable framework for cross-species cell type annotation by embedding both cynomolgus monkeys and human (Tabula Sapiens V2) datasets into a shared reference space using Universal Cell Embeddings (UCE), enabling consistent harmonization of cell identities. In total, 27 organs were annotated using human reference labels, while the remaining sets retained author-provided annotations or labels transferred from other cynomolgus studies with available annotations. The resulting atlas comprises over 2.5 million cells and demonstrates concordance in cell-type-specific expression patterns between cynomolgus and humans, including tissue-specific markers and targets relevant for biologics development. Through translational use cases, we illustrate how this resource can be applied to assess target expression in tissues affected by concordant human-NHP toxicities, investigate ocular adverse events associated with antibody-drug conjugates (ADCs), and identify species-specific features of immune cell subtypes with known safety implications. By enabling scalable, high-resolution, cross-species comparisons of gene expression across organs, tissues, and cell states, this atlas supports improved target qualification, more mechanistic interpretation of toxicities, and evidence-based decisions on the relevance and design of NHP studies. Collectively, this work provides a unified cross-species single-cell resource for cynomolgus monkey and a modular computational framework that advances new approach methodologies and contributes to the refinement and reduction of NHP use in preclinical research.

bioinformatics↗

bioRxiv2024

Combined inhibition of MDM2 and PARP lead to a synergistic anti-tumoral response in p53 wild-type rhabdomyosarcoma models

Targeting MDM2-p53 interaction to enhance p53 activity represents a promising antitumoral strategy for p53 wild-type pediatric tumors, including soft-tissue sarcomas. However, results from early-phase clinical trials in hematological and solid cancers have shown limited efficacy of MDM2 inhibitors, underscoring the necessity to explore more effective combinations with other agents. In this study, we provide results from a 22-drug combination screening demonstrating the therapeutic potential of combining siremadlin (MDM2 inhibitor) and olaparib (PARP inhibitor) for treating p53 wild-type rhabdomyosarcoma (p53 WT RMS). Cell survival, cell death, and apoptosis analysis revealed synergistic effects of combining siremadlin plus olaparib in vitro. The combination of both drugs led to a significant increase in p53 activity, as evidenced by p53 accumulation and K382 acetylation, along with an increased expression of bona fide p53 targets. Furthermore, treatment with both drugs resulted in significant reduction of tumor growth and increased mice overall survival when compared to single treatments and control in cell line-derived orthotopic xenograft models. Overall, our study demonstrates, for the first time, the synergistic effect of combining siremadlin plus olaparib in inhibiting p53 WT RMS tumor growth in vitro and in vivo. Our findings support the potential to study the combination of both drugs in clinical trials and warrants further investigation in other tumors with similar molecular features.

cancer biology↗

bioRxiv2024

BPTF cooperates with MYCN and MYC to link neuroblastoma cell cycle control to epigenetic cellular states

The nucleosome remodeling factor BPTF is required for the deployment of the MYC-driven transcriptional program. Deletion of one Bptf allele delays tumor progression in mouse models of pancreatic cancer and lymphoma. In neuroblastoma, MYCN cooperates with the transcriptional core regulatory circuitry (CRC). High BPTF levels are associated with high-risk features and decreased survival. BPTF depletion results in a dramatic decrease of cell proliferation. Bulk RNA-seq, single-cell sequencing, and tissue microarrays reveal a positive correlation of BPTF and CRC transcription factor expression. Immunoprecipitation/mass spectrometry shows that BPTF interacts with MYCN and the CRC proteins. Genome-wide distribution analysis of BPTF and CRC in neuroblastoma reveals a dual role for BPTF: 1) it co-localizes with MYCN/MYC at the promoter of genes involved in cell cycle and 2) it co-localizes with the CRC at super-enhancers to regulate cell identity. The critical role of BPTF across neuroblastoma subtypes supports its relevance as a therapeutic target.

genomics↗

bioRxiv2023

TRIB3 silencing promotes the downregulation of Akt pathway and PAX3-FOXO1 in high-risk rhabdomyosarcoma

BackgroundRhabdomyosarcoma (RMS), such as other childhood tumors, has witnessed treatment advancements in recent years. However, high-risk patients continue to face poor survival rates, often attributed to the presence of the PAX3/7-FOXO1 fusion proteins, which has been associated with metastasis and treatment resistance. Despite efforts to directly target these chimeric proteins, clinical success remains elusive. In this study, the main aim was to address this challenge by investigating regulators of FOXO1. Specifically, we focused on TRIB3, a potential regulator of the fusion protein in RMS. MethodsTRIB3 expression was examined through the analysis of patient datasets, including gene expression profiling and gene set enrichment analyses. In cell lines, the DepMap dataset for RMS was utilized alongside Western blot analysis to assess TRIB3 expression. The functional significance of TRIB3 in RMS was assessed through constitutive and inducible shRNA-mediated knockdowns. Subsequent in vitro and in vivo analyses, including orthotopic tumor models in immune-compromised mice, were conducted to delineate the role and underlying molecular mechanisms exerted by TRIB3 in RMS ResultsOur findings revealed a prominent TRIB3 expression in RMS tumors, highlighting its correlation with several clinical features. By conducting TRIB3 genetic inhibition experiments, we observed an impairment on cell proliferation. Notably, the knockdown of TRIB3 led to a decrease in PAX3-FOXO1 and its target genes at protein level, accompanied by a reduction in the activity of the Akt signaling pathway. Furthermore, TRIB3 influenced posttranslational modifications, such as phosphorylation together with proteasomal degradation of PAX3-FOXO1 protein. Additionally, inducible silencing of TRIB3 significantly delayed tumor growth and improved overall survival in vivo. ConclusionsBased on our comprehensive analysis, we propose that TRIB3 holds therapeutic potential for treating the most aggressive subtype of RMS. The findings herein reported contribute to our understanding of the underlying molecular mechanisms driving RMS progression and provide novel insights into the potential use of TRIB3 as a therapeutic intervention for high-risk RMS patients.

cancer biology↗

bioRxiv2023

Vitamin D deficiency induces erectile dysfunction: role of superoxide

Epidemiological studies suggest a relationship between vitamin D deficiency and erectile dysfunction (ED) but its causal relationship and the mechanism involved are unclear. Here we demonstrate that isolated corpora cavernosa (CC) from human donors with low vitamin D levels show reduced NO-dependent erectile function. This ED is also reproduced in vitamin D deficient rats and vitamin D receptor knockout mice in vivo and ex vivo and is associated with penile fibrosis. Vitamin D deficiency also blunts the response of CC to the phosphodiesterase 5 inhibitor sildenafil. CC from deficient rats show increased superoxide and their impaired erectile function is restored by superoxide scavengers. These results suggest that vitamin D deficiency induces ED via increased superoxide production.

pharmacology and toxicology↗

bioRxiv2022

Analysis of cancer genomic amplifications identifies druggable collateral dependencies within the amplicon

The identification of novel therapeutic targets for specific cancer molecular subtypes is crucial for the development of precision oncology. In the last years, CRISPR/Cas9 screens have accelerated the discovery and validation of new targets associated with different tumor types, mutations or fusions. However, there are still many cancer vulnerabilities associated with specific molecular features that remain to be explored. Here we used data from CRISPR/Cas9 screens in 954 cancer cell lines to identify gene dependencies associated with 16 common cancer genomic amplifications. We found that high-copy number genomic amplifications generate multiple collateral dependencies within the amplified region in 94% of cases. Further, to prioritize candidate targets for each chromosomal region amplified, we integrated gene dependency parameters with both druggability data and subcellular location. Finally, analysis of the relationship between gene expression and gene dependency leads to the identification of genes, the expression of which may constitute predictive biomarkers of dependency.

cancer biology↗

bioRxiv2022

Structural disruption of BAF chromatin remodeller impairs neuroblastoma metastasis by reverting an invasiveness epigenomic program

BackgroundEpigenetic programming during development is essential for determining cell lineages, and alterations in this programming contribute to the initiation of embryonal tumour development. In neuroblastoma, neural crest progenitors block their course of natural differentiation into sympathoadrenergic cells, leading to the development of aggressive and metastatic paediatric cancer. Research of the epigenetic regulators responsible for oncogenic epigenomic networks is crucial for developing new epigenetic-based therapies against these tumours. Mammalian switch/sucrose non-fermenting (mSWI/SNF) ATP-dependent chromatin remodelling complexes act genome-wide translating epigenetic signals into open chromatin states. The present study aimed to understand the contribution of mSWI/SNF to the oncogenic epigenomes of neuroblastoma and its potential as a therapeutic target. MethodsFunctional characterisation of the mSWI/SNF complexes was performed in neuroblastoma cells using proteomic approaches, loss-of-function experiments, transcriptome and chromatin accessibility analyses, and in vitro and in vivo assays. ResultsNeuroblastoma cells contain three main mSWI/SNF subtypes, but only BRG1-associated factor (BAF) complex disruption through silencing of its key structural subunits, ARID1A and ARID1B, impairs cell proliferation by promoting cell cycle blockade. Genome-wide chromatin remodelling and transcriptomic analyses revealed that BAF disruption results in the epigenetic repression of an extensive invasiveness-related expression program involving integrins, cadherins, and key mesenchymal regulators, thereby reducing adhesion to the extracellular matrix and the subsequent invasion in vitro and drastically inhibiting the initiation and growth of neuroblastoma metastasis in vivo. ConclusionsWe report a novel ATPase-independent role for the BAF complex in maintaining an epigenomic program that allows neuroblastoma invasiveness and metastasis, urging for the development of new BAF pharmacological structural disruptors for therapeutic exploitation in metastatic neuroblastoma.

cancer biology↗

bioRxiv2020

A healthy childhood environment helps to combat inherited susceptibility to obesity

ObjectivesTo investigate the degree by which the inherited susceptibility to obesity is modified by environmental factors during childhood and adolescence. DesignCohort study with repeated measurements of diet, lifestyle factors and anthropometry. SettingThe pan-European IDEFICS/I.Family cohort Participants8,609 repeated observations from 3,098 children aged 2 to 16 years, examined between 2007 and 2014. Main outcome measuresBody mass index (BMI) and waist circumference. Genome-wide polygenic risk scores (PRS) to capture the inherited susceptibility of obesity were calculated using summary statistics from independent genome-wide association studies of BMI. Gene-environment interactions of the PRS with sociodemographic (European region, socioeconomic status) and lifestyle factors (diet, screen time, physical activity) were estimated. ResultsThe PRS was strongly associated with BMI (r2 = 0.11, p-value = 7.9 x 10-81) and waist circumference (r2 = 0.09, p-value = 1.8 x 10-71) in our cohort. The associations with BMI increased from r2=0.03 in 3-year olds to r2=0.18 in 14-year olds and associations with waist circumference from r2=0.03 to r2=0.14. Being in the top decile of the PRS distribution was associated with 3.63 times higher odds for obesity (95% confidence interval (CI): [2.57, 5.14]). We observed significant interactions with demographic and lifestyle factors for BMI as well as waist circumference. The risk of becoming obese among those with higher genetic susceptibility was ~38% higher in children from Southern Europe (BMI: p-interaction = 0.0066, Central vs. Southern Europe) and ~61% higher in children with a low parental education (BMI: p-interaction = 0.0012, low vs. high). Furthermore, the risk was attenuated by a higher intake of dietary fiber (BMI: p-interaction=0.0082) and shorter screen times (BMI: p-interaction=0.018). ConclusionsOur results highlight that a healthy childhood environment might partly offset a genetic predisposition to obesity during childhood and adolescence.

genetics↗

bioRxiv2018

Mitochondrial Na+ import controls oxidative phosphorylation and hypoxic redox signalling

All metazoans depend on O2 delivery and consumption by the mitochondrial oxidative phosphorylation (OXPHOS) system to produce energy. A decrease in O2 availability (hypoxia) leads to profound metabolic rewiring. In addition, OXPHOS uses O2 to produce reactive oxygen species (ROS) that can drive cell adaptations through redox signalling, but also trigger cell damage1-4, and both phenomena occur in hypoxia4-8. However, the precise mechanism by which acute hypoxia triggers mitochondrial ROS production is still unknown. Ca2+ is one of the best known examples of an ion acting as a second messenger9, yet the role ascribed to Na+ is to serve as a mere mediator of membrane potential and collaborating in ion transport10. Here we show that Na+ acts as a second messenger regulating OXPHOS function and ROS production by modulating fluidity of the inner mitochondrial membrane (IMM). We found that a conformational shift in mitochondrial complex I during acute hypoxia11 drives the acidification of the matrix and solubilization of calcium phosphate precipitates. The concomitant increase in matrix free-Ca2+ activates the mitochondrial Na+/Ca2+ exchanger (NCLX), which imports Na+ into the matrix. Na+ interacts with phospholipids reducing IMM fluidity and mobility of free ubiquinone between complex II and complex III, but not inside supercomplexes. As a consequence, superoxide is produced at complex III, generating a redox signal. Inhibition of mitochondrial Na+ import through NCLX is sufficient to block this pathway, preventing adaptation to hypoxia. These results reveal that Na+ import into the mitochondrial matrix controls OXPHOS function and redox signalling through an unexpected interaction with phospholipids, with profound consequences in cellular metabolism.

biochemistry↗

bioRxiv2017

Development of a targeted sequencing approach to identify prognostic, predictive and diagnostic markers in paediatric solid tumours

The implementation of personalised medicine in childhood cancers has been limited by a lack of clinically validated multi-target sequencing approaches specific for paediatric solid tumours. In order to support innovative clinical trials in high-risk patients with unmet need, we have developed a clinically relevant targeted sequencing panel spanning 311 kb and comprising 78 genes involved in childhood cancers. A total of 132 samples were used for the validation of the panel, including Horizon Discovery cell blends (n=4), cell lines (n=15), formalin-fixed paraffin embedded (FFPE, n=83) and fresh frozen tissue (FF, n=30) patient samples. Cell blends containing known single nucleotide variants (SNVs, n=528) and small insertion-deletions (indels n=108) were used to define panel sensitivities of [≥]98% for SNVs and [≥]83% for indels [95% CI] and panel specificity of [≥]98% [95% CI] for SNVs. FFPE samples performed comparably to FF samples (n=15 paired). Of 95 well-characterised genetic abnormalities in 33 clinical specimens and 13 cell lines (including SNVs, indels, amplifications, rearrangements and chromosome losses), 94 (98.9%) were detected by our approach. We have validated a robust and practical methodology to guide clinical management of children with solid tumours based on their molecular profiles. Our work demonstrates the value of targeted gene sequencing in the development of precision medicine strategies in paediatric oncology.

genomics↗