Biology subjects

Carvalho, D.

Publications and source records attributed to Carvalho, D..

5 recordsLinked to original sources

bioRxiv2026

Combination of ALK2 and cholesterol targeting agents exploits linked genetic and metabolic dependencies in diffuse midline glioma

Diffuse midline glioma is an epigenetically driven disease defined by alterations targeting the histone post-translational modification H3K27me3 resulting in epigenetic rewiring and imposing unique metabolic dependencies. ACVR1-mutations arise in ~25% of DMG H3K27-altered patients and impart a selective dependency on the kinase it encodes (ALK2), however ALK2 inhibitors show modest single-agent efficacy in vivo. In an attempt to better understand the cellular consequences of ALK2 inhibition to identify mechanistically-driven drug combinations, integrated multi-omics analysis was performed and revealed a novel role for ALK2 in cholesterol homeostasis while CRISPR and high-throughput drug screens identified hits targeting cholesterol metabolism as sensitisers to ALK2i. In vivo assessment of ALK2i plus clinically well-tolerated statins revealed a significant increase in the median survival compared to vehicle. Forced differentiation of DMG cells from an oligodendrocyte precursor-like to an astrocyte-like cell-state and led to a significant decrease in ALK2i sensitivity and synergy with statins, which was phenocopied when DMG cells were co-cultured with normal astrocytes. We identify a previously unappreciated role for ALK2 signalling in cholesterol homeostasis, showing cell-state dependency, and identify a rational combinatorial strategy for clinical translation.

cancer biology↗

bioRxiv2026

Microphysiological Flow Batteries For Dynamic EDC Screening Of mESC-derived Thyroid Organoids

Endocrine disrupting chemicals (EDCs) are ubiquitous environmental contaminants capable of dysregulating the production of thyroid hormones. Traditional thyroid toxicological assays rely on 2D cell cultures and animal models, both of which fail to accurately recapitulate human thyroid physiology and provide limited mechanistic insight into EDC toxicity. To overcome these limitations, we report a novel thyroid-on-chip platform integrating mouse embryonic stem cell-derived thyroid organoids with advanced organ-on-chip (OoC) technology and downstream multi-omics analysis. The platform leverages a reversibly-sealed microphysiological flow battery (MFB) to allow scale up of dynamic organoid culture and controlled chemical exposure while reducing operational complexity. Upon EDC exposure, transcriptomic and proteomic analysis revealed new molecular signatures of thyroid disruption across four different EDC classes, even at very low EDC concentrations (1nM), validating the capacity of this system to mechanistically dissect EDC-induced responses. This represents an integrated platform consists of an advanced physiologically relevant assay framework for next-generation endocrine toxicity testing, bridging the gap between in vitro screening and in vivo thyroid physiology.

bioengineering↗

bioRxiv2026

HP2NET: Empowering Efficient Phylogenetic Network Analysis through High-Performance Computing

Advances in High-Performance Computing (HPC) have enabled increasingly complex genomic analyses, including those in phylogenomics. These analyses contribute to understanding the evolution of viruses and pathogens, improving our knowledge of disease transmission, and supporting targeted public health strategies. However, due to the increasing number of tools and processing steps involved, executing these analyses manually, step by step, becomes error-prone and inefficient. To address this challenge, we present HP2NET, a robust framework for reproducible, efficient, and scalable phylogenetic network analysis. HP2NET integrates five workflows based on state-of-the-art tools such as PhyloNetworks and PhyloNet, allowing the analysis of multiple datasets and workflows in a single execution. The framework includes features such as task packaging and data reuse to improve performance and resource utilization in HPC environments. We perform a comprehensive performance evaluation of the software used within HP2NET, identifying bottlenecks and analyzing gains from parallel processing. Data reuse provided up to 15.35% time reduction, for a small dataset, in our experimental environment, while parallel execution of the five pipelines reduced total runtime by up to 90.96% compared to sequential runs. Finally, we validate HP2NET in a real-world case study by analyzing Dengue virus genomes, demonstrating its applicability value for large-scale phylogenetic analyses.

bioinformatics↗

bioRxiv2020

Drug screening linked to molecular profiling identifies novel dependencies in patient-derived primary cultures of paediatric high grade glioma and DIPG

Paediatric high grade glioma and diffuse midline glioma (including DIPG) are comprised of multiple biological and clinical subgroups, the majority of which urgently require novel therapies. Patient-derived in vitro primary cell cultures represent potentially useful tools for mechanistic and preclinical investigation based upon their retention of key features of tumour subgroups under experimental conditions amenable to high-throughput approaches. We present 17 novel primary cultures derived from patients in London, Dublin and Belfast, and together with cultures established or shared from Barcelona, Brisbane, Rome and Stanford, assembled a panel of 52 models under 2D (laminin matrix) and/or 3D (neurospheres) conditions, fully credentialed by phenotypic and molecular comparison to the original tumour sample (methylation BeadArray, panel/exome sequencing, RNAseq). In screening a subset of these against a panel of ~400 approved chemotherapeutics and small molecules, we identified specific dependencies associated with tumour subgroups and/or specific molecular markers. These included MYCN-amplified cells and ATM/DNA-PK inhibitors, and DIPGs with PPM1D activating truncating mutations and inhibitors of MDM2 or PARP1. Specific mutations in PDGFRA were found to confer sensitivity to a range of RTK inhibitors, though not all such mutations conferred sensitivity to targeted agents. Notably, dual PDGFRA/FGFR and downstream pathway MEK inhibitors showed profound effects against both PDGFRA-sensitising mutant and FGFR1-dependent non-brainstem pHGG and DIPG. In total, 85% cells were found to have at least one drug screening hit in short term assays linked to the underlying biology of the patients tumour, providing a rational approach for individualised clinical translation.

cancer biology↗

bioRxiv2017

Differentially regulated ortholog analysis demonstrations that early transcriptional responses to cold have diverged slowly than downstream responses in panicoid grasses

Cross-species comparisons of transcriptional regulation have the potential to identify functionally constrained transcriptional regulation and genes for which a change in transcriptional regulation correlates with a change in phenotype. Conventional differential gene expression analysis and a different approach based on identifying differentially regulated orthologs (DROs) are compared using paired time course gene expression data from two species which respond similarly to cold - maize (Zea mays) and sorghum (Sorghum bicolor). Both approaches suggest that, for genes conserved at syntenic positions for millions of years, the majority of cold responsive transcriptional regulation is species specific, although initial transcriptional responses to cold appear to be more conserved between the two species than later responses. In maize, the promoters of genes with both species specific and conserved transcriptional responses to cold tend to contain more micrococcal nuclease hypersensitive sites in their promoters, a proxy for open chromatin. However, genes with conserved patterns of transcriptional regulation between the two species show lower ratios of nonsynonymous to synonymous substitutions consistent with this population of genes experiencing stronger purifying selection. We hypothesize that cold responsive transcriptional regulation is a fast evolving and largely neutral molecular phenotype for the majority of genes in Andropogoneae, while a smaller core set of genes involved in perceiving and responding to cold stress are subject to functionally constrained cold responsive regulation.

genetics↗