Biology subjects

Branco, L.

Publications and source records attributed to Branco, L..

5 recordsLinked to original sources

bioRxiv2026

Organotchi: an open-source tool for the automated segmentation, morphological characterization, and longitudinal tracking of organoids

Neural organoids are three-dimensional stem cell-derived models widely used to study brain development and model disease. Brightfield imaging offers a non-invasive readout of their growth and morphology, and recent advances have made automated organoid segmentation from such images increasingly attainable. Yet existing tools largely leave morphological characterization, quality assessment, and comparisons between conditions to manual or ad hoc analysis. Here we present Organotchi, an open-source tool that integrates automated segmentation with longitudinal morphological analysis of neural organoids. Organotchi quantifies ten morphological features, including area, perimeter, and eccentricity, and tracks cystic structures over time, reports variability within and between batches, and flags outlier organoids and segmentation failures, supporting objective organoid characterization and enhancing downstream analysis. As a proof of concept, we apply Organotchi to disease modelling, pharmacological perturbation, and protocol optimization in neural organoids. One use case assesses drug response in breast cancer spheroids, demonstrating its use beyond its development domain.

bioinformatics↗

bioRxiv2026

Comprehensive in silico analysis reveals candidate regulatory mechanisms underlying selective cerebellar vulnerability in pontocerebellar hypoplasia

Pontocerebellar hypoplasia (PCH) is a group of ultrarare, neurodegenerative disorders characterized by cerebellar and pontine hypoplasia. Genetic analysis over the last two decades has revealed an increasing number of pathogenic variants in a wide range of broadly expressed genes functioning in RNA processing, tRNA metabolism, and translation. However, the mechanisms linking these ubiquitous processes to brain region-specific vulnerability are unknown. Here, we established a multi-level variant-to-function in silico framework to predict the molecular consequences of PCH-associated variants in TSEN complex genes. These variants were predicted to have heterogeneous effects on diverse protein properties, including stability, subcellular localization, and degradation, supporting variant-specific rather than uniform disease mechanisms. Complementary transcriptomic analyses showed that PCH-associated genes were not globally enriched in the prenatal cerebellum. Instead, their expression was coordinated in a stage- and cell type-specific manner during cerebellar development. We therefore hypothesize that multiple PCH-associated genes are regulated by a common set of transcription factors, providing an explanation of the selective vulnerability of the cerebellum and to the phenotypic convergence of genetically diverse PCH subtypes. In summary, this study prioritizes candidate variants for biochemical, cellular, and in vivo validation, and identifies regulatory programs, cell lineages, and developmental windows for targeted, mechanistically informed disease modelling.

systems biology↗

bioRxiv2025

Mistranslation protects against lifespan reduction due to mating in Drosophila melanogaster females.

Accurate translation of genes into proteins is critical to organism fitness, and errors in this process are usually detrimental and cause proteotoxic stress. Mistranslation occurs when the amino acid that is incorporated into the nascent polypeptide chain does not match what is dictated by the genetic code. Valine-to-serine (V[->]S) and threonine-to-serine (T[->]S) mistranslating models of the fruit fly Drosophila melanogaster have demonstrated a surprising, sex-specific increase in virgin female longevity. We predict that the added stressor of reproduction would eliminate this mistranslation-induced lifespan increase since females prioritize reproductive tissues over somatic tissues, and proteotoxic stress would therefore lead to higher protein damage in the soma of mated females. We measured the impact of reproduction on V[->]S and T[->]S mistranslating D. melanogaster by measuring longevity, egg laying, and fecundity. Counter to our prediction, both V[->]S and T[->]S mistranslation led to a sex-specific increase in mated female longevity compared to non-mistranslating controls. Additionally, the risk of death decreased for mated females with mistranslation, beyond the pure additive benefits of mistranslation alone. These effects could not be explained by reduced egg laying or fertilization rates in mistranslating females. Thus, we find that the added proteotoxic stress caused by mistranslation does not exacerbate the detrimental effects of reproduction and instead can ameliorate lifespan decreases due to female reproduction.

genetics↗

bioRxiv2025

Multiomics analysis identifies VPA-induced changes in neural progenitor cells, ventricular-like regions, and cellular microenvironment in dorsal forebrain organoids

Pharmaceutical agents, such as antiepileptic medications, can cross fetal barriers and affect the developing brain. Prenatal exposure to the antiepileptic drug valproate (VPA) is associated with an increased risk of neurodevelopmental disorders, including congenital malformations and autism spectrum disorder. In animal models and neural organoids, VPA has been shown to alter signaling pathways, such as Wnt pathway, providing insights into VPA-induced neurodevelopmental defects. Here, we exposed dorsal forebrain organoids to VPA for 30 days and examined effects at the tissue, cellular, and molecular level. VPA treatment disrupted ventricular-like regions, indicating defects in cell-cell and cell-matrix interactions. Transcriptomics analysis confirmed altered expression of extracellular matrix (ECM) genes and single cell RNA sequencing analysis identified genes involved in microenvironment sensing, such as cellular mechanosensing and Hippo-YAP/TAZ signaling pathway. Finally, proteomics analysis corroborated that VPA alters the microenvironment of the human dorsal forebrain organoids by disrupting the secretion of ECM proteins. Altogether, our study suggests that VPA-treated dorsal forebrain organoids serve as a model to investigate the role of extracellular processes in brain development and to understand how their disruptions might contribute to neurodevelopmental disorders.

neuroscience↗

bioRxiv2020

Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

Viral hemorrhagic fevers (VHFs) remain some of the most devastating human diseases, and recent outbreaks of Ebola virus disease (EVD) 1,2 and Lassa fever (LF) 3,4 highlight the urgent need for sensitive, field-deployable tests to diagnose them 5,6. Here we develop CRISPR-Cas13a-based (SHERLOCK) diagnostics targeting Ebola virus (EBOV) and Lassa virus (LASV), with both fluorescent and lateral flow readouts. We demonstrate on laboratory and clinical samples the sensitivity of these assays and the capacity of the SHERLOCK platform to handle virus-specific diagnostic challenges. Our EBOV diagnostic detects both the L and NP genes, thereby eliminating the potential for false positive results caused by the rVSV{Delta}G-ZEBOV-GP live attenuated vaccine. Our two LASV diagnostics together capture 90% of known viral diversity and demonstrate that CRISPR-RNAs (crRNAs) can be effectively multiplexed to provide greater coverage of known viral diversity. We performed safety testing to demonstrate the efficacy of our HUDSON protocol in heat-inactivating and chemically treating VHF viruses before SHERLOCK testing, eliminating the need for an extraction. We developed a user-friendly field protocol and mobile application (HandLens) to report results, facilitating SHERLOCKs use in endemic regions. Finally, we successfully deployed our tests in Sierra Leone and Nigeria in response to recent outbreaks.

molecular biology↗