Biology subjects

Wood, D.

Publications and source records attributed to Wood, D..

16 recordsLinked to original sources

bioRxiv2026

Human organoid screen links transient translational modulation to progenitor progression in corticogenesis

Human pluripotent stem cell-derived models are increasingly used to recapitulate aspects of human corticogenesis, including the emergence of diverse cortical cell types and their progression through developmental states. These systems offer an opportunity to dissect the molecular mechanisms regulating transitions between cell states, but methods for perturbing them systematically at scale remain limited. Here, we developed a semi-automated culture and high-throughput arrayed screening platform for human cortical organoids. Using a library of 1,280 small molecules designed to systematically target major signaling and regulatory pathways, we screened for modulators of EOMES, which encodes for the transcription factor TBR2, and identified Emetine, an inhibitor of translation elongation, as the top hit. The effect of Emetine on cortical cell-state progression was reproduced across human pluripotent stem cell lines, non-human primate cortical organoids, and primary human cortical tissue but not broadly across translation inhibitors. Moreover, transient exposure resulted in a shift from dividing radial glia towards cortical glutamatergic neurons. Mechanistically, nascent-proteome profiling revealed an early and coordinated remodeling of newly translated proteins that preceded detectable transcriptional changes, placing translational regulation upstream of the ensuing cell-state transition. Together, these findings highlight a role for specific translational inhibitors in promoting cortical cell-state progression and establish a scalable platform for systematic perturbation and discovery in human neural organoids.

neuroscience↗

bioRxiv2026

Redox activation of ATG5 licenses autophagy upon nutrient restriction

Dietary restriction (DR) protects against metabolic disease, extends lifespan, and is associated with remodeling of tissue reactive oxygen species (ROS). ROS control biological adaptation through reversible oxidation of protein cysteines, yet the targets of DR-initiated redox signaling are unknown. Here we generate OxiDR, a tissue-resolved atlas of the cysteine redox proteome that quantifies oxidation state under DR. Rather than oxidizing the proteome broadly, DR selectively targets a high-amplitude set of cysteines in a tissue-specific manner, allowing systematic classification of biological processes subject to DR-mediated redox regulation. Among the cysteines most highly oxidized upon DR is Cys19 of the core autophagy protein ATG5. We show oxidation of Cys19 is required for ATG5-mediated autophagosome formation and for autophagy triggered by nutrient restriction in human cells and mice. Reversible oxidation of this cysteine promotes ATG5 binding to ATG10, thus forming the ATG5-ATG12 conjugate that lipidates LC3B/ATG8 and matures the autophagosome. In mice, loss of this redox switch prevents effective initiation of autophagy upon nutrient restriction, resulting in gross tissue pathology and rapid onset of mortality. The autophagic response to nutrient restriction is thus gated by oxidation of a single cysteine.

cell biology↗

bioRxiv2026

VesSynth: Tubes Are All You Need for Robust Cross-Scale Cross-Modal 3D Vessel Segmentation

The cerebral vasculature is central to brain function, with alterations linked to numerous cerebrovascular and neurological disorders. Yet, no single imaging modality can capture the entire cerebral vascular network in humans. Instead, an array of techniques are sensitized to different spatial scales, while trading off resolution for coverage. Magnetic Resonance Imaging (MRI) typically resolves only large pial vessels, while high-resolution microscopy allows micrometer-scale vessels to be mapped over limited spatial extents. These techniques must therefore be combined to obtain a complete mapping of the cerebral angioarchitecture, which underscores the need for automatic, cross-modal vessel segmentation. Here, we introduce VesSynth, a flexible vessel segmentation framework that achieves state-of-the-art accuracy across multiple modalities and spatial resolutions (MR, optical and X-ray imaging), despite being trained entirely on synthetic data. By enabling consistent vascular mapping across scales, this framework paves the way to comprehensive investigation of cerebrovascular organization and its role in health and disease.

bioengineering↗

bioRxiv2026

Lunar gravity predicts sleep timing

Biological rhythms are fundamental to survival, synchronizing physiological and behavioural processes like the sleep-wake cycle with predictable environmental cycles like the solar day1. However, the extent to which human sleep responds to the lunar cycle remains a subject of controversy, particularly given the ubiquity of artificial light and conflicting reports regarding the influence of moonlight2-5. While lunar illuminance has been the primary candidate for such modulation, it fails to account for semilunar rhythms2,6 or effects observed during the dark new moon phase2,7. Here, we show that human and non-human primate sleep timing is synchronized with the gravimetric cycles exerted by the Moon and Sun. By analysing longitudinal actigraphic recordings from urban cohorts in Seattle, indigenous Toba/Qom communities in Argentina, and captive titi monkeys with attenuated access to natural light, we found that sleep onset is consistently delayed around periods of maximal gravitational variations. Crucially, this synchronization aligns with gravimetric peaks regardless of whether they occur at the full or new moon. Furthermore, while human sleep timing is heavily influenced by social constraints and self-selected light exposure, this synchronization persists in titi monkeys, in which these confounds are absent. These findings identify lunar gravity as a distinct environmental cue that may regulate sleep-wake behaviour. Although this regulation may be mediated by other geophysical factors oscillating with lunisolar gravitational tides, the results suggest that the mechanism is an evolutionarily conserved trait that shapes biological timing beyond the influence of light.

animal behavior and cognition↗

bioRxiv2025

Mechanism of NanR transcriptional activation of sialic acid metabolism in Streptococcus pneumoniae.

In Streptococcus pneumoniae, the RpiR transcriptional regulator NanR (SpNanR) senses sialic acid in the environment and upregulates transcription of the nan and siaA operons to increase uptake and metabolism of sialic acid. The molecular basis of this activation is unknown. Here, we demonstrate that SpNanR binds N-acetylmannosamine-6-phosphate, a metabolite of sialic acid catabolism. SpNanR exists in a dimer-tetramer equilibrium, and N-acetylmannosamine-6-phosphate binding strongly stabilizes the tetramer. Crystal structures and site-specific substitutions demonstrate that N-acetylmannosamine-6-phosphate bridges and stabilizes the SpNanR tetramer. SpNanR binds its DNA recognition sequence with nanomolar affinity. Notably, the effector N-acetylmannosamine-6-phosphate does not affect the affinity of SpNanR for DNA. The DNA binding domains are not structurally coupled to the sugar isomerase domains, explaining why N-acetylmannosamine-6-phosphate binding does not affect DNA binding. Structural analysis reveals that sequence specificity arises through distortion of B-DNA and an unusual {pi}-stack formed by two arginine residues in the minor groove, while affinity is driven by backbone contacts. We propose a mechanism by which S. pneumoniae regulates sialic acid metabolism, consistent with our biophysical experiments and in vivo regulatory behavior. These findings define a unique activation mechanism for an RpiR regulator and provide new insights into carbohydrate-responsive gene regulation in pneumococci.

molecular biology↗

bioRxiv2025

Collagen-Based Tumor Spheroid Model for Investigating Tumor-Macrophage Interactions through Extracellular Matrix Remodeling

Macrophages in the tumor microenvironment (TME) can constitute up to 50% of tumor mass and play a critical role in cancer cell proliferation, invasion, and metastasis. While their contribution to extracellular matrix (ECM) degradation through matrix metalloproteinases (MMPs) has been explored, the role of other macrophage-derived factors in ECM remodeling and their impacts beyond degradation remain poorly understood. Here, we describe the development of a 3D collagen-based tumor spheroid model to investigate the impact of peripheral blood mononuclear cell (PBMC)-derived macrophages on cancer cell-ECM and cancer cell-macrophage interactions within the TME. We observed that cancer cells stimulated PBMC-derived macrophages into an M2-like phenotype and that tumor spheroid conditioned macrophages (TSCMs) shifted cancer cell populations toward phenotypes with greater invasion distances and reduced circularity, indicative of increased malignancy. Such observations can be explained by macrophage-mediated ECM remodeling. Specifically, we demonstrate that TSCMs secreted a variety of soluble factors that are known to contribute to ECM remodeling, including ECM degradation and fiber realignment. These processes collectively create a tumor-favoring environment by loosening the collagen matrix and aligning fibers that serve as invasion tracks for migrating tumor cells that facilitate cancer cell migration and invasion. This model provides a robust platform to study the interactions between cellular and non-cellular components in the TME and to identify the molecular mechanisms underlying cancer progression. These insights may aid in the development of novel therapeutic strategies targeting macrophage-mediated processes in cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/679587v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@17d1f9forg.highwire.dtl.DTLVardef@1a71500org.highwire.dtl.DTLVardef@53deeeorg.highwire.dtl.DTLVardef@510268_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Excitatory Cortical Neurons from CDKL5 Deficiency Disorder Patient-Derived Organoids Show Early Hyperexcitability Not Identified in Neurogenin2 Induced Neurons

CDKL5 deficiency disorder (CDD) is a rare developmental and epileptic encephalopathy resulting from variants in cyclin-dependent kinase-like 5 (CDKL5) that lead to impaired kinase activity or loss of function. CDD is one of the most common genetic etiologies identified in epilepsy cohorts. To study how CDKL5 variants impact human neuronal activity, gene expression and morphology, CDD patient-derived induced pluripotent stem cells and their isogenic controls were differentiated into excitatory neurons using either an NGN2 induction protocol or a guided cortical organoid differentiation. Patient-derived neurons from both differentiation paradigms had decreased phosphorylated EB2, a known molecular target of CDKL5. Induced neurons showed no detectable differences between cases and isogenic controls in network activity using a multielectrode array, or in MAP2+ neurite length, and only two genes were differentially expressed. However, patient-derived neurons from the organoid differentiation showed increased synchrony and weighted mean firing rate on the multielectrode array within the first month of network maturation. CDD patient-derived cortical neurons had lower expression of CDKL5 and HS3ST1, which may change the extracellular matrix around the synapse and contribute to hyperexcitability. Similar to the induced neurons, there were no differences in neurite length across or within patient-control cell lines. Induced neurons have poor cortical specification while the organoid derived neurons expressed cortical markers, suggesting that the changes in neuronal excitability and gene expression are specific to cortical excitatory neurons. Examining molecular mechanisms of early hyperexcitability in cortical neurons is a promising avenue for identification of CDD therapeutics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/622878v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@9d84b8org.highwire.dtl.DTLVardef@1745073org.highwire.dtl.DTLVardef@14dbd20org.highwire.dtl.DTLVardef@bba058_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Light-induced Extracellular Vesicle Adsorption

The role of extracellular vesicles (EVs) in human health and disease has garnered considerable attention over the past two decades. However, while several types of EVs are known to interact dynamically with the extracellular matrix and there is great potential value in producing high-fidelity EV micropatterns, there are currently no label-free, high-resolution, and tunable platform technologies with this capability. We introduce Light-induced Extracellular Vesicle Adsorption (LEVA) as a powerful solution to rapidly advance the study of matrix- and surface-bound EVs and other particles. The versatility of LEVA is demonstrated using commercial GFP-EV standards, EVs from glioblastoma bioreactors, and E. coli outer membrane vesicles (OMVs), with the resulting patterns used for single EV characterization, single cell migration on migrasome-mimetic trails, and OMV-mediated neutrophil swarming. LEVA will enable rapid advancements in the study of matrix- and surface-bound EVs and other particles, and should encourage researchers from many disciplines to create novel diagnostic, biomimetic, immunoengineering, and therapeutic screening assays.

bioengineering↗

bioRxiv2022

Loss of FBXO11 function establishes a stem cell program in acute myeloid leukemia through dysregulation of the mitochondrial protease LONP1

Acute myeloid leukemia (AML) is an aggressive cancer with very poor outcomes. To identify additional drivers of leukemogenesis, we analyzed sequence data from 1,727 unique individual AML patients, which revealed mutations in ubiquitin ligase family genes in 11.2% of adult AML samples with mutual exclusivity. The Skp1/Cul1/Fbox (SCF) E3 ubiquitin ligase complex gene FBXO11 was the most significantly downregulated gene of the SCF complex in AML. FBXO11 catalyzes K63-linked ubiquitination of a novel target, LONP1, which promotes entry into mitochondria, thereby enhancing mitochondrial respiration. Reduced mitochondrial respiration secondary to FBXO11 depletion imparts myeloid-biased stem cell properties in primary CD34+ hematopoietic stem progenitor cells (HSPC). In a human xenograft model, depletion of FBXO11 cooperated with AML1-ETO and mutant KRASG12D to generate serially transplantable AML enriched for primitive cells. Our findings suggest that reduced FBXO11 primes HSPC for myeloid-biased self-renewal through attenuation of LONP1-mediated regulation of mitochondrial respiration.

cancer biology↗

bioRxiv2021

Genetic assimilation of ancestral plasticity during parallel adaptation

Phenotypic plasticity in ancestral populations is hypothesised to facilitate adaptation, but evidence supporting its contribution is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel genetic and phenotypic adaptive changes has not been explored. The most general finding is that nearly all ancestral gene expression plasticity is reversed following adaptation, but this is usually examined transcriptome-wide rather than focused on the genes directly involved in adaptation. We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared to ancestral, zinc-sensitive plants. Our experiments show that reinforcement of ancestral plasticity plays an influential role in the evolution of plasticity in derived populations and, surprisingly, one third of constitutive differences between ecotypes are the result of genetic assimilation of ancestral plasticity. Ancestral plasticity also increases the chance that genes are recruited repeatedly during adaptation. However, despite a high degree of convergence in gene expression levels between independently adapted lineages, genes with ancestral plasticity are as likely to have similar expression levels in adapted populations as genes without. Overall, these results demonstrate that ancestral plasticity does play an important role in adaptive parallel evolution, particularly via genetic assimilation across evolutionary replicates.

evolutionary biology↗

bioRxiv2021

Age-dependent appearance of SARS-CoV-2 entry cells in mouse chemosensory systems reflects COVID-19 anosmia and ageusia symptoms.

COVID-19 pandemic has given rise to a collective scientific effort to study its viral causing agent SARS-CoV-2. Research is focusing in particular on its infection mechanisms and on the associated-disease symptoms. Interestingly, this environmental pathogen directly affects the human chemosensory systems leading to anosmia and ageusia. Evidence for the presence of the cellular entry sites of the virus, the ACE2/TMPRSS2 proteins, has been reported in non-chemosensory cells in the rodents nose and mouth, missing a direct correlation between the symptoms reported in patients and the observed direct viral infection in human sensory cells. Here, mapping the gene and protein expression of ACE2/TMPRSS2 in the mouse olfactory and gustatory cells, we precisely identified the virus target cells to be of basal and sensory origin and we revealed their age-dependent appearance. Our results not only clarify human viral-induced sensory symptoms but also propose new investigative perspectives based on ACE2-humanized mouse models.

neuroscience↗

bioRxiv2021

Stromal architecture directs early dissemination in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDA) is an extremely metastatic and lethal disease. Here in both murine and human PDA we demonstrate that extracellular matrix architecture regulates cell extrusion and subsequent invasion from intact ductal structures through Tumor-Associated Collagen Signatures (TACS), resulting in early dissemination from histologically pre-malignant lesions and continual invasion from well-differentiated disease. Furthermore, we show that pancreatitis results in invasion-conducive architectures, thus priming the stroma prior to malignant disease. Analysis in novel microfluidics-derived microtissues and in vivo demonstrates decreased extrusion and invasion following focal adhesion kinase (FAK) inhibition, consistent with decreased metastasis. Thus, data suggest that targeting FAK or strategies to re-engineer and normalize tumor microenvironments, may have a role not only in also in very early disease but also for limiting continued dissemination from unresectable disease. Likewise, it may be beneficial to employ stroma targeting strategies to resolve precursor diseases such as pancreatitis in order to remove stromal architectures that increase risk for early dissemination. Impact StatementCollagen architectures in the tumor stroma facilitate dissemination of carcinoma cells from the earliest histologically "pre-malignant" lesions and continue to promote disease spread from well-differentiated PDA.

cancer biology↗

bioRxiv2019

Phylogenomics supports a Cenozoic rediversification of the "living fossil" Isoetes

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

evolutionary biology↗

bioRxiv2019

Microscale Collagen and Fibroblast Interactions Enhance Primary Human Hepatocyte Functions in 3-Dimensional Models

Human liver models that are 3-dimensional (3D) in architecture are proving to be indispensable for diverse applications, including compound metabolism and toxicity screening during preclinical drug development, to model human liver diseases for the discovery of novel therapeutics, and for cell-based therapies in the clinic; however, further development of such models is needed to maintain high levels of primary human hepatocyte (PHH) functions for weeks to months in vitro. Therefore, here we determined how microscale 3D collagen-I presentation and fibroblast interaction could affect the long-term functions of PHHs. High-throughput droplet microfluidics was utilized to rapidly generate reproducibly-sized (~300 m diameter) microtissues containing PHHs encapsulated in collagen-I +/- supportive fibroblasts, namely 3T3-J2 murine embryonic fibroblasts or primary human hepatic stellate cells (HSCs); self-assembled spheroids and bulk collagen gels (macrogels) containing PHHs served as gold-standard controls. Hepatic functions (e.g. albumin and cytochrome-P450 or CYP activities) and gene expression were subsequently measured for up to 6 weeks. We found that collagen-based 3D microtissues rescued PHH functions within static multi-well plates at 2- to 30-fold higher levels than self-assembled spheroids or macrogels. Further coating of PHH microtissues with 3T3-J2s led to higher hepatic functions than when the two cell types were either coencapsulated together or when HSCs were used for the coating instead. Additionally, the 3T3-J2-coated PHH microtissues displayed 6+ weeks of relatively stable hepatic gene expression and function at levels similar to freshly thawed PHHs. Lastly, microtissues responded in a clinically-relevant manner to drug-mediated CYP induction or hepatotoxicity. In conclusion, fibroblast-coated collagen microtissues containing PHHs display hepatic functions for 6+ weeks without any fluid perfusion at higher levels than spheroids and macrogels, and such microtissues can be used to assess drug-mediated CYP induction and hepatotoxicity. Ultimately, microtissues may find broader utility for modeling liver diseases and as building blocks for cell-based therapies.

bioengineering↗

bioRxiv2019

Astrocyte redox dysregulation causes prefrontal hypoactivity: sulforaphane treats non-ictal pathophysiology in ALDH7A1-mediated epilepsy

A fundamental but unanswered question in neuropsychiatry is whether the psychiatric symptoms of epilepsy are caused by the same or a separate pathophysiology as seizures. To address this question, we investigated a monogenic form of epilepsy (pyridoxine-dependent epilepsy) caused by aldehyde dehydrogenase 7a1 (ALDH7A1) mutations. ALDH7A1 global knockout mice exhibited both seizure-associated and affective behavioral phenotypes. However, seizure phenotypes were caused by ALDH7A1 deletion in hepatocytes whereas affective behaviors were caused by ALDH7A1 deletion in astrocytes. Deletion in astrocytes disrupted astrocyte redox homeostasis, impairing regulation of extracellular ion concentrations and reducing neuronal activity in the prelimbic cortex. Sulforaphane, which activates the NRF2 antioxidant pathway, restored prelimbic neuronal activity and rescued affective behaviors in ALDH7A1 knockout mice, but did not prevent seizures. These studies implicate astrocyte redox homeostasis and prelimbic hypoactivity in the psychiatric manifestations of a congenital form of epilepsy, which are mechanistically and therapeutically separate from the seizure pathophysiology. TeaserAntioxidant imbalance in astrocytes reduces neuronal activity, causing psychiatric symptoms in epilepsy distinct from seizures.

neuroscience↗

bioRxiv2019

SEMA4C is a novel target to limit osteosarcoma growth, progression, and metastasis

Semaphorins, specifically type IV, are important regulators of axonal guidance and have been increasingly implicated in poor prognoses in a number of different solid cancers. In conjunction with their cognate PLXNB family receptors, type IV members have been increasingly shown to mediate oncogenic functions necessary for tumor development and malignant spread. In this study, we investigated the role of semaphorin 4C (SEMA4C) in osteosarcoma growth, progression, and metastasis. We investigated the expression and localization of SEMA4C in primary osteosarcoma patient tissues and its tumorigenic functions in these malignancies. We demonstrate that overexpression of SEMA4C promotes properties of cellular transformation, while RNAi knockdown of SEMA4C promotes adhesion and reduces cellular proliferation, colony formation, migration, wound healing, tumor growth, and lung metastasis. These phenotypic changes were accompanied by reductions in activated AKT signaling, G1 cell cycle delay, and decreases in expression of mesenchymal marker genes SNAI1, SNAI2, and TWIST1. Lastly, monoclonal antibody blockade of SEMA4C in vitro mirrored that of the genetic studies. Together, our results indicate a multi-dimensional oncogenic role for SEMA4C in metastatic osteosarcoma and more importantly that SEMA4C has actionable clinical potential.

cancer biology↗