Search bioRxiv⌕ Search

Biology subjects

Ho, S.

Publications and source records attributed to Ho, S..

At least 19 recordsLinked to original sources
bioRxiv2026

Evolutionary rates in "living fossils" across the Tree of Life

Lineages that have undergone little apparent evolutionary change over long geological intervals are often described as "living fossils", with iconic examples including the coelacanth, tuatara, and Ginkgo. However, studies of morphological and molecular data have produced mixed evidence regarding whether living fossils have evolved more slowly than their relatives. We tested for reduced evolutionary rates using a sister-pairs approach, analysing a comprehensive set of morphological and molecular data for 45 living-fossil lineages and their close relatives across the Tree of Life. Living-fossil lineages showed substantially reduced rates of morphological evolution, whereas evidence for reduced molecular rates was weaker. To test whether this pattern could be explained by species poverty, we also analysed other depauperate lineages (species-poor clades contrasted with species-rich sister clades) and found a weak tendency towards reduced molecular rates but without a corresponding slowdown in morphological evolution. Our study reveals that the living-fossil concept captures a quantifiable pattern of prolonged morphological conservatism, but also suggests that living fossils lack other shared biological or life-history characteristics that might unite them as a group.

evolutionary biology↗
bioRxiv2026

The luminal and cytosolic domains of CLIMP-63 cooperate to set ER sheet width

The endoplasmic reticulum (ER) synthesized and folds secreted and transmembrane protein in regions composed of flattened sheets with a defined luminal width of [~]50 nm. CLIMP-63 has been proposed to be the principal determinant of this spacing, but the molecular mechanism by which it controls luminal width remains unclear. The luminal domain of CLIMP-63 has been proposed to act as a fixed-length spacer through antiparallel coiled-coil dimerization between molecules on opposing membranes. Here we revise this model. Using systematic cysteine trapping across the luminal domain, we demonstrate that CLIMP-63 assembles into parallel trimers. An AlphaFold-guided screen of CLIMP-63 orthologs combined with cryo-electron microscopy reveals that the luminal domain forms an elongated trimeric rod with intrinsic conformational flexibility at hinge regions. This flexibility is functionally required: replacing the human luminal domain with a more rigid ortholog causes complete ER vacuolation. Higher-order assembly of CLIMP-63 trimers beyond the trimer depends on the cytosolic tail rather than on luminal trans interactions, and the tails role in higher order assembly is separable from its other architectural functions. Together, these findings show that luminal trimeric extension and cytosolic tail-mediated clustering cooperate to determine ER sheet width.

cell biology↗
bioRxiv2026

ZNF185 expression is negatively regulated by CTCF and promotes endometrial cancer growth

CCCTC-binding factor (CTCF) is frequently mutated in endometrial cancer, resulting in genetic haploinsufficiency that contributes to tumour progression. We previously showed that depletion of CTCF disrupted cell polarity in KLE endometrial cancer spheroids; however, the implications for gene dysregulation and endometrial cancer pathophysiology remains poorly understood. ZNF185, an actin-associated and LIM domain-containing protein involved in cytoskeletal remodelling, was identified as a dysregulated target following CTCF haploinsufficiency. In this study, shRNA-mediated knockdown of CTCF was used to model haploinsufficiency in endometrial cancer cells, leading to the identification of a previously unrecognised isoform of ZNF185, named ZNF185B. Unlike the full-length protein, ZNF185B lacked co-localisation with F-actin and exhibited a diffuse cytoplasmic distribution, and ZNF185B was significantly upregulated in CTCF-depleted endometrial cancer cells and in an auxin-inducible degron model in a dose-dependent manner. Functional studies demonstrated that depletion of ZNF185 expression reduced endometrial cancer cell proliferation and clonogenic potential. Together, these findings identify ZNF185B as a novel isoform negatively regulated by CTCF protein dosage and establish ZNF185 as a requirement for endometrial cancer cell proliferation. Our results suggest that dysregulated ZNF185 expression is a crucial downstream consequence of CTCF haploinsufficiency and may contribute to tumour progression in endometrial cancer.

Molecular Biology↗
bioRxiv2026

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants

Cardiovascular diseases often arise in anatomically specialised regions of the heart that remain poorly represented in existing single-cell and spatial atlas references. Here we profiled 28 regions of the adult human heart from 36 donors, combining paired single-nucleus RNA and chromatin accessibility assays with spatial transcriptomics. The resulting atlas integrates 1,059,175 expression profiles and 452,614 chromatin accessibility profiles, and defines spatial niches across the heart. In cardiac valves, we identify a valve fibroblast-macrophage niche that is polarised to the non-fibrosa surface and expands with age. Aortic stenosis genetic risk was enriched in inflammatory regulatory programmes of the Valve Fibroblast Immune cell state. In pulmonary veins, we define PITX2+ Myocardial Sleeve Cells, a region-restricted cardiomyocyte population in which a fine-mapped 4q25 atrial fibrillation variant intersects a cell type-specific open chromatin region. In coronary arteries, we resolve a RUNX1-marked synthetic smooth muscle layer in the subintima that provides a molecular identity for diffuse intimal thickening, a constitutive feature of the healthy vessel wall and a substrate for atherosclerosis, and show by perturbation in human smooth muscle cells that RUNX1 promotes cell-cycle entry while restraining inflammatory cytokine gene expression. Finally, allele-specific accessibility together with deep learning models fine-tuned to predict regulatory activity from DNA sequence identify cell type-specific regulatory effects at GWAS loci for atrial fibrillation, coronary artery disease and calcific aortic valve stenosis, including a variant whose Valve Fibroblast-specific effect on the polyamine transporter ATP13A3 is opposite in direction to the effect seen in bulk-tissue eQTL references that lack valve cells. Together with these cardiac sequence models and CardioSleuth, an AI-powered exploration engine for cardiac regulatory effects, this atlas links cardiac anatomy, gene regulation and disease genetics at single-cell resolution. By placing genetic risk in its precise cellular and anatomical context, it provides a foundation for mechanistic disease understanding, cell-state-specific therapeutic target nomination, and improved interpretation of inherited cardiovascular risk to inform future therapy and management.

Cell Biology↗
bioRxiv2026

Ether lipid remodeling during neuronal differentiation prevents ferroptosis

Ferroptosis is a form of cell death driven by iron-dependent lipid peroxidation, with specific lipid species playing key roles in modulating susceptibility. Among these, ether lipids have shown conflicting effects, being linked to both protection and sensitization. Here, we dissect the relationship between lipid structure and ferroptosis sensitivity and explain how ether lipids exert context-dependent effects. Ether lipids can promote ferroptosis through a metabolic bias towards the accumulation of polyunsaturated acyl chains and ethanolamine head groups, whereas this pro-ferroptotic tendency is counterbalanced by the anti-ferroptotic vinyl ether moiety introduced by plasmanylethanolamine desaturase 1. We show that this protective effect is critical for preventing ferroptosis in hiPSC-derived neurons, which accumulate otherwise pro-ferroptotic ether lipids during differentiation. This effect is not solely due to its antioxidant properties but also stems from the reprogramming of mitochondrial respiration. The lack of vinyl ether bonds leads to multiple mitochondrial defects, including increased mitochondrial reactive oxygen species (ROS), lower membrane potential, and abnormal cristae structures. These findings indicate that vinyl ether bonds in ether lipids offer dual ferroptosis resistance by scavenging ROS and minimizing its production at the mitochondrial level. The disruption of this system in Caenorhabditis elegans leads to iron-induced death and impaired motility. Thus, our study reveals ether lipid structural remodeling as a key regulator of ferroptosis sensitivity in neurons.

cell biology↗
bioRxiv2026

Generation, Characterization and Comparison of Ovine Induced Pluripotent and Embryonic-Disc Stem Cells

Pluripotent stem cells derived from livestock species represent valuable systems for studying early mammalian development and for establishing renewable, well-defined cell sources; however, direct comparative characterization of distinct pluripotent stem cell platforms in sheep remains limited. In this study, we established and evaluated two ovine pluripotent stem cell types: reprogrammed induced pluripotent stem cells (siPSCs) and embryonic disc-derived stem cells (sEDSCs). Both siPSCs and sEDSCs exhibited core features of pluripotency, including compact colony morphology, alkaline phosphatase activity, expression of key pluripotency-associated markers, and maintenance of a normal ovine karyotype. Flow cytometry and quantitative RT-PCR analyses revealed broadly overlapping yet distinguishable pluripotency marker expression profiles between the two cell types. Functional pluripotency was confirmed by embryoid body formation and in vitro differentiation into derivatives of all three germ layers. To further assess lineage-specific differentiation competence and compare functional outputs relevant to mesodermal differentiation, both pluripotent stem cell types were directed towards the adipogenic lineage. While siPSCs and sEDSCs were each capable of adipogenic differentiation, differences in differentiation efficiency and marker expression were observed. Together, these findings demonstrate that ovine siPSCs and sEDSCs share core pluripotency characteristics while retaining distinct molecular and functional properties, providing a robust comparative framework for studies of ovine pluripotency, lineage specification, and stem cell biology.

cell biology↗
bioRxiv2026

High density culture of bovine embryonic stem cell derived mesenchymal cells on edible scaffolds for structured cultivated meat

Developing structured cultivated meat requires integrated solutions that combine scalable cell sources with edible, foodgrade materials capable of supporting highdensity growth and differentiation. Here, we evaluate bovine mesenchymal stem cells derived from embryonic stem cells (ESCderived iMSCs) as a scalable adipogenic cell source and develop an integrated workflow combining these cells with edible plantbased scaffolds for structured biomass generation. Cell identity and functionality were assessed using transcriptomic, morphological, gene expression, flow cytometric, and adipogenic differentiation analyses, in both adherent and suspension culture systems. In parallel, lentil, pea, and soy-based scaffold formulations were screened for cell attachment, proliferation, and biomass accumulation. Soybased scaffolds supported uniform cell distribution and robust growth and outperformed lentil-based scaffolds. Under dynamic culture conditions, bovine iMSCs cultured on soy-based scaffolds achieved highdensity growth, showing biomass accumulation (cell wet weight/scaffold wet weight) reached an average cell wet weight to scaffold wet weight ratio of 15% within three days. Cultures demonstrated active glucose metabolism and retained adipogenic differentiation capacity, confirmed by lipid accumulation and positive oil red O staining. These findings demonstrate an integrated cell-scaffold platform for rapid threedimensional biomass generation. This approach supports the development of a cell culture strategy for structured cultivated meat by combining defined cell sources with foodgrade scaffold technologies to improve scalability, structure, and nutritional relevance. HighlightsO_LIBovine ESC-derived iMSCs enable scalable adipogenic cell production C_LIO_LIEdible soy-based scaffolds support 3D attachment and biomass accumulation C_LIO_LIDynamic culture achieved [~]15% cell wet weight fraction within 3 days C_LIO_LIiMSCs retained adipogenic differentiation capacity on edible scaffolds C_LIO_LIIntegrated cell-scaffold culture supports structured cultivated meat prototypes C_LI

cell biology↗
bioRxiv2025

Unveiling the tempo of molecular and morphological evolution across the Tree of Life

The evolution of Earths vast genetic and morphological diversity has been explained by an array of macroevolutionary models. At opposite ends of the spectrum lie two contrasting evolutionary models: phyletic gradualism and punctuated equilibria. Under a phyletic gradualism framework, evolutionary change accumulates along lineages and species are steadily transformed into new forms over time. In contrast, under punctuated equilibria, evolutionary change tends to occur in bursts at speciation events. Previous studies of molecular and morphological data have found varying levels of support for the two evolutionary models. We examined these models using comprehensive molecular and morphological data sets from 40 clades across the Tree of Life. Testing for associations between species richness and the amount of evolutionary change in sister clades, we find little evidence to support the punctuated equilibria model. However, we found high levels of among-lineage rate variation in molecular evolution and particularly morphological evolution. Our comparison of coding and non-coding genomic regions revealed contrasting patterns of among-lineage rate variation, without clear trends across taxa. Our study confirms that heterotachy is a dominant feature in macroevolution and that molecular and morphological evolution cannot simply be described by either a gradual or punctuated model.

evolutionary biology↗
bioRxiv2025

Molecular Regulation and Physiological Role of 1 GOLPH3-mediated Golgi retention

The Golgi complex serves as the central hub of the biosynthetic pathway, where anterograde and retrograde trafficking converge. How cargo and Golgi-resident proteins traverse this organelle has long been debated. Recent studies have identified a molecular machinery that sorts resident proteins into retrograde-directed COPI vesicles during cisternal maturation. Golgi phosphoprotein 3 (GOLPH3) is a key component of this system; however, its physiological relevance and regulatory mechanisms remain poorly defined. Here, we show that GOLPH3 depletion in mice disrupts both protein and lipid glycosylation, causes partially penetrant embryonic lethality, and severely impairs growth and bone mineralization. At the molecular level, we find that GOLPH3 is regulated by functionally antagonistic S-acylation events that control the topology of its membrane association. To mediate retrograde trafficking of Golgi-resident glycosyltransferases, GOLPH3 must bind their cytosolic tails. This occurs via a negatively charged surface region, which is correctly oriented only in one of the S-acylated GOLPH3 conformations. Together, these findings reveal a lipid-mediated regulatory mechanism for intra-Golgi trafficking and establish the critical role of GOLPH3 in vertebrate development.

cell biology↗
bioRxiv2025

Drivers of avian genomic change revealed by evolutionary rate decomposition

Modern bird diversity spans a striking array of forms, behaviours, and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change, but disentangling the drivers of rate variation has been difficult across large numbers of whole-genomes. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds, we show that clutch size, generation length, and beak shape are dominant predictors of genome-wide mutation rates. To identify the major axes of evolutionary rate variation, we employ covariance matrix eigendecomposition from rates estimated for branches of the avian phylogeny and across genomic loci. We find that the majority of rate variation occurs along the terminal branches of the phylogeny associated with extant families of birds. Additionally, we use principal components analyses to show that several axes of variation are linked with rapid evolution in microchromosomes immediately after the Cretaceous-Palaeogene transition. These apparent pulses of evolution are consistent with major changes in evolutionary rates in the machineries for meiosis, heart performance, and RNA splicing, surveillance, and translation. They also correlate with the diversification of ecological niches reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolutionary rates through time, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage, and niche expansion near the beginning of the Palaeogene period.

evolutionary biology↗
bioRxiv2024

Integrative Co-Registration of Elemental Imag-ing and Histopathology for Enhanced Spatial Multimodal Analysis of Tissue Sections through TRACE

SummaryElemental imaging provides detailed profiling of metal bioaccumulation, offering more precision than bulk analysis by targeting specific tissue areas. However, accurately identifying comparable tissue regions from elemental maps is challenging, requiring the integration of hematoxylin and eosin (H&E) slides for effective comparison. Facilitating the streamlined co-registration of Whole Slide Images (WSI) and elemental maps, TRACE enhances the analysis of tissue regions and elemental abundance in various pathological conditions. Through an interactive containerized web application, TRACE features real-time annotation editing, advanced statistical tools, and data export, supporting comprehensive spatial analysis. Notably, it allows for comparison of elemental abundances across annotated tissue structures and enables integration with other spatial data types through WSI co-registration. Availability and ImplementationAvailable on the following platforms- GitHub: jlevy44/trace_app, PyPI: trace_app, Docker: joshualevy44/trace_app, Singularity: joshualevy44/trace_app. Contactjoshua.levy@cshs.org Supplementary informationSupplementary data are available.

bioinformatics↗
bioRxiv2023

Genome-wide CRISPR/Cas9 screen identifies MAT2A as a critical host factor for BK Polyomavirus

BK polyomavirus (BKPyV) is a ubiquitous human pathogen that causes major complications for renal transplant patients (polyomavirus-associated nephropathy) and hematopoietic stem cell transplant patients (haemorrhagic cystitis). There are currently no effective antivirals available against BKPyV. As polyomaviruses are small DNA viruses that express very few proteins and utilise host DNA polymerases for their replication, there is limited possibility of targeting viral proteins for therapeutic intervention. As such, there is increasing interest in targeting host pathways to inhibit these viruses. To identify host genes required for BKPyV infection we have conducted the first genome-wide CRISPR/Cas9 screen in BKPyV infected cells. This led to the identification of methionine adenosyltransferase 2A (MAT2A), which we have validated as a host dependency factor for BKPyV infection. MAT2A is a druggable host enzyme that synthesises S-adenosylmethionine, the principal co-factor and methyl donor within cells. We have found that a small molecule inhibitor of MAT2A is a potent antiviral drug inhibiting BKPyV replication, offering a new therapeutic option for treatment of BKPyV diseases.

microbiology↗
bioRxiv2023

Transcriptional dysregulation and impaired neuronal activity in FMR1 knock-out and Fragile X patients iPSC-derived models.

The lack of fragile X mental retardation protein (FMRP) protein, due to a repression of the FMR1 gene, causes Fragile X syndrome (FXS), one of the most prevalent forms of syndromic autisms. The FMR1 gene codes for an RNA binding protein involved in the regulation of gene expression through RNA processing, control of local translation, and protein-protein interactions; processes that are crucial for proper brain development. Taking advantage of induced pluripotent stem cells (iPSCs) and CRISPR-Cas9 genome editing technologies, we generated iPSC-derived cortical neural progenitors and cortical neurons from an FMR1 knock-out and patient cell line with the aim of identifying common phenotypes between the two cellular models. Using RNA sequencing, quantitative PCR and multielectrode array approaches, we assessed how the absence of the functional FMR1 gene affects the transcriptional profiles and the activities of iPSC-derived cortical neuronal progenitor cells (NPCs) and neurons with both models. We observed that FMR1 KO and FXS patient cells have a decrease in their mean firing rate; a cellular activity that can also be blocked by tetrodotoxin (TTX) application in wild-type active neurons. Relative to wild-type neurons, in FMR1 KO neurons, increased expression of presynaptic mRNA and transcription factors involved in the forebrain specification and decreased levels of mRNA coding AMPA and NMDA subunits were observed. Intriguingly, 40% of the differentially expressed genes were commonly deregulated between NPCs and differentiating neurons with significant enrichments in FMRP targets and Autism Related Genes found amongst downregulated genes. This implies that an absence of functional FMRP affects transcriptional profiles at the NPC stage, resulting in impaired activity and differentiation of the progenitors into mature neurons over time. These findings from the FMR1 KO lines were also shared with FXS patients iPSC-derived cells that also present with an impairment in activity and neuronal differentiation, illustrating the critical role of FMRP protein in neuronal development.

neuroscience↗
bioRxiv2023

Aub, Vasa and Armi localization to phase separated nuage is dispensable for piRNA biogenesis and transposon silencing in Drosophila

From nematodes to placental mammals, key components of the germline transposon silencing piRNAs pathway localize to phase separated perinuclear granules. In Drosophila, the PIWI protein Aub, DEAD box protein Vasa and helicase Armi localize to nuage granules and are required for ping-pong piRNA amplification and phased piRNA processing. Drosophila piRNA mutants lead to genome instability and Chk2 kinase DNA damage signaling. By systematically analyzing piRNA pathway organization, small RNA production, and long RNA expression in single piRNA mutants and corresponding chk2/mnk double mutants, we show that Chk2 activation disrupts nuage localization of Aub and Vasa, and that the HP1 homolog Rhino, which drives piRNA precursor transcription, is required for Aub, Vasa, and Armi localization to nuage. However, these studies also show that ping-pong amplification and phased piRNA biogenesis are independent of nuage localization of Vasa, Aub and Armi. Dispersed cytoplasmic proteins thus appear to mediate these essential piRNA pathway functions.

developmental biology↗
bioRxiv2023

Rapid disassembly and Piwi-independent reassembly of Drosophila piRNA cluster heterochromatin following acute heat shock

Environmental stress activates transposons and is proposed to generate genetic diversity that facilitates adaptive evolution. piRNAs guide germline transposon silencing, but the impact of stress on the piRNA pathway is not well understood. In Drosophila, the Rhino-Deadlock-Cuff complex (RDC) drives transcription of clusters composed of nested transposon fragments, generating precursors that are processed into mature piRNAs in the cytoplasm. We show that acute heat shock triggers rapid, reversable, loss of RDC localization and cluster transcript expression with coordinate changes in the cytoplasmic processing machinery. Maternal piRNAs bound to Piwi are proposed to guide Rhino localization to clusters during early embryogenesis. However, RDC re-localization after heat shock is accelerated in piwi mutants and delayed in thoc7 mutants, which disrupt piRNA precursor binding to THO complex, and we show that maternally deposited piRNAs are dispensable for RDC localization to the major 42AB cluster. Cluster specification is reconsidered in light of these findings.

developmental biology↗
bioRxiv2022

Microwell-based flow culture reduces hypoxia-induced phenotype and restores drug response in prostate cancer spheroids

3D cancer spheroids represent a highly promising model for study of cancer progression and therapeutic development. Wide-scale adoption of cancer spheroids, however, remains a challenge due to the lack of control over hypoxic gradients that may cloud the assessment of cell morphology and drug response. Here, we present a Microwell Flow Device (MFD) that generates in-well laminar flow around 3D tissues via repetitive tissue sedimentation. Using a prostate cancer cell line, we demonstrate the spheroids in the MFD exhibit improved cell growth, reduced necrotic core formation, enhanced structural integrity, and down-regulated expression of cell stress genes. The flow-cultured spheroids also exhibit an improved sensitivity to chemotherapy with greater transcriptional response. These results demonstrate how fluidic stimuli reveal the cellular phenotype previously masked by severe necrosis. Our platform advances 3D cellular models and enables study into hypoxia modulation, cancer metabolism, and drug screening within pathophysiological conditions.

bioengineering↗
bioRxiv2021

Precise quantification of behavioral individuality from 80 million decisions across 183,000 flies

Individual animals behave differently from each other. This variability is a component of personality and arises even when genetics and environment are held constant. Discovering the biological mechanisms underlying behavioral variability depends on efficiently measuring individual behavioral bias, a requirement that is facilitated by automated, high-throughput experiments. We compiled a large data set of individual locomotor behavior measures, acquired from over 183,000 fruit flies walking in Y-shaped mazes. With this data set we first conducted a "computational ethology natural history" study to quantify the distribution of individual behavioral biases with unprecedented precision and examine correlations between behavioral measures with high power. We discovered a slight, but highly significant, left-bias in spontaneous locomotor decision-making. We then used the data to evaluate standing hypotheses about biological mechanisms affecting behavioral variability, specifically: the neuromodulator serotonin and its precursor transporter, heterogametic sex, and temperature. We found a variety of significant effects associated with each of these mechanisms that were behavior-dependent. This indicates that the relationship between biological mechanisms and behavioral variability may be highly context dependent. Going forward, automation of behavioral experiments will likely be essential in teasing out the complex causality of individuality.

neuroscience↗