Biology subjects

Jones, S.

Publications and source records attributed to Jones, S..

At least 19 recordsLinked to original sources

bioRxiv2026

A quantitative three-dimensional bone mineralisation assay using human dental pulp stem cell spheroids

Matrix mineralisation in three-dimensional (3D) human cell culture is still assessed predominantly by terminal histochemical staining. Alizarin Red S and Von Kossa are destructive, semi-quantitative, and require fixation and dye extraction before a number can be obtained, which precludes longitudinal measurement and makes miniaturised multiwell formats impractical. We describe a scaffold-free assay that renders 3D human bone mineralisation as a continuous, well-level quantity. Primary human dental pulp stem cells (DPSCs) were dispensed by automated liquid handling into 384-well plates, where they formed a single, centrally positioned spheroid per well. Eleven plate geometry and surface-coating combinations were compared, and cell-repellent coating rather than well geometry alone was identified as the determinant of single-aggregate formation. Mineral deposition was measured non-destructively by adding the tetracycline-derived near-infrared probe BoneTag680 directly to the existing culture volume and reading the plate from below, with no spheroid transfer, embedding, sectioning or dye extraction at any point. Spheroids maintained in 10% fetal calf serum (FCS) with osteogenic cocktail were separated from a 1% FCS low-mineralisation condition with an assay window of 13.74 plus-or-minus sign 3.29-fold and a Z-factor of 0.627 plus-or-minus sign 0.119 across four independent plates, with a well-level coefficient of variation of 10.88% compared with 55.81% in a commercial alternative. A DNA content measurement acquired from the same wells after near-infrared acquisition showed no increase in cell number under osteogenic conditions, establishing that the mineral signal is not biomass-driven and providing an internal counter-screen against proliferative and cytotoxic artefacts. All data derive from a single donor; the assay is therefore characterised for technical and within-donor reproducibility, and is presented as a defined quantitative measurement intended as a foundation for bone-anabolic compound screening rather than as a screening-validated platform.

bioengineering↗

bioRxiv2026

Systematic Functional Interrogation of Neurodevelopmental Disorder Risk Variants

Neurodevelopmental disorders (NDDs) are highly polygenic, yet the functional consequences of most associated non-coding variants remain unclear. We used a massively parallel reporter assay (MPRA) to test 727 NDD-associated non-coding variants in human neural progenitors, identifying 38 expression-modulating variants (emVars) with regulatory activity. These emVars were predicted to alter transcription factor binding motifs linked to neurodevelopmental signaling and cellular metabolism. We mapped emVars to candidate target genes using expression quantitative trait loci and activity-by-contact (ABC) models. We then used CRISPR droplet sequencing (CROP-seq) in human pluripotent stem cell-derived neurons to identify endogenous target genes and characterize their downstream transcriptional effects. CROP-seq preferentially supported ABC predictions, identified additional regulatory relationships, and revealed convergence on developmentally regulated programs involving neuronal connectivity, synaptic function, and mitochondrial biology. Together, these results connect NDD risk variants to endogenous target genes and shared neurodevelopmental transcriptional programs.

genomics↗

bioRxiv2026

CYB-4/CDK-1 coordinates timing of meiotic entry, chromosome morphogenesis and oocyte maturation in C. elegans

Meiotic chromosome segregation requires the earlier coordination of chromosome morphogenesis with cell-cycle progression. In C. elegans, the remodeling of chromosomes in preparation for the meiotic divisions and oocyte maturation is regulated by the master cell-cycle regulator cyclin-dependent kinase 1 (CDK-1). Here, we identify CYB-4 as a meiosis-specific B-type cyclin that is required for CDK-1-dependent functions in meiotic prophase. In a genetic suppressor analysis of a mutant defective in chromosome axis assembly, we isolated a null allele that revealed a function for CYB-4 in regulating chromosome structure at two key prophase transitions. Loss of CYB-4 first delays meiotic entry and the onset of chromosome axis formation, and at pachytene exit delays chromatin condensation, bivalent remodeling, and oocyte maturation. The defects in timely CO formation and bivalent packaging that accompany these delays are ultimately resolved before prophase exit, indicating that CYB-4 is required for the scheduling of events rather than if they occur. Together, our findings provide evidence that CDK-1 activity during meiotic prophase is defined by CYB-4 and support a model in which CYB-4/CDK-1 are essential for the sharp transitions at prophase entry and pachytene exit that coordinate chromosome morphogenesis with meiotic progression.

cell biology↗

bioRxiv2026

Kiss1 neurons in the medial amygdala of mice are sexually dimorphic and unique from hypothalamic anteroventral periventricular Kiss1 neurons in their action potential firing properties

Abstract The importance of hypothalamic kisspeptin (Kiss1) neurons in controlling the reproductive axis is well established, while a population of extra-hypothalamic Kiss1 neurons is found in the medial amygdala (MeA) of both males and females in rodents and is less well understood. The MeA is connected with the olfactory bulbs, the hypothalamus and cortical areas. MeA Kiss1 neurons have been implicated in sexual behaviour and modulation of the reproductive axis; however, little is known about their action potential firing properties, which would influence kisspeptin release in target brain regions, nor whether their physiological properties are sex- or estrous cycle-dependent. In this study, whole-cell patch-clamp recordings were made from Kiss1 neurons in brain slices containing the MeA of adult female (estrous and diestrous) and male mice. MeA Kiss1 (Kiss1MeA) neurons were sexually dimorphic, with greater numbers in male compared to female mice and a slower change in excitability in estrous females compared with males. However, combining a range of electrophysiological parameters using principal component analysis did not reveal a distinct sex- or estrous cycle-linked phenotype, suggesting that the properties of Kiss1MeA neurons- and therefore kisspeptin release- are broadly similar. Interestingly, Kiss1MeA neurons had unique electrophysiological properties compared with anteroventral periventricular (AVPV) hypothalamic Kiss1 (Kiss1AVPV) neurons in female mice; with their reduced excitability, achieving action potential firing frequencies greater than 10Hz required a larger current input, indicating that Kiss1MeA neurons require stronger synaptic input to achieve firing frequencies that drive kisspeptin release. These findings provide new information about the physiological properties of Kiss1MeA neurons, showing subtle sex differences and profound regional differences between the MeA and AVPV.

neuroscience↗

bioRxiv2026

Stony coral tissue loss disease outbreak altered reef communities of Carrie Bow Cay, Belize

Stony coral tissue loss disease (SCTLD) has caused one of the most damaging coral epizootics on record, impacting about half of coral species across most of the reef systems of the Caribbean and Florida. To evaluate its impact on the coral reefs surrounding Carrie Bow Cay, Belize, we monitored seven fixed transects before and at two time points during the outbreak using three different methods. We estimated species-specific mortality rates by fate tracking tagged colonies, quantified reef-wide lesion prevalence and resulting changes to colony density and community composition using in situ transect surveys, and finally calculated changes to total coral cover using benthic photoquadrats. SCTLD quickly led to mortality of infected corals. Between October 2019 and May 2022, 32% of the 102 fate-tracked coral colonies had developed lesions consistent with SCTLD and an additional 30% had suffered complete mortality likely due to SCTLD. By December of 2022, 21% of the 33 colonies that had been observed with lesions had died. We documented patterns of species susceptibility largely confirming previous reports in other locations. We documented sharp abundance declines in several species, including the total loss of Meandrina meandrites from survey transects, leading to a significant shift in community composition. Cover of several species declined between October 2019 and May 2022, but only Siderastrea siderea experienced sustained declines into December of 2022. Overall cover of scleractinian corals decreased from 13.2 to 7.9% during the monitoring period. The ecological impacts of SCTLD in the area surrounding Carrie Bow Cay are consistent with reports from elsewhere in the Caribbean, underscoring the magnitude of colony density and coral cover loss caused by SCTLD across the region.

ecology↗

bioRxiv2026

Mutations in severe human H5N1 cases facilitate evasion from human mucus and antivirals

In late 2024, two individuals in Canada and the United States were treated in intensive care for acute respiratory distress caused by infection with the avian Influenza A Virus H5N1 2.3.4.4b genotype D1.1. Viral sequence data obtained from sampling these patients indicated mixed alleles at haemagglutinin (HA) positions 190 and 226. Mutations at these positions are key determinants of HA usage of 2,6-linked sialic acids (SA), the most abundant influenza receptors in human upper respiratory tracts. Thus, these mutations raised concerns about human adaptation and pandemic potential of the H5N1 virus. In this study, we investigated the impact of the mutations at residues 190 and 226 in H5 HA. We studied the receptor binding properties, cell entry phenotypes and fitness impacts of the mutations using recombinant proteins, pseudotyped lentiviruses, and in the context of influenza viruses using reverse genetics. The mutations did not confer any detectable 2,6-linked sialic acid receptor usage either alone or in combination. Rather, viruses carrying these mutations exhibit weakened binding towards 2,3-linked sialic acid receptors. This correlated with an enhanced capacity to evade human airway mucus, and a reduced susceptibility to oseltamivir and zanamivir. This research underscores that in addition to the way HA interacts with SA as entry receptors, other factors that impact the HA/NA balance might influence the evolutionary trajectory of a zoonotic virus in the human respiratory tract. This study presents a new paradigm for the evolutionary drivers of HA, where reduced sialic acid binding can serve as an advantage for escape from host barriers and antivirals.

microbiology↗

bioRxiv2026

Sleep-Related Respiratory Disruption is Associated with Altered Spindle Morphology and Poorer Attention in Children

Study ObjectivesTo determine whether sleep-related respiratory disruption is associated with regionally specific alterations in sleep spindle topography and whether hypopnea-sensitive spindle features are associated with attentional performance in children. MethodsWe recorded overnight high-density EEG in children across a wide range of respiratory disruption severity. Slow and fast spindle metrics were extracted per channel, and channel-wise regression models characterized topographic associations with hypopnea index (HI). Cluster-based permutation testing controlled for multiple comparisons. Hierarchically defined regions of interest were tested as predictors of attentional performance on the Test of Variables of Attention (TOVA). ResultsCanonical slow-anterior and fast-posterior spindle organization was detectable across the cohort. Two HI-related topographic effects survived cluster-based permutation correction: higher HI was associated with shortened anterior fast spindle duration and with slower anterior slow spindle peak frequency. In cognitive models, anterior fast spindle duration was the strongest and most consistent predictor of attentional performance, associated with higher signal detection sensitivity, fewer omission errors, and fewer commission errors. By contrast, slow spindle peak frequency showed no attentional associations. ConclusionsPediatric respiratory disruption is associated with regionally specific alterations in spindle morphology rather than global spindle reduction. Shortened anterior fast spindle duration showed convergent respiratory and attentional associations, suggesting that localized spindle integrity may provide a neurophysiological marker of cognitive vulnerability in pediatric sleep-disordered breathing beyond conventional clinical respiratory metrics. HighlightsO_LIHigher hypopnea index was associated with shortened anterior fast spindle duration and slower anterior slow spindle peak frequency C_LIO_LIAnterior fast spindle duration predicted attentional performance in children C_LIO_LIRespiratory disruption may impair attention by disrupting thalamocortical spindle activity C_LI Statement of SignificanceChildren with sleep-disordered breathing can show neurocognitive difficulties that are not well explained by standard respiratory indices alone. This study uses high-density EEG to show that hypopnea burden is associated with regionally specific alterations in sleep spindle morphology, particularly shortened anterior fast spindle duration, rather than a global reduction in spindle occurrence. Anterior fast spindle duration was also the spindle feature most consistently associated with attentional performance. These findings suggest that localized spindle morphology may provide a sleep-neurophysiological readout of cognitive vulnerability in pediatric sleep-disordered breathing. Longitudinal and treatment studies are needed to determine whether spindle duration changes with respiratory improvement and whether such changes track cognitive recovery.

neuroscience↗

bioRxiv2026

Colletotrichum higginsianum effector ChEC108 binds a plasmodesmal HMA protein and elicits plant defence

To establish infection, phytopathogens deploy effectors to compromise host defences and facilitate invasive growth. As part of this, the battle for control of symplastic connectivity via plasmodesmata is a key determinant of infection outcomes, yet little is known about how fungal effectors directly exploit these channels, and in turn, how hosts defend them. Here, we have identified ChEC108 as a plasmodesmal-targeting, cell-to-cell mobile effector from the anthracnose fungus, Colletotrichum higginsianum. ChEC108 binds the plasmodesmal protein HEAVY METAL-ASSOCIATED (HMA) ISOPRENYLATED PLANT PROTEIN 6 (HIPP6) from Arabidopsis via a tetrahedral metal ion coordination site with either of its HMA domains. Constitutive in planta expression of ChEC108 induces plasmodesmal closure and the upregulation of defence-associated genes in a manner dependent on its capacity to bind HIPP6. Further, HIPP6 binding impairs cell-to-cell mobility of ChEC108. Alongside the finding that loss of ChEC108 favoured C. higginsianum infection, this suggests ChEC108-HIPP6 interaction at plasmodesmata positively regulates defence.

plant biology↗

bioRxiv2026

Metabarcode and transcriptome datasets of Pinus sylvestris to assess fungal phyllosphere and disease dynamics.

Understanding how host-microbiome interactions influence tree disease is critical for understanding forest resilience. Here, we present foliar microbiome ITS2 metabarcoding transcriptomic datasets from Pinus sylvestris to investigate susceptibility to Dothistroma needle blight (DNB), a globally important foliar disease caused by Dothistroma septosporum. We hypothesised that host genotype shapes foliar microbial communities and their interactions, thereby influencing disease outcomes. Samples were collected from a progeny-provenance field trial in the south of Scotland representing a broad spectrum of disease susceptibilities. The dataset comprises ITS2 metabarcoding samples from 200 genotypes across three timepoints and RNAseq samples from 48 genotypes across two timepoints. Sampling captured key stages of pathogen exposure and disease progression. Both standardised and bespoke protocols were used for nucleotide extraction, sequencing, and quality control, including multiple negative and positive controls. These datasets, available in the European Nucleotide Archive (project accession PRJEB88228), enable analysis of temporal dynamics in foliar fungal communities, host-microbiome transcriptional responses, and genotype-dependent variation in disease susceptibility.

bioinformatics↗

bioRxiv2026

A decade of disease survey data in a progeny-provenance trial: Dothistroma needle blight in Scots pine

Longitudinal data on disease susceptibility in forest trees are rare but essential for understanding host-pathogen dynamics and genetic variation in susceptibility traits. We present a long-term multisite common garden dataset quantifying susceptibility of Scots pine (Pinus sylvestris) to Dothistroma needle blight. The dataset comprises annual disease assessments collected from the same trees across 11 years, spanning 168 families and 21 Scottish provenances. This design enables partitioning of genetic and environmental sources of variation, evaluation of temporal stability in host response, and estimation of variance components and narrow-sense heritability of susceptibility. The data support analyses of phenotypic plasticity, provenance-level responses, and interactions between disease susceptibility and other adaptive traits. This resource will facilitate predictive modelling of host susceptibility under current and future environmental conditions.

ecology↗

bioRxiv2026

Translational toolkit for reproducible, cross-study profiling of human ageing hallmarks in human blood and tissue

BackgroundAgeing is a complex, multi-dimensional process, underpinned by interacting biological hallmarks that collectively contribute to functional decline and increased susceptibility to disease. While considerable progress has been made in delineating individual ageing pathways, translation into human studies has been hindered by methodological heterogeneity and a lack of standardised, multi-system approaches. Here, we describe a validated, high-resolution toolkit for the simultaneous quantification of multiple ageing hallmarks in clinically accessible human samples, encompassing cellular senescence, immune ageing, inflammation, mitochondrial function, mTOR signalling, autophagy, genomic instability, and stem cell exhaustion. MethodsBlood (25ml) was obtained from young and aged donors (26-81y). Deep immunophenotyping was performed using a novel 30-colour spectral flow cytometry panel. T-cell mTOR activation and autophagic flux were assessed by flow cytometry. Metabolic flux was measured by Seahorse. From whole blood (4 ml), muscle, and adipose tissue (AT) (obtained during elective hip arthroplasty) RNA, DNA, AT stem cells, and myoblasts were isolated. DNA copy number and senescent cell burden were assessed by q-PCR and SA-{beta}-gal staining, respectively. FindingsUtilising this toolkit, we identified pronounced age-related immune remodelling, increased senescent T-cell burden, diminished mitochondrial capacity and altered mTOR-autophagy signalling between healthy young and aged donors. Furthermore, metabolism was significantly affected by anti-coagulant and freezing sample before analysis. InterpretationThis integrated platform provides a foundation for reproducible, cross-study analyses and facilitates translational investigation of interventions targeting health-span extension. FundingWellcome Leap Dynamic Resilience program (co-funded by Temasek Trust).

immunology↗

bioRxiv2026

Bovine H5N1 influenza viruses have adapted to more efficiently use receptors abundant in cattle

Sustained mammal-to-mammal transmission of high pathogenicity H5N1 avian influenza viruses is reshaping the host range of these pathogens. One of the longest-running mammalian transmission chains involves the B3.13 genotype circulating in U.S. dairy cattle which was detected in early 2024. Genomic analyses revealed selection and rapid fixation of haemagglutinin mutations D104G and V147M. We demonstate, via glycomic profiling, that bovine tissues, including the mammary gland, are enriched in N- and O-linked glycans capped with N-glycolylneuraminic acid (NeuGc), a sialic acid absent in humans and birds, which instead express only N-acetylneuraminic acid (NeuAc). Early cattle H5 viruses poorly recognized NeuGc, but D104G and V147M enabled efficient engagement of both NeuAc- and NeuGc-containing receptors. These mutations enhanced replication in bovine mammary tissue without major attenuation of replication in human lung and primary nasal epithelial cells. NeuGc-driven receptor adaptation therefore promotes viral fitness in cattle while potentially limiting immediate zoonotic risk. Deep mutational scanning further identified alternative haemagglutinin substitutions that confer NeuGc usage and represent surveillance markers for emerging cattle H5 lineages.

microbiology↗

bioRxiv2026

S. cerevisiae Cwc15p Tunes the Spliceosome Active Site for 5' Splice Site Cleavage

Pre-mRNA splicing is an essential step in eukaryotic gene expression during which spliceosomes remove introns from nascent RNAs while ligating the adjacent exons. Spliceosomes are cellular nanomachines composed of five small nuclear (snRNA) components and dozens of proteins, most of which are highly conserved. Despite the high conservation of many splicing factors between S. cerevisiae and H. sapiens, several protein components of the S. cerevisiae spliceosome are not essential for growth under normal laboratory conditions. This is particularly surprising for nonessential factors whose conserved domains contact the spliceosomes catalytic core. Uncovering a function for these splicing factors can be challenging since they are not required for viability, may engage in functionally redundant interactions, and may display only weak phenotypes in the absence of secondary mutations in other spliceosome components. One such nonessential factor is the Cwc15 protein. Cwc15s highly conserved N-terminus directly contacts the U2/U6 di-snRNA within the spliceosome catalytic core; yet its precise role in splicing has not been defined in any organism. In this work, we use molecular genetics in S. cerevisiae combined with splicing reporter assays to study Cwc15p function. We propose that Cwc15p not only promotes the stability of the active site but also its structural transitions. These functions may be critical for splicing in S. cerevisiae under nonoptimal conditions, facilitating use of weak or alternate splice sites, and could have implications for proofreading of spliceosome active site formation.

molecular biology↗

bioRxiv2026

A novel framework for expanding RNNs with biophysical detail to solve cognitive tasks

Recurrent neural networks (RNNs) have proven to be highly successful in emulating human-like cognitive functions such as working memory. In recent years, RNNs are evolving to incorporate more biophysical realism to produce more plausible predictions on how cognitive tasks are solved in real neural circuits. However, there are major challenges in constructing and training networks with the complex and nonlinear properties of real neurons. A major component of the success of RNNs is that they share the same mathematical base as deep neural networks, permitting highly efficient optimization of model parameters using standard deep learning techniques. To do so, they use abstract representations of neurons which fail to capture the impact of cell-level biophysical and morphologic properties that may benefit network-level function. Expanding task-trained RNNs with biophysical properties such as dendrites and active ionic currents poses substantial challenges, as it moves these models away from the validated training regimes known to be highly effective for RNNs. To address this gap, we developed a biophysically detailed reservoir computing (BRC) framework with the goal of extracting mechanistic insights from biophysical neural models, and propose that these insights can be used to guide model choices that will work for specific categories of cognitive tasks. The BRC network was constructed with synaptically coupled excitatory and inhibitory cells, in which the excitatory cells include multicompartment biophysically active dendrites; motivated by empirical studies suggesting dendrites have desirable computational benefits (e.g. pattern classification and coincidence detection). We trained the BRC network to do a simplified working memory task where it had to maintain the representation of an extrinsic "cue" input. We studied the impact of extrinsic input time constants (fast AMPA vs slow NMDA) and location (dendrite vs soma) on the ability of a network to solve the task. Our results revealed that cue inputs through NMDA receptors are particularly efficient for solving the working memory task. Further, the properties of NMDA receptors are uniquely suited for cue inputs delivered at the dendrite, as networks trained with dendritic AMPA cue inputs failed to solve the task. Detailed examination of the cell and network dynamics that solve the task reveals distinct local network configurations and computing principles for the different types of extrinsic input. Overall, much like the body of mechanistic insights that have underpinned the success of training RNNs, this study lays the groundwork for applying the BRC framework to train biophysically detailed neural models to solve complex human-like cognitive tasks.

neuroscience↗

bioRxiv2026

Autophagy induction mitigates FUS aggregate formation and early synaptic dysfunction at the NMJ in the FUS-ALS model

Mutations in Fused in Sarcoma (FUS), a RNA binding protein, cause Amyotrophic Lateral Sclerosis (ALS). ALS is an aggressive neurodegenerative disease resulting in motor neuron degeneration. Defects in synaptic integrity precede neuronal loss in ALS, but the mechanisms responsible for these early synaptic defects are unclear. To investigate early synaptic defects associated with ALS, we expressed an ALS-linked variant of human FUS in adult motor neurons and assessed synaptic pathology at the neuromuscular junction (NMJ). Here we highlight the accumulation of FUS-positive aggregates at synaptic terminals and subsequent reduction in microtubule stability. We show that inducing autophagy via expression of Rab1 or Fragile-X Mental Retardation Protein 1 (FMR1), or treatment with Rapamycin reduces aggregate formation and restores synaptic structure and function. These findings reveal the utility of inducing autophagy to address early synaptic dysfunction in an ALS model and demonstrate a potential therapeutic target to preventing later stages of disease progression.

neuroscience↗

bioRxiv2025

Wherefore the magic? The evolutionary role of psilocybin in nature

Research into psychedelic compounds is in resurgence due to the exciting potential for their use in the treatment of psychiatric and mental health disorders. Despite this revival, remarkably little is known about their evolution. One of the most intriguing psychedelic compounds is psilocybin, the compound found in magic mushrooms and used in ritual ceremonies in Central America for generations. Associated with agaricomycete fungi of the genus Psilocybe, psilocybin acts in a similar way to the neurotransmitter serotonin, yet how and why natural selection favoured its biosynthesis remains unclear. Given the resemblance to serotonin, modulation of invertebrate behaviour for defence is a likely explanation, but neither this nor alternative hypotheses have ever been formally tested. Here, we show that Drosophila larvae exposed to extracts from Psilocybe mushrooms exhibit reduced survival, pupation rates, and inhibited locomotion. Adults exposed during development show reduced thorax and wing size, along with increased fluctuating asymmetry, indicating developmental stress. Conversely, mutants lacking 5HT2A receptors showed the same response to Psilocybe extracts as wild-type flies. Furthermore, DNA metabarcoding revealed that while Psilocybe semilanceata demonstrates a distinct invertebrate community compared to most other grassland fungi, it overlapped with the non-psychedelic species Mycena epipterygia. This study provides a crucial first step toward understanding the evolutionary role of psilocybin-producing fungi and provides a grounding for future research into the molecular mechanisms, ecological interactions and evolutionary origins of psychedelic compounds in nature.

ecology↗

bioRxiv2025

Obesity reprograms adipose extracellular vesicles to induce muscle atrophy via miR-150-5p-mediated transcriptional silencing

BackgroundSarcopenic obesity, where excess body fat coexists with reduced muscle mass and function, is becoming increasingly common in ageing populations and contributes to poor physical and metabolic health. Although adipose tissue-secreted factors are implicated in muscle decline, the specific mechanisms remain unclear. Extracellular vesicles (EVs), which carry regulatory cargo such as microRNAs (miRNAs) between cells, may play a key role in this adipose-muscle communication. MethodsEVs were isolated from adipose-conditioned media (ACM) collected from lean and non-lean human donors using ultracentrifugation. Donors were grouped by BMI (lean: 20.7-24.4; non-lean: 25.3-39.3) and age (younger: 31-56 years; older: 60-84 years). EVs were characterised using nanoparticle tracking analysis (NTA), ExoView, nanoscale flow cytometry (CytoFLEX Nano), and transmission electron microscopy (TEM). Primary human myoblasts were differentiated into myotubes and treated for 24 hours with lean or non-lean EVs (1.3x10 particles/ml) or left untreated. Myotube thickness was measured by immunofluorescence microscopy. Transcriptomic changes were assessed by bulk RNA sequencing. EV miRNA cargo was profiled by small RNA-seq and validated by qPCR. The role of miR-150-5p was tested using antagomir inhibition. ResultsNon-lean EVs significantly reduced myotube thickness compared to both untreated controls (8.7 {+/-} 1.66 {micro}m vs. 12.4 {+/-} 1.72 {micro}m, p < 0.01) and lean EV-treated myotubes (8.7 {+/-} 1.66 {micro}m vs. 13.2 {+/-} 3.84 {micro}m, p < 0.05), indicating a donor BMI-specific effect. This atrophy was restricted to myotubes derived from older donors. MAFbx expression was significantly increased in response to non-lean EVs (p < 0.05). RNA-seq revealed 471 differentially expressed genes (DEGs) in EV-treated vs. untreated cells and 293 DEGs between lean and non-lean EV conditions, with enrichment in inflammatory (TNF, IL1B), oxidative stress, mitochondrial, and chromatin pathways. Small RNA-seq identified 7 differentially expressed miRNAs, including miR-150-5p and miR-193b-5p, both significantly upregulated in non-lean EVs and validated by qPCR. Inhibiting miR-150-5p partially rescued myotube thickness (10.5 {+/-} 1.37 {micro}m vs. 8.7 {+/-} 1.66 {micro}m, p < 0.05) and reduced MAFbx expression. ConclusionsEVs from non-lean adipose tissue drive muscle atrophy and transcriptional changes in an age-dependent manner. These effects are partially mediated by miR-150-5p, highlighting a mechanistic role for EV cargo in adipose-muscle signalling. Targeting EV-derived miRNAs may offer a novel strategy to combat muscle loss in obesity and ageing.

cell biology↗

bioRxiv2025

Spatio-Temporal Multi-Omics Profiling of Mechanisms and Biomarkers in Inhaled Drug-Induced Lung Toxicity

Comprehensive understanding and early detection of drug-induced lung toxicity remain critical challenges in respiratory drug development. In this study, we propose a multi-omics framework that integrates spatial and temporal tissue-specific transcriptomic signatures with proteomics from minimally invasive biofluids to understand mechanisms and identify safety biomarkers associated with lung toxicity. Using this framework, we identified a panel of candidate biomarkers in bronchoalveolar lavage fluid and plasma, including LCN2/NGAL, RETNLA, SP-D, SPP1/osteopontin, and MMP7, that correlate with histopathological features (e.g., inflammation and epithelial remodeling). We confirmed that these molecular biomarkers were consistently dysregulated across a range of inhaled lung toxicants, human disease (IPF), and environmental exposures (smoke, Alternaria), demonstrating broad applicability across different toxic exposures and translatability. Collectively, this study establishes a robust workflow for mechanism-guided biomarker discovery and proposes a panel of candidates for monitoring drug-induced lung injury in humans.

systems biology↗