Biology subjects

Thomas, S.

Publications and source records attributed to Thomas, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Bioenergetic and Proteomic Profiling of ARID1A-Deficient Ovarian Clear Cell Carcinoma under Metabolic Challenge

ARID1A loss is associated with increased mitochondrial respiration in ovarian clear cell carcinoma (OCCC), but whether this phenotype is maintained under metabolic challenge remains unclear. Here, we examined mitochondrial function and electron transport chain (ETC) protein abundance in isogenic ARID1A wild-type (WT) and ARID1A-knockout (KO) OCCC cells cultured under physiological glucose, galactose, or the Complex I inhibitor IACS-010759. Across all conditions, KO cells maintained higher basal, ATP-linked, and maximal respiration, greater spare respiratory capacity, and higher coupling efficiency than WT cells, despite lower steady-state ATP levels. In human OCCC tumors, ARID1A-negative cases showed a higher bioenergetic cellular (BEC) index than ARID1A-positive cases, and high BEC was associated with poorer cancer-specific survival. Quantitative proteomics revealed a trend toward higher ETC complex abundance in KO cells, although whole-complex differences did not reach statistical significance. ARID1A loss was associated with selective increases in Complex III and V proteins, whereas metabolic challenge was associated with increases in Complex I and IV proteins. Together, these findings show that the ARID1A-associated mitochondrial phenotype persists across distinct metabolic challenges and is not explained simply by coordinated increases in ETC protein abundance. The association of mitochondrial bioenergetics with clinical outcomes further supports its relevance in human OCCC.

cancer biology↗

bioRxiv2026

PRISM: A Plasmid-based Reporter for Intracellular Spectral Microscopy

Organelles form an interconnected network whose morphology, positioning and interactions reflect cellular state. However, reproducibly quantifying these organelle phenotypes across large cell populations and diverse cell types remains a significant challenge. Here we present PRISM (Plasmid-based Reporter for Intracellular Spectral Microscopy), a PiggyBac-integrable construct encoding five unique fluorescent organelle reporters for spectral microscopy, with an accompanying modular analysis pipeline. PRISM stably labels the Golgi, peroxisomes, endoplasmic reticulum, mitochondria and lysosomes in multiple cell types while remaining compatible with additional molecular or functional probes. The workflow extracts over 500 metrics per cell, describing organelle morphology and distribution alongside pairwise and higher-order contacts. We use PRISM to characterise organelle responses to cytoskeletal perturbation, map PI(4)P redistribution during lysosomal damage, and reveal how Zika virus remodels the organelle landscape during infection. PRISM provides a reproducible approach for investigating organelle network remodelling across biological contexts

cell biology↗

bioRxiv2026

Chloroplast expression of Chlamydomonas glycolate dehydrogenase en route to an improved photorespiratory bypass

Successes with photorespiratory bypass pathway engineering have relied on nuclear transformation, requiring subcellular targeting and protein localization in the target organelles for photorespiration. In the current study, mitochondrial Chlamydomonas glycolate dehydrogenase (CrGDH) was directly expressed in chloroplasts of Chlamydomonas and tobacco, as the first enzymatic step for a photorespiratory bypass. Proof-of-concept experiments in Chlamydomonas were followed by transgenic tobacco lines that confirmed the chloroplast accumulation of active CrGDH protein. Photosynthetic rates and biomass were comparable or less than those of wild type plants under the tested conditions, indicating that chloroplast expression of CrGDH alone is insufficient to improve plant performance. These results suggest that additional downstream enzymes within a complete photorespiratory bypass are required to metabolize glyoxylate derived from CrGDH activity and thereby benefit growth. One of the chloroplast transformed lines (APP2882) accumulated CrGDH while maintaining wild type levels of photosynthesis and biomass, providing a best candidate chassis for engineering full photorespiratory bypass pathways.

plant biology↗

bioRxiv2026

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

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

bioengineering↗

bioRxiv2026

Species-level controls of foliar methane and nitrous oxide fluxes: roles of traits and microbes in temperate trees

The contribution of tree foliage to atmospheric methane (CH4) and nitrous oxide (N2O) fluxes remains a major uncertainty in global GHG budgets. We made repeated in situ measurements of foliar CH4 and N2O fluxes across 25 temperate tree species interplanted at a forest restoration site using high-resolution laser spectroscopy. Tree foliage was consistently a net CH4 sink and a net N2O source in all species. Foliar CH4 oxidation increased by [~]33% in fall relative to spring and was [~]3-fold higher in shade-tolerant than shade-intolerant angiosperm species. Species differences accounted for most of the variability in fluxes, while correlations with soil emissions were comparatively weak. Microbial DNA sequencing revealed that the highest CH4-oxidizing angiosperm species (Tilia americana) harbored abundant Type I methanotrophs, whereas the lowest-oxidizing species (Prunus virginiana) had nearly 100-fold lower methanotroph abundance, with a foliar microbial community dominated by facultative methylotrophs. Global warming potential (GWP) scaling indicates that foliar CH4 uptake overwhelmingly dominates the net climate forcing effect. Our results suggest that the large and predictable differences in foliar CH4 uptake among tree species and associated differences in foliar microbial communities are of importance in understanding and potentially enhancing the global terrestrial CH4 sink.

ecology↗

bioRxiv2026

Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome

Infant antibiotic treatment is associated with increased risk of developing non-communicable diseases, potentially through disruption of the gut microbiome. However, the impact of indirect antibiotic exposure via human milk remains largely unexplored. Here, we investigate a cohort (n=80) of antibiotic-treated breastfeeding mother-infant dyads and untreated matching controls using integrative multi-omics analyses of fecal, milk, and skin samples (n=1,455). Maternal antibiotic treatment was associated with different infant fecal microbiome and metabolome profiles, including lower abundance of Bacteroides, Lactobacillus, and Bifidobacterium, and higher levels of antimicrobial resistance gene reads. Further, fecal metabolic alterations associated with indirect antibiotic exposure were exacerbated by formula milk supplementation. In a subset of infants (n=61), indirect exposure was associated with higher body mass index (BMI). These findings suggest that maternal antibiotic treatment during lactation may influence the early-life infant gut microbiome with potential long-term implications.

microbiology↗

bioRxiv2026

Adrβ2 in skeletal muscle cells is required for exercise-induced Pgc1α but not for metabolic benefits of exercise on diet-induced obesity

{beta}2-Adrenergic receptor (Adr{beta}2) is the most abundant form of adrenergic receptors in skeletal muscle. Our previous studies have shown that the ventromedial hypothalamic nucleus (VMH) regulates metabolic benefits of exercise, potentially by skeletal muscle Adr{beta}2. Although a large body of literature has shown the importance of Adr{beta}2 on skeletal muscle physiology, it remains unexplored whether skeletal muscle Adr{beta}2 contributes to metabolic benefits of exercise, such as prevention of diet-induced obesity (DIO). Here, we generated mice lacking Adr{beta}2 in skeletal muscle cells (SKMAdr{beta}2) and tested whether SKMAdr{beta}2 is required for metabolic benefits of exercise on DIO. Deletion of SKMAdr{beta}2 completely abolished the induction of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (Pgc-1) in skeletal muscle by {beta}2-agonist, which is a potent activator of Pgc-1. Exercise upregulates Pgc-1, which regulates a broad range of skeletal muscle physiology, including hypertrophy and mitochondrial function. Deletion of SKMAdr{beta}2 hampers augmented Pgc-1 in skeletal muscle by a single bout of exercise. Intriguingly, we found that deletion of SKMAdr{beta}2 increased endurance capacity. Further, our data showed that body weight in DIO mice lacking SKMAdr{beta}2 is comparable to that of control DIO mice during exercise training, suggesting that deletion of SKMAdr{beta}2 did not affect the metabolic benefits of exercise in DIO. Collectively, our data indicate that SKMAdr{beta}2 contributes to exercise-induced transcriptional changes and endurance capacity, however, it is not required for exercise benefits on bodyweight in DIO mice.

physiology↗

bioRxiv2026

A Deep-Learning Atlas of XPO1-Mediated Nuclear Export at Proteome Scale

Exportin 1 (XPO1/CRM1) is the principal nuclear export receptor for cargos bearing hydrophobic nuclear export sequences (NESs). Dysregulation of XPO1-dependent export is implicated in cancer, neurodegeneration, and other diseases, yet a comprehensive view of XPO1 function remains limited by the poor reliability of sequence-based NES prediction. Existing predictors are largely derived from a small set of XPO1-cargo structures and are therefore biased toward canonical docking geometries, limiting their ability to detect NESs that engage XPO1 through noncanonical pocket-occupancy patterns. We hypothesized that deep learning-based structural modeling could overcome this limitation by directly sampling binding geometries. Using AlphaFold 3, we modeled full-length cargo-XPO1-RanGTP complexes for more than 4,000 human proteins and identified over 3,000 previously uncharacterized, high-confidence NESs. Integration of AlphaFold predictions with unsupervised structural geometry analysis and experimental validation identified both canonical NESs and noncanonical sequence patterns exhibiting atypical anchor-residue usage, expanding the structural language of XPO1-recognized NESs. Groove-resolved contact maps further revealed helix rotation within the export groove as a regulatory feature that can rewire pocket usage without altering the core NES sequence, enabling PTM- and cofactor-sensitive tuning of export strength. This exportome atlas resolves many previously ambiguous or unidentified NESs in disease-associated proteins and across major cellular systems, including centrosome organization, mRNA processing, ubiquitin signaling, kinase networks, ribosome quality control, and macroautophagy. We further identified recurrent NES-NLS tandem motifs encoded in primary sequence, suggesting coordinated regulation of nucleocytoplasmic transport. Together, our deep learning-based exportome atlas, integrated with NLS maps and accessible through a web-searchable resource, defines an expanded and regulatable code of nuclear transport at proteome scale and offers a framework for dissecting nuclear trafficking and its dysregulation in human disease.

cell biology↗

bioRxiv2026

Endothelial ACKR1 expression regulates neutrophil infiltration and breast cancer metastatic engraftment in the lung metastatic niche

The formation of the premetastatic niche prepares distant tissues for tumor cell engraftment. Endothelial cells are critical mediators of premetastatic niche formation, orchestrating extravasation of circulating tumor cells and critical pro-tumor immune cells, such as neutrophils. In mouse models of breast cancer, we show that primary tumors upregulate the non-signaling chemokine receptor ACKR1 in the endothelium of the lung premetastatic niche. ACKR1-expressing venules were found to be preferential sites of neutrophil and tumor cell localization within lung tissue. A newly generated conditional ACKR1 allele was used to show that endothelial-specific removal of ACKR1 expression significantly reduces metastatic engraftment in the lung. When ACKR1 is activated by tumor-secreted factors, endothelial ACKR1 functions to promote neutrophil recruitment within the lung parenchyma. We conclude that ACKR1 is a critical component of the endothelial response to tumors at the metastatic site of the lung, leading to neutrophil recruitment and promotion of tumor cell metastasis. SUMMARYEndothelial cells play critical roles in breast cancer metastasis. ACKR1 is upregulated in the endothelium of the lung metastatic niche in response to primary mammary tumors. Endothelial ACKR1 expression was found to promote neutrophil infiltration into the metastatic niche and support breast tumor cell metastasis to the lung.

cancer biology↗

bioRxiv2026

Automated Viability Estimation from Digital Holographic Microscopy: Validation on Heterogeneous Industrial Bioproduction Cultures

Cell viability is a critical parameter in bioproduction, yet most facilities still rely on manual, offline assays. This work introduces a new label-free Digital Holographic Microscopy (DHM)-based viability prediction pipeline using a simple optical design compatible with both on-line and in-line probe implementation. Unlike previous approaches validated under controled laboratory conditions, the proposed pipeline was designed to operate across diverse CHO bioprocess conditions without calibration or parameter tuning. It was validated on a large, heterogeneous dataset comprising 40 cell cultures collected from industrial and academic sites, spanning multiple cell lines, culture media, process modes and cell densities up to 100 million cells/mL. Beyond viability estimation, exploratory analyses suggest that DHM-based monitoring can provide additional process-relevant insights, including early detection of viability decline and correlation with recombinant protein titer. Together, these results indicate that DHM has the potential to enable a new generation of non-invasive, multiparametric monitoring tools for advanced bioproduction control.

bioengineering↗

bioRxiv2025

CANVAS causing AAGGG repeat expansions cause tissue-specific reduction in RFC1 expression and increase sensitivity to DNA damage

Biallelic AAGGG expansions in Replication Factor Complex Subunit 1 (RFC1) are associated with cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and are increasingly recognised as a common cause of adult-onset ataxia and sensory neuropathy. However, the disease-causing mechanisms remain unclear. Here we leveraged in vitro assays, post-mortem brain tissue, patient-derived cell lines and a neuronal Drosophila model to demonstrate that AAGGG expansions are associated with tissue-specific reductions in the expression of RFC1 transcript, along with impaired RFC1 function and increased sensitivity to DNA damage from platinum-based drugs. CRISPR/Cas9 excision of the AAGGG repeat and flanking AluSx3 element normalized RFC1 expression in iPSC-derived neurons and rescued the DNA damage response, providing a framework for future therapeutic strategies. We also show that these biological findings are clinically relevant in heterozygous AAGGG expansion carriers, who display an increased risk and severity of neuropathy with platinum-based chemotherapy.

neuroscience↗

bioRxiv2025

Quality-control Normalization of Fluorescence Microscopy Morphometry and Colocalization Measurements for Improved Accuracy and Cross-instrument Reproducibility

Quantitative fluorescence microscopy is more reproducible when instrument performance is measured and incorporated into the analysis. We show that routinely monitored quality-control (QC) metrics like the system resolution and inter-channel co-registration are determinant variables that can be used to normalize common image readouts and thereby separate instrument-induced variation from genuine biological changes. For intra-channel morphometry, a Gaussian approximation of the fluorescence imaging process yields analytical factors that predict how geometric measurements (length, separation distance, area, volume, etc.) inflate and scale with resolution blur due to optical misalignments or natural optical quality variations. We validate this behavior by deliberately perturbing the system resolution and by exploiting the natural resolution differences in three nominally equivalent objective lenses configured to image the exact same synapses in cultured hippocampal neurons, where structural differences subtle by eye nonetheless produced statistically significant shifts in measured synaptic puncta volumes. For dual-channel colocalization (overlap) measurements, we normalize the inter-channel co-registration QC metric by the measured point-spread function (PSF) resolutions (rather than theoretical limits associated with the objective lens) and demonstrate how fluorescent pre/postsynaptic cleft protein overlap signals decay in a predictable, exponential fashion as the PSF-normalized registration error increases, with the decay rate depending on the imaged object relative to the PSF size ratio. Mapped field-of-view gradients in channel registration also explain feature orientation flips/rotations and overlap loss without any underlying biological change. Finally, we outline a simple QC-aware microscope normalization workflow where each image measurement dataset is paired with its session PSFs and local co-registration error to remove instrument bias and optionally re-project the results to a declared reference PSF without altering the raw images. This approach improves image measurement accuracy and cross-instrument comparability of experiments and reframes light microscope QC from a passive certification of instrument health into a practical normalization that links the acquisition state to quantitative outcomes, thus ensuring the reliability and interpretability of morphometric and colocalization data in fluorescence microscopy.

cell biology↗

bioRxiv2025

Dynamic expression and differential requirement of the myocyte fusogen Myomixer during distinct myogenic episodes in the zebrafish

Skeletal muscle formation involves the fusion of myocytes into precisely aligned, multinucleated myofibres. These fibres continue to grow through reiterative rounds of myocyte fusion, incorporating new myonuclei and supporting muscle growth, repair and regeneration over organismal life span. The vertebrate-specific myocyte fusogens, Myomaker (Mymk) and Myomixer (Mymx), are crucial for generating multinucleated skeletal muscles. While the role of the transmembrane protein Mymk is well established, expression dynamics of mymx and the function of the Mymx micropeptide is less well understood. Here, using quantitative imaging and a mymx knockout strain, we explored the impact on myogenesis at different life stages of the zebrafish. We demonstrate that during the initial phase of muscle formation, mymx has a spatiotemporally varied expression across all axes of the developing myotome. On Mymx loss, myotome morphogenesis is disrupted, with both cell and tissue structure impacted. Moreover, we could show differential effects of Mymk versus Mymx loss on myocyte fusion and muscle growth. Finally, we report that perturbation to adult muscle multinucleation and size impacted bone development, again with different phenotypic severities among the two fusogen mutants. Together, our work provides key insights into the interplay between myocyte fusion, myotome morphogenesis and acquisition of final adult form.

developmental biology↗

bioRxiv2025

Inoculation with arbuscular mycorrhizal fungi can increase the concentration of PFAS compounds in cereal crops

Contamination of agricultural soils with per and poly-fluoroalkyl substances (PFAS) is now widespread and common throughout the world due to management practices such as biosolid application. Crop and pasture plants can readily take up and accumulate PFAS in their tissues, which eventually ends up in food products or livestock feed and presents health issues. We investigated whether arbuscular mycorrhizal (AM) fungi in the soil affect plant PFAS uptake in three important cereal crop species (barley, bread wheat, durum wheat), using a combination of soils that were artificially-spiked or naturally contaminated with PFAS. Spiking soil with PFAS did not interfere with AM colonisation of roots, nor did it detrimentally affect plant biomass. However, the shoots of all three plant species accumulated high concentrations of multiple short- and long-chain PFAS compounds. Inoculation with AM fungi led to increased concentration of all measured PFAS compounds in durum wheat shoots and several compounds in barley shoots, with no effect on any compounds in bread wheat shoots. The effect of AM fungal colonisation on PFAS concentrations in cereal plants is highly dependent on the nature of the soil PFAS contamination (i.e., the concentration and speciation) and the host plant species. It remains to be investigated whether AM fungi can directly take up PFAS from the soil.

plant biology↗

bioRxiv2025

Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuronal Regeneration.

Therapeutic angiogenesis is essential for regenerating brain tissue damaged by stroke, yet it remains an unmet clinical challenge. During brain development, pro-angiogenic genes drive the formation of vascular networks, with their expression tightly regulated in later stages. We found that in adult CNS endothelial cells (ECs), angiogenesis-related genes are epigenetically silenced through histone deacetylase 2 (HDAC2) and the polycomb repressive complex 2 (PRC2). Conditional deletion of Hdac2 in ECs reactivated pro-angiogenic signaling, including Wnt/{beta}-catenin target genes, leading to functional neovascularization with preserved blood-brain barrier (BBB) integrity in the adult brain. In contrast, Ezh2 (PRC2 subunit) deletion reduced vessel density and compromised BBB function. Deletion of Hdac2 and Ezh2 immediately after transient ischemic stroke conferred vascular protection by modulating stroke-induced transcriptional programs in CNS ECs. In contrast, delayed deletion, initiated seven days post-stroke, after significant neuronal loss in the infarct region, induced robust revascularization and promoted post-stroke neurogenesis, with differentiation into both excitatory and inhibitory neurons. These findings highlight CNS EC HDAC2 as a promising therapeutic target for inducing adult brain angiogenesis, facilitating revascularization, and supporting neuronal regeneration following stroke.

neuroscience↗

bioRxiv2025

Environmental and Maternal Imprints on Infant Gut Metabolic Programming

Early life is a critical period for immune and metabolic programming, but developmental patterns remain underexplored in populations from low- and middle-income countries. Here, we profiled the microbiome and metabolome of 55 Bangladeshi mother-infant dyads over the first six months of life. Importantly, we observed an increase in microbially-derived bile amidates and N-acyl lipids with age in conjunction with reads matching the bile salt hydrolase/transferase (bsh) gene. While microbial source tracking confirmed maternal fecal seeding, a substantial environmental contribution was also highlighted. Differences in infant fecal metabolic profiles were associated with delivery mode, maternal milk composition, household assets, and household-level water treatment. C-section delivery and untreated drinking water were linked to transient metabolic differences, including increases in bile amidates, N-acyl lipids, and other host-microbe co-metabolic products, including acylcarnitines. Multi-omics analysis revealed specific microbial-metabolite relationships, highlighting how early environmental and maternal living circumstances shape metabolic gut programming through the microbiome.

microbiology↗

bioRxiv2025

Modulating Cardiac-Gut Microbiome Interaction Post-Myocardial Infarction with Engineered Bacteria

The gut microbiome plays a critical role in the pathophysiology of acute myocardial infarction (MI). MI events significantly impact intestinal integrity which results in leakage of bacterial products into the systemic circulation. We demonstrate that MI not only compromises intestinal integrity, leading to systemic leakage of bacterial products like LPS, but also results in the translocation and colonization of live, intact gut bacteria in the MI heart - a novel aspect of the heart-gut axis. Our initial findings with natural murine gut microbiome were substantiated using orally administered E. coli Nissle 1917 (EcN), as a tracer bacterium. Furthermore, we engineered EcN to express the microbial anti-inflammatory molecule (MAM) derived from the probiotic Faecalibacterium prausnitzii. Treatment with this engineered strain, EcN-MAM, led to significantly improved survival and cardiac function in MI mice. This was attributed to enhanced gut barrier integrity, resulting in reduced systemic bacterial permeation and subsequent inflammation. These findings shed light on a previously unrecognized dimension of the heart-gut axis and highlight the potential of microbiome-based interventions in MI management.

synthetic biology↗

bioRxiv2025

Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles

Indirect exposure to antibiotics during early life, via maternal intrapartum antibiotic prophylaxis (IAP) or postpartum maternal antibiotic usage, is increasingly common and has been epidemiologically linked to altered growth and immune developmental trajectories in offspring. Nevertheless, the underlying mechanisms remain poorly understood. Here, we explored the effects of antepartum and postpartum maternal ampicillin administration on the dams fecal microbiome and metabolic profiles in vivo. Ampicillin caused a reproducible depletion of beneficial bacterial species belonging to the Muribaculaceae family, including Muribaculum intestinale and Duncaniella dubosii, and led to cohort-dependent enrichments of Enterococcus and Prevotella species. These microbial alterations were accompanied by substantial metabolic remodeling, characterized by elevated fecal acylcarnitines and dysregulation of the bile acids profile. Intriguingly, we identified two previously uncharacterized trihydroxylated bile acids conjugated to a hexose moiety, which appeared to be associated with antibiotic exposure across public metabolomics repositories. These alterations in the fecal maternal microbiome and metabolome coincided with increased weight gain in offspring, suggesting a possible role for maternal antibiotic exposure in shaping early developmental trajectories. Further studies are warranted to elucidate the long-term implications of these changes in infant health. IMPORTANCEPerinatal antibiotic administration is a critical intervention to reduce maternal and neonatal infections, including early-onset group B Streptococcus (GBS) disease, a major cause of neonatal mortality. Nevertheless, mounting evidence suggests that the use of broad-spectrum antibiotics during the perinatal period in mothers can affect infant gut microbiome development, with potential consequences for immune maturation and early development. Understanding how maternal antibiotic exposure affects the gut microbiome and metabolome is essential for uncovering the potential pathways by which maternal intervention may influence offspring outcomes and for guiding strategies that balance infection control with long-term infant health.

microbiology↗