Biology subjects

Burton, J.

Publications and source records attributed to Burton, J..

14 recordsLinked to original sources

bioRxiv2026

The lysosomal channel RECS1 regulates extracellular vesicle biogenesis

Lysosomal ion channels play key roles in regulating membrane trafficking, autophagy, and cell death. RECS1 is a pH-sensitive lysosomal calcium channel previously implicated in lysosome-mediated apoptosis. Here, we identify a novel role for RECS1 in exosome biology. Using immunoprecipitation followed by mass spectrometry, we mapped RECS1 interactors under apoptotic and lysosomal stress conditions. Notably, Syntenin-1, a key scaffolding protein in ESCRT-independent exosome biogenesis, emerged as the top hit. We validated the physical interaction between RECS1-Syntenin-1 using various approaches. RECS1 localized to secreted exosomes, and its overexpression increased exosome production, as measured by nanoparticle tracking analysis. Intriguingly, a channel-dead RECS1 retained both Syntenin-1 interaction and the ability to promote exosome release, suggesting a channel-independent mechanism. Our findings identify RECS1 as a structural component of the exosomal trafficking machinery and a modulator of extracellular vesicle biogenesis. This work connects lysosomal signalling with intercellular communication and suggests a broader role for RECS1 in stress-responsive secretion.

cell biology↗

bioRxiv2025

Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis

Endothelial cells (ECs) are critical regulators of vascular function and exhibit specialized, organ-specific roles across tissues. During aging, these cells become dysfunctional, resulting in increased susceptibility to cardiovascular disease and its associated mortality. While single-cell transcriptomics studies have revealed extensive endothelial heterogeneity across tissues and conditions, a comprehensive atlas of human EC transcriptomes over the course of the adult human lifespan is still lacking. Here, we present the Human Aging Endothelial Cell Atlas (HAECA), a harmonized single-cell transcriptomic compendium of over 375,000 ECs from 12 human tissues throughout adulthood. Using HAECA, we identified age-associated transcriptional shifts, including a decline in angiogenic gene expression in venous ECs and widespread alterations in extracellular matrix (ECM)- and mechanotransduction-associated pathways. We validated these findings in aging human skin and further uncovered a p21-linked transcriptional program in ECs, confirmed in both in vitro and in vivo models and linked to cellular senescence. Together, our study provides a high-resolution transcriptome reference across spatial as well as temporal axes of the human endothelium.

cell biology↗

bioRxiv2025

Molecularly informed analysis of histopathology images using natural language

Histopathology refers to the microscopic examination of diseased tissues and routinely guides treatment decisions for cancer and other diseases. Currently, this analysis focuses on morphological features but rarely considers gene expression information, which can add an important molecular dimension. Here, we introduce SpotWhisperer, an AI method that links histopathological images to spatial gene expression profiles and their text annotations, enabling molecularly grounded histopathology analysis through natural language. Our method outperforms pathology vision-language models on a newly curated benchmark dataset, dedicated to spatially resolved H&E annotation. Integrated into a web interface, SpotWhisperer enables interactive exploration of cell types and disease mechanisms using free-text queries with access to inferred spatial gene expression profiles. In summary, SpotWhisperer analyzes cost-effective pathology images with spatial gene expression and natural-language AI, demonstrating a path for routine integration of microscopic molecular information into histopathology.

bioinformatics↗

bioRxiv2025

Optimising CAR-T cell sensitivity by engineering matched extracellular sizes between CAR/antigen and CD2/CD58 adhesion complexes

Chimeric antigen receptor (CAR)-T cells exhibit low antigen sensitivity, which restricts their therapeutic efficacy and leads to patient relapses when cancer cells downregulate antigen expression. Despite the pressing need to overcome this limitation, the underlying mechanisms remain poorly understood. Here, we demonstrate that enhancing CAR sensitivity to match the sensitivity of the T-cell receptor (TCR) can be achieved by engineering matched extracellular sizes of CAR/antigen and CD2/CD58 complexes. We find that different CAR/antigen sizes, which are generated by different CAR architectures and different target antigens, require a different CD2/CD58 size to optimise sensitivity. This extracellular size-matching improves antigen engagement and co-localisation of CAR/antigen and CD2/CD58 complexes. We also find that size-matching controls co-inhibition of CARs by PD-1/PD-L1. These findngs highlight the importance of size-matching for signal integration by surface receptors and offers a new approach to tune CAR-T cell sensitivity by matching or mismatching extracellular sizes. One sentence summaryThe antigen sensitivity of CAR-T cells can be tuned to match the sensitivity of TCR-T cells by varying the relative extracellular size of CAR/antigen and CD2/CD58 complexes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/631424v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@17e6a55org.highwire.dtl.DTLVardef@771b38org.highwire.dtl.DTLVardef@19c3544org.highwire.dtl.DTLVardef@6d1fe1_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats

Single-cell RNA-seq characterizes biological samples at unprecedented scale and detail, but data interpretation remains challenging. Here we introduce CellWhisperer, a multimodal machine learning model and software that connects transcriptomes and text for interactive single-cell RNA-seq data analysis. CellWhisperer enables the chat-based interrogation of transcriptome data in English language. To train our model, we created an AI-curated dataset with over a million pairs of RNA-seq profiles and matched textual annotations across a broad range of human biology, and we established a multimodal embedding of matched transcriptomes and text using contrastive learning. Our model enables free-text search and annotation of transcriptome datasets by cell types, states, and other properties in a zero-shot manner and without the need for reference datasets. Moreover, Cell-Whisperer answers questions about cells and genes in natural-language chats, using a biologically fluent large language model that we fine-tuned to analyze bulk and single-cell transcriptome data across various biological applications. We integrated CellWhisperer with the widely used CELLxGENE browser, allowing users to in-teractively explore RNA-seq data through an integrated graphical and chat interface. Our method demonstrates a new way of working with transcriptome data, leveraging the power of natural language for single-cell data analysis and establishing an important building block for future AI-based bioinformatics research assistants.

bioinformatics↗

bioRxiv2024

The importance of small island populations for the long term survival of endangered large-bodied insular mammals

Island populations of large vertebrates have experienced higher extinction rates than mainland populations over long timescales due to demographic stochasticity, genetic drift and inbreeding. Conversely, small island populations often experience relatively less anthropogenic habitat degradation than populations on larger islands, making them potential targets for conservation interventions such as genetic rescue to improve their overall genetic diversity. Here we determine the consequences and conservation implications of long-term isolation and recent human activities on genetic diversity of island populations of two forest-dependent mammals endemic to the Wallacea archipelago: the anoa (Bubalus spp.) and babirusa (Babyrousa spp.). Using genomic analyses and habitat suitability models, we show that, compared to closely related species, populations on mainland Sulawesi exhibit low heterozygosity, high inbreeding, and a high proportion of deleterious alleles. In contrast, populations on smaller islands possess fewer deleterious mutations despite exhibiting lower heterozygosity and higher inbreeding. Site frequency spectra indicate that these patterns reflect stronger, long-term purging in smaller island populations. Our results thus suggest that conservation efforts should focus on protecting small island habitats and avoiding translocations from mainland populations. This study highlights the crucial role of small offshore islands for the long-term survival of Wallaceas iconic and indigenous mammals in the face of development on the mainland. Significance statementWithin tropical archipelagos, such as the Wallacea biodiversity hotspot, larger islands experience greater resource exploitation compared to smaller ones, highlighting the potential of smaller islands as refuges for conservation. To investigate the genetic health of populations on small islands, we used genomic, occurrence, and environmental data from a system of replicated populations of anoa and babirusa across islands of varying sizes. In contrast to larger islands like Sulawesi, our results demonstrate that smaller offshore islands not only provide higher-quality habitats but also support populations that have efficiently purged harmful mutations. Thus, despite their known vulnerability over geological time-frames, small island populations can provide long term insurance against human-driven extinction and conservation efforts should prioritise habitat management over translocations.

evolutionary biology↗

bioRxiv2024

Discovery of active mouse, plant and fungal cytochrome P450s in endogenous proteomes and upon expression in planta.

Eukaryotes produce a large number of cytochrome P450s that mediate the synthesis and degradation of diverse endogenous and exogenous metabolites. Yet, most of these P450s are uncharacterized and global tools to study these challenging, membrane-resident enzymes remain to be exploited. Here, we applied activity profiling of plant, mouse and fungal P450s with chemical probes that become reactive when oxidized by P450 enzymes. Identification by mass spectrometry revealed labeling of a wide range of active P450s, including six plant P450s, 40 mouse P450s and 13 P450s of the fungal wheat pathogen Zymoseptoria tritici. We next used transient expression of GFP-tagged P450s by agroinfiltration to show ER-targeting and NADPH-dependent, activity-based labeling of plant, mouse and fungal P450s. Both global profiling and transient expression can be used to detect a broad range of active P450s to study e.g. their regulation and discover selective inhibitors.

plant biology↗

bioRxiv2023

Glutathione transferase photoaffinity labeling demonstrates GST activation by safeners and NPR1-independent activation by BTH

Glutathione transferases (GSTs) represent a large and diverse enzyme family involved in detoxification of small molecules by glutathione conjugation in crops, weeds and model plants. Here, we introduce an easy and quick assay for photoaffinity labeling of GSTs to study global GST activation in various plant species. The small molecule probe contains glutathione, a photoreactive group, and a minitag for coupling to reporter tags via click chemistry. Under UV irradiation, this probe quickly and robustly labels GSTs in crude protein extracts. Enrichment and MS analysis of labeled proteins from Arabidopsis identified ten GSTs from the Phi(F) and Tau(U) classes. Photoaffinity labeling of GSTs demonstrated GST activation in wheat seedlings upon treatment with safeners, and in Arabidopsis leaves upon infection with avirulent bacteria. Photoaffinity labeling and proteomics identified six Phi- and Tau-class GSTs that are induced upon treatment with salicylic acid (SA) analog benzothiadiazole (BTH) and these were tested for enhancing immunity in disease assays. Our data confirm that BTH-induced GST activation is independent of NPR1, the master regulator of SA signaling.

plant biology↗

bioRxiv2022

Decreased miRNA-148a-3p expression in skeletal muscle of patients with chronic kidney disease

IntroductionSkeletal muscle wasting is a common complication of chronic kidney disease which leads to a loss of muscle function. The pathogenesis of skeletal muscle wasting is incompletely understood, which is preventing the development of targeted therapeutics. Recent evidence implicates miRNAs in the of skeletal muscle wasting. Our aim was to firstly examine miRNA profiles of CKD human skeletal muscle for the identification of aberrant expression patterns compared to a healthy control (HC) cohort, and secondly, investigate the role these miRNAs may play in inducing or promoting skeletal muscle atrophy using a novel human primary skeletal muscle cell model of CKD skeletal muscle. MethodsFor the comparison between CKD and HC populations, skeletal muscle biopsies were collected from the vastus lateralis of n=15 non-dialysis dependent CKD patients stage 3b-5 CKD patients, and n=15 healthy controls matched for age, gender and physical activity. n=5 biopsies from each group underwent next generation sequencing to obtain complete microRNA profiles in CKD vs HC cohorts, which were then validated in a separate cohort by PCR (N=10 in each group). A causative role in muscle wasting was determined by transfection of key microRNAs into a primary culture model of CKD skeletal muscle and changes in protein degradation determined by L-[3H]- phenylalanine release into the media. ResultsNext Generation Sequencing identified differential expression of 16 miRNAs in skeletal muscle of CKD patients versus controls, and PCR validation confirmed miRNA-148a-3p expression was significantly decreased in CKD patients. The reduced miRNA-148a-3p expression was also maintained in the primary culture model. Upon overexpression of miRNA-148a-3p in CKD myotubes, protein degradation rates were decreased non-significantly (p=0.28) by 16.3% compared to un-transfected CKD cells. ConclusionCKD was associated with a significant reduction in miRNA-148a-3p expression in skeletal muscle compared to non-CKD controls which was retained in our in vitro model. Overexpression of miRNA-148a-3p in primary skeletal myotubes non-significantly decreased muscle protein degradation by 16.3%. In order to determine the importance of miRNA-148a-regulation of protein degradation, a deeper understanding of miRNA-148a-3p targets and their associated pathways with respect to those dysregulated in skeletal muscle wasting is required.

molecular biology↗

bioRxiv2021

Inefficient exploitation of accessory receptors reduces the sensitivity of chimeric antigen receptors.

Chimeric antigen receptors (CARs) can re-direct T cells to target abnormal cells but their activity is limited by a profound defect in antigen sensitivity, the source of which remains unclear. Here we show that, while CARs have a >100-fold lower antigen sensitivity compared to the T cell receptor (TCR) when antigen is presented on antigen-presenting-cells (APCs), they have nearly identical sensitivity when antigen is presented as purified protein on artificial surfaces. We next measured the impact of engaging accessory receptors (CD2, LFA-1, CD28, CD27, 4-1BB) on antigen sensitivity by adding their purified ligands. Unexpectedly, we found that engaging CD2 or LFA-1 improved TCR antigen sensitivity by 125 and 22-fold, respectively, but only improved CAR sensitivity by <5-fold. This differential effect of CD2 and LFA-1 engagement on TCR versus CAR sensitivity was confirmed using APCs. We found that sensitivity to antigen can be partially restored by fusing the CAR variable domains to the TCR CD3{varepsilon} subunit (also known as a TRuC), and fully restored by exchanging the CAR variable domains with the TCR{beta} variable domains (also known as STAR or HIT). Importantly, these improvements in TRuC and STAR/HIT sensitivity can be predicted by their enhanced ability to exploit CD2 and LFA-1. These findings demonstrate that the CAR sensitivity defect is a result of their inefficient exploitation of accessory receptors, and suggest approaches to increase sensitivity.

immunology↗

bioRxiv2021

Inferring kinetic parameters of oscillatory gene regulation from single cell time series data

Gene expression dynamics, such as stochastic oscillations and aperiodic fluctuations, have been associated with cell fate changes in multiple contexts, including development and cancer. Single cell live imaging of protein expression with endogenous reporters is widely used to observe such gene expression dynamics. However, the experimental investigation of regulatory mechanisms underlying the observed dynamics is challenging, since these mechanisms include complex interactions of multiple processes, including transcription, translation, and protein degradation. Here, we present a Bayesian method to infer kinetic parameters of oscillatory gene expression regulation using an auto-negative feedback motif with delay. Specifically, we use a delay-adapted nonlinear Kalman filter within a Metropolis-adjusted Langevin algorithm to identify posterior probability distributions. Our method can be applied to time series data on gene expression from single cells and is able to infer multiple parameters simultaneously. We apply it to published data on murine neural progenitor cells and show that it outperforms alternative methods. We further analyse how parameter uncertainty depends on the duration and time resolution of an imaging experiment, to make experimental design recommendations. This work demonstrates the utility of parameter inference on time course data from single cells and enables new studies on cell fate changes and population heterogeneity.

developmental biology↗

bioRxiv2020

Cast away on Mindoro island: population dynamics of the critically endangered tamaraw (Bubalus mindorensis) at Mounts Iglit-Baco Natural Park

Endangered species, despite often living at low population densities, may undergo unexpected density-dependent feedbacks in the case of successful recovery or marked reduction in range. Because density-dependence dynamics can increase risk of extinction, these effects can hamper conservation efforts. In this study, we analyse the dynamics of the largest population of the tamaraw (Bubalus mindorensis), a critically endangered ungulate species endemic to Mindoro island, Philippines. The population is located within a < 3,000 ha area in Mounts Iglit-Baco Natural Park, with limited expansion possibilities. We took advantage of a 21 year time series of tamaraw counts to estimate annual population growth rate and possible density-dependence, accounting for sampling errors in the counts. The tamaraw population has been increasing at an average rate of +5% per year, as would be expected given its protected status by law. Population growth showed strong spatial structuring, with a population growth close to +10% in the core area of protection, and a reduction of abundance of -5% at the periphery of its range, inside the protected area. This range constriction is concerning because our best population dynamics model suggests significant negative density-dependence (Bayes factor = 0.9). The contraction of tamaraw range is likely caused by anthropogenic pressures forcing the species to live at relatively high densities in the core zone where protection is most effective, creating source-sink dynamics. Our study highlights the fact that, despite the continuous population growth over the last two decades, the long-term viability of the Mounts Iglit-Baco Natural Park tamaraw population remains uncertain.

ecology↗

bioRxiv2018

Microscopy quantification of microbial birth and death dynamics

Microbes live in dynamic environments where nutrient concentrations fluctuate. Quantifying fitness (birth and death) in a wide range of environments is critical for understanding microbial evolution as well as ecological interactions where one species alters the fitness of another. Here, using high-throughput time-lapse microscopy, we have quantified how Saccharomyces cerevisiae mutants incapable of synthesizing an essential metabolite grow or die in various concentrations of the required metabolite. We establish that cells normally expressing fluorescent proteins lose fluorescence upon death and that the total fluorescence in an imaging frame is proportional to the number of live cells even when cells form multiple layers. We validate our microscopy approach of measuring birth and death rates using flow cytometry, cell counting, and chemostat culturing. For lysine-requiring cells, very low concentrations of lysine are not detectably consumed and do not support cell birth, but delay the onset of death phase and reduce the death rate. In contrast, in low hypoxanthine, hypoxanthine-requiring cells can produce new cells, yet also die faster than in the absence of hypoxanthine. For both strains, birth rates under various metabolite concentrations are better described by the sigmoidal-shaped Moser model than the well-known Monod model, while death rates depend on the metabolite concentration and can vary with time. Our work reveals how time-lapse microscopy can be used to discover non-intuitive microbial dynamics and to quantify growth rates in many environments.

microbiology↗

bioRxiv2018

Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesis fauna assembled over the last 15 Myr. Here, we test the hypothesis that recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of the its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesis three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that recent emergence of land on Sulawesi (~1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicates that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

evolutionary biology↗