Biology subjects

Burgess, K.

Publications and source records attributed to Burgess, K..

9 recordsLinked to original sources

bioRxiv2026

TGF-β- and IL-1-dependent fibroblast states differentially shape pancreatic cancer microenvironments and metastasis

Pancreatic ductal adenocarcinoma (PDAC) contains heterogeneous cancer-associated fibroblast (CAF) populations, including interleukin 1 (IL-1)-dependent inflammatory CAFs (iCAFs) and transforming growth factor beta (TGF-{beta})-dependent myofibroblastic CAFs (myCAFs), whose functions at primary and metastatic sites remain incompletely defined. Here, we genetically disrupted IL-1 or TGF-{beta} signalling in fibroblast activation protein (FAP)-expressing CAFs arising from a shared cellular origin to determine how myCAF and iCAF states shape PDAC progression and microenvironments. Depletion of TGF-{beta}-dependent myCAFs, but not IL-1-dependent iCAFs, did not alter primary tumour growth or local metastatic dissemination but significantly reduced liver and lung metastases. Matched primary tumours and liver metastasis analyses also revealed site-specific stromal responses to TGF-{beta} signalling disruption. Experimental models of liver metastasis colonisation and outgrowth indicated that the reduced metastatic phenotype was linked primarily to alterations within pancreatic tumours rather than to impaired malignant cell outgrowth at metastatic sites. Single-cell RNA-sequencing of myCAF-depleted primary tumours revealed extensive transcriptional reprogramming across fibroblast, immune and malignant compartments, highlighting the complexity of assigning myCAF-to-malignant cell signalling mechanisms in vivo. To resolve this crosstalk, we co-cultured PDAC organoids with pancreatic stellate cells engineered to remain in myCAF or iCAF states. Cross-model transcriptomic analyses, together with genetic and pharmacological perturbation studies, showed that myCAF-derived TGF-{beta} directly promotes epithelial-to-mesenchymal transition signalling in PDAC malignant cells, providing a candidate mechanism for the reduced metastasis observed upon myCAF depletion in vivo. These findings reveal distinct, context-dependent roles for TGF-{beta}- and IL-1-dependent CAF states and identify myCAF-derived TGF-{beta} signalling as a stromal mechanism promoting malignant cell plasticity.

cancer biology↗

bioRxiv2025

Multiobjective design of growth media with genome-scale metabolic models and Bayesian optimization

The optimization of culture media is critical for improving the efficiency and cost of cellular production systems. Traditional approaches often rely on extensive experimental trials or statistical methods, which can be both costly and time-consuming. Here, we present gsMOBO, a computational approach for media design that integrates genome-scale metabolic models with multiobjective optimization. Our method employs Flux Balance Analysis coupled with a top-layer Bayesian optimization routine for efficient exploration and optimization of nutrient combinations across high-dimensional spaces. We show that our method finds optimal medium formulations along a Pareto front balancing growth, production and cost of medium components. We illustrate the approach in models of Escherichia coli engineered to produce antibody fragments, as well as Bacillus subtilis strains that synthesize cyclic lipopeptides. Our results show that gsMOBO identifies media compositions and Paretooptimal trade-offs consistent with prior experimental work. Our method provides a broadly applicable tool for the design of cost-effective and productive culture media, and offers a route to accelerate medium development in biomanufacturing.

synthetic biology↗

bioRxiv2024

Optimisation of surfactin yield in Bacillus using active learning and high-throughput mass spectrometry

Integration of machine learning and high throughput measurements are essential to drive the next generation of the design-build-test-learn (DBTL) cycle in synthetic biology. Here, we report the use of active learning in combination with metabolomics for optimising production of surfactin, a complex lipopeptide resulting from a non-ribosomal assembly pathway. We designed a media optimisation algorithm that iteratively learns the yield landscape and steers the media composition toward maximal production. The algorithm led to a 160% yield increase after three DBTL runs as compared to an M9 baseline. Metabolomics data helped to elucidate the underpinning biochemistry for yield improvement and revealed Pareto-like trade-offs in production of other lipopeptides from related pathways. We found positive associations between organic acids and surfactin, suggesting a key role of central carbon metabolism, as well as system-wide anisotropies in how metabolism reacts to shifts in carbon and nitrogen levels. Our framework offers a novel data-driven approach to improve yield of biological products with complex synthesis pathways that are not amenable to traditional yield optimisation strategies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/576661v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@14c41ceorg.highwire.dtl.DTLVardef@1745ad2org.highwire.dtl.DTLVardef@1f6bedforg.highwire.dtl.DTLVardef@6d56c5_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2020

PEA polymer-coated nanotopography delivers solid-state BMP2, enhances mesenchymal stem cell adhesion, prevents bacterial biofilm formation and protects cells from quorum sensing virulence factors

Post-operative infection is a major complication in patients recovering from orthopaedic surgery. As such, there is a clinical need to develop biomaterials for use in regenerative surgery that can promote mesenchymal stem cell (MSC) osteospecific differentiation and that can prevent infection caused by biofilm-forming pathogens. Nanotopographical approaches to pathogen control are being identified, including in orthopaedic materials such as titanium and its alloys. These topographies use high aspect ratio nanospikes or nanowires to prevent bacterial adhesion but these features puncture adhering cells, thus also reducing MSC adhesion. Here, we use a poly(ethyl acrylate) (PEA) polymer coating on titanium nanowires to spontaneously organise fibronectin (FN) and to deliver bone morphogenetic protein 2 (BMP2) to enhance MSC adhesion and osteospecific signalling. This nanotopography when combined with the PEA coating enhanced osteogenesis and reduced adhesion of Pseudomonas aeruginosa in culture. Using a novel MSC-Pseudomonas aeruginosa co-culture, we also show that the coated nanotopographies protect MSCs from cytotoxic quorum sensing and signalling molecules. We conclude that the PEA polymer-coated nanotopography can both support MSCs and prevent pathogens from adhering to a biomaterial surface, thus protecting from biofilm formation and bacterial infection and supporting osteogenic repair.

bioengineering↗

bioRxiv2020

Decomposing metabolite set activity levels with PALS

MotivationRelated metabolites can be grouped into metabolite sets in many ways. Examples of these include the grouping of metabolites through their participation in a series of chemical reactions (forming metabolic pathways); or based on fragmentation spectral similarities and shared chemical substructures. Understanding how such metabolite sets change across samples can be incredibly useful in the interpretation and understanding of complex metabolomics data. However many of the available tools suitable for the enrichment analysis of metabolite sets are based on simple methods that badly handle the missing features inherent in untargeted metabolomics measurements and can be difficult to integrate into existing applications. ResultsWe present PALS (Pathway Activity Level Scoring), a Python library, command-line tool and Web application that performs the ranking of significantly-changing metabolite sets over different experimental conditions. As example applications, PALS is used to analyse metabolites grouped as pathways and by common MS-MS fragmentation structures. A comparison of PALS with two other commonly used methods (ORA and GSEA) is also given, and reveals that PALS is more robust to missing peaks and noisy data than the alternatives. We report results from using PALS to analyse pathways from a study of Human African Trypanosomiasis. Finally, we also report how PALS used tandem MS fragmentation structures to reveal enriched metabolite sets between clades in Rhamnaceae plant data, and on American Gut Project data. AvailabilityPALS is freely available from our project Web site at https://pals.glasgowcompbio.org/. It can be imported as a Python library, run as a stand-alone tool or used as a web application.

bioinformatics↗

bioRxiv2020

Nanovibrational stimulation of mesenchymal stem cells induces therapeutic reactive oxygen species and inflammation for 3D bone tissue engineering

There is a pressing clinical need to develop cell-based bone therapies due to a lack of viable, autologous bone grafts and a growing demand for bone grafts in musculoskeletal surgery. Such therapies can be tissue engineered and cellular, such as osteoblasts combined with a material scaffold. Because mesenchymal stem cells (MSCs) are both available and fast growing compared to mature osteoblasts, therapies that utilise these progenitor cells are particularly promising. We have developed a nanovibrational bioreactor that can convert MSCs into bone-forming osteoblasts in 2D and 3D but the mechanisms involved in this osteoinduction process remain unclear. Here, to elucidate this mechanism, we use increasing vibrational amplitude, from 30 nm (N30) to 90 nm (N90) amplitudes at 1000 Hz, and assess MSC metabolite, gene and protein changes. These approaches reveal that dose-dependent changes occur in MSCs responses to increased vibrational amplitude, particularly in adhesion and mechanosensitive ion channel expression, and that energetic metabolic pathways are activated, leading to low-level reactive oxygen species (ROS) production and to low-level inflammation, as well as to ROS- and inflammation-balancing pathways. These events are analogous to those that occur in the natural bone-healing processes. We have also developed a tissue engineered MSC-laden scaffold designed using cells mechanical memory, driven by the stronger N90 stimulation. These new mechanistic insights and cell-scaffold design are underpinned by a process that is free of inductive chemicals.

bioengineering↗

bioRxiv2020

The use of nanovibration to discover specific and potent bioactive metabolites that stimulate osteogenic differentiation in mesenchymal stem cells

Bioactive metabolites have wide-ranging biological activities and are a potential source of future research and therapeutic tools. Here, we use nanovibrational stimulation to induce the osteogenic differentiation of MSCs, in the absence of off-target differentiation. We show that this differentiation method, which does not rely on the addition of exogenous growth factors to the culture media, provides an artefact-free approach to identifying bioactive metabolites that specifically and potently induce osteogenesis. We first identify a highly specific metabolite as the endogenous steroid, cholesterol sulphate. Next, a screen of other small molecules with a similar steroid scaffold identified fludrocortisone acetate as being both specific and having highly potent osteogenic-inducing activity. These findings demonstrate that physical priciples can be used to identify bioactive metabolites and then metabolite potency can be optimised by examining structure-function relationship.

bioengineering↗

bioRxiv2019

Nanotopography reveals metabolites that maintain the immunosuppressive phenotype of mesenchymal stem cells

Mesenchymal stem cells (MSCs) are multipotent stem cells that are immunosuppressive and thus of considerable therapeutic potential in transplant operations. However, MSCs rapidly differentiate once in culture, making their large-scale expansion for use in immunosuppressive therapies challenging. Although the differentiation mechanisms of MSCs have been extensively investigated using materials, little is known about how materials can modulate paracrine activities of MSCs. Here, we show for the first time that nanotopography can control the immunomodulatory capacity of MSCs through decreased intracellular tension increasing oxidative glycolysis. We also use the nanotopography to identify bioactive metabolites that modulate intracellular tension, growth and immunomodulatory phenotype of MSCs in standard culture. Our findings show a novel route to support large-scale expansion of functional MSCs for therapeutic purposes

bioengineering↗

bioRxiv2019

Changing environments and genetic variation: inbreeding does not compromise short-term physiological responses

O_LISelfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce long-term evolutionary potential. However, short-term capacity to respond appropriately to new conditions might not require high levels of standing genetic variation. The purpose of this study was to directly test whether mating system variation and its associated changes in genetic variability in natural populations affected responses to short-term environmental challenges.\nC_LIO_LIWe compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a long-lived perennial plant, Arabidopsis lyrata, under constant growth chamber conditions and an outdoor common garden environment outside its native range.\nC_LIO_LIWe found no effect of mating system on survival or reproductive output, although several phenological traits showed different associations with latitude for outcrossing and inbreeding populations. Natural inbreeding had no effect on the plasticity of physiological responses, using either multivariate approaches or analysis of variation in individual metabolites. Moreover, while both growing environment and time significantly affected the relative abundance of individual metabolites, inbreeding populations responded similarly to outbreeding populations, suggesting adaptation to the outdoor environment, regardless of mating system.\nC_LIO_LIWe conclude that low genetic diversity in naturally inbred populations may not compromise fitness or short-term capacity for appropriate physiological responses to environmental change. The absence of natural costs of inbreeding could help to explain the global success of clonal or asexual mating strategies for adapting to a wide range of environments.\nC_LI

evolutionary biology↗