Biology subjects

Newton, M.

Publications and source records attributed to Newton, M..

13 recordsLinked to original sources

bioRxiv2026

Oncogenic ESR1 fusions form chromatin-anchored condensates that remodel nuclear architecture

Estrogen receptor (ESR1) fusions are recurrent drivers of endocrine-resistant breast cancer, yet their mechanisms of action remain poorly understood. Here, we show that ESR1-e6 fusion proteins, including ESR1-DAB2, ESR1-SOX9, and ESR1-YAP1, assemble into nuclear condensates across multiple cell types. Sequence analysis reveals that these fusions combine chromatin-targeting domains with increased intrinsic disorder, promoting multivalent interactions and phase separation. Live-cell imaging, fluorescence recovery after photobleaching, and mechanical perturbation demonstrate that condensates exhibit liquid-like properties, but progressively mature into stable, viscoelastic assemblies constrained by chromatin. Disruption of DNA binding abolishes condensate formation, indicating that chromatin engagement is essential for their assembly and organisation. ESR1 fusion condensates localise to chromatin-depleted regions, reduce nuclear stiffness, and promote chromatin decompaction, consistent with active remodelling of nuclear architecture. We propose that ESR1 fusions exploit phase separation to generate chromatin-anchored assemblies that reorganise the nuclear microenvironment, providing a physical framework through which ESR1 fusions may support sustained transcriptional activity, endocrine resistance and tumour progression.

cell biology↗

bioRxiv2026

Decorin-mediated Extracellular Matrix Stabilization Maintains Cartilage Integrity During Aging

Aging is a primary risk factor for osteoarthritis (OA), yet the mechanisms that preserve extracellular matrix integrity in long-lived connective tissues remain poorly defined. The function of articular cartilage depends on maintaining extracellular matrix integrity over a lifetime of mechanical use. Here we identify failure of matrix stabilization as an initiating mechanism of age-associated OA. Cartilage-specific deletion of decorin in mature mice disrupted the superficial collagen II fibrillar network, reduced aggrecan retention, and impaired poroelastic fluid pressurization by 9 months of age, preceding substantial transcriptional changes in resident chondrocytes. With advancing age, these matrix defects culminated in cartilage erosion, fibrotic remodeling, and spontaneous OA by 18 months. Mechanistically, decorin attenuated force-induced collagen II fibril realignment and reinforced the superficial fibrillar network, preserving matrix architecture under sustained physiological loading. These findings establish decorin-mediated extracellular matrix stabilization as a critical determinant of cartilage longevity and support a matrix-first model of age-associated degeneration.

biophysics↗

bioRxiv2026

Bleb formation induced by acidic mixing buffers improves liquid stability of mRNA-LNPs

mRNA-lipid nanoparticles (LNP) have proven their potential as a rapidly adaptable vaccine platform and promise to revolutionize numerous therapeutic areas. A major hurdle towards the widespread adoption of mRNA-LNP vaccines and therapeutics is their limited liquid shelf-life compared to more established modalities currently necessitating an ultralow temperature cold-chain to enable their distribution and storage. While ongoing efforts aim to improve liquid stability through chemical modification of mRNA and lipid components, complementary strategies that are broadly applicable across chemistries may further accelerate translation. Here, we present an approach to improve the liquid shelf-life of mRNA-LNPs that does not rely on modifications to the mRNA or LNP chemistry. In particular, we show that bleb formation induced by high ionic strength acidic citrate buffers during LNP formation reduces mRNA degradation and retains in vitro activity during extended liquid storage. We observed an increase in the in vitro activity storage half-life from 2.8 to 18.9 days at 25{degrees}C when prepared using high ionic strength buffers translating into a [~]7-fold improvement in the liquid shelf-life of MC3-LNPs. This enhanced stability of LNPs with large amount of bleb formation was mainly attributed to reduced rates of lipid-mRNA adduct formation and mRNA fragmentation. Furthermore, the acidic buffer dependent stabilization was observed across different ionizable lipids with the extent dependent on the ionizable lipid head group. We envision that the induction of bleb formation via selection of appropriate acidic mixing buffers may represent a universal approach to enhance mRNA-LNPs stability and enable extended long-term refrigerated storage.

biochemistry↗

bioRxiv2026

Phenotypic dynamics and behaviors of neutrophils during barrier challenge

Neutrophils are intrinsically antimicrobial innate immune cells, but they have recently been observed to play diverse roles across various conditions. The concept of neutrophil heterogeneity has thus emerged, yet a fundamental understanding of the mechanisms and processes underlying neutrophil diversity in vivo is lacking. Here, we interrogated neutrophils native propensities to diversify by studying them in the setting of host defense to barrier challenge. Using both high-parameter, high throughput methods and intravital microscopy, we tracked cellular dynamics, identity, and behaviors and asked how these aligned with critical host defensive functions. We found that neutrophil diversity was underscored by both turnover and plasticity of cells within an infection site, and that environment-specific adaptation occurred rapidly upon extravasation and swarm initiation. The population-level phenotypic landscape shifted considerably through phases of inflammation initiation, peak, and resolution; and adaptation varied substantially between infections and aseptic wounds. Like mature neutrophils, immature neutrophils were capable of phenotypic adaptation in infection sites but were deficient in host defense functions. We unexpectedly identified a novel population of CD101-low, mature neutrophils, expressing elevated levels of PD-L1 and ICAM-1, that was associated with key antimicrobial effector functions and most pronounced during the neutrophil response to large or recalcitrant challenge. Our findings highlight that neutrophil specification is rapid and environment-dependent, and that specific phenotypes are linked to critical host defensive behaviors and functions in vivo.

immunology↗

bioRxiv2025

Acute Effects of Intra-Articular Liposomal IDO-1 following Anterior Cruciate Ligament Injury

Joint injuries, such as rupture of the anterior cruciate ligament (ACL), is associated with the development of post-traumatic osteoarthritis (PTOA). It is known that ACL rupture can lead to disruption of metabolic pathways, including the conversion of the essential amino acid tryptophan to kynurenine, which is associated with a sustained inflammatory response. An in vivo study was undertaken to determine the acute effects of intra-articular administration of liposomes loaded with the tryptophan-catabolizing enzyme indoleamine 2,3-dioxygenase-1 (IDO-1) following ACL rupture. Using an established rat model of non-surgical ACL injury, male and female Lewis rats underwent a single intra-articular injection of empty liposomes, or liposomes loaded with IDO-1 and were subsequently randomized to 1- or 2-week endpoints. IDO-1 treatment after ACL injury was associated with a significant reduction in synovial fluid concentration of tryptophan at both 1-and 2-week endpoints. In addition to a reduction in tryptophan, IDO-1 treatment led to significantly lower synovial fluid concentrations of IL-1b and TNF-a. Intra-articular administration of IDO-1-loaded liposomes also increased the ratio of regulatory T lymphocytes (Tregs) to IL-17-secreting helper T lymphocytes (Th17 cells). Similarly, IDO-1 treatment increased the number of CTLA4+ cells relative to IL-17A+ cells that infiltrated joint tissues at a 2-week endpoint. Contrast-enhanced micro-computed tomography (CE-uCT) was used to quantify treatment-based effects on articular cartilage thickness and surface roughness at at 2-week endpoint. In addition to sex-based differences, IDO-1-loaded liposome treatment was associated with increased cartilage thickness, with no significant effects on surface roughness. Histologic characterization is needed to determine whether this increased cartilage thickness represents a chondroprotective effect, or a degenerative effect of IDO-1-treatment.

physiology↗

bioRxiv2024

Dynamic regulation of engineered T7 RNA polymerases by endogenous metabolites

For many enzymes, activity is regulated post-translationally by endogenous metabolites. Designing liganded control of essential activities like transcription would advance predictive control of biological processes, a fundamental goal of synthetic biology. Here we demonstrate that full-length, single subunit T7-derived RNA polymerases (T7 RNAP) can be controlled by physiologically relevant concentrations of indoles. We used rational design and directed evolution to identify T7 RNAP variants with minimal transcriptional activity in the absence of indole, and a 29-fold increase in activity with an EC50 of 344 {micro}M. Indoles control T7-dependent gene expression exogenously, endogenously, and inter-cellularly. We also demonstrate indole-dependent bacteriophage viability and propagation in trans. Specificity of different indoles, T7 promoter specificities, and portability to different bacteria are shown. Our ligand activated RNA polymerases (LARPs) represent a new chemically inducible platform immediately deployable for novel synthetic biology applications, including for modulation of synthetic co-cultures.

bioengineering↗

bioRxiv2023

Individual genotype but not phenotype predicts river migration success in Atlantic salmon

Migratory species typically undertake demanding long-distance journeys, across different habitat types during which they are exposed to multiple natural and anthropogenic stressors. Mortality during migration is typically high, and may be exacerbated by human-induced pressures. Understanding individual responses to these selection pressures is rarely attempted, because of the challenges of relating individual phenotypic and genetic data to migration success. Here we show distinct Single Nucleotide Polymorphism (SNP) sets significantly differentiated between Atlantic salmon smolts making successful migrations to sea and those that failed to migrate, in two different rivers. In contrast, morphological variation was not diagnostic of migration success. Populations from each river were genetically distinct, and while different genes were possibly implicated in migration success in each river, they related to common biological processes (for example osmoregulation and immune and stress response). Given that migration failure should quickly purge polymorphism at selected SNPs from a population, the question of how genetic diversity in these populations is maintained is an important one. Standing genetic variation could be maintained by different life history strategies and/or environmentally driven balancing selection. Our work highlights the importance of preserving genetic diversity to ensure evolutionary resilience at the population level, and has practical implications for management.

evolutionary biology↗

bioRxiv2022

Is shape in the eye of the beholder? The reproducibility of geometric morphometric analyses on live animals

Geometric morphometrics is widely used to quantify morphological variation between biological specimens, but the fundamental influence of operator bias on data reproducibility is rarely considered, particularly in studies using photographs of live animals taken under field conditions. We examined this using four independent operators that applied an identical landmarking scheme to replicate photographs of 291 live Atlantic salmon (Salmo salar L.) from two rivers. Using repeated measures tests, we found significant inter-operator differences in mean body shape, suggesting that the operators introduced a systematic error despite following the same landmarking scheme. No significant differences were detected when the landmarking process was repeated by the same operator on a random subset of photographs. Importantly, in spite of significant operator bias, small but statistically significant morphological differences between fish from the two rivers were found consistently by all operators. Pairwise tests of angles of vectors of shape change showed that these between-river differences in body shape were analogous across operator datasets, suggesting a general reproducibility of findings obtained by geometric morphometric studies. In contrast, merging landmark data when fish from each river are digitised by different operators had a significant impact on downstream analyses, highlighting an intrinsic risk of bias. Overall, we show that, even when significant inter-operator error is introduced during digitisation, following an identical landmarking scheme can identify morphological differences between populations. This study indicates that operators digitising at least a sub-set of all data groups of interest may be an effective way of mitigating inter-operator error and potentially enabling data sharing.

zoology↗

bioRxiv2021

The benefits of merging passive and active tracking approaches: new insights into riverine migration by salmonid smolts

The process of smolting is a critical phase in the life-cycle of anadromous salmonids and it has been associated with substantial rates of mortality. Survival during freshwater and marine migration is known to have population level effects, thus an understanding of the patterns of mortality has the potential to yield important insights into population bottlenecks. Despite important advancements in tracking techniques, the specifics of mortality events in anadromous salmonids during their initial migration to sea remains somewhat elusive. Here, we develop a framework combining spatial and temporal detections of smolt riverine migration from two tracking techniques, which enable inferences to be made about mortality locations, causes, and rates. In this study, we demonstrate that during their initial riverine transitional phase, smolts were particularly vulnerable to predators. Specifically, avian predation appeared to be the main cause of mortality (42%), although piscine predation events were not trivial (14%). Our results suggested some direct and indirect tagging-induced mortality (e.g., through increased predation vulnerability), which highlights the importance of determining tagging mortality in a telemetry study to ensure adequate interpretation of migration success. Overall, by estimating migration loss and its variability, our study framework should help to guide management actions to mitigate the widespread population declines these species are currently facing.

ecology↗

bioRxiv2021

SpotClean adjusts for spot swapping in spatial transcriptomics data

Spatial transcriptomics (ST) is a powerful and widely-used approach for profiling genome-wide gene expression across a tissue with emerging applications in molecular medicine and tumor diagnostics. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case owing to bleed from nearby spots, an artifact we refer to as spot swapping. We propose SpotClean to adjust for spot swapping and, in doing so, to increase the sensitivity and precision with which downstream analyses are conducted.

genomics↗

bioRxiv2021

Early Patellofemoral Cartilage and Bone Degeneration in a Rat Model of Noninvasive Anterior Cruciate Ligament Rupture

BackgroundAnterior cruciate ligament rupture (ACLR) is a well-known risk factor for the development of post-traumatic osteoarthritis (PTOA). While clinical and pre-clinical studies have characterized the onset and progression of PTOA in the tibiofemoral joint compartment, very little is known about degenerative changes in the patellofemoral compartment after ACL injury. Hypothesis/PurposeTo evaluate the extent to which ACL rupture induces acute patellofemoral joint degeneration by quantifying articular cartilage morphology and remodeling of subchondral and trabecular bone microarchitecture in the patellofemoral compartment. Study DesignDescriptive laboratory study. MethodsAdult female Lewis rats were randomized to undergo either a non-surgical ACL rupture or a Sham procedure (n = 6 per group). Ex vivo contrast-enhanced micro-computed tomography ({micro}CT) and histological evaluation of the patellofemoral compartment were performed at 2-weeks post-injury, representing a timepoint of documented early PTOA in the tibiofemoral compartment in this model. ResultsACL rupture causes osteophyte formation in the patella and mild degeneration in the superficial zone of articular cartilage (AC), including surface fibrillation, fissures, increased cellularity, and abnormal chondrocyte clustering at two weeks post-injury. Contrast-enhanced {micro}CT analysis demonstrates significant increases in AC thickness of patellar and trochlear cartilage. Loss of subchondral bone thickness, bone volume fraction, and tissue mineral density, as well as changes to trabecular microarchitecture in both the patella and trochlea, were indicative of catabolic bone remodeling. ConclusionThese results demonstrate that the patellofemoral joint develops mild but evident degenerative changes in the acute time period following ACL rupture, extending the utility of this rat model to the study of degenerative patellofemoral changes following joint trauma. Clinical RelevanceACL rupture causes mild degeneration and swelling of articular cartilage, coupled with catabolic bone remodeling in the patellofemoral compartment. Characterizing the pathophysiology of patellofemoral PTOA in its early stages may provide a better understanding of disease progression and provide opportunities for preventative therapeutic intervention.

physiology↗

bioRxiv2019

A conserved activity for cohesin in bridging DNA molecules

Essential processes such as accurate chromosome segregation, regulation of gene expression and DNA repair rely on protein-mediated DNA tethering. Sister chromatid cohesion requires the SMC complex cohesin to act as a protein linker that holds replicated chromatids together (1, 2). The molecular mechanism by which cohesins hold sister chromatids has remained controversial. Here, we used a single molecule approach to visualise the activity of cohesin complexes as they hold DNA molecules. We describe a DNA bridging activity that requires ATP and is conserved from yeast to human cohesin. We show that cohesin can form two distinct classes of bridges at physiological conditions, a \"permanent bridge\" able to resists high force (over 80pN) and a \"reversible bridge\" that breaks at lower forces (5-40pN). Both classes of bridges require Scc2/Scc4 in addition to ATP. We demonstrate that bridge formation requires physical proximity of the DNA segments to be tethered and show that \"permanent\" cohesin bridges can move between two DNA molecules but cannot be removed from DNA when they occur in cis. This suggests that separate physical compartments in cohesin molecules are involved in the bridge. Finally, we show that cohesin tetramers, unlike condensin, cannot compact linear DNA molecules against low force, demonstrating that the core activity of cohesin tetramers is bridging DNA rather than compacting it. Our findings carry important implications for the understanding of the basic mechanisms behind cohesin-dependent establishment of sister chromatid cohesion and chromosome architecture.

biochemistry↗

bioRxiv2016

SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data

Normalization of RNA-sequencing data is essential for accurate downstream inference, but the assumptions upon which most methods are based do not hold in the single-cell setting. Consequently, applying existing normalization methods to single-cell RNA-seq data introduces artifacts that bias downstream analyses. To address this, we introduce SCnorm for accurate and efficient normalization of scRNA-seq data.

genomics↗