Biology subjects

Butler, L.

Publications and source records attributed to Butler, L..

18 recordsLinked to original sources

bioRxiv2026

Cholesterol and p53 promote senescence and systemic fibrosis in metabolic dysfunction-associated steatohepatitis

Background & aims: TP53 (p53) coordinates diverse cellular stress response programmes including pro-survival activities, senescence, and cell death. During tissue damage, p53 can shape both the local cellular response to injury, including the fibrotic response, and influence distal organ biology. Fibrosis in the liver is a major driver of hepatocellular carcinoma (HCC) risk within metabolic dysfunction-associated steatohepatitis (MASH). It is also an important determinant of dysfunction in multiple distal tissues including the kidneys, lungs, and heart. Despite significant clinical burden, our understanding of the molecular determinants of fibrotic MASH and its relationship to multiorgan fibrosis remain incomplete. Here, we investigate local and systemic effects of hepatocellular p53 activity and cholesterol during MASH development, with implications for disease prevention. Methods: This study utilised a genetic model of stabilised p53, diet-induced MASH models with varying cholesterol compositions, and an in vitro obesogenic system to investigate p53 activity during liver disease development. Non-invasive imaging and histopathological analyses were employed to monitor p53 activity, MASH, and multiorgan fibrosis in vivo. Complementary approaches, including in vitro human multicomponent liver spheroids, cytokine arrays, and analyses of human MASH transcriptomic and proteomic datasets, were used to examine molecular drivers and patient relevance. Results: Using an inducible mouse model of MDM2 E3 ubiquitin ligase deficiency to stabilise p53, we report that hepatocellular MDM2 E3 loss results in progressive fibrotic damage, robust hepatocellular expression of the p53 target gene CDKN1A/p21 (p21),and induces p21 and fibrosis in the kidneys of male mice in a sex-specific manner. In diet-induced MASH, we observe cholesterol and p53-dependent development of liver fibrosis, high expression of hepatocellular p21, and induction of p21 and fibrosis in the kidneys of male mice-reminiscent of features observed in MDM2 E3-deficient mice. We also observe fibrosis in the lungs and heart of male MASH mice. Both a cholesterol-free obesogenic diet and liver-specific loss of p53 mitigate hepatic fibrosis and systemic induction of p21 and fibrosis. Mechanistically, p53 induces hepatic expression of senescence-associated secretory phenotype (SASP) factors, including GDF15, in vivo. A human multicomponent LiverACE spheroid model showed a concordant trend towards increased GDF15 protein abundance under steatotic stress, while in humans, elevated circulating GDF15 levels in advanced MASH correlate with increased TNFRSF1A and EPHA2, circulating markers linked to kidney injury. Conclusions: Our work identifies undue p53 activity within the liver as a driver of multiorgan fibrosis in a sex-specific manner, affecting male but not female mice. We implicate cholesterol in promoting this pro-fibrotic environment in vivo and highlight circulating factors that could identify at-risk patients for multiorgan fibrosis in MASH.

cancer biology↗

bioRxiv2025

Testing the Vogt-Bailey Index using task-based fMRI across pulse sequence protocols

Local connectivity analyses in fMRI such as the Vogt-Bailey Index, investigate the prevalence of co-fluctuations in the time-series of adjacent voxels. While there have been in silico assessments of the VB Index, this technique has not yet been assessed in vivo. This study has two aims: first, to assess the VB Index using a task paradigm with well established a priori expectations on the brain region predominantly responsible for executing this task to determine whether the VB Index highlights this area. Second, we investigate if, and how, the spatial resolution of the sequence protocols employed, with their inherent effects on the signal-to-noise ratio, affect the resultant VB maps. A cohort of 10 research volunteers underwent fMRI acquisitions utilising a block design finger tapping experiment. Each volunteer was scanned with three sequence protocols, with all parameters equivalent except for the volume of the voxels. The resulting parametric maps derived using the VB Index were compared with those obtained from the conventional General Linear Model approach. Particular emphasis was placed on the identification of the hand portion of the motor homunculus. Across sequence protocols, the VB Index consistently identified elevated local connectivity in, qualitatively, the same portion of the motor cortex as that yielded by the General Linear Model based on the task paradigm. However, the VB Index also detected elevated local connectivity outside the motor cortex while the General Linear Model results were mostly restricted to the motor cortex. The consistently high VB Index, across sequence protocols, in the cortical region associated with an fMRI task paradigm, despite the approachs agnosticism to that task, provides support for the biological relevance of such local connectivity measures.

neuroscience↗

bioRxiv2024

Inclusivity in fNIRS Studies: Quantifying the Impact of Hair and Skin Characteristics on Signal Quality with Practical Recommendations for Improvement

Functional Near-Infrared Spectroscopy (fNIRS) holds transformative potential for research and clinical applications in neuroscience due to its non-invasive nature and adaptability to real-world settings. However, despite its promise, fNIRS signal quality is sensitive to individual differences in biophysical factors such as hair and skin characteristics, which can significantly impact the absorption and scattering of near-infrared light. If not properly addressed, these factors risk biasing fNIRS research by disproportionately affecting signal quality across diverse populations. Our results quantify the impact of various hair properties, skin pigmentation as well as head size, sex and age on signal quality, providing quantitative guidance for future hardware advances and methodological standards to help overcome these critical barriers to inclusivity in fNIRS studies. We provide actionable guidelines for fNIRS researchers, including a suggested metadata table and recommendations for cap and optode configurations, hair management techniques, and strategies to optimize data collection across varied participants. This research paves the way for the development of more inclusive fNIRS technologies, fostering broader applicability and improved interpretability of neuroimaging data in diverse populations.

neuroscience↗

bioRxiv2024

Artificial intelligence and species distribution ensemble models inform resource interactions with offshore wind development

Development of offshore wind energy resources has led to growing concerns for marine wildlife. However, significant uncertainty remains regarding the technologys potential to impact species of interest that may occupy planned development sites. This is further compounded by the difficulty of monitoring highly migratory or data-poor species in marine waters, making practical assessment of site- or species-specific threats that could require additional management intervention particularly problematic. Here, I identify a highly generalizable framework to inform species interactions in marine habitats allocated for offshore resource exploitation, using telemetry-derived artificial intelligence species distribution models. Results from a case study of the federally protected Atlantic Sturgeon (Acipenser oxyrinchus) demonstrate excellent discriminatory capacity (i.e., AUC [≥] 0.9) at a relatively fine scale (raster resolution = 1 km2), while providing critical information on predicted occurrence over a broad swath of unmonitored marine habitats (i.e., the Atlantic OCS region of the US; area > 620,000 km2). Furthermore, ensemble map products developed from these models are readily scalable to ongoing management needs and, when overlaid with offshore wind energy lease areas, can feed directly into management strategies to inform best practices for potential habitat influences on Atlantic Sturgeon, as well as other species of commercial or conservation interest.

ecology↗

bioRxiv2024

p53 and TIGAR promote redox control to protect against metabolic dysfunction-associated steatohepatitis

TP53 is a potent tumour suppressor that coordinates diverse stress response programmes within the cell. The activity of p53 is frequently context and cell type-dependent, and ranges from pro-survival activities, including the implementation of transient cell cycle arrest and metabolic rewiring, through to cell death. In addition to tumour suppressor functions, p53 also has established roles in the pathological response to stress that occurs during tissue damage and repair, including within the liver. Metabolic dysfunction-associated steatohepatitis (MASH) is a major driver of hepatocellular carcinoma (HCC), but our understanding of the molecular determinants of MASH development remains incomplete. Here, using a p53 reporter mouse, we report early and sustained activation of hepatic p53 in response to an obesogenic high fat and high sugar diet. In this context, liver-specific loss of p53 accelerates the progression of benign fatty liver disease to MASH that is characterised by high levels of reactive oxygen species (ROS), extensive fibrosis, and chronic inflammation. Using an in vitro culture system, we show that p53 functions to control ROS and protect against the development of MASH, in part through induction of the antioxidant gene TP53-induced glycolysis and apoptosis regulator (TIGAR). Our work demonstrates an important role for the p53-TIGAR axis in protecting against MASH, and identifies redox control as an essential barrier against liver disease progression.

cancer biology↗

bioRxiv2023

hnRNPUL1 ensures efficient Integrator-mediated cleavage of snRNAs and is mutated in amyotrophic lateral sclerosis

Integrator cleaves nascent RNA, triggering RNA polymerase II transcription termination, but how cleavage is regulated is poorly understood. Here we show hnRNPUL1 ensures efficient Integrator-mediated cleavage of nascent RNA downstream of snRNA genes and, in the case of U2 snRNA, binds a terminal stem-loop involved in this process. In the nucleoplasm, hnRNPUL1 binds U4 snRNA and SART3 and enables efficient reformation of the U4:U6 di-snRNP for further rounds of pre-mRNA splicing. Sustained hnRNPUL1 loss leads to reduced levels of snRNAs, defects in histone mRNA 3' end processing and loss of Cajal bodies. hnRNPUL1 binds RNA through multiple domains, including a globular central domain comprising tightly juxtaposed SPRY and dead polynucleotide kinase folds. This latter fold allows binding to 5'-monophosphorylated RNAs in a mutually exclusive manner with ATP binding and functions as an XRN2 antagonist when overexpressed. We identify a cohort of amyotrophic lateral sclerosis patients harbouring disruptive mutations in hnRNPUL1. SMN loss in spinal muscular atrophy and hnRNPUL1 loss both disrupt snRNP biogenesis, leading to motor neuron death, suggesting a common aetiology.

molecular biology↗

bioRxiv2023

Synthetic autotetraploid Caenorhabditis elegans resist severe cold stress by escaping cold induced death at the gravid adult stage.

Whole genome duplication (WGD) is a well-studied yet enigmatic phenomenon. While it has long been recognised as contributing numerous genes to many eukaryotic lineages and often implicated in evolutionary radiations, how these lineages overcome the known burdens of polyploidy is poorly understood. Circumstantial evidence of many WGD events coinciding with periods of otherwise mass extinction is consistent with the hypothesis that polyploidy is conditionally advantageous under stress conditions. While support for this comes from both theoretical work and field studies, direct evidence is lacking, especially in animals. Here we compare diploid and neo-tetraploid Caenorhabditis elegans and show that tetraploid animals exhibit increased resilience under specific stress conditions related to temperature changes. Most notably, under severe cold stress gravid neo-tetraploids massively escape cold-induced death, and generate more progeny, of similar quality, than diploid animals. This is the first demonstration of the effects of polyploidy on stress resistance and physiology in animals.

cell biology↗

bioRxiv2023

Temporal transcriptome analysis of the endothelial response to tumour necrosis factor

The vascular endothelium acts as a dynamic interface between blood and tissue and provides an anti-inflammatory and anti-thrombotic surface under normal conditions. Tumour necrosis factor- (TNF), a cytokine that drives acute and chronic inflammation, induces numerous transcriptional changes in endothelial cells (EC). However, the overall temporal dynamics of this response have not been fully elucidated. Here, we conducted an extended time-course analysis of the EC response to TNF, from 30 minutes to 72 hours. We identified TNF-regulated genes and used weighted gene correlation network analysis (WGCNA) to decipher co-expression profiles, uncovering two distinct temporal phases - an acute response initiated between 1-4 hours, followed by a later phase initiated between 12-24 hours. Several previously uncharacterised genes were strongly regulated during the acute phase, while the majority in the later phase were interferon-stimulated genes (ISGs). A lack of interferon transcription indicated that this TNF-induced ISG expression was independent of de novo interferon production and autocrine signalling. Furthermore, we observed two different groups of genes whose transcription was inhibited by TNF, those that resolved towards baseline levels over time, and those that did not. Our study provides insights into the global temporal dynamics of the EC transcriptional response to TNF, highlighting distinct gene expression patterns during the acute and later phases. These findings may be useful in understanding the role of EC in inflammation and developing TNF signalling-targeting therapies.

cell biology↗

bioRxiv2023

A human stomach cell type transcriptome atlas

The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single cell sequencing-based atlases. Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell and plasma cells, identifying over 1600 cell type-enriched genes. We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.

systems biology↗

bioRxiv2023

A tissue centric atlas of cell type transcriptome enrichment signatures

Genes with cell type specific expression typically encode for proteins that have cell type specific functions. Single cell RNAseq (scRNAseq) has facilitated the identification of such genes, but various challenges limit the analysis of certain cell types and lowly expressed genes. Here, we performed an integrative network analysis of over 6000 bulk RNAseq datasets from 15 human organs, to generate a tissue-by-tissue cell type enrichment prediction atlas for all protein coding genes. We profile all the major constituent cell types, including several that are fragile or difficult to process and thus absent from existing scRNAseq-based atlases. The stability and read depth of bulk RNAseq data, and the high number of biological replicates analysed, allowed us to identify lowly expressed cell type enriched genes that are difficult to classify using existing methods. We identify co-enriched gene panels shared by pancreatic alpha and beta cells, chart temporal changes in cell enrichment signatures during spermatogenesis, and reveal that cells in the hair root are a major source of skin enriched genes. In a cross-tissue analysis, we identify shared gene enrichment signatures between highly metabolic and motile cell types, and core identity profiles of cell types found in across tissue types. Our study provides the only cell type gene enrichment atlas generated independently of scRNAseq, representing a new addition to our existing toolbox of resources for the understanding of gene expression across human tissues.

systems biology↗

bioRxiv2022

Genome-wide single cell annotation of the human protein-coding genes

An important quest for the life science community is to deliver a complete annotation of the human building-blocks of life, the genes and the proteins. Here, we report on a genome-wide effort to annotate all protein-coding genes based on single cell transcriptomics data representing all major tissues and organs in the human body, integrated with data from bulk transcriptomics and antibody-based tissue profiling. Altogether, 25 tissues have been analyzed with single cell transcriptomics resulting in genome-wide expression in 444 single cell types using a strategy involving pooling data from individual cells to obtain genome-wide expression profiles of individual cell type. We introduce a new genome-wide classification tool based on clustering of similar expression profiles across single cell types, which can be visualized using dimensional reduction maps (UMAP). The clustering classification is integrated with a new "tau" score classification for all protein-coding genes, resulting in a measure of single cell specificity across all cell types for all individual genes. The analysis has allowed us to annotate all human protein-coding genes with regards to function and spatial distribution across individual cell types across all major tissues and organs in the human body. A new version of the open access Human Protein Atlas (www.proteinatlas.org) has been launched to enable researchers to explore the new genome-wide annotation on an individual gene level.

systems biology↗

bioRxiv2022

HDAC6 inhibition partially alleviates mitochondrial trafficking defects and restores motor function in human motor neuron and zebrafish models of Charcot-Marie-Tooth Disease Type 2A

Charcot Marie Tooth Disease (CMT) is a group of inherited progressive conditions affecting distal motor and sensory neurons, leading to muscle weakness, pain and loss of sensation in limbs. There are currently no treatments for this debilitating disease. To investigate disease mechanisms and facilitate treatment discovery, here we developed an in vitro model for CMT type 2A by introducing the patient-specific MFN2R94Q mutation into human embryonic stem cells (hESCs). Isogenic mutant and wild-type hESCs differentiated to spinal motor neurons with similar efficiency and gave rise to functional motor neurons in vitro. However, MFN2R94Q/+ spinal motor neurons displayed impaired mitochondrial trafficking, resulting in reduced numbers of mitochondria in distal parts of axons. Importantly, we showed that mitochondrial trafficking defects can be alleviated by treatment with an HDAC6 inhibitor. Chemical and genetic inhibition of HDAC6 also significantly rescued the motor phenotype in a zebrafish CMT2A model. Taken together, our study reveals a mutation-specific insight into CMT2A disease mechanism and confirms HDAC6 as a promising target for further therapeutic development.

cell biology↗

bioRxiv2022

Dynamic proteomic and phosphoproteomic atlas of corticostriatal axon neurodevelopment

Mammalian axonal development begins in embryonic stages and continues postnatally. After birth, axonal proteomic landscape changes rapidly, coordinated by transcription, protein turnover, and post-translational modifications. Comprehensive profiling of axonal proteomes across neurodevelopment is limited, with most studies lacking cell-type and neural circuit specificity, resulting in substantial information loss. We create a Cre-dependent APEX2 reporter mouse line and map cell-type specific proteome of corticostriatal projections across postnatal development. We synthesize analysis frameworks to define temporal patterns of axonal proteome and phosphoproteome, identifying co-regulated proteins and phosphorylations associated with genetic risk for human brain disorders. We discover proline-directed kinases as major developmental regulators. APEX2 transgenic reporter proximity labeling offers flexible strategies for subcellular proteomics with cell type specificity in early neurodevelopment, a critical period for neuropsychiatric disease.

neuroscience↗

bioRxiv2021

A rapid method to quantify small-scale vegetation patch structure to complement conventional quadrat surveys

AimsVegetation sampling typically involves the use of quadrats, often 1m2, to estimate species cover-abundance. Such surveys do not generally record small-scale vegetation patch structure at sub-quadrat scales, for example 10 cm2. Here we test a simple method to quantify patch structure that complements conventional techniques. We compare the two methods, and analyse metrics derived from small-scale patch surveys with environment / management data. LocationNorthumberland, United Kingdom MethodsWe recorded cover-abundance of all species in an upland moor with 1m2 quadrats. These were divided into 100 sub-quadrats, 10 x 10 cm, and the dominant and subdominant species identified. Patch metrics (number, area and shape) for individual species recorded as dominant or subdominant in the sub-quadrat survey were analysed using multivariate generalised linear models with environmental and management data. Sub-quadrat data were also aggregated for each quadrat, to create species composition data. The two sets of compositional data, from whole-quadrat and sub-quadrat aggregations, were compared via Procrustes rotation of ordination scores. ResultsPatch number, area and shape for dominant and subdominant species were all significantly affected by soil pH, soil water content, slope and elevation. Effects of proximity to sheep tracks and drainage ditches were less consistent amongst species. Ordinations of vegetation data from conventional and sub-quadrats were similar, with significant Procrustes R-squared of 67% and 70% for dominant and subdominant species respectively. ConclusionsSub-quadrat surveys can easily be used to complement existing whole-quadrat surveys at little cost in time or resources. Their patch metrics can provide additional insights into the environmental and management drivers that may affect the growth of individual plants or clumps, potentially in relation to plant traits, and thus alter the overall community composition. The methods we describe can readily be adapted to other sizes of quadrats and sub-quadrats in a wide range of vegetation communities.

ecology↗

bioRxiv2020

Defining the signalling determinants of a posterior ventral spinal cord identity in human neuromesodermal progenitor derivatives

The anteroposterior axial identity of motor neurons (MNs) determines their functionality and vulnerability to neurodegeneration. Thus it is a critical parameter in the design of strategies aiming to produce MNs from human pluripotent stem cells (hPSCs) for regenerative medicine and disease modelling applications. However, the in vitro generation of posterior spinal cord MNs has been challenging. Although the induction of cells resembling neuromesodermal progenitors (NMPs), the bona fide precursors of the mammalian spinal cord, offers a promising solution, the progressive specification of posterior MNs from these cells is not well-defined. Here we determine the signals guiding the transition of human NMP-like cells toward posterior ventral spinal cord neurectoderm. We show that combined WNT-FGF activities drive a posterior dorsal early neural state while suppression of TGFβ-BMP signalling pathways, combined with SHH stimulation, promotes a ventral identity. Based on these results, we define an optimised protocol for the generation of posterior MNs that can efficiently integrate within the neural tube of chick embryos. We expect that our findings will facilitate the functional comparison of hPSC-derived spinal cord cells of distinct axial identities.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2019

A tree-planting decision support tool for urban heat island mitigation

Heat poses an urgent threat to public health in cities, as the urban heat island (UHI) effect can amplify exposures, contributing to high heat-related mortality and morbidity. Urban trees have the potential to mitigate by providing substantial cooling, as well as co-benefits such as reductions in energy consumption. The City of Boston has attempted to expand its urban canopy, yet maintenance costs and high tree mortality have hindered successful canopy expansion. Here, we present an interactive web application called "Right Place, Right Tree - Boston" that aims to support informed decision-making for planting new trees. To highlight priority regions for canopy expansion, we developed a Boston-specific Heat Vulnerability Index (HVI) and present this alongside maps of summer temperatures. We also provide information about tree pests and diseases, suitability of species for various conditions, land ownership, maintenance tips, and alternatives to tree planting.

scientific communication and education↗

bioRxiv2019

A systems-based map of human brain cell-type enriched genes and malignancy-associated endothelial changes

Changes in the endothelium of the cerebral vasculature can contribute to inflammatory, thrombotic and malignant disorders. The importance of defining cell type-specific genes and how they are modified in disease is increasingly recognised. Here, we developed a bioinformatics-based approach to identify normal brain cell-enriched genes, using bulk RNAseq data from 238 normal human cortex samples from 2 independent cohorts. We compared endothelial cell-enriched gene profiles with astrocyte, oligodendrocyte and neuron profiles. Global modifications to the endothelium in malignant disease were characterised, using RNAseq data from 516 human lower grade gliomas and 401 human glioblastoma multiforme samples. Lower grade glioma appeared to be an endothelial intermediate between normal brain and glioblastoma multiforme. We identify the most highly glioblastoma multiforme-specific endothelial cell biomarkers, providing potential diagnostic or therapeutic targets. In summary, we provide a roadmap of endothelial cell identity in normal and malignant brain tissue, using a bioinformatics-based method developed to resolve bulk RNAseq datasets into constituent cell type-enriched profiles.

cell biology↗

bioRxiv2018

GSK3β-SCF-FBXW7 mediated phosphorylation and ubiquitination of IRF1 are required for its transcription-dependent turnover.

IRF1 (Interferon Regulatory Factor-1) is the prototype of the IRF family of DNA binding transcription factors. IRF1 protein expression is regulated by transient up-regulation in response to external stimuli followed by rapid degradation via the ubiquitin-proteasome system. Here we report that DNA bound IRF1 turnover is promoted by GSK3{beta} (Glycogen Synthase Kinase 3{beta}) via phosphorylation of the T181 residue which generates a phosphodegron for the SCF (Skp-Cul-Fbox) ubiquitin E3-ligase receptor protein Fbxw7 (F-box/WD40 7). This regulated turnover is essential for IRF1 activity, as mutation of T181 results in an improperly stabilised protein that accumulates at target promoters but fails to induce RNA-Pol-II elongation and subsequent transcription of target genes. Consequently, the anti-proliferative activity of IRF1 is lost in cell lines expressing T181A mutant. Further, cell lines with dysfunctional Fbxw7 are less sensitive to IRF1 overexpression, suggesting an important co-activator function for this ligase complex. As T181 phosphorylation requires both DNA binding and RNA-Pol-II elongation, we propose that this event acts to clear \"spent\" molecules of IRF1 from transcriptionally engaged target promoters.

molecular biology↗