Biology subjects

Burns, J.

Publications and source records attributed to Burns, J..

9 recordsLinked to original sources

bioRxiv2024

RNA mis-splicing in children with myotonic dystrophy is associated with physical function

ObjectivesDysregulated RNA alternative splicing is the hallmark of myotonic dystrophy type 1 (DM1). However, the association between RNA mis-splicing and physical function in children with the most severe form of disease, congenital myotonic dystrophy (CDM), is unknown. Methods82 participants (42 DM1 adults & 40 CDM children) with muscle biopsies and measures of myotonia, motor function, and strength were combined from five observational studies. Data were normalized and correlated with an aggregate measure of alternative splicing dysregulation, [MBNL]inferred in skeletal muscle biopsies. Multiple linear regression analysis was performed to predict [MBNL]inferred using clinical outcome measures alone. Similar analyses were performed to predict 12-month physical function using baseline metrics. ResultsMyotonia (measured via vHOT) was significantly correlated with RNA mis-splicing in our cross-sectional population of all DM1 individuals; CDM participants alone displayed no myotonia despite a similar range of RNA mis-splicing. Measures of motor performance and muscle strength were significantly associated with [MBNL]inferred in our cohort of all DM1 individuals and when assessing CDM children independently. Multiple linear regression analyses yielded two models capable of predicting [MBNL]inferred from select clinical outcome assessments alone in all subjects (adjusted R2 = 0.6723) or exclusively in CDM children (adjusted R2 = 0.5875). InterpretationOur findings establish significant correlations between skeletal muscle performance and a composite measure of alternative splicing dysregulation, [MBNL]inferred, in DM1. The strength of these correlations and the development of the predictive models will assist in designing efficacious clinical trials for individuals with DM1, particularly CDM.

genetics↗

bioRxiv2023

Proteomic Features of Adolescents and Young Adults with Soft Tissue Tumours

Adolescents and young adult (AYA) patients with soft tissue tumours (STT) including sarcomas are an underserved group with disparities in treatment outcomes. To define the molecular features between AYA and older adult (OA) patients, we analysed the proteomic profiles of a large cohort of STT across 10 histological subtypes (AYA n=66, OA n=243). AYA tumours are enriched in proteins involved in mitochondrial metabolism while OA patients have elevated inflammatory and cell cycle signalling. By integrating the patient-level proteomic data with functional genomic profiles from sarcoma cell lines, we show that the mRNA splicing pathway is an intrinsic vulnerability in cell lines from OA patients and that components of the spliceosome complex are independent prognostic factors for metastasis free survival in AYA patients. Our study highlights the importance of performing age-specific molecular profiling studies to identify risk stratification tools and targeted agents tailored for the clinical management of AYA patients.

cancer biology↗

bioRxiv2023

Proteomic characterisation of Sarculator nomogram-defined risk groups in soft tissue sarcomas of the extremities and trunk wall

BackgroundHigh-risk soft tissue sarcomas of the extremities and trunk wall (eSTS), as defined by the Sarculator nomogram, are more likely to benefit from (neo)adjuvant anthracycline-based therapy compared to low/intermediate-risk patients. The biology underpinning these differential treatment outcomes remain unknown. MethodsWe analysed proteomic profiles and clinical outcomes of 123 eSTS patients. A Cox model for overall survival including the Sarculator was fitted to individual data to define 4 risk groups. A DNA replication protein signature - Sarcoma Proteomic Module 6 (SPM6) was evaluated for association with clinicopathological factors and risk groups. SPM6 was added as a covariate together with Sarculator in a multivariable Cox model to assess improvement in prognostic risk stratification. ResultsDNA replication and cell cycle proteins were upregulated in high risk versus very low risk patients. Evaluation of the functional effects of CRISPR-Cas9 gene knockdown of proteins enriched in high risk patients identified candidate drug targets. SPM6 was significantly associated with tumour malignancy grade (p = 1.6e-06), histology (p = 1.4e-05) and risk groups (p = 2.6e-06). Cox model analysis showed that SPM6 substantially contributed to a better calibration of the Sarculator nomogram (Index of Prediction Accuracy =0.109 for Sarculator alone versus 0.165 for Sarculator + SPM6). ConclusionsRisk stratification of patient with STS is defined by distinct biological pathways across a range of cancer hallmarks. Incorporation of SPM6 protein signature improves prognostic risk stratification of the Sarculator nomogram. This study highlights the utility of integrating protein signatures for the development of next-generation nomograms.

cancer biology↗

bioRxiv2021

Pancreatic ductal adenocarcinoma cells employ integrin α6β4 to form hemidesmosomes and regulate cell proliferation

Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis due to its aggressive progression, late detection and lack of druggable driver mutations, which often combine to result in unsuitability for surgical intervention. Together with activating mutations of the small GTPase KRas, which are found in over 90% of PDAC tumours, a contributory factor for PDAC tumour progression is formation of a rigid extracellular matrix (ECM) and associated desmoplasia. This response leads to aberrant integrin signalling, and accelerated proliferation and invasion. To identify the integrin adhesion systems that operate in PDAC, we analysed a range of pancreatic ductal epithelial cell models using 2D, 3D and organoid culture systems. Proteomic analysis of isolated integrin receptor complexes from human pancreatic ductal epithelial (HPDE) cells predominantly identified integrin 6{beta}4 and hemidesmosome components, rather than classical focal adhesion components. Electron microscopy, together with immunofluorescence, confirmed the formation of hemidesmosomes by HPDE cells, both in 2D and 3D culture systems. Similar results were obtained for the human PDAC cell line, SUIT-2. Analysis of HPDE cell secreted proteins and cell-derived matrices (CDM) demonstrated that HPDE cells secrete a range of laminin subunits and form a hemidesmosome-specific, laminin 332-enriched ECM. Expression of mutant KRas (G12V) did not affect hemidesmosome composition or formation by HPDE cells. Cell-ECM contacts formed by mouse and human PDAC organoids were also assessed by electron microscopy. Organoids generated from both the PDAC KPC mouse model and human patient-derived PDAC tissue displayed features of acinar-ductal cell polarity, and hemidesmosomes were visible proximal to prominent basement membranes. Furthermore, electron microscopy identified hemidesmosomes in normal human pancreas. Depletion of integrin {beta}4 using siRNA reduced cell proliferation in both SUIT-2 and HPDE cells, reduced the number of SUIT-2 cells in S-phase, and induced G1 cell cycle arrest, indicating a requirement for 6{beta}4-mediated adhesion for cell cycle progression and growth. Taken together, these data suggest that laminin-binding adhesion mechanisms in general, and hemidesmosome-mediated adhesion in particular, may be under-appreciated in the context of PDAC. Proteomic data are available via ProteomeXchange with the identifiers PXD027803, PXD027823 and PXD027827.

cancer biology↗

bioRxiv2021

Kawasaki Disease patient stratification and pathway analysis based on host transcriptomic and proteomic profiles

The aetiology of Kawasaki Disease (KD), an acute inflammatory disorder of childhood, remains unknown despite various triggers of KD having been proposed. Host omic profiles offer insights into the host response to infection and inflammation, with the interrogation of multiple omic levels in parallel providing a more comprehensive picture. We used differential abundance analysis, pathway analysis, clustering and classification techniques to explore whether the host response in KD is more similar to the response to bacterial or viral infection at the transcriptomic and proteomic levels through comparison of omic profiles from children with KD to those with bacterial and viral infections. Pathways activated in patients with KD included those involved in anti-viral and anti-bacterial responses. Unsupervised clustering showed that the majority of KD patients clustered with bacterial patients on both omic levels, whilst application of diagnostic signatures specific for bacterial and viral infections revealed that many transcriptomic KD samples had low probabilities of having bacterial or viral infections, suggesting that KD may be triggered by a different process not typical of either common bacterial or viral infections. Clustering based on the transcriptomic and proteomic responses during KD revealed three clusters of KD patients on both omic levels, suggesting heterogeneity within the inflammatory response during KD. The observed heterogeneity may reflect differences in the host response to a common trigger, or variation dependent on different triggers of the condition.

bioinformatics↗

bioRxiv2020

Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary

Food limitation can dampen survival and growth of fish during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on the guts of these fishes and on environmental zooplankton samples. Differential abundance analysis suggested that both species consumed the most abundant zooplankton at a lower rate than their availability in the environment. Both fish consumed the prey that were commonly available and relatively abundant. Prey taxa substantially overlapped between the two species (Schoeners index = 0.66), and alpha diversity analysis suggested high variability in the content of individual guts. Abundant prey taxa in both fish species included the copepods Eurytemora carolleeae, Acanthocyclops americanus, and A. robustus; the Acanthocyclops spp. are difficult to identify morphologically. A few uncommon prey in the diets hint at variable feeding strategies, such as herring (presumably egg) DNA in the longfin smelt diets, which suggests feeding near substrates. Herring consumed the small (<0.5 mm) copepod Limnoithona tetraspina more frequently (30%) than did smelt (2%), possibly indicating differences in foraging behavior or sensory abilities. Among the unexpected prey found in the diets was the cnidarian Hydra oligactis, the polychaete Dasybranchus sp., and a newly identified species Mesocyclops pehpeiensis. "Unknown" DNA was in 56% of longfin smelt diets and 57% of herring diets, and made up 17% and 21% of the relative read abundance in the two species, respectively. Our results suggest that these two fishes, which overlap in nursery habitat, also largely overlap in food resources necessary for larval survival.

ecology↗

bioRxiv2020

A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method overcomes the challenge of high sequence similarity between mouse and human proteins, facilitating the study of host microenvironment-tumour interactions from bulk tumour measurements. We apply the XenoSWATH pipeline to characterise an intraductal xenograft model of breast ductal carcinoma in-situ and uncover complex regulation of cell migration pathways that are not restricted to tumour cells but also operate in the mouse stroma upon progression to invasive disease. MouseRefSWATH and XenoSWATH opens new opportunities for in-depth and reproducible proteomic assessment to address wide-ranging biological questions involving this important model organism.

biochemistry↗

bioRxiv2018

Physical activity in children and adolescents with Charcot-Marie-Tooth disease: A cross-sectional case-controlled study

BackgroundDisability related to the progressive and degenerative neuropathies known as Charcot-Marie-Tooth disease (CMT) affects gait and function, increasing with age and influencing physical activity in adults with CMT. The relationship between disease, ambulatory function and physical activity in children and adolescents with CMT is unknown.\n\nMethodA cross-sectional case-controlled study of 50 children with CMT and age- and gender-matched typically developing (TD) controls [mean age 12.5 (SD 3.9) years]. A 7-day recall questionnaire assessed physical activity; disease severity and gait-related function were measured to explore factors associated with physical activity.\n\nResultsChildren with CMT were less active than TD controls (estimated weekly moderate to vigorous physical activity CMT 283.6 (SD 211.6) mins, TD 318.0 (SD 202.5) mins; p < 0.001). The children with CMT had moderate disability [CMT Pediatric Scale mean score 20 (SD 8) /44] and reduced ambulatory capacity in a six-minute walk test [CMT 485.1 (SD 160.9) metres, TD 639.8 (83.1) metres; p < 0.001]. Physical activity correlated with greater disease severity ({rho} = -0.52, p < 0.001) and six-minute walk distance ({rho} = 0.71, p < 0.001).\n\nConclusionsDisease-related disability affects physical activity and gait-related function in children and adolescents with CMT compared to TD peers. Reduced physical activity adversely affects function across the timespan of childhood and adolescence into adulthood.

neuroscience↗

bioRxiv2017

The transcriptome of Paraphelidium tribonemae illuminates the ancestry of Fungi and Opisthosporidia

Aphelids constitute a group of diverse, yet poorly known, parasites of algae [1, 2]. Their life cycle and morphology resemble those of zoosporic fungi (chytrids) and rozellids (Cryptomycota/Rozellosporidia), another specious group of parasites of fungi and oomycetes [3, 4]. Unlike fungi, which are osmotrophs, aphelids and rozellids are phagotrophs, feeding on the hosts cytoplasm. Combined RNA polymerase and rRNA gene trees [5] suggested that aphelids and rozellids relate to Microsporidia, extremely reduced parasites with remnant mitochondria [6]. Accordingly, aphelids, rozellids and Microsporidia were proposed to form a monophyletic clade, called Opisthosporidia, sister to Fungi [1]. Microsporidia would have subsequently lost the ancestral opisthosporidian phagotrophy. However, the limited phylogenetic signal of those genes combined with microsporidian fast-evolving sequences have resulted in incongruent tree topologies, showing either rozellids [5, 7] or aphelids [8] as the earliest-branching lineages of Opisthosporidia. We have generated the first transcriptome data for one aphelid species, Paraphelidium tribonemae [2]. In-depth multi-gene phylogenomic analyses using various protein datasets place aphelids in a deep, pivotal position as a sister group to Fungi, making Opisthosporidia paraphyletic. We infer a rich, free-living-like proteome for P. tribonemae, which includes cellulases likely involved in algal cell-wall penetration, enzymes involved in chitin biosynthesis and several metabolic pathways that were lost in the comparatively reduced Rozella allomycis genome [9]. Our results suggest that Fungi evolved from a complex phagotrophic opisthosporidian ancestor, likely a specialized endobiotic predator, which became osmotrophic at the fungal root and evolved towards phagotrophic parasitism in the rozellid/microsporidian line.

evolutionary biology↗