Biology subjects

Nicholson, T.

Publications and source records attributed to Nicholson, T..

7 recordsLinked to original sources

bioRxiv2026

Multimodal imaging suggests potential immune-vascular contributions to altered regional brain perfusion and oxygen metabolism in Post-COVID-19 Syndrome

Post-COVID-19 Syndrome (PCS) frequently presents with persistent fatigue, cognitive impairment, and emotional symptoms. Although structural brain changes remain subtle, growing evidence implicates functional and metabolic disruptions in ongoing symptomatology. We used multimodal MRI to investigate cerebral perfusion and oxygen metabolism in PCS and examined their associations with cognitive function and peripheral biomarkers. We enrolled 40 individuals with prior mild SARS-CoV-2 infection, including 20 with persistent fatigue and 20 recovered controls matched for age, sex, BMI, and acute COVID-19 severity. Participants underwent structural MRI, arterial spin labelling (ASL) to quantify regional cerebral blood flow (CBF), and asymmetric spin echo imaging to estimate oxygen extraction fraction (OEF) and cerebral metabolic rate of oxygen consumption (CMRO{square}). We assessed cognition using an online battery and measured serum levels of TNF-, IL-6, IL-8, IL-13, IFN-{gamma}, GFAP, and S100{beta}, alongside blood routine tests. We performed ANCOVAs on predefined regions of interest (hippocampus, anterior cingulate cortex [ACC], insula, amygdala, striatum), followed by Bayesian inference and exploratory whole-brain analyses. PCS participants showed increased CMRO{square} in the hippocampus and decreased CMRO{square} in the ACC. Subfield analysis revealed elevated OEF and CMRO{square} across most hippocampal regions, excluding the entorhinal cortex. Whole-brain analyses identified increased perfusion in salience-related regions (insula, ACC, thalamus) and decreased perfusion in posterior cortical and cerebellar areas, in the absence of grey matter volume differences. Higher hippocampal metabolism positively correlated with cognitive performance, suggesting compensatory adaptation to sustain function. In contrast, lower ACC CMRO{square} correlated with depressive symptoms, reduced motivation, and elevated TNF- and GFAP, consistent with neurovascular uncoupling possibly driven by immune-glial activation. These findings reveal distinct physiological disruptions in PCS, with potential implications for stratified, metabolism-focused interventions.

neuroscience↗

bioRxiv2026

Brain dynamics of attentional, default-mode and limbic networks are disrupted at rest in Post-COVID-19 Syndrome

BackgroundPost-COVID-19 Syndrome (PCS) is characterised by persistent fatigue, cognitive impairments, and affective symptoms, yet its underlying neural mechanisms remain poorly understood. While static neuroimaging studies have identified resting-state connectivity abnormalities in PCS, such approaches fail to capture the brains dynamic functional organisation. This represents a missed opportunity to understand how alterations at the dynamic macroscale interactions give rise to the complex and fluctuating symptom profile of PCS. Cognitive and emotional processes rely on the brains capacity to flexibly reconfigure large-scale networks over time; disruptions in the exploration and transition between brain states may therefore play a central role in PCS pathophysiology. MethodsResting-state fMRI data were acquired from 20 individuals with PCS (mean age = 41.8 years, SD = 9.4) and 20 age- and sex-matched healthy controls (mean age = 40.6 years, SD = 8.1) using a multi-echo sequence. Following denoising with multi-echo independent component analysis, we applied Leading Eigenvector Dynamics Analysis (LEiDA) to identify recurrent patterns of whole-brain phase synchrony. The optimal number of dynamic brain states was determined using the Dunn index. For each state, we quantified probability of occurrence, lifetime, and transition probabilities, and mapped spatial topographies onto canonical functional networks. Group differences were assessed using ANCOVAs controlling for age, sex, and handedness. Exploratory associations with clinical symptoms, cognitive performance, and inflammatory markers were examined using both frequentist and Bayesian approaches. ResultsFive recurrent dynamic brain states were identified. Compared with controls, PCS participants showed reduced probability of occurrence and shorter lifetime of a visual/dorsal attention state, alongside increased probability of a limbic/default mode network (DMN) state. PCS was also characterised by reduced transitions between visual/dorsal attention and frontoparietal-DMN states, and increased transitions from somatomotor/visual states toward the limbic-DMN configuration. Exploratory analyses revealed that greater expression of the limbic-DMN state was negatively associated with global cognitive performance (MoCA) and positively associated with serum IL-1{beta} levels. ConclusionsPCS is associated with a reorganisation of intrinsic brain dynamics, marked by a shift from externally oriented attentional states toward limbic-DMN configurations. This imbalance may reflect reduced cognitive flexibility and increased sensitivity to interoceptive or affective signals. The observed links between dynamic brain-state expression, cognitive impairment, and peripheral inflammation support a systems-level mechanism through which immune signalling may influence neural function in PCS. Dynamic functional connectivity offers a sensitive framework for capturing these alterations and may inform future mechanistic models of post-viral dysfunction and therapeutic targeting. HighlightsO_LIPost-COVID-19 Syndrome (PCS) is linked to altered intrinsic brain dynamics at rest. C_LIO_LIPatients show reduced engagement of visual and attentional brain states. C_LIO_LIIncreased recruitment of limbic-DMN states suggests a shift toward more internally, emotionally charged focussed brain activity. C_LIO_LIBrain-state dynamics are putatively associated with global cognition and IL-1{beta}. C_LIO_LIReduced brain-state flexibility may underlie cognitive and emotional symptoms in PCS. C_LI

neuroscience↗

bioRxiv2025

Obesity reprograms adipose extracellular vesicles to induce muscle atrophy via miR-150-5p-mediated transcriptional silencing

BackgroundSarcopenic obesity, where excess body fat coexists with reduced muscle mass and function, is becoming increasingly common in ageing populations and contributes to poor physical and metabolic health. Although adipose tissue-secreted factors are implicated in muscle decline, the specific mechanisms remain unclear. Extracellular vesicles (EVs), which carry regulatory cargo such as microRNAs (miRNAs) between cells, may play a key role in this adipose-muscle communication. MethodsEVs were isolated from adipose-conditioned media (ACM) collected from lean and non-lean human donors using ultracentrifugation. Donors were grouped by BMI (lean: 20.7-24.4; non-lean: 25.3-39.3) and age (younger: 31-56 years; older: 60-84 years). EVs were characterised using nanoparticle tracking analysis (NTA), ExoView, nanoscale flow cytometry (CytoFLEX Nano), and transmission electron microscopy (TEM). Primary human myoblasts were differentiated into myotubes and treated for 24 hours with lean or non-lean EVs (1.3x10 particles/ml) or left untreated. Myotube thickness was measured by immunofluorescence microscopy. Transcriptomic changes were assessed by bulk RNA sequencing. EV miRNA cargo was profiled by small RNA-seq and validated by qPCR. The role of miR-150-5p was tested using antagomir inhibition. ResultsNon-lean EVs significantly reduced myotube thickness compared to both untreated controls (8.7 {+/-} 1.66 {micro}m vs. 12.4 {+/-} 1.72 {micro}m, p < 0.01) and lean EV-treated myotubes (8.7 {+/-} 1.66 {micro}m vs. 13.2 {+/-} 3.84 {micro}m, p < 0.05), indicating a donor BMI-specific effect. This atrophy was restricted to myotubes derived from older donors. MAFbx expression was significantly increased in response to non-lean EVs (p < 0.05). RNA-seq revealed 471 differentially expressed genes (DEGs) in EV-treated vs. untreated cells and 293 DEGs between lean and non-lean EV conditions, with enrichment in inflammatory (TNF, IL1B), oxidative stress, mitochondrial, and chromatin pathways. Small RNA-seq identified 7 differentially expressed miRNAs, including miR-150-5p and miR-193b-5p, both significantly upregulated in non-lean EVs and validated by qPCR. Inhibiting miR-150-5p partially rescued myotube thickness (10.5 {+/-} 1.37 {micro}m vs. 8.7 {+/-} 1.66 {micro}m, p < 0.05) and reduced MAFbx expression. ConclusionsEVs from non-lean adipose tissue drive muscle atrophy and transcriptional changes in an age-dependent manner. These effects are partially mediated by miR-150-5p, highlighting a mechanistic role for EV cargo in adipose-muscle signalling. Targeting EV-derived miRNAs may offer a novel strategy to combat muscle loss in obesity and ageing.

cell biology↗

bioRxiv2025

Increased Quadriceps Intermuscular Adipose Tissue in Chronic Liver Disease is Associated with an Altered Muscle Transcriptome compared with Healthy Age Matched Controls.

Muscle fat infiltration (i.e., myosteatosis) is an important index of muscle health and pathology in disease states, such as chronic liver disease (CLD). However, it is unknown whether myosteatosis differs due to anatomical location. Further, the mechanistic implications of divergent intermuscular adipose tissue (IMAT) deposition remains unknown in patients with CLD. 33 patients with CLD (55.0{+/-}10.5years) and 17 healthy controls (HC) (49.6{+/-}15.4years) were recruited. Quadriceps IMAT was estimated between 20-80% of muscle length and psoas IMAT at L3 via MRI. Body composition, muscle strength and habitual activity were assessed. Fasted vastus lateralis muscle biopsies were collected and subjected to RNA sequencing analysis. https://ClinicalTrials.gov identifier: NCT04734496. IMAT was greater in CLD compared with HC in both quadriceps and psoas (P<0.0001). Quadriceps IMAT positively correlated with BMI (r=0.62), body fat (r=0.65), age (r=0.36) and negatively correlated with maximal knee extensor strength (r=-0.45) and habitual physical activity (r=-0.50) in CLD and HC. 169 differentially expressed genes (DEGs) were identified in low IMAT CLD vs HC, and 178 DEGs were identified in high IMAT CLD vs HC. CLD patients with high and low IMAT exhibited defined expression profiles, with only 39 DEGs (representing 12.7%) in common. Pathway analysis of DEGs revealed enrichment of atrophic and pro-inflammatory pathways in the high IMAT group. IMAT is greater in patients with CLD compared to HC, irrespective of anatomical location and is associated with reductions in muscle function and may be exacerbated by physical inactivity. IMAT appears to alter the muscle transcriptome in COLD, potentially exacerbating muscle loss.

physiology↗

bioRxiv2025

Systemic drivers and molecular mechanisms of sarcopenia in aetiology-specific end-stage liver disease

IntroductionPatients with end-stage liver disease (ESLD) often present with sarcopenia, defined as loss of skeletal muscle mass and quality, which is associated with reduced quality of life and increased mortality. However, the molecular mechanisms driving sarcopenia in ESLD are not fully understood and there are currently no therapeutic interventions. This study aimed to identify potential circulating factors contributing to sarcopenia progression in ESLD by assessing their role in driving transcriptomic alterations in skeletal muscle. MethodsQuadriceps muscle tissue, plasma and serum were obtained from ESLD patients (n=24) and age/sex-matched healthy controls (HC; n=18) (clinical trial ID: NCT04734496, ethical approval 18/WM/0167). Total RNA from snap-frozen vastus lateralis muscle biopsies underwent RNA sequencing (Illumina). Serum concentrations of 60 cytokines were profiled by Luminex and ELISA, with comparisons made both between ESLD and HC, and across ESLD aetiologies (alcohol-related, NAFLD, viral hepatitis, other). In vitro, primary human myotubes (from non-ESLD aged donors, NRES #16/SS/0172) were treated with 10% ESLD or HC plasma (24 h, n=6 per group) followed by RNA sequencing (BGI Genomics). Differentially expressed genes (p<0.05, fold-change >1.5) were identified via Qlucore and DESeq2, and pathway analysis performed using Ingenuity (Qiagen). The impact of physiological concentrations of candidate cytokines (IL-1, GDF-15, HGF) on myotube thickness, differentiation and mitochondrial function was assessed by immunofluorescence microscopy, RT-qPCR and metabolic flux assays. ResultsIn ESLD muscle, 387 and 225 genes were significantly up- and downregulated compared to HC respectively, with cellular senescence identified as a top dysregulated function. Upstream regulator analysis predicted activation of hepatocyte growth factor (HGF) and interleukin-1 signalling. Subgroup analysis revealed distinct transcriptomic profiles based on disease aetiology. Serum profiling identified 15 cytokines significantly elevated (p<0.05) and 5 reduced (p<0.05) in ESLD, including increased HGF and reduced interleukin-1 receptor antagonist. Stratified analysis also revealed aetiology specific cytokine profiles, with only GDF-15 significantly (P<0.0001) elevated in all groups. 24h ESLD plasma treatment induced 423 differentially expressed genes in human myotubes, which were again associated with significant activation of senescence pathways, with IL-1 identified as a key upstream driver. In vitro, IL-1, GDF-15, and HGF significantly reduced myotube thickness, nuclear fusion index and perturbed metabolism (Increased glycolysis, impaired oxidative phosphorylation). ConclusionsCollectively, these findings suggest that sarcopenia in ESLD is driven by aetiology-specific mechanisms, highlighting the potential for targeted therapies to improve muscle mass and function.

molecular biology↗

bioRxiv2020

Protein-carbohydrate ingestion alters Vps34 cellular localization independent of changes in kinase activity in human skeletal muscle

The mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) regulates cell size and growth in response to nutrients, however, the mechanisms by which nutrient levels are sensed by mTORC1 in human skeletal muscle are yet to be fully elucidated. The Class III PI3Kinase Vps34 has recently been proposed as a sensor essential for mTORC1 activation following nutrient stimulation. We therefore investigated the effects of increasing nutrient availability through protein-carbohydrate (PRO-CHO) feeding on Vps34 kinase activity and cellular localization in human skeletal muscle. Eight young, healthy males (age - 21 {+/-} 0.5yrs, mean {+/-} SEM) ingested a PRO-CHO beverage containing 20/44/1g PRO/CHO/FAT respectively, with skeletal muscle biopsies obtained at baseline and 1h and 3h post-feeding. PRO-CHO feeding did not alter Vps34 kinase activity, but did stimulate Vps34 translocation toward the cell periphery (PRE (mean{+/-}SEM) - 0.273{+/-}0.021, 1h - 0.347{+/-}0.022, Pearsons Coefficient (r)) where it co-localized with mTOR (PRE - 0.312{+/-}0.018, 1h - 0.348{+/-}0.024, Pearsons Coefficient (r))). These alterations occurred in parallel to an increase in S6K1 kinase activity - 941{+/-}164% of PRE at 1h post-feeding). Subsequent in vitro experiments in C2C12 and human primary myotubes displayed no effect of the Vps34-specific inhibitor SAR405 on mTORC1 signalling responses to elevated nutrient availability. Therefore, in summary, PRO-CHO ingestion does not increase Vps34 activity in human skeletal muscle, whilst pharmacological inhibition of Vps34 does not prevent nutrient stimulation of mTORC1 in vitro. However, PRO-CHO ingestion promotes Vps34 translocation to the cell periphery, enabling Vps34 to associate with mTOR. Therefore, our data suggests that interaction between Vps34 and mTOR, rather than changes in Vps34 activity per se may be involved in PRO-CHO activation of mTORC1 in human skeletal muscle.

physiology↗

bioRxiv2019

Injection molded open microfluidic well plate inserts for user-friendly coculture and microscopy

Open microfluidic cell culture systems are powerful tools for interrogating biological mechanisms. We have previously presented a microscale cell culture system, based on spontaneous capillary flow of biocompatible hydrogels, that is integrated into a standard cell culture well plate, with flexible cell compartment geometries and easy pipet access. Here, we present two new injection molded open microfluidic devices that also easily insert into standard cell culture well plates and standard culture workflows, allowing seamless adoption by biomedical researchers. These platforms allow culture and study of soluble factor communication among multiple cell types, and the microscale dimensions are well-suited for rare primary cells. Unique advances include optimized evaporation control within the well, manufacture with reproducible and cost-effective rapid injection molding, and compatibility with sample preparation workflows for high resolution microscopy (following well-established coverslip mounting procedures). In this work, we present several use cases that highlight the usability and widespread utility of our platform including culture of limited primary testis cells from surgical patients, microscopy readouts including immunocytochemistry and single molecule fluorescence in situ hybridization (smFISH), and coculture to study interactions between adipocytes and prostate cancer cells.

bioengineering↗