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Garnham, A.

Publications and source records attributed to Garnham, A..

At least 19 recordsLinked to original sources

Molecular responsiveness to testosterone is uncoupled from skeletal muscle mass and strength in males aged 18 - 80 years

Objective Testosterone exerts wide-ranging physiological effects, including the regulation of anabolic processes in skeletal muscle. However, its role in skeletal muscle ageing remains unclear. This study aimed to establish the association between endogenous testosterone levels and skeletal muscle phenotype across the adult lifespan and determine whether ageing modulates this relationship. Methods Eighty-one healthy males aged 18-80 underwent comprehensive phenotypic assessment. Body composition and muscle morphology were assessed using dual-energy X-ray absorptiometry (DEXA) and peripheral quantitative computed tomography (pQCT). Muscle strength was estimated leg press one-repetition maximum (e1RM). Vastus lateralis biopsies were used to assess fibre type, sequence the transcriptome and establish primary myocytes. Cell lines from young (n=5) and older (n=7) donors were cultured and compared under control and testosterone-treated conditions for cellular phenotype. Results Ageing was associated with lower free testosterone, muscle mass and strength, altered type IIa fibre characteristics, and widespread transcriptional changes in skeletal muscle. Free, but not total, testosterone was strongly associated with the muscle transcriptome, although neither fraction was associated with muscle mass or strength. In primary myocytes, testosterone increased androgen receptor abundance and nuclear localisation and enriched pathways involved in protein translation. Conclusion Testosterone is biologically active in male skeletal muscle, with its free fraction strongly associated with the transcriptome; however, these molecular effects do not translate into differences in muscle mass or strength. Testosterone may therefore play a primary role in establishing the male muscle phenotype during puberty, before transitioning to a more ancillary role in adult skeletal muscle.

physiology↗

3D genome remodelling underlies PU.1-dependent granulocyte maturation

PU.1 is an ETS-domain transcription factor that has critical roles in many aspects of hematopoiesis and immune cell fate and function. In addition, aberrant PU.1 expression has been implicated in the development of acute myeloid leukemia (AML). Loss of PU.1 during adult murine hematopoiesis results in the expansion of immature granulocytes suggesting that PU.1 plays an important role in granulocyte maturation. To understand the molecular underpinnings of this process, we combined gene expression, transcription factor binding and 3D genome analyses with conditional deletion of PU.1 in vivo. We find that in contrast to normal granulocytes, PU.1-deficient cells possessed a transcriptome of immature granulocytes, in line with their cellular phenotype. Furthermore PU.1-deficient granulocytes display altered 3D genome architecture with a significant loss of interactivity in regions bound by PU.1 in control cells. Overall, this study implicates PU.1 as a key regulator of granulocyte maturation and lineage commitment through control of transcriptional programs and 3D chromatin architecture.

immunology↗

Muscle mass and denervation explain variability in maximal power and rapid force across the adult female lifespan

BackgroundDynamic power declines earlier across the lifespan and shows a more pronounced and complex pattern than isometric strength, particularly in ageing females. However, the functional, skeletal muscle and molecular mechanisms underpinning power loss across the female lifespan remain to be collectively examined. MethodsEighty-six females aged 18-80 years and stratified per decade of age completed a series of maximal voluntary knee extensions to construct torque-velocity and power-velocity relationships of the quadriceps. Data points corresponding to >95% maximal power were selected for the evaluation of rate of torque development (RTD) and quadriceps surface electromyography (EMG). Outcomes were quantified within discrete 50ms time bins from torque onset to +200ms and included absolute RTD, RTD normalised to peak force, and EMG amplitude and rate of rise normalised to the maximal compound action potential. Quadriceps morphology was assessed via computed tomography, and a vastus lateralis muscle biopsy was collected to assess markers of denervation and expression of genes associated with the neuromuscular junction and calcium-handling transcriptome. ResultsAgeing led to linear reductions in maximal power (-1.39 {+/-} 0.01% p/year), torque (-0.98 {+/-} 0.13% p/year) and velocity (-0.38 {+/-} 0.01% p/year) (all p < 0.05). Quadriceps skeletal muscle CSA attenuated power loss by [~]40% (p < 0.001), largely through reduction of the decline in torque ([~]50%), with no effect on the decline in velocity. During early time bins, older females generated higher relative RTD accompanied by higher EMG amplitude, whereas during later time bins, older females generated less absolute and relative RTD accompanied by lower EMG amplitude and rate of rise (all p < 0.05). Ageing increased neural cell adhesion molecule (NCAM) positive fibres and fibrosis (both p < 0.05). The presence of NCAM{square} fibres was associated with attenuation of the age-related decline in maximal power ([~]15%), torque ([~]35%) and velocity ([~]60%), suggesting that NCAM{square} fibre prevalence may partially explain the observed age associations. Within the neuromuscular junction transcriptome, ageing reduced acetylcholinesterase and increased laminin alpha-2 and muscle-specific kinase (all FDR < 0.05), whereas lesser changes were observed within the calcium-handling transcriptome. ConclusionsSkeletal muscle CSA explains [~]40% of the age-related decline in quadriceps dynamic maximal power across the female lifespan, whereas a neurodegenerative profile mainly evidenced by age-related changes in voluntary neural drive, denervation and markers of neuromuscular junction instability further contribute to the decline.

physiology↗

Normobaric hypoxia alters the transcriptional response of healthy human skeletal muscles to a single session of high-intensity interval exercise

Given its well-documented effects on human physiology, hypoxia has garnered increasing interest for its potential to enhance specific adaptations to exercise. However, the molecular response of skeletal muscle to exercise under normobaric hypoxia remains poorly understood. To address this gap in knowledge, ten healthy young males completed a crossover study in which exercise in hypoxia was compared to exercise in normoxia matched by either absolute or relative intensity. This design allowed us to identify shared transcriptomic responses across all three conditions, as well as changes that were specific to exercise intensity or hypoxic exposure. Skeletal muscle biopsies were collected before, immediately after, and at 3 and 24 hours following each exercise session, with RNA sequencing performed to assess changes in gene expression. Following exercise, a greater number of differentially expressed genes were observed in hypoxia compared to normoxia at 24 h post-exercise. This hypoxia-specific response involved the downregulation of multiple mitochondrial pathways and appears to be regulated by a transcriptional network comprising both positive and negative regulators of HIF-1 activity. These findings highlight the ability of normobaric hypoxia to influence exercise-induced gene expression and suggests that it may promote distinct molecular adaptations in skeletal muscle following longer-term training.

physiology↗

Exercise induces time-dependent but not sex-specific transcriptomic changes in healthy human skeletal muscle

Elucidating the time-dependent transcriptional response of skeletal muscle to exercise is essential for uncovering the molecular mechanisms that drive its health-promoting effects. However, previous studies have been limited by a small number of muscle biopsies, often collected at arbitrary time points post-exercise, and in predominantly male subjects. Using the most comprehensive skeletal muscle biopsy time course following a single session of exercise in both males and females, we identified over 16,600 differentially expressed genes (DEGs), including more than 7,000 novel exercise-responsive genes. Of these DEGs, the magnitude of differential expression in 60% of genes was influenced by cardiorespiratory fitness. Although most mitochondrial genes were differentially expressed after exercise, the majority were downregulated at 24-48 hours, suggesting that mitochondrial protein expression may be regulated by post-transcriptional regulation. Despite 1,193 genes showing sex-specific expression at baseline, exercise-induced gene expression differences were minimal between males and females, suggesting that when cardiorespiratory fitness and exercise stimulus are matched, skeletal muscle adaptations are similar between sexes. To enhance data accessibility, we created an interactive Shiny app (https://BishopLab.shinyapps.io/EXERgene/) that allows users to investigate specific genes and interrogate potential mechanisms of skeletal muscle adaptation to exercise.

physiology↗

Differentiation of Toxoplasma into latent forms is linked to central carbon metabolism and requires a GID/CTLH-type E3 ubiquitin ligase

Toxoplasma and other Apicomplexan parasites, switch between different developmental stages to persist in and transmit between hosts. Toxoplasma can alternate between systemic tachyzoites and encysted bradyzoite forms found in the CNS and muscle tissues. How parasites sense these tissue types and trigger differentiation remains largely unknown. We show that Toxoplasma differentiation is induced under glucose-limiting conditions and using a CRISPR screen identify parasite genes required for growth under these conditions. From [~]25 identified genes important for differentiation we show that lactate and glutamine metabolism is linked to differentiation and demonstrate the importance of an E3 ubiquitin ligase complex, orthologous to glucose induced degradation deficient (GID) complex in yeast and CTLH complex in humans. We show that TgGID likely regulates translational repression of a key transcription factor required for differentiation, BFD1, through its 3 utr. Overall, this work provides important new insight into how these divergent parasites sense different host cell niches and trigger stage conversion through a ubiquitination-dependent program.

microbiology↗

ARAP2 regulates responses to interferon-gamma by restricting SOCS1

Interferon-gamma (IFN{gamma}) is critical for immunity against intra-macrophagic pathogens, signaling through the JAK-STAT pathway to induce a tyrosine-phosphorylation cascade that ensures a potent immune response. Excessive JAK-STAT signaling can drive hyperinflammation and autoimmunity, and thus signaling is tightly and selectively regulated by the IFN{gamma}-inducible protein, Suppressor of Cytokine Signaling 1 (SOCS1). SOCS1 inhibits signaling by directly blocking JAK kinase activity. Here we identified a SOCS1-interacting partner, ARAP2 that fine-tunes SOCS1 function. We report that tyrosine 415 in ARAP2 binds the SOCS1-Src Homology 2 (SH2) domain and limits the ability of SOCS1 to inhibit IFN{gamma} signaling. Our findings show that ARAP2 promotes the IFN{gamma} response through a phosphorylation dependent interaction with the negative regulator SOCS1.

cell biology↗

Expression of the Close homolog of L-1 and embigin identifies activated myofibroblasts.

AbstractFibrosis is driven by the emergence of myofibroblasts, which are the primary producers of the extracellular matrix proteins that form fibrotic lesions. Despite this critical role, detecting myofibroblasts remains challenging due to the paucity of selective markers. We therefore screened for novel myofibroblast-specific markers, discovering that the expression of the close homolog of L1 (ChL-1) and embigin (Emb) distinguish activated myofibroblasts from their quiescent precursors. We report that ChL-1+/Emb+ fibroblasts: (1) emerge during cardiac inflammation, (2) have elevated expression of collagens and inflammatory factors and (3) localise to fibrotic zones - consistent with activated myofibroblasts. Mechanistically, Chl1+/Emb+ myofibroblasts differentiate from resident fibroblasts which upregulate these markers in response to proinflammatory cytokines, such as IL-1 and IL-17. Moreover, we show that embigin could be exploited to target antibody-based therapies to myofibroblasts and confirm this protein as a conserved marker of activated fibroblasts in multiple tissues and settings. Collectively, these findings identify ChL-1 and embigin as novel myofibroblast surface-markers that could be used to identify, enumerate and target this pathogenic population.

cell biology↗

Sprint interval exercise disrupts mitochondrial ultrastructure driving a unique mitochondrial stress response and remodelling in humans

Exercise remains the most effective lifestyle intervention to remodel the mitochondrial network and to prevent most non-communicable diseases. Despite this, the molecular mechanisms by which different exercise prescriptions dictate mitochondrial remodelling are poorly understood in humans. Here, we show that, compared to moderate-intensity continuous exercise (MICE), sprint-interval exercise (SIE) - a known time-efficient high-intensity exercise - leads to mitochondrial stress and activates the mitochondrial unfolded protein response (UPRmt). The SIE-specific signature is characterized by a morphological and ultrastructural mitochondrial disturbance, concurrent with the activation of the integrated stress response (ISR) and mitochondrial quality control (MQC) pathways. When the respective exercises are repeated over time (8 weeks), our results demonstrate that moderate-intensity continuous training (MICT) and sprint-interval training (SIT) lead to a divergent mitochondrial remodelling. MICT elicits a mitochondrial adaptation characterized by an increase in markers of mitochondrial content, complex I activity, and enrichment of proteins involved in tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) system. On the other hand, SIT leads to proteomic enrichment of pathways involved in mitochondrial 1-Carbon metabolism and protein quality control, concurrently with improvements in mitochondrial respiratory function. Lastly, we have identified COX7A2L as a divergently regulated protein across groups, significantly accumulating in III2+IV1 respiratory supercomplexes only following SIT. In conclusion, our study provides mechanistic insights on how SIE and MICE divergently impact the post-exercise mitochondrial signalling, and subsequent long-term mitochondrial remodelling following training. These findings provide a strong basis for targeted exercise prescription to modulate specific mitochondrial adaptations in human skeletal muscle.

molecular biology↗

The transcriptomic signature of age and sex is not conserved in human primary myocytes

BackgroundHuman primary muscle cell (HPMC) lines derived from skeletal muscle biopsies are potentially powerful tools to interrogate the molecular pathways underlying fundamental muscle mechanisms. HPMCs retain their genome in culture, but many endogenous circulating factors are not present in the in vitro environment, or at concentrations that do not mirror physiological levels. To address the assumption that HPMCs are valid models of age and sex-specificity in human muscle research, we examined to what extent HPMC lines retain their source phenotype in culture. MethodsBiopsies from the vastus lateralis muscle were collected from ten males aged 18-30, ten females aged 18-30 and ten males aged 60-75 recruited from a general, healthy population. A portion of the muscle was used for the establishment of 30 individual HMPC lines. The remaining sample was immediately snap frozen and stored for further analysis. RNA was extracted from muscle tissue samples and their corresponding, fully differentiated HMPCs and analysed using RNA Sequencing. To compare their transcriptomic signature, principal component analysis (PCA), differential expression analysis, single-cell deconvolution and pathway enrichment analysis were conducted in R. ResultsA comparison of the transcriptomic signature of 30 human muscle biopsies and their corresponding HPMCs indicated a near-complete lack of retention of the genes and pathways differentially regulated in vivo when compared to their in vitro equivalent, with the exception of several genes encoded on the Y-chromosome. ConclusionsThe diversity of resident cell populations in muscle tissue and the lack of sex- and age-dependent circulating factors in the cellular milieu likely contribute to these observations, which call for caution when using HPMCs as an experimental model of human muscle sex or age.

cell biology↗

Transcriptomic alterations including p53 pathway dysregulation prime DNMT3A mutant cells for transformation

DNMT3A mutations are prevalent in haematologic malignancies. Our mouse model introduced the murine homologue (R878H) of the human hotspot R882H mutation into the mouse Dnmt3a locus, resulting in globally reduced DNA methylation in all tissues. Mice with heterozygous R878H mutations developed {gamma}-radiation induced thymic lymphoma more rapidly than control mice, suggesting a vulnerability to stress stimuli in Dnmt3aR878H/+ cells. In competitive transplantations, Dnmt3aR878H/+ Lin-Sca-1+Kit+ (LSK) cells had a competitive advantage over wt cells, indicating a self-renewal phenotype at the expense of differentiation. RNA-sequencing of Dnmt3aR878H/+ LSKs exposed to low dose {gamma}-radiation showed downregulation of the p53 pathway. Accordingly, reduced PUMA expression was observed by flow cytometry in the bone marrow of {gamma}-irradiated Dnmt3aR878H/+ mice due to altered p53 signalling. These findings provide new insights as to how DNMT3A mutations cause subtle changes in the transcriptome of LSK cells which contribute to their increased self-renewal and propensity for malignant transformation. SIGNIFICANCEHotspot DNMT3A R882H mutations are overrepresented in leukaemia suggesting that they confer a susceptibility to disease if further mutations are acquired. To advance therapies for DNMT3A mutant disease, it is essential to understand the mechanisms by which this mutation primes cells for malignant transformation.

cancer biology↗

Molecular Landscape of Modality-Specific Exercise Adaptation in Human Skeletal Muscle through Large-Scale Multi-OMICs Integration

We conducted a large-scale, statistically powered, meta-analysis of exercise adaptations in human skeletal muscles, integrating epigenetic, transcriptomic, transcription factors, and proteomic data across 12 independent cohorts comprising over 1000 participants and 2340 human muscle samples. Our study identified distinctive signatures associated with maximal oxygen consumption (VO2max), and identified five genes robustly intersecting multi-OMIC layers. Notably, transcription factors predominantly functioned as activators across these layers, regulating expression of target genes irrespective of whether DNA methylation levels were low or high, indicating a synergistic effect between TFs and the methylome. Analysis of distinct exercise modalities (aerobic and resistance exercise) revealed unique gene pathways, contrasting with patterns observed in inactivity (muscle disuse) studies. These findings offer a comprehensive understanding of exercise and modality-specific adaptations, shedding light on muscle health and the molecular mechanisms associated with cardiorespiratory fitness, aging, and disease prevention.

molecular biology↗

Total testosterone is not associated with muscle mass, function or exercise adaptations in pre-menopausal females

Key pointsO_LIBioavailable testosterone was positively related to exercise-induced muscle hypertrophy in pre-menopausal females. C_LIO_LINuclear localisation of the androgen receptor was positively related to muscle mass in pre-menopausal females before resistance training, but not with resistance-training induced hypertrophy. C_LIO_LITotal testosterone is not related to muscle mass or strength in pre-menopausal females. C_LIO_LITestosterone treatment induced androgen receptor nuclear translocation, but did not induce mTOR signalling in myocytes from pre-menopausal females. C_LI Testosterone, the major androgen hormone, influences the reproductive and non-reproductive systems in males and females via binding to the androgen receptor (AR). Both circulating endogenous testosterone and muscle AR protein content are positively associated with muscle mass and strength in males, but there is no such evidence in females. Here, we tested whether circulating testosterone levels were associated with muscle mass, function, or the muscle anabolic response to resistance training in pre-menopausal females. Twenty-seven pre-menopausal, untrained females (aged 23.5 {+/-} 4.8) underwent a 12-week resistance training program. Muscle strength, size, power and plasma and urine androgen hormone levels were measured. Skeletal muscle biopsies were collected before and after the training program to quantify the effect of resistance training on AR protein and mRNA content, and nuclear localisation. Primary muscle cell lines were cultured from a subset (n=6) of the participants biopsies and treated with testosterone to investigate its effect on myotube diameter, markers of muscle protein synthesis and AR cellular localisation. Total testosterone was not associated with muscle mass or strength at baseline or with the changes in muscle mass and strength that occurred in response to resistance training. In vitro, supra-physiological doses of testosterone increased myocyte diameter, but this did not occur via the Akt/mTOR pathway as previously suggested. Instead, we show a marked increase in AR nuclear localisation with testosterone administration. In conclusion, we found that, bioavailable testosterone and the proportion of nuclear-localised AR, but not total testosterone, with skeletal muscle mass and strength in pre-menopausal females.

physiology↗

The interactive effect of sustained sleep restriction and resistance exercise on skeletal muscle transcriptomics in young females

IntroductionBoth sleep loss and exercise regulate gene expression in skeletal muscle, yet little is known about how the interaction of these stressors affects the transcriptome. The aim of this study was to investigate the effect of nine nights of sleep restriction, with repeated resistance exercise (REx) sessions, on the skeletal muscle transcriptome of young, trained females. MethodsTen healthy females aged 18-35 years undertook a randomised cross-over study of nine nights sleep restriction (SR; 5-h time in bed) and normal sleep (NS; [&ge;]7 h time in bed) with a minimum 6-week washout. Participants completed four REx sessions per condition (day 3, 5, 7 and 9). Muscle biopsies were collected both pre- and post-REx on days 3 and 9. Gene and protein expression were assessed by RNA sequencing and Western Blot, respectively. ResultsThree or nine nights of sleep restriction had no effect on the muscle transcriptome independently of exercise. However, close to 3000 transcripts were differentially regulated (FDR < 0.05) 48 h post the completion of three resistance exercise sessions in both NS and SR conditions. Only 39% of downregulated and 18% of upregulated genes were common between both conditions, indicating a moderating effect of sleep restriction on the response to exercise. ConclusionSleep restriction and resistance exercise interacted to alter the enrichment of skeletal muscle transcriptomic pathways in young, resistance-trained females. Performing exercise when sleep restricted may not provide the same adaptive response for individuals as if they were fully rested.

genomics↗

Clonal analysis of fetal hematopoietic stem/progenitor cell subsets reveals how post-transplantation capabilities are distributed

It has been proposed that adult haematopoiesis is sustained by multipotent progenitor (MPP) clones that are specified during development. From an immunophenotypic perspective, it is known that hematopoietic stem cell (HSC) and MPPs are present in the fetal liver yet our understanding of how fetal MPPs functionally compare to those in the adult bone marrow is incomplete. Using acute-term transplantations, we found that at a population-level fetal immunophenotypic MPP classes exhibited similar lineage biases as adult cells, albeit with some difference in lymphoid output. Clonal assessment of fetal MPPs engraftment revealed that lineage biases largely resulted from differences in the pattern of single-or bi-lineage differentiation. Immunophenotypic long-term (LT)-and short-term (ST)-HSCs in the fetal liver were distinguished from MPPs according to propensity for clonal multi-lineage differentiation. We also discovered that a large cohort of long-term repopulating units (LT-RU) were within the immunophenotypic ST-HSC population, a significant portion of these were labelled using Flt3-cre. This finding has two implications: (1) use of the CD150+ LT-HSC immunophenotype alone will systematically underestimate the size and diversity of the fetal LT-RU pool; and, (2), given fetal LT-RUs with a ST-HSC immunophenotype have the functional attributes required to persist into adulthood.

developmental biology↗

Whole body cell map tracks tissue-specific immune cell accumulation and plasticity loss through ageing

Understanding tissue biologys heterogeneity is crucial for advancing precision medicine. Despite the centrality of the immune system in tissue homeostasis, a detailed and comprehensive map of immune cell distribution and interactions across human tissues and demographics remains elusive. To fill this gap, we harmonised data from 12,981 single-cell RNA sequencing samples and curated 29 million cells from 45 anatomical sites to create a comprehensive compositional and transcriptional healthy map of the healthy immune system. We used this resource and a novel multilevel modelling approach to track immune ageing and test differences across sex and ethnicity. We uncovered conserved and tissue-specific immune-ageing programs, resolved sex-dependent differential ageing and identified ethnic diversity in clinically critical immune checkpoints. This study provides a quantitative baseline of the immune system, facilitating advances in precision medicine. By sharing our immune map, we hope to catalyse further breakthroughs in cancer, infectious disease, immunology and precision medicine.

immunology↗

Deletion of the transcriptional regulator TFAP4 accelerates c-MYC-driven lymphomagenesis

Many lymphoid malignancies arise from deregulated c-MYC expression in cooperation with additional genetic lesions. While many of these cooperative genetic lesions have been discovered, DNA sequence data suggest that many more do exist. However, their contributions to c-MYC driven lymphomagenesis have not yet been investigated. We identified TFAP4 as a potent suppressor of c-MYC driven lymphoma development in a previous genome-wide CRISPR knockout screen in primary cells in vivo (Mizutani et al, 2022). CRISPR deletion of TFAP4 in E-MYC transgenic hematopoietic stem and progenitor cells (HSPCs) significantly accelerated c-MYC-driven lymphoma development in mice. TFAP4 deficient E-MYC lymphomas all arose at the pre-B cell stage. Characterization of the transcriptional profile of pre-leukemic pre-B cells in E-MYC/Cas9/sgTFAP4 transplanted mice, revealed that TFAP4 deletion reduced expression of several master regulators of B cell differentiation, such as Spi1, SpiB and Pax5, which all have been shown to be bound by TFAP4. We therefore conclude that loss of TFAP4 leads to a block in differentiation during early B cell development, causing accelerated c-MYC-driven lymphoma development.

cancer biology↗

MLKL deficiency protects against low-grade, sterile inflammation in aged mice

MLKL and RIPK3 are the core signaling proteins of the inflammatory cell death pathway, necroptosis, which is a known mediator and modifier of human disease. Necroptosis has been implicated in the progression of disease in almost every physiological system and recent reports suggest a role for necroptosis in aging. Here we present the first comprehensive analysis of age-related histopathological and immunological phenotypes in a cohort of Mlkl-/- and Ripk3-/- mice on a congenic C57BL/6J genetic background. We show that genetic deletion of Mlkl, but not Ripk3, in female mice interrupts immune system aging, specifically delaying the age-related reduction of circulating lymphocytes. Mlkl-/- female mice were also protected against age-related, low-grade chronic sterile inflammation, with a reduced number of inflammatory infiltrates present in the connective and muscle tissue at 17 months relative to wild-type littermates. These observations implicate MLKL in age-related sterile inflammation, suggesting a possible application for long-term anti-necroptotic therapy in humans.

immunology↗