Time trajectories in the transcriptomic response to exercise - a meta-analysis.
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ABSTRACT:
SUBMITTER: Amar D
PROVIDER: S-EPMC8190306 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:This study aimed to provide a more comprehensive molecular insight into the effects of aerobic exercise (AE), protein intake (PI), and AE combined with PI on human skeletal muscle by comparing their transcriptomic profiles. Fourteen published datasets obtained from the Gene Expression Omnibus (GEO) database were used. The hub genes were identified in response to acute AE (ACTB, IL6), training AE (UBB, COL1A1), PI (EZH2), acute AE combined with PI (DDIT3), and training AE combined with PI (MYC). Both FOS and MYC were upregulated in response to acute AE, and they were, respectively, downregulated by higher PI and a combination of AE and PI. COL1A1 was upregulated by training AE but was downregulated by higher PI. Results from the gene set enrichment analysis (p < 0.05 and FDR < 25%) showed that AE and PI delivered their impacts on human skeletal muscle in analogous pathways, including aerobic respiration, mitochondrial complexes, extracellular matrix (ECM) remodeling, metabolic process, and immune/inflammatory responses, whereas, PI may attenuate the response of immune/inflammation and ECM remodeling which would be promoted by AE, irrespective of its types. Compared to PI alone, acute AE combined with PI would further promote protein turnover and synthesis, but suppress skeletal muscle contraction and movement.
| S-EPMC10421363 | biostudies-literature
Project description:Background Knowledge gaps exist regarding the effect of time elapsed after stroke on the effectiveness of exercise training interventions, offering incomplete guidance to clinicians. Methods and Results To determine the associations between time after stroke and 6-minute walk distance, 10-meter walk time, cardiorespiratory fitness and balance (Berg Balance Scale score [BBS]) in exercise training interventions, relevant studies in post-stroke populations were identified by systematic review. Time after stroke as continuous or dichotomized (≤3 months versus >3 months, and ≤6 months versus >6 months) variables and weighted mean differences in postintervention outcomes were examined in meta-regression analyses adjusted for study baseline mean values (pre-post comparisons) or baseline mean values and baseline control-intervention differences (controlled comparisons). Secondary models were adjusted additionally for mean age, sex, and aerobic exercise intensity, dose, and modality. We included 148 studies. Earlier exercise training initiation was associated with larger pre-post differences in mobility; studies initiated ≤3 months versus >3 months after stroke were associated with larger differences (weighted mean differences [95% confidence interval]) in 6-minute walk distance (36.3 meters; 95% CI, 14.2-58.5), comfortable 10-meter walk time (0.13 m/s; 95% CI, 0.06-0.19) and fast 10-meter walk time (0.16 m/s; 95% CI, 0.03-0.3), in fully adjusted models. Initiation ≤3 months versus >3 months was not associated with cardiorespiratory fitness but was associated with a higher but not clinically important Berg Balance Scale score difference (2.9 points; 95% CI, 0.41-5.5). In exercise training versus control studies, initiation ≤3 months was associated with a greater difference in only postintervention 6-minute walk distance (baseline-adjusted 27.3 meters; 95% CI, 6.1-48.5; fully adjusted, 24.9 meters; 95% CI, 0.82-49.1; a similar association was seen for ≤6 months versus >6 months after stroke (fully adjusted, 26.6 meters; 95% CI, 2.6-50.6). Conclusions There may be a clinically meaningful benefit to mobility outcomes when exercise is initiated within 3 months and up to 6 months after stroke.
| S-EPMC9075264 | biostudies-literature
Project description:We performed genome-wide and transcriptome-wide profiling to identify genes and single nucleotide polymorphisms (SNPs) associated with the response of triglycerides (TG) to exercise training.Plasma TG levels were measured before and after a 20-week endurance training programme in 478 white participants from the HERITAGE Family Study. Illumina HumanCNV370-Quad v3.0 BeadChips were genotyped using the Illumina BeadStation 500GX platform. Affymetrix HG-U133+2 arrays were used to quantitate gene expression levels from baseline muscle biopsies of a subset of participants (N=52). Genome-wide association study (GWAS) analysis was performed using MERLIN, while transcriptomic predictor models were developed using the R-package GALGO.The GWAS results showed that eight SNPs were associated with TG training-response (?TG) at p<9.9×10(-6), while another 31 SNPs showed p values <1×10(-4). In multivariate regression models, the top 10 SNPs explained 32.0% of the variance in ?TG, while conditional heritability analysis showed that four SNPs statistically accounted for all of the heritability of ?TG. A molecular signature based on the baseline expression of 11 genes predicted 27% of ?TG in HERITAGE, which was validated in an independent study. A composite SNP score based on the top four SNPs, each from the genomic and transcriptomic analyses, was the strongest predictor of ?TG (R(2)=0.14, p=3.0×10(-68)).Our results indicate that skeletal muscle transcript abundance at 11 genes and SNPs at a number of loci contribute to TG response to exercise training. Combining data from genomics and transcriptomics analyses identified a SNP-based gene signature that should be further tested in independent samples.
| S-EPMC4672639 | biostudies-literature
Project description:BackgroundMeans-based analysis of maximal rate of oxygen consumption (VO2max) has traditionally been used as the exercise response indicator to assess the efficacy of endurance (END), high intensity interval (HIIT) and resistance exercise training (RET) for improving cardiorespiratory fitness and whole-body health. However, considerable heterogeneity exists in the interindividual variability response to the same or different training modalities.ObjectivesWe performed a systematic review and meta-analysis to investigate exercise response rates in the context of VO2max: (1) in each training modality (END, HIIT and RET) versus controls, (2) in END versus either HIIT or RET and (3) exercise response rates as measured by VO2max versus other indicators of positive exercise response in each exercise modality.MethodsThree databases (EMBASE, MEDLINE, CENTRAL) and additional sources were searched. Both individual response rate and population average data were incorporated through continuous data, respectively. Of 3268 identified manuscripts, a total of 29 studies were suitable for qualitative synthesis and a further 22 for quantitative. Stratification based on intervention duration (less than 12 weeks; more than or equal to 12 weeks) was undertaken.ResultsA total of 62 data points were procured. Both END and HIIT training exhibited differential improvements in VO2max based on intervention duration. VO2max did not adequately differentiate between END and HIIT, irrespective of intervention length. Although none of the other exercise response indicators achieved statistical significance, LT and HRrest demonstrated common trajectories in pooled and separate analyses between modalities. RET data were highly limited. Heterogeneity was ubiquitous across all analyses.ConclusionsThe potential for LT and HRrest as indicators of exercise response requires further elucidation, in addition to the exploration of interventional and intrinsic sources of heterogeneity.
| S-EPMC8728353 | biostudies-literature
Project description:BackgroundSkeletal muscle atrophy manifests across numerous diseases; however, the extent of similarities/differences in causal mechanisms between atrophying conditions in unclear. Ageing and disuse represent two of the most prevalent and costly atrophic conditions, with resistance exercise training (RET) being the most effective lifestyle countermeasure. We employed gene-level and network-level meta-analyses to contrast transcriptomic signatures of disuse and RET, plus young and older RET to establish a consensus on the molecular features of, and therapeutic targets against, muscle atrophy in conditions of high socio-economic relevance.MethodsIntegrated gene-level and network-level meta-analysis was performed on publicly available microarray data sets generated from young (18-35 years) m. vastus lateralis muscle subjected to disuse (unilateral limb immobilization or bed rest) lasting ≥7 days or RET lasting ≥3 weeks, and resistance-trained older (≥60 years) muscle.ResultsDisuse and RET displayed predominantly separate transcriptional responses, and transcripts altered across conditions were mostly unidirectional. However, disuse and RET induced directly inverted expression profiles for mitochondrial function and translation regulation genes, with COX4I1, ENDOG, GOT2, MRPL12, and NDUFV2, the central hub components of altered mitochondrial networks, and ZMYND11, a hub gene of altered translation regulation. A substantial number of genes (n = 140) up-regulated post-RET in younger muscle were not similarly up-regulated in older muscle, with young muscle displaying a more pronounced extracellular matrix (ECM) and immune/inflammatory gene expression response. Both young and older muscle exhibited similar RET-induced ubiquitination/RNA processing gene signatures with associated PWP1, PSMB1, and RAF1 hub genes.ConclusionsDespite limited opposing gene profiles, transcriptional signatures of disuse are not simply the converse of RET. Thus, the mechanisms of unloading cannot be derived from studying muscle loading alone and provides a molecular basis for understanding why RET fails to target all transcriptional features of disuse. Loss of RET-induced ECM mechanotransduction and inflammatory profiles might also contribute to suboptimal ageing muscle adaptations to RET. Disuse and age-dependent molecular candidates further establish a framework for understanding and treating disuse/ageing atrophy.
| S-EPMC8200445 | biostudies-literature
Project description:BackgroundPsychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C.ResultsWe observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures.ConclusionsThe results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.
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Project description:INTRODUCTION:The number of inconclusive physical rehabilitation randomised controlled trials for patients with critical illness is increasing. Evidence suggests critical illness patient subgroups may exist that benefit from targeted physical rehabilitation interventions that could improve their recovery trajectory. We aim to identify critical illness patient subgroups that respond to physical rehabilitation and map recovery trajectories according to physical function and quality of life outcomes. Additionally, the utilisation of healthcare resources will be examined for subgroups identified. METHODS AND ANALYSIS:This is an individual participant data meta-analysis protocol. A systematic literature review was conducted for randomised controlled trials that delivered additional physical rehabilitation for patients with critical illness during their acute hospital stay, assessed chronic disease burden, with a minimum follow-up period of 3?months measuring performance-based physical function and health-related quality of life outcomes. From 2178 records retrieved in the systematic literature review, four eligible trials were identified by two independent reviewers. Principal investigators of eligible trials were invited to contribute their data to this individual participant data meta-analysis. Risk of bias will be assessed (Cochrane risk of bias tool for randomised trials). Participant and trial characteristics, interventions and outcomes data of included studies will be summarised. Meta-analyses will entail a one-stage model, which will account for the heterogeneity across and the clustering between studies. Multiple imputation using chained equations will be used to account for the missing data. ETHICS AND DISSEMINATION:This individual participant data meta-analysis does not require ethical review as anonymised participant data will be used and no new data collected. Additionally, eligible trials were granted approval by institutional review boards or research ethics committees and informed consent was provided for participants. Data sharing agreements are in place permitting contribution of data. The study findings will be disseminated at conferences and through peer-reviewed publications. PROSPERO REGISTRATION NUMBER:CRD42019152526.
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Project description:Connectivity of terrestrial deep biosphere microbial communities with surface communities
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Project description:Metallic nanoparticles are increasingly present in our environment, raising concerns on their interactions with living organisms and potential toxicity. Indeed, metallic nanoparticles release metal ions that can be toxic, bioessential, therapeutically active, or combine several of these features. However, human cell responses to different metallic nanoparticles and ions have rarely been compared so far. We propose here a meta-analysis of the transcriptomic responses of human cells to nanoparticles and ions of various metals (titanium, iron, copper, zinc, silver, cadmium, platinum, gold), in order to identify the commonalities and differences between cell responses to these compounds. This analysis revealed that the chemical properties of metals are more important than their known biological functions (i.e., essential metals, toxicity) in governing the cell transcriptome. Particularly, we evidence that the response to nanoparticles is dominated by the response to the ions they contain, and depend on the nanoparticles' solubility. The formulation as nanoparticles impacts the cell response at lower intensity than the released ions, by altering genes related to vesicle intracellular transport and the cytoskeleton. Moreover, we put into light that several metals (i.e., copper, zinc, silver, cadmium, and gold) trigger a common cell response governed by metallothioneins, which coexist with singular signatures that are specific to a given element.
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