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1.
FASEB J ; 37(5): e22863, 2023 05.
Article in English | MEDLINE | ID: mdl-37016990

ABSTRACT

Duchenne muscular dystrophy (DMD) is a life-limiting neuromuscular disorder characterized by muscle weakness and wasting. Previous proof-of-concept studies demonstrate that the dystrophic phenotype can be mitigated with the pharmacological stimulation of AMP-activated protein kinase (AMPK). However, first-generation AMPK activators have failed to translate from bench to bedside due to either their lack of potency or toxic, off-target effects. The identification of safe and efficacious molecules that stimulate AMPK in dystrophic muscle is of particular importance as it may broaden the therapeutic landscape for DMD patients regardless of their specific dystrophin mutation. Here, we demonstrate that a single dose of the next generation, orally-bioactive AMPK agonist MK-8722 (MK) to mdx mice evoked skeletal muscle AMPK and extensive downstream stimulation within 12 h post-treatment. Specifically, MK elicited a gene expression profile indicative of a more disease-resistant slow, oxidative phenotype including increased peroxisome proliferator-activated receptor É£ coactivator-1⍺ activity and utrophin levels. In addition, we observed augmented autophagy signaling downstream of AMPK, as well as elevations in critical autophagic genes such as Map1lc3 and Sqstm1 subsequent to the myonuclear accumulation of the master regulator of the autophagy gene program, transcription factor EB. Lastly, we show that pharmacological AMPK stimulation normalizes the expression of myogenic regulatory factors and amends activated muscle stem cell content in mdx muscle. Our results indicate that AMPK activation via MK enhances disease-mitigating mechanisms in dystrophic muscle and prefaces further investigation on the chronic effects of novel small molecule AMPK agonists.


Subject(s)
AMP-Activated Protein Kinases , Muscular Dystrophy, Duchenne , Mice , Animals , AMP-Activated Protein Kinases/genetics , AMP-Activated Protein Kinases/metabolism , Mice, Inbred mdx , Muscle, Skeletal/metabolism , Muscular Dystrophy, Duchenne/drug therapy , Muscular Dystrophy, Duchenne/genetics , Muscular Dystrophy, Duchenne/metabolism , Utrophin/metabolism , Gene Expression , Disease Models, Animal
2.
J Physiol ; 597(5): 1361-1381, 2019 03.
Article in English | MEDLINE | ID: mdl-30628727

ABSTRACT

KEY POINTS: Myotonic dystrophy type 1 (DM1), the second most common muscular dystrophy and most prevalent adult form of muscular dystrophy, is characterized by muscle weakness, wasting and myotonia. A microsatellite repeat expansion mutation results in RNA toxicity and dysregulation of mRNA processing, which are the primary downstream causes of the disorder. Recent studies with DM1 participants demonstrate that exercise is safe, enjoyable and elicits benefits in muscle strength and function; however, the molecular mechanisms of exercise adaptation in DM1 are undefined. Our results demonstrate that 7 weeks of volitional running wheel exercise in a pre-clinical DM1 mouse model resulted in significantly improved motor performance, muscle strength and endurance, as well as reduced myotonia. At the cellular level, chronic physical activity attenuated RNA toxicity, liberated Muscleblind-like 1 protein from myonuclear foci and improved mRNA alternative splicing. ABSTRACT: Myotonic dystrophy type 1 (DM1) is a trinucleotide repeat expansion neuromuscular disorder that is most prominently characterized by skeletal muscle weakness, wasting and myotonia. Chronic physical activity is safe and satisfying, and can elicit functional benefits such as improved strength and endurance in DM1 patients, but the underlying cellular basis of exercise adaptation is undefined. Our purpose was to examine the mechanisms of exercise biology in DM1. Healthy, sedentary wild-type (SED-WT) mice, as well as sedentary human skeletal actin-long repeat animals, a murine model of DM1 myopathy (SED-DM1), and DM1 mice with volitional access to a running wheel for 7 weeks (EX-DM1), were utilized. Chronic exercise augmented strength and endurance in vivo and in situ in DM1 mice. These alterations coincided with normalized measures of myopathy, as well as increased mitochondrial content. Electromyography revealed a 70-85% decrease in the duration of myotonic discharges in muscles from EX-DM1 compared to SED-DM1 animals. The exercise-induced enhancements in muscle function corresponded at the molecular level with mitigated spliceopathy, specifically the processing of bridging integrator 1 and muscle-specific chloride channel (CLC-1) transcripts. CLC-1 protein content and sarcolemmal expression were lower in SED-DM1 versus SED-WT animals, but they were similar between SED-WT and EX-DM1 groups. Chronic exercise also attenuated RNA toxicity, as indicated by reduced (CUG)n foci-positive myonuclei and sequestered Muscleblind-like 1 (MBNL1). Our data indicate that chronic exercise-induced physiological improvements in DM1 occur in concert with mitigated primary downstream disease mechanisms, including RNA toxicity, MBNL1 loss-of-function, and alternative mRNA splicing.


Subject(s)
Myotonic Dystrophy/therapy , Physical Conditioning, Animal , Alternative Splicing , Animals , Disease Models, Animal , Female , Male , Mice , Muscle, Skeletal/physiology , Myotonic Dystrophy/genetics , Myotonic Dystrophy/physiopathology , RNA, Messenger/metabolism
3.
Can J Surg ; 62(4): 224-226, 2019 08 01.
Article in English | MEDLINE | ID: mdl-31348627

ABSTRACT

Summary: In Ontario, Canada, wait times for magnetic resonance imaging (MRI) scans continue to exceed provincial targets. We sought to determine the incidence of inappropriate hip MRI scan referrals, based on accepted indications for hip MRI. We developed an algorithm to appraise each MRI referral based on a prescan patient questionnaire and the interpretation of the MRI by a musculoskeletal radiologist. After reviewing 84 patient questionnaires, we considered 32.1% of MRI referrals to be inappropriate; 25.9% of the inappropriate MRI referrals were ordered as a preoperative test for potential hip arthroscopy despite the patients showing severe osteoarthritis. Having no prior radiographic examination was the most common reason for inappropriate referrals, regardless of pathology (48.1%). With limited MRI scanner time available in Ontario, it is essential that guidelines and training be improved on the indications for hip MRI to reduce the wait times for these specialized tests.


Subject(s)
Hip/diagnostic imaging , Magnetic Resonance Imaging , Medical Overuse/statistics & numerical data , Ambulatory Care , Contraindications, Procedure , Hip Injuries/diagnostic imaging , Hip Joint/diagnostic imaging , Humans , Joint Diseases/diagnostic imaging , Ontario , Referral and Consultation/statistics & numerical data , Waiting Lists
4.
Am J Physiol Cell Physiol ; 314(2): C177-C190, 2018 02 01.
Article in English | MEDLINE | ID: mdl-29092819

ABSTRACT

Protein arginine methyltransferase 1 (PRMT1), PRMT4, and PRMT5 catalyze the methylation of arginine residues on target proteins. Previous work suggests that these enzymes regulate skeletal muscle plasticity. However, the function of PRMTs during disuse-induced muscle remodeling is unknown. The purpose of our study was to determine whether denervation-induced muscle disuse alters PRMT expression and activity in skeletal muscle, as well as to contextualize PRMT biology within the early disuse-evoked events that precede atrophy, which remain largely undefined. Mice were subjected to 6, 12, 24, 72, or 168 h of unilateral hindlimb denervation. Muscle mass decreased by ~30% after 72 or 168 h of neurogenic disuse, depending on muscle fiber type composition. The expression, localization, and activities of PRMT1, PRMT4, and PRMT5 were modified, exhibiting changes in gene expression and activity that were PRMT-specific. Rapid alterations in canonical muscle atrophy signaling such as forkhead box protein O1, muscle RING-finger protein-1, as well as peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) content, AMP-activated protein kinase (AMPK) and p38 mitogen-activated protein kinase, were observed before measurable decrements in muscle mass. Denervation-induced modifications in AMPK-PRMT1 and PGC-1α-PRMT1 binding revealed a novel, putative PRMT1-AMPK-PGC-1α signaling axis in skeletal muscle. Here, PGC-1α-PRMT1 binding was elevated after 6 h of disuse, whereas AMPK-PRMT1 interactions were reduced following 168 h of denervation. Our data suggest that PRMT biology is integral to the mechanisms that precede and initiate skeletal muscle atrophy during conditions of neurogenic disuse. This study furthers our understanding of the role of PRMTs in governing skeletal muscle plasticity.


Subject(s)
Cell Plasticity , Muscle, Skeletal/enzymology , Muscle, Skeletal/innervation , Muscular Atrophy/enzymology , Protein-Arginine N-Methyltransferases/metabolism , AMP-Activated Protein Kinases/metabolism , Animals , Disease Models, Animal , Male , Mice, Inbred C57BL , Muscle Denervation , Muscle, Skeletal/pathology , Muscular Atrophy/genetics , Muscular Atrophy/pathology , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism , Phenotype , Protein Binding , Protein-Arginine N-Methyltransferases/genetics , Signal Transduction , Time Factors
5.
Lancet ; 385 Suppl 1: S42, 2015 Feb 26.
Article in English | MEDLINE | ID: mdl-26312864

ABSTRACT

BACKGROUND: Incomplete understanding of mechanisms and clinicopathobiological heterogeneity in asthma hinders research progress. Pathogenic roles for T-helper-type 17 (Th17) cells and invariant T cells implied by murine data have yet to be assessed in man. We aimed to investigate the role of Th17 and mucosal associated invariant T (MAIT) cells in airway inflammation; to characterise associations between diverse clinical and immunological features of asthma; and to identify novel multidimensional asthma endotypes. METHODS: In this single-centre, cross-sectional observational study in the UK, we assessed volunteers with mild-to-severe asthma and healthy non-atopic controls using clinical and physiological assessment and immunological sampling of blood, induced sputum, endobronchial biopsy, and bronchoalveolar lavage for flow cytometry and multiplex-electrochemiluminescence assays. Primary outcomes were changes in frequencies of Th17 and MAIT cells between health and asthma using Mann-Whitney U tests and the Jonckheere-Terpstra test (linear trend across ranked groups). The study had 80% power to detect 60% differences in T-cell frequencies at p<0·05. Bayesian Network Analysis (BNA) was used to explore associations between parameters. Topological Data Analysis (TDA) was used to identify multidimensional endotypes. The study had local research ethics approval. All participants provided informed consent. FINDINGS: Participants were 84 male and female volunteers (60 with mild-to-severe asthma and 24 healthy, non-atopic controls) aged 18-70 years recruited from clinics and research cohorts. Th17 cells and γδ17 cells were not associated with asthma, even in severe neutrophilic forms. MAIT-cell frequencies were strikingly reduced in asthma compared with health (median frequency in blood 0·9% of CD3+ cells [IQR 0·3-1·8] in asthma vs 1·6 [1·2-2·6] in health, p=0·005; in sputum 1·1 [0·7-2·0] vs 1·8 [1·6-2·3], p=0·002; and in biopsy samples 1·3 [0·7-2·3] vs 3·9% [1·3-5·3%], p=0·02), especially in severe asthma where BAL regulatory T cells were also reduced compared with those in health (4·4, 3·1-6·1, vs 8·1, 5·6-10; p=0·02). BNA and TDA identified six novel clinicopathobiological clusters of underlying disease mechanisms, with elevated mast cell mediators tryptase (p<0·0001), chymase (p=0·02), and carboxypeptidase A3 (p=0·02) in severe asthma. INTERPRETATION: This study suggests that Th17 cells do not have a major pathogenic role in human asthma. We describe a novel deficiency of MAIT cells in severe asthma. We also provide proof of concept for application of TDA to identification of multidimensional clinicopathobiological endotypes. Endotypes will require validation in further cohorts. FUNDING: Wellcome Trust.

6.
J Allergy Clin Immunol ; 136(2): 323-33, 2015 Aug.
Article in English | MEDLINE | ID: mdl-25746968

ABSTRACT

BACKGROUND: Asthma is a chronic inflammatory disease involving diverse cells and mediators whose interconnectivity and relationships to asthma severity are unclear. OBJECTIVE: We performed a comprehensive assessment of TH17 cells, regulatory T cells, mucosal-associated invariant T (MAIT) cells, other T-cell subsets, and granulocyte mediators in asthmatic patients. METHODS: Sixty patients with mild-to-severe asthma and 24 control subjects underwent detailed clinical assessment and provided induced sputum, endobronchial biopsy, bronchoalveolar lavage, and blood samples. Adaptive and invariant T-cell subsets, cytokines, mast cells, and basophil mediators were analyzed. RESULTS: Significant heterogeneity of T-cell phenotypes was observed, with levels of IL-13-secreting T cells and type 2 cytokines increased at some, but not all, asthma severities. TH17 cells and γδ-17 cells, proposed drivers of neutrophilic inflammation, were not strongly associated with asthma, even in severe neutrophilic forms. MAIT cell frequencies were strikingly reduced in both blood and lung tissue in relation to corticosteroid therapy and vitamin D levels, especially in patients with severe asthma in whom bronchoalveolar lavage regulatory T-cell numbers were also reduced. Bayesian network analysis identified complex relationships between pathobiologic and clinical parameters. Topological data analysis identified 6 novel clusters that are associated with diverse underlying disease mechanisms, with increased mast cell mediator levels in patients with severe asthma both in its atopic (type 2 cytokine-high) and nonatopic forms. CONCLUSION: The evidence for a role for TH17 cells in patients with severe asthma is limited. Severe asthma is associated with a striking deficiency of MAIT cells and high mast cell mediator levels. This study provides proof of concept for disease mechanistic networks in asthmatic patients with clusters that could inform the development of new therapies.


Subject(s)
Adaptive Immunity , Asthma/immunology , Immunity, Innate , Th17 Cells/immunology , Th2 Cells/immunology , Adolescent , Adrenal Cortex Hormones/therapeutic use , Adult , Aged , Anti-Asthmatic Agents/therapeutic use , Asthma/drug therapy , Asthma/genetics , Asthma/pathology , Basophils/immunology , Basophils/pathology , Bayes Theorem , Bronchoalveolar Lavage Fluid/chemistry , Bronchoalveolar Lavage Fluid/cytology , Case-Control Studies , Female , Gene Expression , Humans , Interleukin-13/genetics , Interleukin-13/immunology , Male , Mast Cells/immunology , Mast Cells/pathology , Middle Aged , Receptors, Antigen, T-Cell, gamma-delta/genetics , Receptors, Antigen, T-Cell, gamma-delta/immunology , Severity of Illness Index , Sputum/chemistry , Sputum/cytology , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/pathology , Th17 Cells/pathology , Th2 Cells/pathology
7.
Med Sci Sports Exerc ; 56(3): 486-498, 2024 Mar 01.
Article in English | MEDLINE | ID: mdl-37882083

ABSTRACT

PURPOSE: The purpose of this study was to determine how the intersection of coactivator-associated arginine methyltransferase 1 (CARM1) and biological sex affects skeletal muscle adaptations to chronic physical activity. METHODS: Twelve-week-old female (F) and male (M) wild-type (WT) and CARM1 skeletal muscle-specific knockout (mKO) mice were randomly assigned to sedentary (SED) or voluntary wheel running (VWR) experimental groups. For 8 wk, the animals in the VWR cohort had volitional access to running wheels. Subsequently, we performed whole-body functional tests, and 48 h later muscles were harvested for molecular analysis. Western blotting, enzyme activity assays, as well as confocal and transmission electron microscopy were used to examine skeletal muscle biology. RESULTS: Our data reveal a sex-dependent reduction in VWR volume caused by muscle-specific ablation of CARM1, as F CARM1 mKO mice performed less chronic, volitional exercise than their WT counterparts. Regardless of VWR output, exercise-induced adaptations in physiological function were similar between experimental groups. A broad panel of protein arginine methyltransferase (PRMT) biology measurements, including markers of arginine methyltransferase expression and activity, were unaffected by VWR, except for CARM1 and PRMT7 protein levels, which decreased and increased with VWR, respectively. Changes in myofiber morphology and mitochondrial protein content showed similar trends among animals. However, a closer examination of transmission electron microscopy images revealed contrasting responses to VWR in CARM1 mKO mice compared with WT littermates, particularly in mitochondrial size and fractional area. CONCLUSIONS: The present findings demonstrate that CARM1 mKO reduces daily running volume in F mice, as well as exercise-evoked skeletal muscle mitochondrial plasticity, which indicates that this enzyme plays an essential role in sex-dependent differences in exercise performance and mitochondrial health.


Subject(s)
Physical Conditioning, Animal , Protein-Arginine N-Methyltransferases , Humans , Male , Female , Mice , Animals , Protein-Arginine N-Methyltransferases/genetics , Protein-Arginine N-Methyltransferases/metabolism , Motor Activity/physiology , Physical Conditioning, Animal/physiology , Muscle, Skeletal/metabolism , Mice, Inbred C57BL
8.
Acta Physiol (Oxf) ; 237(4): e13943, 2023 04.
Article in English | MEDLINE | ID: mdl-36726043

ABSTRACT

AIM: Myotonic dystrophy type 1 (DM1) is the second most common muscular dystrophy after Duchenne and is the most prevalent muscular dystrophy in adults. DM1 patients that participate in aerobic exercise training experience several physiological benefits concomitant with improved muscle mitochondrial function without alterations in typical DM1-specific disease mechanisms, which suggests that correcting organelle health is key to ameliorate the DM1 pathology. However, our understanding of the molecular mechanisms of mitochondrial turnover and dynamics in DM1 skeletal muscle is lacking. METHODS: Skeletal muscle tissue was sampled from healthy and DM1 mice under sedentary conditions and at several recovery time points following an exhaustive treadmill run. RESULTS: We demonstrate that DM1 patients exhibit an imbalance in the transcriptional apparatus for mitochondrial turnover and dynamics in skeletal muscle. Additionally, DM1 mice displayed elevated expression of autophagy and mitophagy regulators. A single dose of exercise successfully enhanced canonical exercise molecular pathways and skeletal muscle mitochondrial biogenesis despite failing to alter the cellular pathology in DM1 mice. However, treadmill running stimulated coordinated organelle fusion and fission signaling, as well as improved alternative splicing of Optic atrophy 1. Exercise also evoked autophagy and mitophagy pathways in DM1 skeletal muscle resulting in the normalized expression of autophagy- and lysosome-related machinery responsible for the clearance of dysfunctional organelles. CONCLUSION: Collectively, our data indicate that mitochondrial dynamics and turnover processes in DM1 skeletal muscle are initiated with a single dose of exercise, which may underlie the adaptive benefits previously documented in DM1 mice and patients.


Subject(s)
Muscular Dystrophies , Myotonic Dystrophy , Mice , Animals , Myotonic Dystrophy/genetics , Myotonic Dystrophy/metabolism , Myotonic Dystrophy/pathology , Muscle, Skeletal/metabolism , Muscular Dystrophies/metabolism , Muscular Dystrophies/pathology , Mitochondria/metabolism , Signal Transduction
9.
J Clin Invest ; 132(10)2022 05 16.
Article in English | MEDLINE | ID: mdl-35316212

ABSTRACT

BackgroundMyotonic dystrophy type 1 (DM1) is a complex life-limiting neuromuscular disorder characterized by severe skeletal muscle atrophy, weakness, and cardiorespiratory defects. Exercised DM1 mice exhibit numerous physiological benefits that are underpinned by reduced CUG foci and improved alternative splicing. However, the efficacy of physical activity in patients is unknown.MethodsEleven genetically diagnosed DM1 patients were recruited to examine the extent to which 12 weeks of cycling can recuperate clinical and physiological metrics. Furthermore, we studied the underlying molecular mechanisms through which exercise elicits benefits in skeletal muscle of DM1 patients.RESULTSDM1 was associated with impaired muscle function, fitness, and lung capacity. Cycling evoked several clinical, physical, and metabolic advantages in DM1 patients. We highlight that exercise-induced molecular and cellular alterations in patients do not conform with previously published data in murine models and propose a significant role of mitochondrial function in DM1 pathology. Finally, we discovered a subset of small nucleolar RNAs (snoRNAs) that correlated to indicators of disease severity.ConclusionWith no available cures, our data support the efficacy of exercise as a primary intervention to partially mitigate the clinical progression of DM1. Additionally, we provide evidence for the involvement of snoRNAs and other noncoding RNAs in DM1 pathophysiology.Trial registrationThis trial was approved by the HiREB committee (no. 7901) and registered under ClinicalTrials.gov (NCT04187482).FundingNeil and Leanne Petroff. Canadian Institutes of Health Research Foundation (no. 143325).


Subject(s)
Myotonic Dystrophy , Physical Conditioning, Animal , Alternative Splicing , Animals , Canada , Humans , Mice , Muscle, Skeletal/metabolism , Myotonic Dystrophy/genetics , Myotonic Dystrophy/metabolism , Myotonic Dystrophy/therapy
10.
iScience ; 23(11): 101755, 2020 Nov 20.
Article in English | MEDLINE | ID: mdl-33241200

ABSTRACT

Coactivator-associated arginine methyltransferase 1 (CARM1) is an emerging mediator of skeletal muscle plasticity. We employed genetic, physiologic, and pharmacologic approaches to determine whether CARM1 regulates the master neuromuscular phenotypic modifier AMP-activated protein kinase (AMPK). CARM1 skeletal muscle-specific knockout (mKO) mice displayed reduced muscle mass and dysregulated autophagic and atrophic processes downstream of AMPK. We observed altered interactions between CARM1 and AMPK and its network, including forkhead box protein O1, during muscle disuse. CARM1 methylated AMPK during the early stages of muscle inactivity, whereas CARM1 mKO mitigated progression of denervation-induced atrophy and was accompanied by attenuated phosphorylation of AMPK targets such as unc-51 like autophagy-activating kinase 1Ser555. Lower acetyl-coenzyme A corboxylaseSer79 phosphorylation, as well as reduced peroxisome proliferator-activated receptor-γ coactivator-1α, was also observed in mKO animals following acute administration of the direct AMPK activator MK-8722. Our study suggests that targeting CARM1-AMPK interplay may have broad impacts on neuromuscular health and disease.

11.
Appl Physiol Nutr Metab ; 43(11): 1194-1206, 2018 Nov.
Article in English | MEDLINE | ID: mdl-29944848

ABSTRACT

Neuromuscular disorders (NMDs) are chronic conditions that affect the neuromuscular system. Many NMDs currently have no cure; however, as more effective therapies become available for NMD patients, these individuals will exhibit improved health and/or prolonged lifespans. As a result, persons with NMDs will likely desire to engage in a more diverse variety of activities of daily living, including increased physical activity or exercise. Therefore, there is a need to increase our knowledge of the effects of acute exercise and chronic training on the neuromuscular system in NMD contexts. Here, we discuss the disease mechanisms and exercise biology of Duchenne muscular dystrophy (DMD), spinal muscular atrophy (SMA), and myotonic dystrophy type 1 (DM1), which are among the most prevalent NMDs in children and adults. Evidence from clinical and preclinical studies are reviewed, with emphasis on the functional outcomes of exercise, as well as on the putative cellular mechanisms that drive exercise-induced remodelling of the neuromuscular system. Continued investigation of the molecular mechanisms of exercise adaptation in DMD, SMA, and DM1 will assist in enhancing our understanding of the biology of these most prevalent NMDs. This information may also be useful for guiding the development of novel therapeutic targets for future pursuit.


Subject(s)
Exercise/physiology , Muscular Atrophy, Spinal , Muscular Dystrophy, Duchenne , Myotonic Dystrophy , Humans , Muscular Atrophy, Spinal/physiopathology , Muscular Atrophy, Spinal/therapy , Muscular Dystrophy, Duchenne/physiopathology , Muscular Dystrophy, Duchenne/therapy , Myotonic Dystrophy/physiopathology , Myotonic Dystrophy/therapy
12.
Trends Endocrinol Metab ; 29(5): 300-312, 2018 05.
Article in English | MEDLINE | ID: mdl-29572064

ABSTRACT

AMP-activated protein kinase (AMPK) is a primary regulator of cellular metabolism. Recent studies have revealed that AMPK also mediates the maintenance and plasticity of α-motoneurons, the neuromuscular junction, and skeletal muscle. Furthermore, AMPK stimulation by either genetic, pharmacological, or physiological approaches elicits beneficial phenotypic remodeling in neuromuscular disorders (NMDs). Here, we review the role of AMPK as a governor of neuromuscular biology, and present evidence for AMPK as an effective molecular target for therapeutic pursuit in the context of the most prevalent NMDs, including Duchenne muscular dystrophy, spinal muscular atrophy, and myotonic dystrophy type 1. This information may be useful for engineering AMPK-targeted pharmacological- or lifestyle-based strategies to treat disorders of the neuromuscular system.


Subject(s)
AMP-Activated Protein Kinases/metabolism , Autophagy/physiology , AMP-Activated Protein Kinases/genetics , Animals , Autophagy/genetics , Humans , Motor Neurons/metabolism , Muscle, Skeletal/metabolism , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism , Utrophin/metabolism
13.
BMC Syst Biol ; 12(1): 60, 2018 05 29.
Article in English | MEDLINE | ID: mdl-29843806

ABSTRACT

BACKGROUND: Multilevel data integration is becoming a major area of research in systems biology. Within this area, multi-'omics datasets on complex diseases are becoming more readily available and there is a need to set standards and good practices for integrated analysis of biological, clinical and environmental data. We present a framework to plan and generate single and multi-'omics signatures of disease states. METHODS: The framework is divided into four major steps: dataset subsetting, feature filtering, 'omics-based clustering and biomarker identification. RESULTS: We illustrate the usefulness of this framework by identifying potential patient clusters based on integrated multi-'omics signatures in a publicly available ovarian cystadenocarcinoma dataset. The analysis generated a higher number of stable and clinically relevant clusters than previously reported, and enabled the generation of predictive models of patient outcomes. CONCLUSIONS: This framework will help health researchers plan and perform multi-'omics big data analyses to generate hypotheses and make sense of their rich, diverse and ever growing datasets, to enable implementation of translational P4 medicine.


Subject(s)
Disease/genetics , Systems Biology/methods , Biomarkers/metabolism , Cluster Analysis , False Positive Reactions , Machine Learning , Quality Control
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