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Timmons JA, Brenner C. The information theory of aging has not been tested. Cell 2024; 187:1101-1102. [PMID: 38428390 DOI: 10.1016/j.cell.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/03/2023] [Accepted: 01/10/2024] [Indexed: 03/03/2024]
Affiliation(s)
- James A Timmons
- William Harvey Research Institute, Queen Mary University of London, London, UK
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2
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Stokes T, Cen HH, Kapranov P, Gallagher IJ, Pitsillides AA, Volmar C, Kraus WE, Johnson JD, Phillips SM, Wahlestedt C, Timmons JA. Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq. Adv Genet (Hoboken) 2023; 4:2200024. [PMID: 37288167 PMCID: PMC10242409 DOI: 10.1002/ggn2.202200024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Indexed: 06/09/2023]
Abstract
Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are used to study the bulk transcriptome; but now short-read RNA sequencing (RNA-seq) predominates. Positioned as a superior technology, that makes the discovery of novel transcripts routine, most RNA-seq analyses are in fact modeled on the known transcriptome. Limitations of the RNA-seq methodology have emerged, while the design of, and the analysis strategies applied to, arrays have matured. An equitable comparison between these technologies is provided, highlighting advantages that modern arrays hold over RNA-seq. Array protocols more accurately quantify constitutively expressed protein coding genes across tissue replicates, and are more reliable for studying lower expressed genes. Arrays reveal long noncoding RNAs (lncRNA) are neither sparsely nor lower expressed than protein coding genes. Heterogeneous coverage of constitutively expressed genes observed with RNA-seq, undermines the validity and reproducibility of pathway analyses. The factors driving these observations, many of which are relevant to long-read or single-cell sequencing are discussed. As proposed herein, a reappreciation of bulk transcriptomic methods is required, including wider use of the modern high-density array data-to urgently revise existing anatomical RNA reference atlases and assist with more accurate study of lncRNAs.
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Affiliation(s)
- Tanner Stokes
- Faculty of ScienceMcMaster UniversityHamiltonL8S 4L8Canada
| | - Haoning Howard Cen
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | - Iain J Gallagher
- School of Applied SciencesEdinburgh Napier UniversityEdinburghEH11 4BNUK
| | | | | | | | - James D. Johnson
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | | | - James A. Timmons
- Miller School of MedicineUniversity of MiamiMiamiFL33136USA
- William Harvey Research InstituteQueen Mary University LondonLondonEC1M 6BQUK
- Augur Precision Medicine LTDStirlingFK9 5NFUK
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3
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Dennison JL, Volmar CH, Modarresi F, Ke D, Wang J, Gravel E, Hammond-Vignini S, Li Z, Timmons JA, Lohse I, Hayward MA, Brothers SP, Wahlestedt C. Erratum to: JOTROL, a Novel Formulation of Resveratrol, Shows Beneficial Effects in the 3xTg-AD Mouse Model. J Alzheimers Dis 2022; 88:385. [PMID: 35723129 DOI: 10.3233/jad-229006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Nath M, Romaine SP, Koekemoer A, Hamby S, Webb TR, Nelson CP, Castellanos‐Uribe M, Papakonstantinou M, Anker SD, Lang CC, Metra M, Zannad F, Filippatos G, van Veldhuisen DJ, Cleland JG, Ng LL, May ST, Marelli‐Berg F, Voors AA, Timmons JA, Samani NJ. Whole blood transcriptomic profiling identifies molecular pathways related to cardiovascular mortality in heart failure. Eur J Heart Fail 2022; 24:1009-1019. [PMID: 35570197 PMCID: PMC9546237 DOI: 10.1002/ejhf.2540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 12/01/2022] Open
Abstract
AIMS Chronic heart failure (CHF) is a systemic syndrome with a poor prognosis and a need for novel therapies. We investigated whether whole blood transcriptomic profiling can provide new mechanistic insights into cardiovascular (CV) mortality in CHF. METHODS AND RESULTS Transcriptome profiles were generated at baseline from 944 CHF patients from the BIOSTAT-CHF study, of whom 626 survived and 318 died from a CV cause during a follow-up of 21 months. Multivariable analysis, including adjustment for cell count, identified 1153 genes (6.5%) that were differentially expressed between those that survived or died and strongly related to a validated clinical risk score for adverse prognosis. The differentially expressed genes mainly belonged to five non-redundant pathways: adaptive immune response, proteasome-mediated ubiquitin-dependent protein catabolic process, T-cell co-stimulation, positive regulation of T-cell proliferation, and erythrocyte development. These five pathways were selectively related (RV coefficients >0.20) with seven circulating protein biomarkers of CV mortality (fibroblast growth factor 23, soluble ST2, adrenomedullin, hepcidin, pentraxin-3, WAP 4-disulfide core domain 2, and interleukin-6) revealing an intricate relationship between immune and iron homeostasis. The pattern of survival-associated gene expression matched with 29 perturbagen-induced transcriptome signatures in the iLINCS drug-repurposing database, identifying drugs, approved for other clinical indications, that were able to reverse in vitro the molecular changes associated with adverse prognosis in CHF. CONCLUSION Systematic modelling of the whole blood protein-coding transcriptome defined molecular pathways that provide a link between clinical risk factors and adverse CV prognosis in CHF, identifying both established and new potential therapeutic targets.
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Affiliation(s)
- Mintu Nath
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
- Institute of Applied Health SciencesUniversity of AberdeenAberdeenUK
| | - Simon P.R. Romaine
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
| | - Andrea Koekemoer
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
| | - Stephen Hamby
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
| | - Thomas R. Webb
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
| | - Christopher P. Nelson
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
| | | | - Manolo Papakonstantinou
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
| | - Stefan D. Anker
- German Centre for Cardiovascular Research (DZHK) Partner Site Berlin, Charité – Universitätsmedizin BerlinBerlinGermany
| | - Chim C. Lang
- Division of Molecular and Clinical Medicine, School of MedicineUniversity of DundeeDundeeUK
| | - Marco Metra
- Department of Medical and Surgical Specialties, Radiological Sciences and Public HealthUniversity of BresciaBresciaItaly
| | - Faiez Zannad
- Clinical Investigation Center 1433, Centre Hospitalier Regional et Universitaire de NancyVandoeuvre les NancyFrance
| | | | - Dirk J. van Veldhuisen
- Department of Cardiology, University of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - John G. Cleland
- National Heart and Lung Institute, Royal Brompton and Harefield Hospitals, Imperial College, London, UK and Robertson Centre for Biostatistics and Clinical TrialsUniversity of GlasgowGlasgowUK
| | - Leong L. Ng
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
| | - Sean T. May
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLoughboroughUK
| | | | - Adriaan A. Voors
- Department of Cardiology, University of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - James A. Timmons
- Barts & The London School of MedicineQueen Mary University of LondonLondonUK
- Augur Precision Medicine LtdStirling University Innovation ParkUK
| | - Nilesh J. Samani
- Department of Cardiovascular SciencesUniversity of Leicester and NIHR Leicester Biomedical Research CentreGlenfield Hospital, LeicesterUK
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5
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Dennison JL, Volmar CH, Ke D, Wang J, Gravel E, Hammond-Vignini S, Li Z, Timmons JA, Lohse I, Hayward MA, Brothers SP, Wahlestedt C. JOTROL, a Novel Formulation of Resveratrol, Shows Beneficial Effects in the 3xTg-AD Mouse Model. J Alzheimers Dis 2022; 86:173-190. [PMID: 35034905 DOI: 10.3233/jad-215370] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) has minimally effective treatments currently. High concentrations of resveratrol, a polyphenol antioxidant found in plants, have been reported to affect several AD-related and neuroprotective genes. To address the low bioavailability of resveratrol, we investigated a novel oral formulation of resveratrol, JOTROL™, that has shown increased pharmacokinetic properties compared to non-formulated resveratrol in animals and in humans. OBJECTIVE We hypothesized that equivalent doses of JOTROL, compared to non-formulated resveratrol, would result in greater brain exposure to resveratrol, and more efficacious responses on AD biomarkers. METHODS For sub-chronic reversal studies, 15-month-old male triple transgenic (APPSW/PS1M146V/TauP301L; 3xTg-AD) AD mice were treated orally with vehicle or 50 mg/kg JOTROL for 36 days. For prophylactic studies, male and female 3xTg-AD mice were similarly administered vehicle, 50 mg/kg JOTROL, or 50 mg/kg resveratrol for 9 months starting at 4 months of age. A behavioral battery was run, and mRNA and protein from brain and blood were analyzed for changes in AD-related gene and protein expression. RESULTS JOTROL displays significantly increased bioavailability over non-formulated resveratrol. Treatment with JOTROL resulted in AD-related gene expression changes (Adam10, Bace1, Bdnf, Psen1) some of which were brain region-dependent and sex-specific, as well as changes in inflammatory gene and cytokine levels. CONCLUSION JOTROL may be effective as a prophylaxis and/or treatment for AD through increased expression and/or activation of neuroprotective genes, suppression of pro-inflammatory genes, and regulation of central and peripheral cytokine levels.
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Affiliation(s)
- Jessica L Dennison
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Claude-Henry Volmar
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Danbing Ke
- KDM Laboratories Inc., Montreal, QC, Canada
| | - James Wang
- KDM Laboratories Inc., Montreal, QC, Canada
| | | | | | - Zuomei Li
- NuChem Sciences Inc., St. Laurent, QC, Canada
| | | | - Ines Lohse
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Shaun P Brothers
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Claes Wahlestedt
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
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6
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Timmons JA, Anighoro A, Brogan RJ, Stahl J, Wahlestedt C, Farquhar DG, Taylor-King J, Volmar CH, Kraus WE, Phillips SM. A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease. eLife 2022; 11:68832. [PMID: 35037854 PMCID: PMC8763401 DOI: 10.7554/elife.68832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 11/26/2021] [Indexed: 12/22/2022] Open
Abstract
Insulin resistance (IR) contributes to the pathophysiology of diabetes, dementia, viral infection, and cardiovascular disease. Drug repurposing (DR) may identify treatments for IR; however, barriers include uncertainty whether in vitro transcriptomic assays yield quantitative pharmacological data, or how to optimise assay design to best reflect in vivo human disease. We developed a clinical-based human tissue IR signature by combining lifestyle-mediated treatment responses (>500 human adipose and muscle biopsies) with biomarkers of disease status (fasting IR from >1200 biopsies). The assay identified a chemically diverse set of >130 positively acting compounds, highly enriched in true positives, that targeted 73 proteins regulating IR pathways. Our multi-gene RNA assay score reflected the quantitative pharmacological properties of a set of epidermal growth factor receptor-related tyrosine kinase inhibitors, providing insight into drug target specificity; an observation supported by deep learning-based genome-wide predicted pharmacology. Several drugs identified are suitable for evaluation in patients, particularly those with either acute or severe chronic IR.
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Affiliation(s)
- James A Timmons
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom.,Augur Precision Medicine LTD, Stirling, United Kingdom
| | | | | | - Jack Stahl
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, United States
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, United States
| | | | | | - Claude-Henry Volmar
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, United States
| | | | - Stuart M Phillips
- Faculty of Science, Kinesiology, McMaster University, Hamilton, Canada
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7
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Cen HH, Hussein B, Botezelli JD, Wang S, Zhang JA, Noursadeghi N, Jessen N, Rodrigues B, Timmons JA, Johnson JD. Human and mouse muscle transcriptomic analyses identify insulin receptor mRNA downregulation in hyperinsulinemia-associated insulin resistance. FASEB J 2022; 36:e22088. [PMID: 34921686 PMCID: PMC9255858 DOI: 10.1096/fj.202100497rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 01/03/2023]
Abstract
Hyperinsulinemia is commonly viewed as a compensatory response to insulin resistance, yet studies have demonstrated that chronically elevated insulin may also drive insulin resistance. The molecular mechanisms underpinning this potentially cyclic process remain poorly defined, especially on a transcriptome-wide level. Transcriptomic meta-analysis in >450 human samples demonstrated that fasting insulin reliably and negatively correlated with INSR mRNA in skeletal muscle. To establish causality and study the direct effects of prolonged exposure to excess insulin in muscle cells, we incubated C2C12 myotubes with elevated insulin for 16 h, followed by 6 h of serum starvation, and established that acute AKT and ERK signaling were attenuated in this model of in vitro hyperinsulinemia. Global RNA-sequencing of cells both before and after nutrient withdrawal highlighted genes in the insulin receptor (INSR) signaling, FOXO signaling, and glucose metabolism pathways indicative of 'hyperinsulinemia' and 'starvation' programs. Consistently, we observed that hyperinsulinemia led to a substantial reduction in Insr gene expression, and subsequently a reduced surface INSR and total INSR protein, both in vitro and in vivo. Bioinformatic modeling combined with RNAi identified SIN3A as a negative regulator of Insr mRNA (and JUND, MAX, and MXI as positive regulators of Irs2 mRNA). Together, our analysis identifies mechanisms which may explain the cyclic processes underlying hyperinsulinemia-induced insulin resistance in muscle, a process directly relevant to the etiology and disease progression of type 2 diabetes.
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Affiliation(s)
- Haoning Howard Cen
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bahira Hussein
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - José Diego Botezelli
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Su Wang
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiashuo Aaron Zhang
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nilou Noursadeghi
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Brian Rodrigues
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - James A Timmons
- Augur Precision Medicine LTD, Stirling University Innovation Park, Stirling, Scotland.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - James D Johnson
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
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8
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Cao H, Salazar-García L, Gao F, Wahlestedt T, Wu CL, Han X, Cai Y, Xu D, Wang F, Tang L, Ricciardi N, Cai D, Wang H, Chin MPS, Timmons JA, Wahlestedt C, Kapranov P. Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells. Nat Commun 2019; 10:5799. [PMID: 31862872 PMCID: PMC6925131 DOI: 10.1038/s41467-019-13602-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022] Open
Abstract
Single-strand breaks (SSBs) represent the major form of DNA damage, yet techniques to map these lesions genome-wide with nucleotide-level precision are limited. Here, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realms of cellular biology, not obtainable with current approaches.
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Affiliation(s)
- Huifen Cao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lorena Salazar-García
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Thor Wahlestedt
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Chun-Lin Wu
- Department of Pathology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, China
| | - Xueer Han
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ye Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fang Wang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lu Tang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Natalie Ricciardi
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - DingDing Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifang Wang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Mario P S Chin
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - James A Timmons
- Augur Precision Medicine LTD, Scion House, Stirling University Innovation Park, Stirling, FK9 4NF, UK
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, 33136, USA.
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
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9
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Timmons JA, Gallagher IJ, Sood S, Phillips B, Crossland H, Howard R, Kraus WE, Atherton PJ. A statistical and biological response to an informatics appraisal of healthy aging gene signatures. Genome Biol 2019; 20:152. [PMID: 31375147 PMCID: PMC6676519 DOI: 10.1186/s13059-019-1734-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/10/2019] [Indexed: 11/10/2022] Open
Abstract
Jacob and Speed did not identify even a single example of a '150-gene-set' that was statistically significant at classifying Alzheimer's disease (AD) samples, or age in independent studies. We attempt to clarify the various misunderstandings, below.
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10
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Timmons JA, Volmar C, Crossland H, Phillips BE, Sood S, Janczura KJ, Törmäkangas T, Kujala UM, Kraus WE, Atherton PJ, Wahlestedt C. Longevity-related molecular pathways are subject to midlife "switch" in humans. Aging Cell 2019; 18:e12970. [PMID: 31168962 PMCID: PMC6612641 DOI: 10.1111/acel.12970] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022] Open
Abstract
Emerging evidence indicates that molecular aging may follow nonlinear or discontinuous trajectories. Whether this occurs in human neuromuscular tissue, particularly for the noncoding transcriptome, and independent of metabolic and aerobic capacities, is unknown. Applying our novel RNA method to quantify tissue coding and long noncoding RNA (lncRNA), we identified ~800 transcripts tracking with age up to ~60 years in human muscle and brain. In silico analysis demonstrated that this temporary linear "signature" was regulated by drugs, which reduce mortality or extend life span in model organisms, including 24 inhibitors of the IGF-1/PI3K/mTOR pathway that mimicked, and 5 activators that opposed, the signature. We profiled Rapamycin in nondividing primary human myotubes (n = 32 HTA 2.0 arrays) and determined the transcript signature for reactive oxygen species in neurons, confirming that our age signature was largely regulated in the "pro-longevity" direction. Quantitative network modeling demonstrated that age-regulated ncRNA equaled the contribution of protein-coding RNA within structures, but tended to have a lower heritability, implying lncRNA may better reflect environmental influences. Genes ECSIT, UNC13, and SKAP2 contributed to a network that did not respond to Rapamycin, and was associated with "neuron apoptotic processes" in protein-protein interaction analysis (FDR = 2.4%). ECSIT links inflammation with the continued age-related downwards trajectory of mitochondrial complex I gene expression (FDR < 0.01%), implying that sustained inhibition of ECSIT may be maladaptive. The present observations link, for the first time, model organism longevity programs with the endogenous but temporary genome-wide responses to aging in humans, revealing a pattern that may ultimately underpin personalized rates of health span.
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Affiliation(s)
- James A. Timmons
- Division of Genetics and Molecular MedicineKing's College LondonLondonUK
- Scion HouseStirling University Innovation ParkStirlingUK
| | - Claude‐Henry Volmar
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic InnovationUniversity of Miami Miller School of MedicineMiamiFlorida
| | - Hannah Crossland
- Division of Genetics and Molecular MedicineKing's College LondonLondonUK
- School of Medicine, Royal Derby HospitalUniversity of NottinghamDerbyUK
| | | | - Sanjana Sood
- Division of Genetics and Molecular MedicineKing's College LondonLondonUK
| | - Karolina J. Janczura
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic InnovationUniversity of Miami Miller School of MedicineMiamiFlorida
| | - Timo Törmäkangas
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Urho M. Kujala
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | | | | | - Claes Wahlestedt
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic InnovationUniversity of Miami Miller School of MedicineMiamiFlorida
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11
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Timmons JA, Atherton PJ, Larsson O, Sood S, Blokhin IO, Brogan RJ, Volmar CH, Josse AR, Slentz C, Wahlestedt C, Phillips SM, Phillips BE, Gallagher IJ, Kraus WE. A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease. Nucleic Acids Res 2019; 46:7772-7792. [PMID: 29986096 PMCID: PMC6125682 DOI: 10.1093/nar/gky570] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWAS), relying on hundreds of thousands of individuals, have revealed >200 genomic loci linked to metabolic disease (MD). Loss of insulin sensitivity (IS) is a key component of MD and we hypothesized that discovery of a robust IS transcriptome would help reveal the underlying genomic structure of MD. Using 1,012 human skeletal muscle samples, detailed physiology and a tissue-optimized approach for the quantification of coding (>18,000) and non-coding (>15,000) RNA (ncRNA), we identified 332 fasting IS-related genes (CORE-IS). Over 200 had a proven role in the biochemistry of insulin and/or metabolism or were located at GWAS MD loci. Over 50% of the CORE-IS genes responded to clinical treatment; 16 quantitatively tracking changes in IS across four independent studies (P = 0.0000053: negatively: AGL, G0S2, KPNA2, PGM2, RND3 and TSPAN9 and positively: ALDH6A1, DHTKD1, ECHDC3, MCCC1, OARD1, PCYT2, PRRX1, SGCG, SLC43A1 and SMIM8). A network of ncRNA positively related to IS and interacted with RNA coding for viral response proteins (P < 1 × 10−48), while reduced amino acid catabolic gene expression occurred without a change in expression of oxidative-phosphorylation genes. We illustrate that combining in-depth physiological phenotyping with robust RNA profiling methods, identifies molecular networks which are highly consistent with the genetics and biochemistry of human metabolic disease.
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Affiliation(s)
- James A Timmons
- Division of Genetics and Molecular Medicine, King's College London, London, UK.,Scion House, Stirling University Innovation Park, Stirling, UK
| | | | - Ola Larsson
- Department of Oncology-Pathology, Science For Life Laboratory, Stockholm, Sweden
| | - Sanjana Sood
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | | | - Robert J Brogan
- Scion House, Stirling University Innovation Park, Stirling, UK
| | | | | | - Cris Slentz
- Duke University School of Medicine, Durham, USA
| | - Claes Wahlestedt
- Department of Oncology-Pathology, Science For Life Laboratory, Stockholm, Sweden
| | | | | | - Iain J Gallagher
- Scion House, Stirling University Innovation Park, Stirling, UK.,School of Health Sciences and Sport, University of Stirling, Stirling, UK
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Crossland H, Timmons JA, Atherton PJ. A dynamic ribosomal biogenesis response is not required for IGF-1-mediated hypertrophy of human primary myotubes. FASEB J 2017; 31:5196-5207. [PMID: 28774889 PMCID: PMC5690393 DOI: 10.1096/fj.201700329r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/17/2017] [Indexed: 12/11/2022]
Abstract
Increased ribosomal DNA transcription has been proposed to limit muscle protein synthesis, making ribosome biogenesis central to skeletal muscle hypertrophy. We examined the relationship between ribosomal RNA (rRNA) production and IGF-1-mediated myotube hypertrophy in vitro Primary skeletal myotubes were treated with IGF-1 (50 ng/ml) with or without 0.5 µM CX-5461 (CX), an inhibitor of RNA polymerase I. Myotube diameter, total protein, and RNA and DNA levels were measured along with markers of RNA polymerase I regulatory factors and regulators of protein synthesis. CX treatment reduced 45S pre-rRNA expression (-64 ± 5% vs. IGF-1; P < 0.001) and total RNA content (-16 ± 2% vs. IGF-1; P < 0.001) in IGF-1-treated myotubes. IGF-1-mediated increases in myotube diameter (1.27 ± 0.09-fold, P < 0.05 vs. control) and total protein (+20 ± 2%; P < 0.001 vs. control) were not prevented by CX treatment. Suppression of rRNA synthesis during IGF-1 treatment did not prevent early increases in AKT (+203 ± 39% vs. CX; P < 0.001) and p70 S6K1 (269 ± 41% vs. CX; P < 0.001) phosphorylation. Despite robust inhibition of the dynamic ribosomal biogenesis response to IGF-1, myotube diameter and protein accretion were sustained. Thus, while ribosome biogenesis represents a potential site for the regulation of skeletal muscle protein synthesis and muscle mass, it does not appear to be a prerequisite for IGF-1-induced myotube hypertrophy in vitro.-Crossland, H., Timmons, J. A., Atherton, P. J. A dynamic ribosomal biogenesis response is not required for IGF-1-mediated hypertrophy of human primary myotubes.
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Affiliation(s)
- Hannah Crossland
- Division of Genetics and Molecular Medicine, Guy's Hospital, King's College London, London, United Kingdom; and
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, United Kingdom
| | - James A Timmons
- Division of Genetics and Molecular Medicine, Guy's Hospital, King's College London, London, United Kingdom; and
| | - Philip J Atherton
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, United Kingdom
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Dinas PC, Lahart IM, Timmons JA, Svensson PA, Koutedakis Y, Flouris AD, Metsios GS. Effects of physical activity on the link between PGC-1a and FNDC5 in muscle, circulating Ιrisin and UCP1 of white adipocytes in humans: A systematic review. F1000Res 2017; 6:286. [PMID: 28620456 PMCID: PMC5461915 DOI: 10.12688/f1000research.11107.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/16/2017] [Indexed: 11/13/2023] Open
Abstract
Background: Exercise may activate a brown adipose-like phenotype in white adipose tissue. The aim of this systematic review was to identify the effects of physical activity on the link between peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1a) and fibronectin type III domain-containing protein 5 (FNDC5) in muscle, circulating Irisin and uncoupling protein one (UCP1) of white adipocytes in humans. Methods: Two databases (PubMed 1966 to 08/2016 and EMBASE 1974 to 08/2016) were searched using an appropriate algorithm. We included articles that examined physical activity and/or exercise in humans that met the following criteria: a) PGC-1a in conjunction with FNDC5 measurements, and b) FNDC5 and/or circulating Irisin and/or UCP1 levels in white adipocytes. Results: We included 51 studies (12 randomised controlled trials) with 2474 participants. Out of the 51 studies, 16 examined PGC-1a and FNDC5 in response to exercise, and only four found increases in both PGC-1a and FNDC5 mRNA and one showed increased FNDC5 mRNA. In total, 22 out of 45 studies that examined circulating Irisin in response to exercise showed increased concentrations when ELISA techniques were used; two studies also revealed increased Irisin levels measured via mass spectrometry. Three studies showed a positive association of circulating Irisin with physical activity levels. One study found no exercise effects on UCP1 mRNA in white adipocytes. Conclusions: The effects of physical activity on the link between PGC-1a, FNDC5 mRNA in muscle and UCP1 in white human adipocytes has attracted little scientific attention. Current methods for Irisin identification lack precision and, therefore, the existing evidence does not allow for conclusions to be made regarding Irisin responses to physical activity. We found a contrast between standardised review methods and accuracy of the measurements used. This should be considered in future systematic reviews.
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Affiliation(s)
- Petros C. Dinas
- Institute of Sport, Faculty of Education Health and Wellbeing, University of Wolverhampton, Walsall, WS1 3BD, UK
- FAME Laboratory, Department of Physical Education and Exercise Science, University of Thessaly, Trikala, GR42100, Greece
| | - Ian M. Lahart
- Institute of Sport, Faculty of Education Health and Wellbeing, University of Wolverhampton, Walsall, WS1 3BD, UK
| | - James A. Timmons
- Genetics and Molecular Medicine, King’s College London, London, SE1 9RT, UK
| | - Per-Arne Svensson
- Department of Molecular and Clinical Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-413 45, Sweden
| | - Yiannis Koutedakis
- Institute of Sport, Faculty of Education Health and Wellbeing, University of Wolverhampton, Walsall, WS1 3BD, UK
- Department of Physical Education and Exercise Science, University of Thessaly, Trikala, GR42100, Greece
- Institute for Research and Technology, Trikala, GR42100, Greece
| | - Andreas D. Flouris
- FAME Laboratory, Department of Physical Education and Exercise Science, University of Thessaly, Trikala, GR42100, Greece
| | - George S. Metsios
- Institute of Sport, Faculty of Education Health and Wellbeing, University of Wolverhampton, Walsall, WS1 3BD, UK
- Department of Physical Education and Exercise Science, University of Thessaly, Trikala, GR42100, Greece
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14
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Dinas PC, Lahart IM, Timmons JA, Svensson PA, Koutedakis Y, Flouris AD, Metsios GS. Effects of physical activity on the link between PGC-1a and FNDC5 in muscle, circulating Ιrisin and UCP1 of white adipocytes in humans: A systematic review. F1000Res 2017; 6:286. [PMID: 28620456 PMCID: PMC5461915 DOI: 10.12688/f1000research.11107.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2017] [Indexed: 01/08/2023] Open
Abstract
Background: Exercise may activate a brown adipose-like phenotype in white adipose tissue. The aim of this systematic review was to identify the effects of physical activity on the link between peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1a) and fibronectin type III domain-containing protein 5 (FNDC5) in muscle, circulating Irisin and uncoupling protein one (UCP1) of white adipocytes in humans. Methods: Two databases (PubMed 1966 to 08/2016 and EMBASE 1974 to 08/2016) were searched using an appropriate algorithm. We included articles that examined physical activity and/or exercise in humans that met the following criteria: a) PGC-1a in conjunction with FNDC5 measurements, and b) FNDC5 and/or circulating Irisin and/or UCP1 levels in white adipocytes. Results: We included 51 studies (12 randomised controlled trials) with 2474 participants. Out of the 51 studies, 16 examined PGC-1a and FNDC5 in response to exercise, and only four found increases in both PGC-1a and FNDC5 mRNA and one showed increased FNDC5 mRNA. In total, 22 out of 45 studies that examined circulating Irisin in response to exercise showed increased concentrations when ELISA techniques were used; two studies also revealed increased Irisin levels measured via mass spectrometry. Three studies showed a positive association of circulating Irisin with physical activity levels. One study found no exercise effects on UCP1 mRNA in white adipocytes. Conclusions: The effects of physical activity on the link between PGC-1a, FNDC5 mRNA in muscle and UCP1 in white human adipocytes has attracted little scientific attention. Current methods for Irisin identification lack precision and, therefore, the existing evidence does not allow for conclusions to be made regarding Irisin responses to physical activity. We found a contrast between standardised review methods and accuracy of the measurements used. This should be considered in future systematic reviews.
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Affiliation(s)
- Petros C. Dinas
- Institute of Sport, Faculty of Education Health and Wellbeing, University of Wolverhampton, Walsall, WS1 3BD, UK
- FAME Laboratory, Department of Physical Education and Exercise Science, University of Thessaly, Trikala, GR42100, Greece
| | - Ian M. Lahart
- Institute of Sport, Faculty of Education Health and Wellbeing, University of Wolverhampton, Walsall, WS1 3BD, UK
| | - James A. Timmons
- Genetics and Molecular Medicine, King’s College London, London, SE1 9RT, UK
| | - Per-Arne Svensson
- Department of Molecular and Clinical Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-413 45, Sweden
| | - Yiannis Koutedakis
- Institute of Sport, Faculty of Education Health and Wellbeing, University of Wolverhampton, Walsall, WS1 3BD, UK
- Department of Physical Education and Exercise Science, University of Thessaly, Trikala, GR42100, Greece
- Institute for Research and Technology, Trikala, GR42100, Greece
| | - Andreas D. Flouris
- FAME Laboratory, Department of Physical Education and Exercise Science, University of Thessaly, Trikala, GR42100, Greece
| | - George S. Metsios
- Institute of Sport, Faculty of Education Health and Wellbeing, University of Wolverhampton, Walsall, WS1 3BD, UK
- Department of Physical Education and Exercise Science, University of Thessaly, Trikala, GR42100, Greece
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Phillips BE, Kelly BM, Lilja M, Ponce-González JG, Brogan RJ, Morris DL, Gustafsson T, Kraus WE, Atherton PJ, Vollaard NBJ, Rooyackers O, Timmons JA. A Practical and Time-Efficient High-Intensity Interval Training Program Modifies Cardio-Metabolic Risk Factors in Adults with Risk Factors for Type II Diabetes. Front Endocrinol (Lausanne) 2017; 8:229. [PMID: 28943861 PMCID: PMC5596071 DOI: 10.3389/fendo.2017.00229] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/22/2017] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Regular physical activity (PA) can reduce the risk of developing type 2 diabetes, but adherence to time-orientated (150 min week-1 or more) PA guidelines is very poor. A practical and time-efficient PA regime that was equally efficacious at controlling risk factors for cardio-metabolic disease is one solution to this problem. Herein, we evaluate a new time-efficient and genuinely practical high-intensity interval training (HIT) protocol in men and women with pre-existing risk factors for type 2 diabetes. MATERIALS AND METHODS One hundred eighty-nine sedentary women (n = 101) and men (n = 88) with impaired glucose tolerance and/or a body mass index >27 kg m-2 [mean (range) age: 36 (18-53) years] participated in this multi-center study. Each completed a fully supervised 6-week HIT protocol at work-loads equivalent to ~100 or ~125% [Formula: see text]. Change in [Formula: see text] was used to monitor protocol efficacy, while Actiheart™ monitors were used to determine PA during four, weeklong, periods. Mean arterial (blood) pressure (MAP) and fasting insulin resistance [homeostatic model assessment (HOMA)-IR] represent key health biomarker outcomes. RESULTS The higher intensity bouts (~125% [Formula: see text]) used during a 5-by-1 min HIT protocol resulted in a robust increase in [Formula: see text] (136 participants, +10.0%, p < 0.001; large size effect). 5-by-1 HIT reduced MAP (~3%; p < 0.001) and HOMA-IR (~16%; p < 0.01). Physiological responses were similar in men and women while a sizeable proportion of the training-induced changes in [Formula: see text], MAP, and HOMA-IR was retained 3 weeks after cessation of training. The supervised HIT sessions accounted for the entire quantifiable increase in PA, and this equated to 400 metabolic equivalent (MET) min week-1. Meta-analysis indicated that 5-by-1 HIT matched the efficacy and variability of a time-consuming 30-week PA program on [Formula: see text], MAP, and HOMA-IR. CONCLUSION With a total time-commitment of <15 min per session and reliance on a practical ergometer protocol, 5-by-1 HIT offers a new solution to modulate cardio-metabolic risk factors in adults with pre-existing risk factors for type 2 diabetes while approximately meeting the MET min week-1 PA guidelines. Long-term randomized controlled studies will be required to quantify the ability for 5-by-1 HIT to reduce the incidence of type 2 diabetes, while strategies are required to harmonize the adaptations to exercise across individuals.
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Affiliation(s)
- Bethan E. Phillips
- Clinical, Metabolic and Molecular Physiology Research Group, School of Medicine, University of Nottingham, Derby, United Kingdom
| | | | - Mats Lilja
- Department of Laboratory Medicine, Karolinska University Hospital, Stockholm, Sweden
| | | | - Robert J. Brogan
- Scion House, Stirling University Innovation Park, Stirling, United Kingdom
| | - David L. Morris
- Division of Genetics and Molecular Medicine, King’s College London, London, United Kingdom
| | - Thomas Gustafsson
- Department of Laboratory Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - William E. Kraus
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States
| | - Philip J. Atherton
- Clinical, Metabolic and Molecular Physiology Research Group, School of Medicine, University of Nottingham, Derby, United Kingdom
| | - Niels B. J. Vollaard
- Faculty of Health Sciences and Sport, University of Stirling, Stirling, United Kingdom
| | - Olav Rooyackers
- CLINTEC, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - James A. Timmons
- Scion House, Stirling University Innovation Park, Stirling, United Kingdom
- Division of Genetics and Molecular Medicine, King’s College London, London, United Kingdom
- *Correspondence: James A. Timmons,
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16
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Timmons JA. Molecular Diagnostics of Ageing and Tackling Age-related Disease. Trends Pharmacol Sci 2016; 38:67-80. [PMID: 27979318 DOI: 10.1016/j.tips.2016.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/08/2016] [Accepted: 11/08/2016] [Indexed: 10/25/2022]
Abstract
As average life expectancy increases there is a greater focus on health-span and, in particular, how to treat or prevent chronic age-associated diseases. Therapies which were able to control 'biological age' with the aim of postponing chronic and costly diseases of old age require an entirely new approach to drug development. Molecular technologies and machine-learning methods have already yielded diagnostics that help guide cancer treatment and cardiovascular procedures. Discovery of valid and clinically informative diagnostics of human biological age (combined with disease-specific biomarkers) has the potential to alter current drug-discovery strategies, aid clinical trial recruitment and maximize healthy ageing. I will review some basic principles that govern the development of 'ageing' diagnostics, how such assays could be used during the drug-discovery or development process. Important logistical and statistical considerations are illustrated by reviewing recent biomarker activity in the field of Alzheimer's disease, as dementia represents the most pressing of priorities for the pharmaceutical industry, as well as the chronic disease in humans most associated with age.
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Affiliation(s)
- James A Timmons
- Division of Genetics and Molecular Medicine, King's College London, London, England; XRGenomics Ltd, Scion House, Stirlingshire, Scotland.
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17
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Hangelbroek RWJ, Fazelzadeh P, Tieland M, Boekschoten MV, Hooiveld GJEJ, van Duynhoven JPM, Timmons JA, Verdijk LB, de Groot LCPGM, van Loon LJC, Müller M. Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness. J Cachexia Sarcopenia Muscle 2016; 7:604-614. [PMID: 27239416 PMCID: PMC4863830 DOI: 10.1002/jcsm.12099] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/17/2015] [Accepted: 12/04/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The skeletal muscle system plays an important role in the independence of older adults. In this study we examine differences in the skeletal muscle transcriptome between healthy young and older subjects and (pre-)frail older adults. Additionally, we examine the effect of resistance-type exercise training on the muscle transcriptome in healthy older subjects and (pre-)frail older adults. METHODS Baseline transcriptome profiles were measured in muscle biopsies collected from 53 young, 73 healthy older subjects, and 61 frail older subjects. Follow-up samples from these frail older subjects (31 samples) and healthy older subjects (41 samples) were collected after 6 months of progressive resistance-type exercise training. Frail older subjects trained twice per week and the healthy older subjects trained three times per week. RESULTS At baseline genes related to mitochondrial function and energy metabolism were differentially expressed between older and young subjects, as well as between healthy and frail older subjects. Three hundred seven genes were differentially expressed after training in both groups. Training affected expression levels of genes related to extracellular matrix, glucose metabolism ,and vascularization. Expression of genes that were modulated by exercise training was indicative of muscle strength at baseline. Genes that strongly correlated with strength belonged to the protocadherin gamma gene cluster (r = -0.73). CONCLUSIONS Our data suggest significant remaining plasticity of ageing skeletal muscle to adapt to resistance-type exercise training. Some age-related changes in skeletal muscle gene expression appear to be partially reversed by prolonged resistance-type exercise training. The protocadherin gamma gene cluster may be related to muscle denervation and re-innervation in ageing muscle.
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Affiliation(s)
- Roland W J Hangelbroek
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Parastoo Fazelzadeh
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Michael Tieland
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Mark V Boekschoten
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Guido J E J Hooiveld
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - John P M van Duynhoven
- Laboratory of Biophysics Wageningen University Wageningen the Netherlands; Netherlands Metabolomics Centre Leiden the Netherlands
| | | | - Lex B Verdijk
- Top Institute Food and Nutrition Wageningen the Netherlands; Department of Human Movement Sciences, NUTRIM School of Nutrition and Translational Research in Metabolism Maastricht University Maastricht the Netherlands
| | - Lisette C P G M de Groot
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Luc J C van Loon
- Top Institute Food and Nutrition Wageningen the Netherlands; Department of Human Movement Sciences, NUTRIM School of Nutrition and Translational Research in Metabolism Maastricht University Maastricht the Netherlands
| | - Michael Müller
- Top Institute Food and Nutrition Wageningen the Netherlands; Division of Human Nutrition Wageningen University Wageningen the Netherlands; Norwich Medical School University of East Anglia Norwich UK
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18
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Crossland H, Atherton PJ, Strömberg A, Gustafsson T, Timmons JA. A reverse genetics cell-based evaluation of genes linked to healthy human tissue age. FASEB J 2016; 31:96-108. [PMID: 27698205 PMCID: PMC5161526 DOI: 10.1096/fj.201600296rrr] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 09/16/2016] [Indexed: 11/11/2022]
Abstract
We recently developed a binary (i.e., young vs. old) classifier using human muscle RNA profiles that accurately distinguished the age of multiple tissue types. Pathway analysis did not reveal regulators of these 150 genes, so we used reverse genetics and pharmacologic methods to explore regulation of gene expression. Using small interfering RNA, well-studied age-related factors (i.e., rapamycin, resveratrol, TNF-α, and staurosporine), quantitative real-time PCR and clustering analysis, we studied gene-gene interactions in human skeletal muscle and renal epithelial cells. Individual knockdown of 10 different age genes yielded a consistent pattern of gene expression in muscle and renal cells, similar to in vivo. Potential epigenetic interactions included HIST1H3E knockdown, leading to decreased PHF19 and PCDH9, and increased ICAM5 in muscle and renal cells, while ICAM5 knockdown reduced HIST1H3E expression. Resveratrol, staurosporine, and TNF-α significantly regulated the in vivo aging genes, while only rapamycin perturbed the healthy-age gene expression signature in a manner consistent with in vivo. In vitro coordination of gene expression for this in vivo tissue age signature indicates a degree of direct coordination, and the observed link with mTOR activity suggests a direct link between a robust biomarker of healthy neuromuscular age and a major axis of life span in model systems.-Crossland, H., Atherton, P. J., Strömberg, A., Gustafsson, T., Timmons, J. A. A reverse genetics cell-based evaluation of genes linked to healthy human tissue age.
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Affiliation(s)
- Hannah Crossland
- Division of Genetics and Molecular Medicine, King's College London, Guy's Hospital, London, United Kingdom; and
| | - Philip J Atherton
- School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, United Kingdom; and
| | - Anna Strömberg
- Department of Laboratory Medicine, Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Gustafsson
- Department of Laboratory Medicine, Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - James A Timmons
- Division of Genetics and Molecular Medicine, King's College London, Guy's Hospital, London, United Kingdom; and
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19
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Nakhuda A, Josse AR, Gburcik V, Crossland H, Raymond F, Metairon S, Good L, Atherton PJ, Phillips SM, Timmons JA. Biomarkers of browning of white adipose tissue and their regulation during exercise- and diet-induced weight loss. Am J Clin Nutr 2016; 104:557-65. [PMID: 27488235 PMCID: PMC4997298 DOI: 10.3945/ajcn.116.132563] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/09/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND A hypothesis exists whereby an exercise- or dietary-induced negative energy balance reduces human subcutaneous white adipose tissue (scWAT) mass through the formation of brown-like adipocyte (brite) cells. However, the validity of biomarkers of brite formation has not been robustly evaluated in humans, and clinical data that link brite formation and weight loss are sparse. OBJECTIVES We used rosiglitazone and primary adipocytes to stringently evaluate a set of biomarkers for brite formation and determined whether the expression of biomarker genes in scWAT could explain the change in body composition in response to exercise training combined with calorie restriction in obese and overweight women (n = 79). DESIGN Gene expression was derived from exon DNA microarrays and preadipocytes from obesity-resistant and -sensitive mice treated with rosiglitazone to generate candidate brite biomarkers from a microarray. These biomarkers were evaluated against data derived from scWAT RNA from obese and overweight women before and after supervised exercise 5 d/wk for 16 wk combined with modest calorie restriction (∼0.84 MJ/d). RESULTS Forty percent of commonly used brite gene biomarkers exhibited an exon or strain-specific regulation. No biomarkers were positively related to weight loss in human scWAT. Greater weight loss was significantly associated with less uncoupling protein 1 expression (P = 0.006, R(2) = 0.09). In a follow-up global analysis, there were 161 genes that covaried with weight loss that were linked to greater CCAAT/enhancer binding protein α activity (z = 2.0, P = 6.6 × 10(-7)), liver X receptor α/β agonism (z = 2.1, P = 2.8 × 10(-7)), and inhibition of leptin-like signaling (z = -2.6, P = 3.9 × 10(-5)). CONCLUSION We identify a subset of robust RNA biomarkers for brite formation and show that calorie-restriction-mediated weight loss in women dynamically remodels scWAT to take on a more-white rather than a more-brown adipocyte phenotype.
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Affiliation(s)
- Asif Nakhuda
- School of Medicine, Derby Royal Hospital, University of Nottingham, Nottingham, United Kingdom
| | - Andrea R Josse
- Department of Kinesiology, Brock University, St. Catharines, Canada
| | | | - Hannah Crossland
- Division of Genetics and Molecular Medicine, King's College London, London, United Kingdom
| | - Frederic Raymond
- Functional Genomics, Nestle Institute of Health Sciences, Lausanne, Switzerland; and
| | - Sylviane Metairon
- Functional Genomics, Nestle Institute of Health Sciences, Lausanne, Switzerland; and
| | - Liam Good
- Royal Veterinary College, London, United Kingdom
| | - Philip J Atherton
- School of Medicine, Derby Royal Hospital, University of Nottingham, Nottingham, United Kingdom
| | - Stuart M Phillips
- Exercise Metabolism Research Group, McMaster University, Hamilton, Canada
| | - James A Timmons
- Division of Genetics and Molecular Medicine, King's College London, London, United Kingdom;
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Abstract
The purpose of an F1000 review is to reflect on the bigger picture, exploring controversies and new concepts as well as providing opinion as to what is limiting progress in a particular field. We reviewed about 200 titles published in 2015 that included reference to 'skeletal muscle, exercise, and ageing' with the aim of identifying key articles that help progress our understanding or research capacity while identifying methodological issues which represent, in our opinion, major barriers to progress. Loss of neuromuscular function with chronological age impacts on both health and quality of life. We prioritised articles that studied human skeletal muscle within the context of age or exercise and identified new molecular observations that may explain how muscle responds to exercise or age. An important aspect of this short review is perspective: providing a view on the likely 'size effect' of a potential mechanism on physiological capacity or ageing.
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Affiliation(s)
- James A Timmons
- Division of Genetics & Molecular Medicine, King's College London, London, UK
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21
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Sood S, Szkop KJ, Nakhuda A, Gallagher IJ, Murie C, Brogan RJ, Kaprio J, Kainulainen H, Atherton PJ, Kujala UM, Gustafsson T, Larsson O, Timmons JA. iGEMS: an integrated model for identification of alternative exon usage events. Nucleic Acids Res 2016; 44:e109. [PMID: 27095197 PMCID: PMC4914109 DOI: 10.1093/nar/gkw263] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/02/2016] [Indexed: 12/16/2022] Open
Abstract
DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabetes drug, rosiglitazone. iGEMS identified 555 genes with AEU, and robust verification by RT-qPCR (∼90%). Second, in a three-way human tissue comparison (muscle, adipose and blood, n = 41) iGEMS identified 4421 genes with at least one AEU event, with excellent RT-qPCR verification (95%, n = 22). Importantly, iGEMS identified a variety of AEU events, including 3′UTR extension, as well as exon inclusion/exclusion impacting on protein kinase and extracellular matrix domains. In conclusion, iGEMS is a robust method for identification of AEU while the variety of exon usage between human tissues is 5–10 times more prevalent than reported by the Genotype-Tissue Expression consortium using RNA sequencing.
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Affiliation(s)
- Sanjana Sood
- Division of Genetics and Molecular Medicine, King's College London, WC2R 2LS, London, UK Research Department, XRGenomics Ltd, 35 Kingsland Road, London E2 8AA, UK
| | - Krzysztof J Szkop
- Division of Genetics and Molecular Medicine, King's College London, WC2R 2LS, London, UK Research Department, XRGenomics Ltd, 35 Kingsland Road, London E2 8AA, UK
| | - Asif Nakhuda
- Division of Genetics and Molecular Medicine, King's College London, WC2R 2LS, London, UK School of Medicine, University of Nottingham, Derby Royal Hospital, Derbyshire, DE22 3DT, UK
| | - Iain J Gallagher
- School of Health Sciences, University of Stirling, Stirling, FK9 4LA, Scotland
| | - Carl Murie
- Department of Oncology-Pathology, SciLifeLab, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Robert J Brogan
- Research Department, XRGenomics Ltd, 35 Kingsland Road, London E2 8AA, UK
| | - Jaakko Kaprio
- Department of Public Health and the Institute for Molecular Medicine (FIMM), University of Helsinki, FI-00014, Helsinki, Finland National Institute for Health and Welfare, University of Helsinki, FI-00014, Helsinki, Finland
| | - Heikki Kainulainen
- Department of Biology of Physical Activity, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Philip J Atherton
- School of Medicine, University of Nottingham, Derby Royal Hospital, Derbyshire, DE22 3DT, UK
| | - Urho M Kujala
- Department of Health Sciences, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Thomas Gustafsson
- Department of Laboratory Medicine, Division of Clinical Physiology, Karolinska University Hospital, 14186, Huddinge, Sweden
| | - Ola Larsson
- Department of Oncology-Pathology, SciLifeLab, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - James A Timmons
- Division of Genetics and Molecular Medicine, King's College London, WC2R 2LS, London, UK Research Department, XRGenomics Ltd, 35 Kingsland Road, London E2 8AA, UK
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Sood S, Gallagher IJ, Lunnon K, Rullman E, Keohane A, Crossland H, Phillips BE, Cederholm T, Jensen T, van Loon LJC, Lannfelt L, Kraus WE, Atherton PJ, Howard R, Gustafsson T, Hodges A, Timmons JA. A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status. Genome Biol 2015; 16:185. [PMID: 26343147 PMCID: PMC4561473 DOI: 10.1186/s13059-015-0750-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/12/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Diagnostics of the human ageing process may help predict future healthcare needs or guide preventative measures for tackling diseases of older age. We take a transcriptomics approach to build the first reproducible multi-tissue RNA expression signature by gene-chip profiling tissue from sedentary normal subjects who reached 65 years of age in good health. RESULTS One hundred and fifty probe-sets form an accurate classifier of young versus older muscle tissue and this healthy ageing RNA classifier performed consistently in independent cohorts of human muscle, skin and brain tissue (n = 594, AUC = 0.83-0.96) and thus represents a biomarker for biological age. Using the Uppsala Longitudinal Study of Adult Men birth-cohort (n = 108) we demonstrate that the RNA classifier is insensitive to confounding lifestyle biomarkers, while greater gene score at age 70 years is independently associated with better renal function at age 82 years and longevity. The gene score is 'up-regulated' in healthy human hippocampus with age, and when applied to blood RNA profiles from two large independent age-matched dementia case-control data sets (n = 717) the healthy controls have significantly greater gene scores than those with cognitive impairment. Alone, or when combined with our previously described prototype Alzheimer disease (AD) RNA 'disease signature', the healthy ageing RNA classifier is diagnostic for AD. CONCLUSIONS We identify a novel and statistically robust multi-tissue RNA signature of human healthy ageing that can act as a diagnostic of future health, using only a peripheral blood sample. This RNA signature has great potential to assist research aimed at finding treatments for and/or management of AD and other ageing-related conditions.
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Affiliation(s)
- Sanjana Sood
- XRGenomics Ltd, London, UK
- Division of Genetics & Molecular Medicine, King's College London, 8th Floor, Tower Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Iain J Gallagher
- XRGenomics Ltd, London, UK
- School of Health, Stirling University, Stirling, Scotland, UK
| | - Katie Lunnon
- Department of Old Age Psychiatry, King's College London, London, UK
- Present address: University of Exeter Medical School, Exeter, UK
| | - Eric Rullman
- Division of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Aoife Keohane
- Department of Old Age Psychiatry, King's College London, London, UK
| | - Hannah Crossland
- Division of Genetics & Molecular Medicine, King's College London, 8th Floor, Tower Wing, Guy's Hospital, London, SE1 9RT, UK
- School of Medicine, Derby Royal Hospital, Derbyshire, UK
| | | | - Tommy Cederholm
- Department of Public Health, Caring Sciences, Clinical Nutrition and Metabolism, Uppsala University, Uppsala, Sweden
| | | | | | - Lars Lannfelt
- Department of Public Health and Caring Sciences/Molecular Geriatrics, Uppsala University, Uppsala, Sweden
| | - William E Kraus
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Robert Howard
- Department of Old Age Psychiatry, King's College London, London, UK
| | - Thomas Gustafsson
- Division of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Angela Hodges
- Department of Old Age Psychiatry, King's College London, London, UK
| | - James A Timmons
- XRGenomics Ltd, London, UK.
- Division of Genetics & Molecular Medicine, King's College London, 8th Floor, Tower Wing, Guy's Hospital, London, SE1 9RT, UK.
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Abstract
Serious and underappreciated sources of bias mean that extreme caution should be applied when using or interpreting functional enrichment analysis to validate findings from global RNA- or protein-expression analyses.
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Affiliation(s)
- James A Timmons
- Division of Genetics and Molecular Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
| | - Krzysztof J Szkop
- Division of Genetics and Molecular Medicine, King's College London, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Iain J Gallagher
- School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
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Abstract
This article is devoted to the role of genetic variation and gene-exercise interactions in the biology of adaptation to exercise. There is evidence from genetic epidemiology research that DNA sequence differences contribute to human variation in physical activity level, cardiorespiratory fitness in the untrained state, cardiovascular and metabolic response to acute exercise, and responsiveness to regular exercise. Methodological and technological advances have made it possible to undertake the molecular dissection of the genetic component of complex, multifactorial traits, such as those of interest to exercise biology, in terms of tissue expression profile, genes, and allelic variants. The evidence from animal models and human studies is considered. Data on candidate genes, genome-wide linkage results, genome-wide association findings, expression arrays, and combinations of these approaches are reviewed. Combining transcriptomic and genomic technologies has been shown to be more powerful as evidenced by the development of a recent molecular predictor of the ability to increase VO2max with exercise training. For exercise as a behavior and physiological fitness as a state to be major players in public health policies will require that the role of human individuality and the influence of DNA sequence differences be understood. Likewise, progress in the use of exercise in therapeutic medicine will depend to a large extent on our ability to identify the favorable responders for given physiological properties to a given exercise regimen.
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Affiliation(s)
- Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA.
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Kennedy R, Timmons JA. Winning the Translational Race: Making Good Choices in Biomarker Assay Development for the Clinic. Science 2013. [DOI: 10.1126/science.342.6154.133-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In an effort to develop more tailored approaches to managing disease, there has been a surge in biomarker research aimed at providing truly personalized medicine. The increase in interest over the past 20 years suggests great promise that biomarkers will transform patient treatment. However, despite the optimism and intense research, relatively few are in routine clinical use today. Attention has now turned to actively translating actionable biomarkers and biomarker signatures into clinical utility—not an easy task. The major reasons for clinical failure of biomarkers are poor experimental design and inappropriate choice of assay. It is therefore critical to carefully construct biomarker discovery and validation studies using the most appropriate assays, and to develop these into validated analytical methods suitable for clinical practice. This webinar will review the unprecedented range of technology choices, and provide insight into the challenges confronting researchers when selecting the right biomarker to pursue and the best assay to develop for the clinic.
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Ghosh S, Vivar JC, Sarzynski MA, Sung YJ, Timmons JA, Bouchard C, Rankinen T. Integrative pathway analysis of a genome-wide association study of (V)O(2max) response to exercise training. J Appl Physiol (1985) 2013; 115:1343-59. [PMID: 23990238 DOI: 10.1152/japplphysiol.01487.2012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We previously reported the findings from a genome-wide association study of the response of maximal oxygen uptake (Vo2max) to an exercise program. Here we follow up on these results to generate hypotheses on genes, pathways, and systems involved in the ability to respond to exercise training. A systems biology approach can help us better establish a comprehensive physiological description of what underlies Vo2maxtrainability. The primary material for this exploration was the individual single-nucleotide polymorphism (SNP), SNP-gene mapping, and statistical significance levels. We aimed to generate novel hypotheses through analyses that go beyond statistical association of single-locus markers. This was accomplished through three complementary approaches: 1) building de novo evidence of gene candidacy through informatics-driven literature mining; 2) aggregating evidence from statistical associations to link variant enrichment in biological pathways to Vo2max trainability; and 3) predicting possible consequences of variants residing in the pathways of interest. We started with candidate gene prioritization followed by pathway analysis focused on overrepresentation analysis and gene set enrichment analysis. Subsequently, leads were followed using in silico analysis of predicted SNP functions. Pathways related to cellular energetics (pantothenate and CoA biosynthesis; PPAR signaling) and immune functions (complement and coagulation cascades) had the highest levels of SNP burden. In particular, long-chain fatty acid transport and fatty acid oxidation genes and sequence variants were found to influence differences in Vo2max trainability. Together, these methods allow for the hypothesis-driven ranking and prioritization of genes and pathways for future experimental testing and validation.
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Affiliation(s)
- Sujoy Ghosh
- Laboratory of Computational Biology, Pennington Biomedical Research Center, Baton Rouge, Louisiana
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Lessard SJ, Rivas DA, Alves-Wagner AB, Hirshman MF, Gallagher IJ, Constantin-Teodosiu D, Atkins R, Greenhaff PL, Qi NR, Gustafsson T, Fielding RA, Timmons JA, Britton SL, Koch LG, Goodyear LJ. Resistance to aerobic exercise training causes metabolic dysfunction and reveals novel exercise-regulated signaling networks. Diabetes 2013; 62:2717-27. [PMID: 23610057 PMCID: PMC3717870 DOI: 10.2337/db13-0062] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Low aerobic exercise capacity is a risk factor for diabetes and a strong predictor of mortality, yet some individuals are "exercise-resistant" and unable to improve exercise capacity through exercise training. To test the hypothesis that resistance to aerobic exercise training underlies metabolic disease risk, we used selective breeding for 15 generations to develop rat models of low and high aerobic response to training. Before exercise training, rats selected as low and high responders had similar exercise capacities. However, after 8 weeks of treadmill training, low responders failed to improve their exercise capacity, whereas high responders improved by 54%. Remarkably, low responders to aerobic training exhibited pronounced metabolic dysfunction characterized by insulin resistance and increased adiposity, demonstrating that the exercise-resistant phenotype segregates with disease risk. Low responders had impaired exercise-induced angiogenesis in muscle; however, mitochondrial capacity was intact and increased normally with exercise training, demonstrating that mitochondria are not limiting for aerobic adaptation or responsible for metabolic dysfunction in low responders. Low responders had increased stress/inflammatory signaling and altered transforming growth factor-β signaling, characterized by hyperphosphorylation of a novel exercise-regulated phosphorylation site on SMAD2. Using this powerful biological model system, we have discovered key pathways for low exercise training response that may represent novel targets for the treatment of metabolic disease.
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Affiliation(s)
| | - Donato A. Rivas
- Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts
| | | | | | | | | | - Ryan Atkins
- University of Nottingham, University Park, Nottinghamshire, United Kingdom
| | - Paul L. Greenhaff
- University of Nottingham, University Park, Nottinghamshire, United Kingdom
| | - Nathan R. Qi
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | | | - Roger A. Fielding
- Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts
| | - James A. Timmons
- Karolinska Institutet, Huddinge, Sweden
- Loughborough University, Leicestershire, United Kingdom
| | - Steven L. Britton
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan
| | - Lauren G. Koch
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan
| | - Laurie J. Goodyear
- Joslin Diabetes Center, Boston, Massachusetts
- Corresponding author: Laurie J. Goodyear,
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Crossland H, Kazi AA, Lang CH, Timmons JA, Pierre P, Wilkinson DJ, Smith K, Szewczyk NJ, Atherton PJ. Focal adhesion kinase is required for IGF-I-mediated growth of skeletal muscle cells via a TSC2/mTOR/S6K1-associated pathway. Am J Physiol Endocrinol Metab 2013; 305:E183-93. [PMID: 23695213 PMCID: PMC3725543 DOI: 10.1152/ajpendo.00541.2012] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Focal adhesion kinase (FAK) is an attachment complex protein associated with the regulation of muscle mass through as-of-yet unclear mechanisms. We tested whether FAK is functionally important for muscle hypertrophy, with the hypothesis that FAK knockdown (FAK-KD) would impede cell growth associated with a trophic stimulus. C₂C₁₂ skeletal muscle cells harboring FAK-targeted (FAK-KD) or scrambled (SCR) shRNA were created using lentiviral transfection techniques. Both FAK-KD and SCR myotubes were incubated for 24 h with IGF-I (10 ng/ml), and additional SCR cells (±IGF-1) were incubated with a FAK kinase inhibitor before assay of cell growth. Muscle protein synthesis (MPS) and putative FAK signaling mechanisms (immunoblotting and coimmunoprecipitation) were assessed. IGF-I-induced increases in myotube width (+41 ± 7% vs. non-IGF-I-treated) and total protein (+44 ± 6%) were, after 24 h, attenuated in FAK-KD cells, whereas MPS was suppressed in FAK-KD vs. SCR after 4 h. These blunted responses were associated with attenuated IGF-I-induced FAK Tyr³⁹⁷ phosphorylation and markedly suppressed phosphorylation of tuberous sclerosis complex 2 (TSC2) and critical downstream mTOR signaling (ribosomal S6 kinase, eIF4F assembly) in FAK shRNA cells (all P < 0.05 vs. IGF-I-treated SCR cells). However, binding of FAK to TSC2 or its phosphatase Shp-2 was not affected by IGF-I or cell phenotype. Finally, FAK-KD-mediated suppression of cell growth was recapitulated by direct inhibition of FAK kinase activity in SCR cells. We conclude that FAK is required for IGF-I-induced muscle hypertrophy, signaling through a TSC2/mTOR/S6K1-dependent pathway via means requiring the kinase activity of FAK but not altered FAK-TSC2 or FAK-Shp-2 binding.
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MESH Headings
- Algorithms
- Animals
- Blotting, Western
- Cells, Cultured
- Focal Adhesion Protein-Tyrosine Kinases/antagonists & inhibitors
- Focal Adhesion Protein-Tyrosine Kinases/genetics
- Focal Adhesion Protein-Tyrosine Kinases/physiology
- Genetic Vectors
- Immunoprecipitation
- Insulin-Like Growth Factor I/physiology
- Lentivirus/genetics
- Mice
- Muscle Fibers, Skeletal/drug effects
- Muscle Fibers, Skeletal/physiology
- Muscle Fibers, Skeletal/ultrastructure
- Muscle, Skeletal/cytology
- Muscle, Skeletal/growth & development
- Phosphorylation/drug effects
- RNA Interference
- RNA, Small Interfering/genetics
- Ribosomal Protein S6 Kinases, 90-kDa/metabolism
- Ribosomal Protein S6 Kinases, 90-kDa/physiology
- Signal Transduction/physiology
- TOR Serine-Threonine Kinases/metabolism
- TOR Serine-Threonine Kinases/physiology
- Tuberous Sclerosis Complex 2 Protein
- Tumor Suppressor Proteins/metabolism
- Tumor Suppressor Proteins/physiology
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Affiliation(s)
- Hannah Crossland
- Medical Research Council-Arthritis Research United Kingdom Centre of Excellence for Musculoskeletal Ageing Research, School of Graduate Entry Medicine and Health, University of Nottingham, Royal Derby Hospital, Derby, United Kingdom
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30
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Abstract
Failure of white adipose tissue to appropriately store excess metabolic substrate seems to underpin obesity-associated type 2 diabetes. Encouraging "browning" of white adipose has been suggested as a therapeutic strategy to help dispose of excess stored lipid and ameliorate the resulting insulin resistance. Genetic variation at the DNA locus encoding the novel proteolipid neuronatin has been associated with obesity, and we recently observed that neuronatin expression is reduced in subcutaneous adipose tissue from obese humans. Thus, to explore the function of neuronatin further, we used RNAi to silence its expression in murine primary adipocyte cultures and examined the effects on adipocyte phenotype. We found that primary adipocytes express only the longer isoform of neuronatin. Loss of neuronatin led to increased mitochondrial biogenesis, indicated by greater intensity of MitoTracker Green staining. This was accompanied by increased expression of UCP1 and the key genes in mitochondrial oxidative phosphorylation, PGC-1α, Cox8b, and Cox4 in primary subcutaneous white adipocytes, indicative of a "browning" effect. In addition, phosphorylation of AMPK and ACC was increased, suggestive of increased fatty acid utilization. Similar, but less pronounced, effects of neuronatin silencing were also noted in primary brown adipocytes. In contrast, loss of neuronatin caused a reduction in both basal and insulin-stimulated glucose uptake and glycogen synthesis, likely mediated by a reduction in Glut1 protein upon silencing of neuronatin. In contrast, loss of neuronatin had no effect on insulin signaling. In conclusion, neuronatin appears to be a novel regulator of browning and metabolic substrate disposal in white adipocytes.
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Affiliation(s)
- Valentina Gburcik
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
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31
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Poulet B, Ulici V, Stone TC, Pead M, Gburcik V, Constantinou E, Palmer DB, Beier F, Timmons JA, Pitsillides AA. Time-series transcriptional profiling yields new perspectives on susceptibility to murine osteoarthritis. ACTA ACUST UNITED AC 2013; 64:3256-66. [PMID: 22833266 DOI: 10.1002/art.34572] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Chronological age is a powerful epidemiologic risk factor for osteoarthritis (OA), a multifactorial disease that is characterized by articular cartilage (AC) degradation. It is unclear from a molecular perspective how aging interacts with OA to produce this risk to AC integrity. To address this key question, we used in vivo time-course analysis of OA development and murine interstrain variability in natural susceptibility to OA to examine changes in non-OA-prone CBA mice versus OA-prone STR/Ort mice, which develop disease that bears significant histologic resemblance to human OA. Through global transcriptome profiling, we attempted to discover the molecular signature linked with both OA vulnerability and progression. METHODS Affymetrix Mouse Gene 1.0 ST Array profiles were generated from AC samples derived from CBA and STR/Ort mice at 3 different ages, corresponding to the stages prior to, at, and late after the natural onset of OA in the STR/Ort mice. RESULTS We found that the OA in STR/Ort mice exhibited a molecular phenotype resembling human OA, and we pinpointed a central role of NF-κB signaling and the emergence of an immune-related signature in OA cartilage over time. We discovered that, strikingly, young healthy AC has a highly expressed skeletal muscle gene expression program, which is switched off during maturation, but is intriguingly retained in AC during OA development in STR/Ort mice. CONCLUSION This study is the first to show that AC chondrocytes share a high-abundance gene-expression program with skeletal muscle. We show that failure to switch this program off, as well as the restoration of this program, is associated with inappropriate expression of NF-κB signaling pathways, skeletal muscle-related genes, and induction and/or progression of OA.
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Gburcik V, Cawthorn WP, Nedergaard J, Timmons JA, Cannon B. An essential role for Tbx15 in the differentiation of brown and "brite" but not white adipocytes. Am J Physiol Endocrinol Metab 2012; 303:E1053-60. [PMID: 22912368 DOI: 10.1152/ajpendo.00104.2012] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The transcription factor Tbx15 is expressed predominantly in brown adipose tissue and in those white adipose depots that are capable of giving rise to brown-in-white ("brite"/"beige") adipocytes. Therefore, we have investigated a possible role here of Tbx15 in brown and brite adipocyte differentiation in vitro. Adipocyte precursors were isolated from interscapular and axilliary brown adipose tissues, inguinal white ("brite") adipose tissue, and epididymal white adipose tissue in 129/Sv mouse pups and differentiated in culture. Differentiation was enhanced by chronic treatment with the PPARγ agonist rosiglitazone plus the sympathetic neurotransmitter norepinephrine. Using short interfering RNAs (siRNA) directed toward Tbx15 in these primary adipocyte cultures, we decreased Tbx15 expression >90%. This resulted in reduced expression levels of adipogenesis markers (PPARγ, aP2). Importantly, Tbx15 knockdown reduced the expression of brown phenotypic marker genes (PRDM16, PGC-1α, Cox8b/Cox4, UCP1) in brown adipocytes and even more markedly in inguinal white adipocytes. In contrast, Tbx15 knockdown had no effect on white adipocytes originating from a depot that is not brite competent in vivo (epididymal). Therefore, Tbx15 may be essential for the development of the adipogenic and thermogenic programs in adipocytes/adipomyocytes capable of developing brown adipocyte features.
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Affiliation(s)
- Valentina Gburcik
- Royal Veterinary College, University of London, London, United Kingdom
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Gallagher IJ, Stephens NA, MacDonald AJ, Skipworth RJE, Husi H, Greig CA, Ross JA, Timmons JA, Fearon KCH. Suppression of skeletal muscle turnover in cancer cachexia: evidence from the transcriptome in sequential human muscle biopsies. Clin Cancer Res 2012; 18:2817-27. [PMID: 22452944 DOI: 10.1158/1078-0432.ccr-11-2133] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The mechanisms underlying muscle wasting in patients with cancer remain poorly understood, and consequently there remains an unmet clinical need for new biomarkers and treatment strategies. EXPERIMENTAL DESIGN Microarrays were used to examine the transcriptome in single biopsies from healthy controls (n = 6) and in paired biopsies [pre-resection baseline (weight-loss 7%) and 8 month post-resection follow-up (disease-free/weight-stable for previous 2 months)] from quadriceps muscle of patients with upper gastrointestinal cancer (UGIC; n = 12). RESULTS Before surgery, 1,868 genes were regulated compared with follow-up (false discovery rate, 6%). Ontology analysis showed that regulated genes belonged to both anabolic and catabolic biologic processes with overwhelming downregulation in baseline samples. No literature-derived genes from preclinical cancer cachexia models showed higher expression in baseline muscle. Comparison with healthy control muscle (n = 6) revealed that despite differences in the transcriptome at baseline (941 genes regulated), the muscle of patients at follow-up was similar to control muscle (2 genes regulated). Physical activity (step count per day) did not differ between the baseline and follow-up periods (P = 0.9), indicating that gene expression differences reflected the removal of the cancer rather than altered physical activity levels. Comparative gene expression analysis using exercise training signatures supported this interpretation. CONCLUSIONS Metabolic and protein turnover-related pathways are suppressed in weight-losing patients with UGIC whereas removal of the cancer appears to facilitate a return to a healthy state, independent of changes in the level of physical activity.
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Affiliation(s)
- Iain J Gallagher
- Department of Clinical and Surgical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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35
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Abstract
Mainly from cell culture studies, a series of genes that have been suggested to be characteristic of different types of adipocytes have been identified. Here we have examined gene expression patterns in nine defined adipose depots: interscapular BAT, cervical BAT, axillary BAT, mediastinic BAT, cardiac WAT, inguinal WAT, retroperitoneal WAT, mesenteric WAT, and epididymal WAT. We found that each depot displayed a distinct gene expression fingerprint but that three major types of depots were identifiable: the brown, the brite, and the white. Although differences in gene expression pattern were generally quantitative, some gene markers showed, even in vivo, remarkable depot specificities: Zic1 for the classical BAT depots, Hoxc9 for the brite depots, Hoxc8 for the brite and white in contrast to the brown, and Tcf21 for the white depots. The effect of physiologically induced recruitment of thermogenic function (cold acclimation) on the expression pattern of the genes was quantified; in general, the depot pattern dominated over the recruitment effects. The significance of the gene expression patterns for classifying the depots and for understanding the developmental background of the depots is discussed, as are the possible regulatory functions of the genes.
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Affiliation(s)
- Tomas B Waldén
- The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, Stockholm, Sweden
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36
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Keller P, Gburcik V, Petrovic N, Gallagher IJ, Nedergaard J, Cannon B, Timmons JA. Gene-chip studies of adipogenesis-regulated microRNAs in mouse primary adipocytes and human obesity. BMC Endocr Disord 2011; 11:7. [PMID: 21426570 PMCID: PMC3070678 DOI: 10.1186/1472-6823-11-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 03/22/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Adipose tissue abundance relies partly on the factors that regulate adipogenesis, i.e. proliferation and differentiation of adipocytes. While components of the transcriptional program that initiates adipogenesis is well-known, the importance of microRNAs in adipogenesis is less well studied. We thus set out to investigate whether miRNAs would be actively modulated during adipogenesis and obesity. METHODS Several models exist to study adipogenesis in vitro, of which the cell line 3T3-L1 is the most well known, albeit not the most physiologically appropriate. Thus, as an alternative, we produced EXIQON microarray of brown and white primary murine adipocytes (prior to and following differentiation) to yield global profiles of miRNAs. RESULTS We found 65 miRNAs regulated during in vitro adipogenesis in primary adipocytes. We evaluated the similarity of our responses to those found in non-primary cell models, through literature data-mining. When comparing primary adipocyte profiles, with those of cell lines reported in the literature, we found a high degree of difference in 'adipogenesis' regulated miRNAs suggesting that the model systems may not be accurately representing adipogenesis. The expression of 10 adipogenesis-regulated miRNAs were studied using real-time qPCR and then we selected 5 miRNAs, that showed robust expression, were profiled in subcutaneous adipose tissue obtained from 20 humans with a range of body mass indices (BMI, range = 21-48, and all samples have U133+2 Affymetrix profiles provided). Of the miRNAs tested, mir-21 was robustly expressed in human adipose tissue and positively correlated with BMI (R2 = 0.49, p < 0.001). CONCLUSION In conclusion, we provide a preliminary analysis of miRNAs associated with primary cell in vitro adipogenesis and demonstrate that the inflammation-associated miRNA, mir-21 is up-regulated in subcutaneous adipose tissue in human obesity. Further, we provide a novel transcriptomics database of EXIQON and Affymetrix adipocyte profiles to facilitate data mining.
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Affiliation(s)
- Pernille Keller
- Royal Veterinary College, University of London, UK
- Department of Molecular Genetics, Novo Nordisk A/S, DK-2760 Måløv Denmark
| | | | - Natasa Petrovic
- Department of Physiology, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Iain J Gallagher
- Royal Veterinary College, University of London, UK
- Tissue Injury & Repair Group, The Chancellor's Building, University of Edinburgh, EH16 4SB, UK
| | - Jan Nedergaard
- Department of Physiology, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Barbara Cannon
- Royal Veterinary College, University of London, UK
- Department of Physiology, The Wenner-Gren Institute, Stockholm University, Sweden
| | - James A Timmons
- Royal Veterinary College, University of London, UK
- Department of Physiology, The Wenner-Gren Institute, Stockholm University, Sweden
- Department of Molecular Genetics, Novo Nordisk A/S, DK-2760 Måløv Denmark
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Timmons JA. Genes that AKTto determine physiological heterogeneity in response to exercise. Exp Physiol 2011; 96:259-60. [DOI: 10.1113/expphysiol.2010.056234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Davidsen PK, Gallagher IJ, Hartman JW, Tarnopolsky MA, Dela F, Helge JW, Timmons JA, Phillips SM. High responders to resistance exercise training demonstrate differential regulation of skeletal muscle microRNA expression. J Appl Physiol (1985) 2011; 110:309-17. [DOI: 10.1152/japplphysiol.00901.2010] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNA), small noncoding RNA molecules, may regulate protein synthesis, while resistance exercise training (RT) is an efficient strategy for stimulating muscle protein synthesis in vivo. However, RT increases muscle mass, with a very wide range of effectiveness in humans. We therefore determined the expression level of 21 abundant miRNAs to determine whether variation in these miRNAs was able to explain the variation in RT-induced gains in muscle mass. Vastus lateralis biopsies were obtained from the top and bottom ∼20% of responders from 56 young men who undertook a 5 day/wk RT program for 12 wk. Training-induced muscle mass gain was determined by dual-energy X-ray absorptiometry, and fiber size was evaluated by histochemistry. The expression level of each miRNA was quantified using TaqMan-based quantitative PCR, with the analysis carried out in a blinded manner. Gene ontology and target gene profiling were used to predict the potential biological implications. Of the 21 mature miRNAs examined, 17 were stable during RT in both groups. However, miR-378, miR-29a, miR-26a, and miR-451 were differentially expressed between low and high responders. miR-378, miR-29a, and miR-26a were downregulated in low responders and unchanged in high responders, while miR-451 was upregulated only in low responders. Interestingly, the training-induced change in miR-378 abundance was positively correlated with muscle mass gains in vivo. Gene ontology analysis of the target gene list of miR-378, miR-29a, miR-26a, and miR-451, from the weighted cumulative context ranking methodology, indicated that miRNA changes in the low responders may be compensatory, reflecting a failure to “activate” growth and remodeling genes. We report, for the first time, that RT-induced hypertrophy in human skeletal muscle is associated with selected changes in miRNA abundance. Our analysis indicates that miRNAs may play a role in the phenotypic change and pronounced intergroup variation in the RT response.
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Affiliation(s)
- Peter K. Davidsen
- Centre for Healthy Ageing, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej, Denmark
- Lifestyle Research Group, The Royal Veterinary College, University of London, London, United Kingdom; and
| | - Iain J. Gallagher
- Lifestyle Research Group, The Royal Veterinary College, University of London, London, United Kingdom; and
| | | | - Mark A. Tarnopolsky
- Pediatrics and Medicine, McMaster University Medical Centre, Hamilton, Ontario, Canada
| | - Flemming Dela
- Centre for Healthy Ageing, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej, Denmark
| | - Jørn W. Helge
- Centre for Healthy Ageing, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej, Denmark
| | - James A. Timmons
- Centre for Healthy Ageing, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej, Denmark
- Lifestyle Research Group, The Royal Veterinary College, University of London, London, United Kingdom; and
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Abstract
When human skeletal muscle is exposed to exercise training, the outcomes, in terms of physiological adaptation, are unpredictable. The significance of this fact has long been underappreciated, and only recently has progress been made in identifying some of the molecular bases for the heterogeneous response to exercise training. It is not only of great medical importance that some individuals do not substantially physiologically adapt to exercise training, but the study of the heterogeneity itself provides a powerful opportunity to dissect out the genetic and environmental factors that limit adaptation, directly in humans. In the following review I will discuss new developments linking genetic and transcript abundance variability to an individual's potential to improve their aerobic capacity or endurance performance or induce muscle hypertrophy. I will also comment on the idea that certain gene networks may be associated with muscle “adaptability” regardless the stimulus provided.
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Affiliation(s)
- James A Timmons
- Royal Veterinary College, Univ. of London, Camden NW1 0TU, United Kingdom.
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Keller P, Vollaard NBJ, Gustafsson T, Gallagher IJ, Sundberg CJ, Rankinen T, Britton SL, Bouchard C, Koch LG, Timmons JA. A transcriptional map of the impact of endurance exercise training on skeletal muscle phenotype. J Appl Physiol (1985) 2010; 110:46-59. [PMID: 20930125 DOI: 10.1152/japplphysiol.00634.2010] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The molecular pathways that are activated and contribute to physiological remodeling of skeletal muscle in response to endurance exercise have not been fully characterized. We previously reported that ∼800 gene transcripts are regulated following 6 wk of supervised endurance training in young sedentary males, referred to as the training-responsive transcriptome (TRT) (Timmons JA et al. J Appl Physiol 108: 1487-1496, 2010). Here we utilized this database together with data on biological variation in muscle adaptation to aerobic endurance training in both humans and a novel out-bred rodent model to study the potential regulatory molecules that coordinate this complex network of genes. We identified three DNA sequences representing RUNX1, SOX9, and PAX3 transcription factor binding sites as overrepresented in the TRT. In turn, miRNA profiling indicated that several miRNAs targeting RUNX1, SOX9, and PAX3 were downregulated by endurance training. The TRT was then examined by contrasting subjects who demonstrated the least vs. the greatest improvement in aerobic capacity (low vs. high responders), and at least 100 of the 800 TRT genes were differentially regulated, thus suggesting regulation of these genes may be important for improving aerobic capacity. In high responders, proangiogenic and tissue developmental networks emerged as key candidates for coordinating tissue aerobic adaptation. Beyond RNA-level validation there were several DNA variants that associated with maximal aerobic capacity (Vo(₂max)) trainability in the HERITAGE Family Study but these did not pass conservative Bonferroni adjustment. In addition, in a rat model selected across 10 generations for high aerobic training responsiveness, we found that both the TRT and a homologous subset of the human high responder genes were regulated to a greater degree in high responder rodent skeletal muscle. This analysis provides a comprehensive map of the transcriptomic features important for aerobic exercise-induced improvements in maximal oxygen consumption.
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Affiliation(s)
- Pernille Keller
- Translational Biomedicine, Heriot-Watt University, Edinburgh, UK
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Koch LG, Britton SL, Wisloff U, Kainulainen H, Timmons JA. Development of Rat Models for Low and High Response to Exercise Training. Med Sci Sports Exerc 2010. [DOI: 10.1249/01.mss.0000389367.67612.9f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Timmons JA, Knudsen S, Rankinen T, Koch LG, Sarzynski M, Jensen T, Keller P, Scheele C, Vollaard NBJ, Nielsen S, Akerström T, MacDougald OA, Jansson E, Greenhaff PL, Tarnopolsky MA, van Loon LJC, Pedersen BK, Sundberg CJ, Wahlestedt C, Britton SL, Bouchard C. Using molecular classification to predict gains in maximal aerobic capacity following endurance exercise training in humans. J Appl Physiol (1985) 2010; 108:1487-96. [PMID: 20133430 DOI: 10.1152/japplphysiol.01295.2009] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A low maximal oxygen consumption (VO2max) is a strong risk factor for premature mortality. Supervised endurance exercise training increases VO2max with a very wide range of effectiveness in humans. Discovering the DNA variants that contribute to this heterogeneity typically requires substantial sample sizes. In the present study, we first use RNA expression profiling to produce a molecular classifier that predicts VO2max training response. We then hypothesized that the classifier genes would harbor DNA variants that contributed to the heterogeneous VO2max response. Two independent preintervention RNA expression data sets were generated (n=41 gene chips) from subjects that underwent supervised endurance training: one identified and the second blindly validated an RNA expression signature that predicted change in VO2max ("predictor" genes). The HERITAGE Family Study (n=473) was used for genotyping. We discovered a 29-RNA signature that predicted VO2max training response on a continuous scale; these genes contained approximately 6 new single-nucleotide polymorphisms associated with gains in VO2max in the HERITAGE Family Study. Three of four novel candidate genes from the HERITAGE Family Study were confirmed as RNA predictor genes (i.e., "reciprocal" RNA validation of a quantitative trait locus genotype), enhancing the performance of the 29-RNA-based predictor. Notably, RNA abundance for the predictor genes was unchanged by exercise training, supporting the idea that expression was preset by genetic variation. Regression analysis yielded a model where 11 single-nucleotide polymorphisms explained 23% of the variance in gains in VO2max, corresponding to approximately 50% of the estimated genetic variance for VO2max. In conclusion, combining RNA profiling with single-gene DNA marker association analysis yields a strongly validated molecular predictor with meaningful explanatory power. VO2max responses to endurance training can be predicted by measuring a approximately 30-gene RNA expression signature in muscle prior to training. The general approach taken could accelerate the discovery of genetic biomarkers, sufficiently discrete for diagnostic purposes, for a range of physiological and pharmacological phenotypes in humans.
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Affiliation(s)
- James A Timmons
- Panum Institutet and Center for Healthy Ageing, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Stephens NA, Gallagher IJ, Rooyackers O, Skipworth RJ, Tan BH, Marstrand T, Ross JA, Guttridge DC, Lundell L, Fearon KC, Timmons JA. Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia. Genome Med 2010; 2:1. [PMID: 20193046 PMCID: PMC2829926 DOI: 10.1186/gm122] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Revised: 12/09/2009] [Accepted: 01/15/2010] [Indexed: 01/17/2023] Open
Abstract
Background Cancer cachexia is a multi-organ tissue wasting syndrome that contributes to morbidity and mortality in many cancer patients. Skeletal muscle loss represents an established key feature yet there is no molecular understanding of the disease process. In fact, the postulated molecular regulators of cancer cachexia originate largely from pre-clinical models and it is unclear how these translate to the clinical environment. Methods Rectus abdominis muscle biopsies were obtained from 65 upper gastrointestinal (UGI) cancer patients during open surgery and RNA profiling was performed on a subset of this cohort (n = 21) using the Affymetrix U133+2 platform. Quantitative analysis revealed a gene signature, which underwent technical validation and independent confirmation in a separate clinical cohort. Results Quantitative significance analysis of microarrays produced an 83-gene signature that was able to identify patients with greater than 5% weight loss, while this molecular profile was unrelated to markers of systemic inflammation. Selected genes correlating with weight loss were validated using quantitative real-time PCR and independently studied as general cachexia biomarkers in diaphragm and vastus lateralis from a second cohort (n = 13; UGI cancer patients). CaMKIIβ correlated positively with weight loss in all muscle groups and CaMKII protein levels were elevated in rectus abdominis. TIE1 was also positively associated with weight loss in both rectus abdominis and vastus lateralis muscle groups while other biomarkers demonstrated tissue-specific expression patterns. Candidates selected from the pre-clinical literature, including FOXO protein and ubiquitin E3 ligases, were not related to weight loss in this human clinical study. Furthermore, promoter analysis identified that the 83 weight loss-associated genes had fewer FOXO binding sites than expected by chance. Conclusion We were able to discover and validate new molecular biomarkers of human cancer cachexia. The exercise activated genes CaMKIIβ and TIE1 related positively to weight-loss across muscle groups, indicating that this cachexia signature is not simply due to patient inactivity. Indeed, excessive CaMKIIβ activation is a potential mechanism for reduced muscle protein synthesis. Our genomics analysis also supports the view that the available preclinical models do not accurately reflect the molecular characteristics of human muscle from cancer cachexia patients.
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Affiliation(s)
- Nathan A Stephens
- Department of Clinical and Surgical Sciences (Surgery), School of Clinical Sciences and Community Health, University of Edinburgh, EH16 4SB, UK.
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Petrovic N, Walden TB, Shabalina IG, Timmons JA, Cannon B, Nedergaard J. Chronic peroxisome proliferator-activated receptor gamma (PPARgamma) activation of epididymally derived white adipocyte cultures reveals a population of thermogenically competent, UCP1-containing adipocytes molecularly distinct from classic brown adipocytes. J Biol Chem 2009; 285:7153-64. [PMID: 20028987 DOI: 10.1074/jbc.m109.053942] [Citation(s) in RCA: 1011] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The recent insight that brown adipocytes and muscle cells share a common origin and in this respect are distinct from white adipocytes has spurred questions concerning the origin and molecular characteristics of the UCP1-expressing cells observed in classic white adipose tissue depots under certain physiological or pharmacological conditions. Examining precursors from the purest white adipose tissue depot (epididymal), we report here that chronic treatment with the peroxisome proliferator-activated receptor gamma agonist rosiglitazone promotes not only the expression of PGC-1alpha and mitochondriogenesis in these cells but also a norepinephrine-augmentable UCP1 gene expression in a significant subset of the cells, providing these cells with a genuine thermogenic capacity. However, although functional thermogenic genes are expressed, the cells are devoid of transcripts for the novel transcription factors now associated with classic brown adipocytes (Zic1, Lhx8, Meox2, and characteristically PRDM16) or for myocyte-associated genes (myogenin and myomirs (muscle-specific microRNAs)) and retain white fat characteristics such as Hoxc9 expression. Co-culture experiments verify that the UCP1-expressing cells are not proliferating classic brown adipocytes (adipomyocytes), and these cells therefore constitute a subset of adipocytes ("brite" adipocytes) with a developmental origin and molecular characteristics distinguishing them as a separate class of cells.
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Affiliation(s)
- Natasa Petrovic
- Wenner-Gren Institute, The Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
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Vollaard NBJ, Constantin-Teodosiu D, Fredriksson K, Rooyackers O, Jansson E, Greenhaff PL, Timmons JA, Sundberg CJ. Systematic analysis of adaptations in aerobic capacity and submaximal energy metabolism provides a unique insight into determinants of human aerobic performance. J Appl Physiol (1985) 2009; 106:1479-86. [PMID: 19196912 DOI: 10.1152/japplphysiol.91453.2008] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
It has not been established which physiological processes contribute to endurance training-related changes (Delta) in aerobic performance. For example, the relationship between intramuscular metabolic responses at the intensity used during training and improved human functional capacity has not been examined in a longitudinal study. In the present study we hypothesized that improvements in aerobic capacity (Vo(2max)) and metabolic control would combine equally to explain enhanced aerobic performance. Twenty-four sedentary males (24 +/- 2 yr; 1.81 +/- 0.08 m; 76.6 +/- 11.3 kg) undertook supervised cycling training (45 min at 70% of pretraining Vo(2max)) 4 times/wk for 6 wk. Performance was determined using a 15-min cycling time trial, and muscle biopsies were taken before and after a 10-min cycle at 70% of pretraining Vo(2max) to quantify substrate metabolism. Substantial interindividual variability in training-induced adaptations was observed for most parameters, yet "low responders" for DeltaVo(2max) were not consistently low responders for other variables. While Vo(2max) and time trial performance were related at baseline (r(2) = 0.80, P < 0.001), the change in Vo(2max) was completely unrelated to the change in aerobic performance. The maximal parameters DeltaVe(max) and DeltaVeq(max) (DeltaVe/Vo(2max)) accounted for 64% of the variance in DeltaVo(2max) (P < 0.001), whereas Deltaperformance was related to changes in the submaximal parameters Veq(submax) (r(2) = 0.33; P < 0.01), muscle Deltalactate (r(2) = 0.32; P < 0.01), and Deltaacetyl-carnitine (r(2) = 0.29; P < 0.05). This study demonstrates that improvements in high-intensity aerobic performance in humans are not related to altered maximal oxygen transport capacity. Altered muscle metabolism may provide the link between training stimulus and improved performance, but metabolic parameters do not change in a manner that relates to aerobic capacity changes.
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Affiliation(s)
- Niels B J Vollaard
- The Wenner-Gren Institute, Arrhenius Laboratories, Stockholm Univ., Sweden
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Babraj JA, Vollaard NBJ, Keast C, Guppy FM, Cottrell G, Timmons JA. Extremely short duration high intensity interval training substantially improves insulin action in young healthy males. BMC Endocr Disord 2009; 9:3. [PMID: 19175906 PMCID: PMC2640399 DOI: 10.1186/1472-6823-9-3] [Citation(s) in RCA: 239] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 01/28/2009] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Traditional high volume aerobic exercise training reduces cardiovascular and metabolic disease risk but involves a substantial time commitment. Extremely low volume high-intensity interval training (HIT) has recently been demonstrated to produce improvements to aerobic function, but it is unknown whether HIT has the capacity to improve insulin action and hence glycemic control. METHODS Sixteen young men (age: 21 +/- 2 y; BMI: 23.7 +/- 3.1 kg x m-2; VO2peak: 48 +/- 9 ml x kg-1 x min-1) performed 2 weeks of supervised HIT comprising of a total of 15 min of exercise (6 sessions; 4-6 x 30-s cycle sprints per session). Aerobic performance (250-kJ self-paced cycling time trial), and glucose, insulin and NEFA responses to a 75-g oral glucose load (oral glucose tolerance test; OGTT) were determined before and after training. RESULTS Following 2 weeks of HIT, the area under the plasma glucose, insulin and NEFA concentration-time curves were all reduced (12%, 37%, 26% respectively, all P < 0.001). Fasting plasma insulin and glucose concentrations remained unchanged, but there was a tendency for reduced fasting plasma NEFA concentrations post-training (pre: 350 +/- 36 v post: 290 +/- 39 micromol x l-1, P = 0.058). Insulin sensitivity, as measured by the Cederholm index, was improved by 23% (P < 0.01), while aerobic cycling performance improved by approximately 6% (P < 0.01). CONCLUSION The efficacy of a high intensity exercise protocol, involving only ~250 kcal of work each week, to substantially improve insulin action in young sedentary subjects is remarkable. This novel time-efficient training paradigm can be used as a strategy to reduce metabolic risk factors in young and middle aged sedentary populations who otherwise would not adhere to time consuming traditional aerobic exercise regimes.
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Affiliation(s)
- John A Babraj
- Translational Biomedicine, School of Engineering and Physical Sciences, Heriot-Watt University Edinburgh, Scotland, UK
| | - Niels BJ Vollaard
- Translational Biomedicine, School of Engineering and Physical Sciences, Heriot-Watt University Edinburgh, Scotland, UK
| | - Cameron Keast
- Translational Biomedicine, School of Engineering and Physical Sciences, Heriot-Watt University Edinburgh, Scotland, UK
| | - Fergus M Guppy
- Translational Biomedicine, School of Engineering and Physical Sciences, Heriot-Watt University Edinburgh, Scotland, UK
| | - Greg Cottrell
- Translational Biomedicine, School of Engineering and Physical Sciences, Heriot-Watt University Edinburgh, Scotland, UK
| | - James A Timmons
- Translational Biomedicine, School of Engineering and Physical Sciences, Heriot-Watt University Edinburgh, Scotland, UK
- The Wenner-Gren Institute, Arrhenius Laboratories, Stockholm University, Sweden
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Abstract
Genome sequencing projects have provided the substrate for an unimaginable number of biological experiments. Further, genomic technologies such as microarrays and quantitative and exquisitely sensitive techniques such as real-time quantitative polymerase chain reaction have made it possible to reliably generate millions of data points per experiment. The data can be high quality and yield entirely new insights into how gene expression is coordinated under complex physiological situations. It can also be that the data and interpretation are meaningless because of a lack of physiological context or experimental control. Thus, functional genomics is now being applied to study metabolic physiology with varying degrees of success. From the genome sequencing projects we also have the information needed to design chemical tools that can knock down a gene transcript, even distinguishing between splice variants in mammalian cells. Use of such technologies, inspired by nature's endogenous RNAi mechanism-microRNA targeting, comes with significant caveats. While the discipline of Pharmacology taught us last century that inhibitor action specificity is dependent on the concentration used, these experiences have been ignored by users of siRNA technologies. What we provide in this chapter is some considerations and observations from functional genomic studies. We are largely concerned with the phase that follows a microarray study, where a candidate gene is selected for manipulation in a system that is considered to be simpler than the in vivo mammalian tissue and thus the methods discussed largely apply to this cell biology phase. We apologize for not referring to all relevant publications and for any technical considerations we have also failed to factor into our discussion.
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Affiliation(s)
- Camilla Scheele
- The Centre of Inflammation and Metabolism, Department of Infectious Diseases and CMRC, Rigshospitalet, The Faculty of Health Sciences, University of Copenhagen, Denmark
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Walden TB, Timmons JA, Keller P, Nedergaard J, Cannon B. Distinct expression of muscle-specific microRNAs (myomirs) in brown adipocytes. J Cell Physiol 2008; 218:444-9. [PMID: 18937285 DOI: 10.1002/jcp.21621] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs, a novel class of post-transcriptional gene regulators, have been demonstrated to be involved in several cellular processes regulating the expression of protein-coding genes. Here we examine murine white and brown primary cell cultures for differential expression of miRNAs. The adipogenesis-related miRNA miR-143 was highly expressed in mature white adipocytes but was low in mature brown adipocytes. Three classical "myogenic" miRNAs miR-1, miR-133a and miR-206 were absent from white adipocytes but were specifically expressed both in brown pre- and mature adipocytes, reinforcing the concept that brown adipocytes and myocytes derive from a common cell lineage that specifies energy-dissipating cells. Augmentation of adipocyte differentiation status with norepinephrine or rosiglitazone did not affect the expression of the above miRNAs, the expression levels of which were thus innately regulated. However, expression of the miRNA miR-455 was enhanced during brown adipocyte differentiation, similarly to the expression pattern of the brown adipocyte differentiation marker UCP1. In conclusion, miRNAs are differentially expressed in white and brown adipocytes and may be important in defining the common precursor cell for myocytes and brown adipocytes and thus have distinct roles in energy-storing versus energy-dissipating cells.
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Affiliation(s)
- Tomas B Walden
- The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, Stockholm, Sweden.
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