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Drummer DJ, Lavin KM, Graham ZA, O'Bryan SM, McAdam JS, Lixandrão ME, Seay R, Aban I, Siegel HJ, Ghanem E, Singh JA, Bonfitto A, Antone J, Reiman R, Hutchins E, Van Keuren-Jensen K, Schutzler SE, Barnes CL, Ferrando AA, Bridges SL, Bamman MM. Muscle transcriptomic circuits linked to periarticular physiology in end-stage osteoarthritis. Physiol Genomics 2022; 54:501-513. [PMID: 36278270 PMCID: PMC9762959 DOI: 10.1152/physiolgenomics.00092.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 02/01/2023] Open
Abstract
The ability of individuals with end-stage osteoarthritis (OA) to functionally recover from total joint arthroplasty is highly inconsistent. The molecular mechanisms driving this heterogeneity have yet to be elucidated. Furthermore, OA disproportionately impacts females, suggesting a need for identifying female-specific therapeutic targets. We profiled the skeletal muscle transcriptome in females with end-stage OA (n = 20) undergoing total knee or hip arthroplasty using RNA-Seq. Single-gene differential expression (DE) analyses tested for DE genes between skeletal muscle overlaying the surgical (SX) joint and muscle from the contralateral (CTRL) leg. Network analyses were performed using Pathway-Level Information ExtractoR (PLIER) to summarize genes into latent variables (LVs), i.e., gene circuits, and link them to biological pathways. LV differences in SX versus CTRL muscle and across sources of muscle tissue (vastus medialis, vastus lateralis, or tensor fascia latae) were determined with ANOVA. Linear models tested for associations between LVs and muscle phenotype on the SX side (inflammation, function, and integrity). DE analysis revealed 360 DE genes (|Log2 fold-difference| ≥ 1, FDR ≤ 0.05) between the SX and CTRL limbs, many associated with inflammation and lipid metabolism. PLIER analyses revealed circuits associated with protein degradation and fibro-adipogenic cell gene expression. Muscle inflammation and function were linked to an LV associated with endothelial cell gene expression highlighting a potential regulatory role of endothelial cells within skeletal muscle. These findings may provide insight into potential therapeutic targets to improve OA rehabilitation before and/or following total joint replacement.
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Affiliation(s)
- Devin J Drummer
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kaleen M Lavin
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Florida Institute for Human and Machine Cognition, Pensacola, Florida
| | - Zachary A Graham
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Florida Institute for Human and Machine Cognition, Pensacola, Florida
- Birmingham VA Medical Center, Birmingham, Alabama
| | - Samia M O'Bryan
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jeremy S McAdam
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Florida Institute for Human and Machine Cognition, Pensacola, Florida
| | - Manoel E Lixandrão
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Regina Seay
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Inmaculada Aban
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Herrick J Siegel
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Orthopaedic Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Elie Ghanem
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Orthopaedic Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jasvinder A Singh
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Birmingham VA Medical Center, Birmingham, Alabama
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Comprehensive Arthritis, Musculoskeletal, Bone, and Autoimmunity Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Anna Bonfitto
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Elizabeth Hutchins
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, Arizona
| | | | - Scott E Schutzler
- Department of Geriatrics and Center for Translational Research in Aging and Longevity, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - C Lowry Barnes
- Department of Orthopaedic Surgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Arny A Ferrando
- Department of Geriatrics and Center for Translational Research in Aging and Longevity, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - S Louis Bridges
- Department of Medicine, Hospital for Special Surgery, New York, New York
- Division of Rheumatology, Weill Cornell Medical Center, New York, New York
| | - Marcas M Bamman
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Florida Institute for Human and Machine Cognition, Pensacola, Florida
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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] [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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Dulhunty AF, Wei-LaPierre L, Casarotto MG, Beard NA. Core skeletal muscle ryanodine receptor calcium release complex. Clin Exp Pharmacol Physiol 2017; 44:3-12. [PMID: 27696487 DOI: 10.1111/1440-1681.12676] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 12/15/2022]
Abstract
The core skeletal muscle ryanodine receptor (RyR1) calcium release complex extends through three compartments of the muscle fibre, linking the extracellular environment through the cytoplasmic junctional gap to the lumen of the internal sarcoplasmic reticulum (SR) calcium store. The protein complex is essential for skeletal excitation-contraction (EC)-coupling and skeletal muscle function. Its importance is highlighted by perinatal death if any one of the EC-coupling components are missing and by myopathies associated with mutation of any of the proteins. The proteins essential for EC-coupling include the DHPR α1S subunit in the transverse tubule membrane, the DHPR β1a subunit in the cytosol and the RyR1 ion channel in the SR membrane. The other core proteins are triadin and junctin and calsequestrin, associated mainly with SR. These SR proteins are not essential for survival but exert structural and functional influences that modify the gain of EC-coupling and maintain normal muscle function. This review summarises our current knowledge of the individual protein/protein interactions within the core complex and their overall contribution to EC-coupling. We highlight significant areas that provide a continuing challenge for the field. Additional important components of the Ca2+ release complex, such as FKBP12, calmodulin, S100A1 and Stac3 are identified and reviewed elsewhere.
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Affiliation(s)
- Angela F Dulhunty
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Lan Wei-LaPierre
- Department of Physiology and Pharmacology, University of Rochester Medical Center, Rochester, NY, USA
| | - Marco G Casarotto
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Nicole A Beard
- Health Research Institute, University of Canberra, Canberra, ACT, Australia
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