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Lovett J, McColl RS, Durcan P, Vechetti I, Myburgh KH. Analysis of plasma-derived small extracellular vesicle characteristics and microRNA cargo following exercise-induced skeletal muscle damage in men. Physiol Rep 2024; 12:e70056. [PMID: 39304515 PMCID: PMC11415274 DOI: 10.14814/phy2.70056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/23/2024] [Accepted: 09/02/2024] [Indexed: 09/22/2024] Open
Abstract
Extracellular vesicle (EV) cargo is known to change in response to stimuli such as muscle damage. This study aimed to assess particle size, concentration and microRNA (miR) content within small EV-enriched separations prepared from human blood taken before and after unaccustomed eccentric-biased exercise-induced muscle damage. Nine male volunteers underwent plyometric jumping and downhill running, with blood samples taken at baseline, 2, and 24 h post-exercise. EVs were separated using size exclusion chromatography (SEC) and their characteristics evaluated by nanoparticle tracking. No changes in EV size or concentration were seen following the muscle-damaging exercise. Small RNA sequencing identified 240 miRs to be consistently present within the EVs. RT-qPCR analysis was performed: specifically, for known muscle-enriched/important miRs, including miR-1, -206, -133a, -133b, -31, -208b, -451a, -486 and - 499 and the immune-important miR-21, -146a and - 155. Notably, none of the immune-important miRs within the EVs tested changed in response to the muscle damage. Of the muscle-associated miRs tested, only the levels of miR-31-5p were seen to change with decreased levels at 24 h compared to baseline and 2 h, indicating involvement in the damage response. These findings shed light on the dynamic role of EV miRs in response to exercise-induced muscle damage.
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Affiliation(s)
- Jason Lovett
- Department of Physiological SciencesStellenbosch UniversityStellenboschSouth Africa
| | - Rhys S. McColl
- Department of Physiological SciencesStellenbosch UniversityStellenboschSouth Africa
| | - Peter Durcan
- Department of Physiological SciencesStellenbosch UniversityStellenboschSouth Africa
| | - Ivan Vechetti
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Kathryn H. Myburgh
- Department of Physiological SciencesStellenbosch UniversityStellenboschSouth Africa
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2
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Ji E, Pandey PR, Martindale JL, Yang X, Yang JH, Tsitsipatis D, Shin CH, Piao Y, Fan J, Mazan-Mamczarz K, Banskota N, De S, Gorospe M. FUS-Mediated Inhibition of Myogenesis Elicited by Suppressing TNNT1 Production. Mol Cell Biol 2024; 44:391-409. [PMID: 39133076 PMCID: PMC11376412 DOI: 10.1080/10985549.2024.2383296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 08/13/2024] Open
Abstract
Myogenesis is a highly orchestrated process whereby muscle precursor cells, myoblasts, develop into muscle fibers to form skeletal muscle during embryogenesis and regenerate adult muscle. Here, we studied the RNA-binding protein FUS (fused in sarcoma), which has been implicated in muscular and neuromuscular pathologies but is poorly characterized in myogenesis. Given that FUS levels declined in human and mouse models of skeletal myogenesis, and that silencing FUS enhanced myogenesis, we hypothesized that FUS might be a repressor of myogenic differentiation. Interestingly, overexpression of FUS delayed myogenesis, accompanied by slower production of muscle differentiation markers. To identify the mechanisms through which FUS inhibits myogenesis, we uncovered RNA targets of FUS by ribonucleoprotein immunoprecipitation (RIP) followed by RNA-sequencing (RNA-seq) analysis. Stringent selection of the bound transcripts uncovered Tnnt1 mRNA, encoding troponin T1 (TNNT1), as a major effector of FUS influence on myogenesis. We found that in myoblasts, FUS retained Tnnt1 mRNA in the nucleus, preventing TNNT1 expression; however, reduction of FUS during myogenesis or by silencing FUS released Tnnt1 mRNA for export to the cytoplasm, enabling TNNT1 translation and promoting myogenesis. We propose that FUS inhibits myogenesis by suppressing TNNT1 expression through a mechanism of nuclear Tnnt1 mRNA retention.
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Affiliation(s)
- Eunbyul Ji
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Chang Hoon Shin
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Jinshui Fan
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Nirad Banskota
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
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3
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Seco-Cervera M, Ibáñez-Cabellos JS, Pallardo FV, García-Giménez JL, Aulinas A, Martel-Duguech L, Webb SM, Valassi E. Circulating miR-28-5p is overexpressed in patients with sarcopenia despite long-term remission of Cushing's syndrome: a pilot study. Front Endocrinol (Lausanne) 2024; 15:1410080. [PMID: 39086897 PMCID: PMC11289718 DOI: 10.3389/fendo.2024.1410080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/21/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Patients with Cushing's syndrome (CS) in remission show sustained fatigue, myopathy, and an increased prevalence of sarcopenia. The mechanisms that determine these persistent muscle problems are not well known. We aimed to identify circulating microRNAs (miRNAs) with differential expression that could be potential biomarkers for the diagnosis and/or prognosis in CS. Patients and methods Thirty-six women in sustained remission for 13 ± 7 years (mean ± SD) from CS, with a median age (IQ range) of 51 (45.2-60) years and mean ± SD BMI of 27 ± 4 Kg/m2, and 36 matched healthy controls were investigated. In 7 patients sarcopenia was present according to the European Working Group on Sarcopenia in Older People (EWGSOP) criteria. Small RNA libraries were generated and indexed using a modified Illumina TruSeq small RNA-sequencing protocol. MiRNAs were identified in plasma using bioinformatic analysis, and validation was carried out using RT-qPCR. For the validation, Taqman probes were performed on QuantStudio 5 equipment (Applied Biosystems). Results In a first discovery group using RNA-sequencing, plasma samples of 18 CS patients and 18 healthy subjects were investigated; circulating miR-28-5p, miR-495-3p and miR-654-5p were upregulated in CS patients as compared with controls (p<0.05). In a validation study of the 3 upregulated miRNAs in 36 patients and 26 controls, no differences were observed by RT-qPCR; however, the expression of circulating miR-28-5p was upregulated in CS patients with sarcopenia as compared with those without (AUC for fold-change in the ROC analysis, 0.798; p=0.0156). The optimized cut-off value for miR-28-5p to identify CS patients with sarcopenia was 3.80, which yielded a sensitivity of 86% and a specificity of 69%. Conclusion MiR-28-5p, a muscle-specific microRNA involved in myotube proliferation and differentiation in vivo, may serve as an independent non-invasive biomarker for identifying CS patients at high-risk of sarcopenia despite biochemical remission.
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Affiliation(s)
- Marta Seco-Cervera
- Unit 733, Centre for Biomedical Network Research on Rare Diseases [CIBERER- Instituto de Salud Carlos III (ISCIII)], Madrid, Spain
- Mixed Unit for rare diseases INCLIVA-CIPF, INCLIVA Health Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | | | - Federico V. Pallardo
- Unit 733, Centre for Biomedical Network Research on Rare Diseases [CIBERER- Instituto de Salud Carlos III (ISCIII)], Madrid, Spain
- Mixed Unit for rare diseases INCLIVA-CIPF, INCLIVA Health Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - José-Luis García-Giménez
- Unit 733, Centre for Biomedical Network Research on Rare Diseases [CIBERER- Instituto de Salud Carlos III (ISCIII)], Madrid, Spain
- Mixed Unit for rare diseases INCLIVA-CIPF, INCLIVA Health Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Anna Aulinas
- Department of Endocrinology, Hospital S Pau, Research Center for Pituitary Diseases, Institut de Recerca Sant Pau (IIB-Sant Pau), Barcelona, Spain
- CIBERER Unit 747, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - Luciana Martel-Duguech
- Department of Endocrinology, Hospital S Pau, Research Center for Pituitary Diseases, Institut de Recerca Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Susan M. Webb
- Department of Endocrinology, Hospital S Pau, Research Center for Pituitary Diseases, Institut de Recerca Sant Pau (IIB-Sant Pau), Barcelona, Spain
- CIBERER Unit 747, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, Univ Autonoma Barcelona, Bellaterra, Spain
| | - Elena Valassi
- CIBERER Unit 747, Instituto de Salud Carlos III, Madrid, Spain
- Endocrinology and Nutrition Department, Germans Trias i Pujol Hospital and Research Institute, Badalona, Spain
- School of Medicine, Universitat Internacional de Catalunya (UIC), Sant Cugat del Vallès, Barcelona, Spain
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Yun SH, Lee DY, Lee J, Mariano E, Choi Y, Park J, Han D, Kim JS, Hur SJ. Current Research, Industrialization Status, and Future Perspective of Cultured Meat. Food Sci Anim Resour 2024; 44:326-355. [PMID: 38764517 PMCID: PMC11097034 DOI: 10.5851/kosfa.2024.e13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 05/21/2024] Open
Abstract
Expectations for the industrialization of cultured meat are growing due to the increasing support from various sectors, such as the food industry, animal welfare organizations, and consumers, particularly vegetarians, but the progress of industrialization is slower than initially reported. This review analyzes the main issues concerning the industrialization of cultured meat, examines research and media reports on the development of cultured meat to date, and presents the current technology, industrialization level, and prospects for cultured meat. Currently, over 30 countries have companies industrializing cultured meat, and around 200 companies that are developing or industrializing cultured meat have been surveyed globally. By country, the United States has over 50 companies, accounting for more than 20% of the total. Acquiring animal cells, developing cell lines, improving cell proliferation, improving the efficiency of cell differentiation and muscle production, or developing cell culture media, including serum-free media, are the major research themes related to the development of cultured meat. In contrast, the development of devices, such as bioreactors, which are crucial in enabling large-scale production, is relatively understudied, and few of the many companies invested in the development of cultured meat have presented products for sale other than prototypes. In addition, because most information on key technologies is not publicly available, it is not possible to determine the level of technology in the companies, and it is surmised that the technology of cultured meat-related startups is not high. Therefore, further research and development are needed to promote the full-scale industrialization of cultured meat.
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Affiliation(s)
- Seung Hyeon Yun
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Da Young Lee
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Juhyun Lee
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Ermie Mariano
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Yeongwoo Choi
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Jinmo Park
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Dahee Han
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Jin Soo Kim
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Sun Jin Hur
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
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Yun SH, Lee DY, Lee SY, Lee J, Mariano EJ, Joo ST, Choi I, Choi JS, Kim GD, Hur SJ. Improved culture procedure for bovine muscle satellite cells for cultured meat. Food Res Int 2023; 174:113660. [PMID: 37981377 DOI: 10.1016/j.foodres.2023.113660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023]
Abstract
Many researchers and companies around the world are reported to have developed cultured meat, but their specific techniques have rarely been disclosed. Thus, the purpose of this study is to provide an improved procedure for cultured meat. There are four major steps in this cultured meat production: muscle cell isolation, proliferation, differentiation, and validation. The improved isolation enabled the efficient removal of unnecessary cells and tissues compared to previous procedures. In addition, proper use of basal media can improve the proliferation efficiency by about 2-fold. During the differentiation process, improved procedure was performed by using 10 % horse serum-containing media after 3 days of initial differentiation for myotube induction. This method demonstrated significantly enhanced myotube formation, up to 2.6-fold increase in area and up to 1.9-fold increase in fusion index compared to the previous method. This study provides a simple, improved procedure to enable more effective cultured meat production compared to previous procedures and is expected to help produce inexpensive and safe cultured meat.
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Affiliation(s)
- Seung Hyeon Yun
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Da Young Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Seung Yun Lee
- Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Juhyun Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Ermie Jr Mariano
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Seon-Tea Joo
- Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Jung Seok Choi
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Gap-Don Kim
- Graduate School of International Agricultural Technology, Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Sun Jin Hur
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea.
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Mierzejewski B, Pulik Ł, Grabowska I, Sibilska A, Ciemerych MA, Łęgosz P, Brzoska E. Coding and noncoding RNA profile of human heterotopic ossifications - Risk factors and biomarkers. Bone 2023; 176:116883. [PMID: 37597797 DOI: 10.1016/j.bone.2023.116883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Heterotopic ossification (HO) means the formation of bone in muscles and soft tissues, such as ligaments or tendons. HO could have a genetic history or develop after a traumatic event, as a result of muscle injury, fractures, burns, surgery, or neurological disorders. Many lines of evidence suggest that the formation of HO is related to the pathological differentiation of stem or progenitor cells present within soft tissues or mobilized from the bone marrow. The cells responsible for the initiation and progression of HO are generally called HO precursor cells. The exact mechanisms behind the development of HO are not fully understood. However, several factors have been identified as potential contributors. For example, local tissue injury and inflammation disturb soft tissue homeostasis. Inflammatory cells release growth factors and cytokines that promote osteogenic or chondrogenic differentiation of HO precursor cells. The bone morphogenetic protein (BMP) is one of the main factors involved in the development of HO. In this study, next-generation sequencing (NGS) and RT-qPCR were performed to analyze the differences in mRNA, miRNA, and lncRNA expression profiles between muscles, control bone samples, and HO samples coming from patients who underwent total hip replacement (THR). As a result, crucial changes in the level of gene expression between HO and healthy tissues were identified. The bioinformatic analysis allowed to describe the processes most severely impacted, as well as genes which level differed the most significantly between HO and control samples. Our analysis showed that the level of transcripts involved in leukocyte migration, differentiation, and activation, as well as markers of chronic inflammatory diseases, that is, miR-148, increased in HO, as compared to muscle. Furthermore, the levels of miR-195 and miR-143, which are involved in angiogenesis, were up-regulated in HO, as compared to bone. Thus, we suggested that inflammation and angiogenesis play an important role in HO formation. Importantly, we noticed that HO is characterized by a higher level of TLR3 expression, compared to muscle and bone. Thus, we suggest that infection may also be a risk factor in HO development. Furthermore, an increased level of transcripts coding proteins involved in osteogenesis and signaling pathways, such as ALPL, SP7, BGLAP, BMP8A, BMP8B, SMPD3 was noticed in HO, as compared to muscles. Interestingly, miR-99b, miR-146, miR-204, and LINC00320 were up-regulated in HO, comparing to muscles and bone. Therefore, we suggested that these molecules could be important biomarkers of HO formation and a potential target for therapies.
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Affiliation(s)
- Bartosz Mierzejewski
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096 Warsaw, Poland
| | - Łukasz Pulik
- Department of Orthopedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005 Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096 Warsaw, Poland
| | - Aleksandra Sibilska
- Department of Orthopedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005 Warsaw, Poland
| | - Maria Anna Ciemerych
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096 Warsaw, Poland
| | - Paweł Łęgosz
- Department of Orthopedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005 Warsaw, Poland.
| | - Edyta Brzoska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096 Warsaw, Poland.
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Muñoz-Braceras S, Pinal-Fernandez I, Casal-Dominguez M, Pak K, Milisenda JC, Lu S, Gadina M, Naz F, Gutierrez-Cruz G, Dell’Orso S, Torres-Ruiz J, Grau-Junyent JM, Selva-O’Callaghan A, Paik JJ, Albayda J, Christopher-Stine L, Lloyd TE, Corse AM, Mammen AL. Identification of Unique microRNA Profiles in Different Types of Idiopathic Inflammatory Myopathy. Cells 2023; 12:2198. [PMID: 37681930 PMCID: PMC10487266 DOI: 10.3390/cells12172198] [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: 07/16/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
Dermatomyositis (DM), antisynthetase syndrome (AS), immune-mediated necrotizing myopathy (IMNM), and inclusion body myositis (IBM) are four major types of idiopathic inflammatory myopathy (IIM). Muscle biopsies from each type of IIM have unique transcriptomic profiles. MicroRNAs (miRNAs) target messenger RNAs (mRNAs), thereby regulating their expression and modulating transcriptomic profiles. In this study, 18 DM, 12 IMNM, 6 AS, 6 IBM, and 6 histologically normal muscle biopsies underwent miRNA profiling using the NanoString nCounter system. Eleven miRNAs were exclusively differentially expressed in DM compared to controls, seven miRNAs were only differentially expressed in AS, and nine miRNAs were specifically upregulated in IBM. No differentially expressed miRNAs were identified in IMNM. We also analyzed miRNA-mRNA associations to identify putative targets of differentially expressed miRNAs. In DM and AS, these were predominantly related to inflammation and cell cycle progression. Moreover, our analysis showed an association between miR-30a-3p, miR-30e-3p, and miR-199b-5p downregulation in DM and the upregulation of target genes induced by type I interferon. In conclusion, we show that muscle biopsies from DM, AS, and IBM patients have unique miRNA signatures and that these miRNAs might play a role in regulating the expression of genes known to be involved in IIM pathogenesis.
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Affiliation(s)
- Sandra Muñoz-Braceras
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
| | - Iago Pinal-Fernandez
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
| | - Maria Casal-Dominguez
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
| | - Katherine Pak
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
| | - José César Milisenda
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Muscle Research Unit, Internal Medicine Service, Hospital Clinic de Barcelona, 08036 Barcelona, Spain;
- CIBERER, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Shajia Lu
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (S.L.); (M.G.)
| | - Massimo Gadina
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (S.L.); (M.G.)
| | - Faiza Naz
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.N.); (G.G.-C.)
| | - Gustavo Gutierrez-Cruz
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.N.); (G.G.-C.)
| | - Stefania Dell’Orso
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.N.); (G.G.-C.)
| | - Jiram Torres-Ruiz
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Josep Maria Grau-Junyent
- Muscle Research Unit, Internal Medicine Service, Hospital Clinic de Barcelona, 08036 Barcelona, Spain;
- CIBERER, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Albert Selva-O’Callaghan
- Systemic Autoimmune Diseases Unit, Vall d’Hebron General Hospital, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
| | - Julie J. Paik
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (J.J.P.); (J.A.)
| | - Jemima Albayda
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (J.J.P.); (J.A.)
| | - Lisa Christopher-Stine
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (J.J.P.); (J.A.)
| | - Thomas E. Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
| | - Andrea M. Corse
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
| | - Andrew L. Mammen
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (J.J.P.); (J.A.)
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8
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Pomella S, Danielli SG, Alaggio R, Breunis WB, Hamed E, Selfe J, Wachtel M, Walters ZS, Schäfer BW, Rota R, Shipley JM, Hettmer S. Genomic and Epigenetic Changes Drive Aberrant Skeletal Muscle Differentiation in Rhabdomyosarcoma. Cancers (Basel) 2023; 15:2823. [PMID: 37345159 DOI: 10.3390/cancers15102823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Rhabdomyosarcoma (RMS), the most common soft-tissue sarcoma in children and adolescents, represents an aberrant form of skeletal muscle differentiation. Both skeletal muscle development, as well as regeneration of adult skeletal muscle are governed by members of the myogenic family of regulatory transcription factors (MRFs), which are deployed in a highly controlled, multi-step, bidirectional process. Many aspects of this complex process are deregulated in RMS and contribute to tumorigenesis. Interconnected loops of super-enhancers, called core regulatory circuitries (CRCs), define aberrant muscle differentiation in RMS cells. The transcriptional regulation of MRF expression/activity takes a central role in the CRCs active in skeletal muscle and RMS. In PAX3::FOXO1 fusion-positive (PF+) RMS, CRCs maintain expression of the disease-driving fusion oncogene. Recent single-cell studies have revealed hierarchically organized subsets of cells within the RMS cell pool, which recapitulate developmental myogenesis and appear to drive malignancy. There is a large interest in exploiting the causes of aberrant muscle development in RMS to allow for terminal differentiation as a therapeutic strategy, for example, by interrupting MEK/ERK signaling or by interfering with the epigenetic machinery controlling CRCs. In this review, we provide an overview of the genetic and epigenetic framework of abnormal muscle differentiation in RMS, as it provides insights into fundamental mechanisms of RMS malignancy, its remarkable phenotypic diversity and, ultimately, opportunities for therapeutic intervention.
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Affiliation(s)
- Silvia Pomella
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS Istituto Ospedale Pediatrico Bambino Gesu, Viale San Paolo 15, 00146 Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Sara G Danielli
- Department of Oncology and Children's Research Center, University Children's Hospital of Zurich, 8032 Zürich, Switzerland
| | - Rita Alaggio
- Department of Pathology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Viale San Paolo 15, 00146 Rome, Italy
| | - Willemijn B Breunis
- Department of Oncology and Children's Research Center, University Children's Hospital of Zurich, 8032 Zürich, Switzerland
| | - Ebrahem Hamed
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, 79106 Freiburg, Germany
| | - Joanna Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London SM2 FNG, UK
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital of Zurich, 8032 Zürich, Switzerland
| | - Zoe S Walters
- Translational Epigenomics Team, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital of Zurich, 8032 Zürich, Switzerland
| | - Rossella Rota
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS Istituto Ospedale Pediatrico Bambino Gesu, Viale San Paolo 15, 00146 Rome, Italy
| | - Janet M Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London SM2 FNG, UK
| | - Simone Hettmer
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), 79104 Freiburg, Germany
- Comprehensive Cancer Centre Freiburg (CCCF), University Medical Center Freiburg, 790106 Freiburg, Germany
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9
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Corbett RJ, Luttman AM, Herrera-Uribe J, Liu H, Raney NE, Grabowski JM, Loving CL, Tuggle CK, Ernst CW. Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits. BMC Genomics 2022; 23:575. [PMID: 35953767 PMCID: PMC9367135 DOI: 10.1186/s12864-022-08773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
Background Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope. Results We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21+ and CD21− B cells, four T cell fractions (CD4+, CD8+, CD8+CD4+, and SWC6γδ+), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1). Conclusion Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08773-5.
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Affiliation(s)
- Ryan J Corbett
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA
| | - Andrea M Luttman
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA
| | | | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Jenna M Grabowski
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | | | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA.
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10
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Parker E, Mendhe B, Ruan L, Marshall B, Zhi W, Liu Y, Fulzele S, Tang YL, McGee-Lawrence M, Lee TJ, Sharma A, Johnson M, Chen J, Hamrick MW. MicroRNA cargo of extracellular vesicles released by skeletal muscle fibro-adipogenic progenitor cells is significantly altered with disuse atrophy and IL-1β deficiency. Physiol Genomics 2022; 54:296-304. [PMID: 35759450 PMCID: PMC9342138 DOI: 10.1152/physiolgenomics.00177.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/31/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
Fibro-adipogenic progenitor cells (FAPs) are a population of stem cells in skeletal muscle that play multiple roles in muscle repair and regeneration through their complex secretome; however, it is not well understood how the FAP secretome is altered with muscle disuse atrophy. Previous work suggests that the inflammatory cytokine IL-1β is increased in FAPs with disuse and denervation. Inflammasome activation and IL-1β secretion are also known to stimulate the release of extracellular vesicles (EVs). Here, we examined the microRNA (miRNA) cargo of FAP-derived, platelet-derived growth factor receptor A (PDGFRα+) EVs from hindlimb muscles of wild-type and IL-1β KO mice after 14 days of single-hindlimb immobilization. Hindlimb muscles were isolated from mice following the immobilization period, and PDGFRα+ extracellular vesicles were isolated using size-exclusion chromatography and immunoprecipitation. Microarrays were performed to detect changes in miRNAs with unloading and IL-1β deficiency. Results indicate that the PDGFRα+, FAP-derived EVs show a significant increase in miRNAs, such as miR-let-7c, miR-let-7b, miR-181a, and miR-124. These miRNAs have previously been demonstrated to play important roles in cellular senescence and muscle atrophy. Furthermore, the expression of these same miRNAs was not significantly altered in FAP-derived EVs isolated from the immobilized IL-1β KO. These data suggest that disuse-related activation of IL-1β can mediate the miRNA cargo of FAP-derived EVs, contributing directly to the release of senescence- and atrophy-related miRNAs. Therapies targeting FAPs in settings associated with muscle disuse atrophy may therefore have the potential to preserve muscle function and enhance muscle recovery.
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Affiliation(s)
- Emily Parker
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Bharati Mendhe
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Ling Ruan
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Brendan Marshall
- EM/Histology Core Laboratory, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Sadanand Fulzele
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Yao Liang Tang
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Meghan McGee-Lawrence
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Maribeth Johnson
- Division of Biostatistics and Data Science, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Jie Chen
- Division of Biostatistics and Data Science, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Mark W Hamrick
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, Georgia
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11
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Widmann M, Mattioni Maturana F, Burgstahler C, Erz G, Schellhorn P, Fragasso A, Schmitt A, Nieß AM, Munz B. miRNAs as markers for the development of individualized training regimens: A pilot study. Physiol Rep 2022; 10:e15217. [PMID: 35274816 PMCID: PMC8915711 DOI: 10.14814/phy2.15217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/24/2022] Open
Abstract
Small, non‐coding RNAs (microRNAs) have been shown to regulate gene expression in response to exercise in various tissues and organs, thus possibly coordinating their adaptive response. Thus, it is likely that differential microRNA expression might be one of the factors that are responsible for different training responses of different individuals. Consequently, determining microRNA patterns might be a promising approach toward the development of individualized training strategies. However, little is known on (1) microRNA patterns and their regulation by different exercise regimens and (2) possible correlations between these patterns and individual training adaptation. Here, we present microarray data on skeletal muscle microRNA patterns in six young, female subjects before and after six weeks of either moderate‐intensity continuous or high‐intensity interval training on a bicycle ergometer. Our data show that n = 36 different microRNA species were regulated more than twofold in this cohort (n = 28 upregulated and n = 8 downregulated). In addition, we correlated baseline microRNA patterns with individual changes in VO2max and identified some specific microRNAs that might be promising candidates for further testing and evaluation in the future, which might eventually lead to the establishment of microRNA marker panels that will allow individual recommendations for specific exercise regimens.
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Affiliation(s)
- Manuel Widmann
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Felipe Mattioni Maturana
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Christof Burgstahler
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Gunnar Erz
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Philipp Schellhorn
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Annunziata Fragasso
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Angelika Schmitt
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Andreas M Nieß
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Barbara Munz
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Research Institute for Sports and Physical Activity, Eberhard Karls University of Tübingen, Tübingen, Germany
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12
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Yedigaryan L, Sampaolesi M. Therapeutic Implications of miRNAs for Muscle-Wasting Conditions. Cells 2021; 10:cells10113035. [PMID: 34831256 PMCID: PMC8616481 DOI: 10.3390/cells10113035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that are mainly involved in translational repression by binding to specific messenger RNAs. Recently, miRNAs have emerged as biomarkers, relevant for a multitude of pathophysiological conditions, and cells can selectively sort miRNAs into extracellular vesicles for paracrine and endocrine effects. In the overall context of muscle-wasting conditions, a multitude of miRNAs has been implied as being responsible for the typical dysregulation of anabolic and catabolic pathways. In general, chronic muscle disorders are associated with the main characteristic of a substantial loss in muscle mass. Muscular dystrophies (MDs) are a group of genetic diseases that cause muscle weakness and degeneration. Typically, MDs are caused by mutations in those genes responsible for upholding the integrity of muscle structure and function. Recently, the dysregulation of miRNA levels in such pathological conditions has been reported. This revelation is imperative for both MDs and other muscle-wasting conditions, such as sarcopenia and cancer cachexia. The expression levels of miRNAs have immense potential for use as potential diagnostic, prognostic and therapeutic biomarkers. Understanding the role of miRNAs in muscle-wasting conditions may lead to the development of novel strategies for the improvement of patient management.
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Affiliation(s)
- Laura Yedigaryan
- Translational Cardiomyology Laboratory, Stem Cell Biology and Embryology, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium;
| | - Maurilio Sampaolesi
- Translational Cardiomyology Laboratory, Stem Cell Biology and Embryology, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium;
- Histology and Medical Embryology Unit, Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence:
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13
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Abiusi E, Infante P, Cagnoli C, Lospinoso Severini L, Pane M, Coratti G, Pera MC, D'Amico A, Diano F, Novelli A, Spartano S, Fiori S, Baranello G, Moroni I, Mora M, Pasanisi MB, Pocino K, Le Pera L, D'Amico D, Travaglini L, Ria F, Bruno C, Locatelli D, Bertini ES, Morandi LO, Mercuri E, Di Marcotullio L, Tiziano FD. SMA-miRs (miR-181a-5p, -324-5p, and -451a) are overexpressed in spinal muscular atrophy skeletal muscle and serum samples. eLife 2021; 10:68054. [PMID: 34542403 PMCID: PMC8486378 DOI: 10.7554/elife.68054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/13/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Spinal muscular atrophy (SMA) is a neuromuscular disorder characterized by the degeneration of the second motor neuron. The phenotype ranges from very severe to very mild forms. All patients have the homozygous loss of the SMN1 gene and a variable number of SMN2 (generally 2–4 copies), inversely related to the severity. The amazing results of the available treatments have made compelling the need of prognostic biomarkers to predict the progression trajectories of patients. Besides the SMN2 products, few other biomarkers have been evaluated so far, including some miRs. Methods: We performed whole miRNome analysis of muscle samples of patients and controls (14 biopsies and 9 cultures). The levels of muscle differentially expressed miRs were evaluated in serum samples (51 patients and 37 controls) and integrated with SMN2 copies, SMN2 full-length transcript levels in blood and age (SMA-score). Results: Over 100 miRs were differentially expressed in SMA muscle; 3 of them (hsa-miR-181a-5p, -324-5p, -451a; SMA-miRs) were significantly upregulated in the serum of patients. The severity predicted by the SMA-score was related to that of the clinical classification at a correlation coefficient of 0.87 (p<10-5). Conclusions: miRNome analyses suggest the primary involvement of skeletal muscle in SMA pathogenesis. The SMA-miRs are likely actively released in the blood flow; their function and target cells require to be elucidated. The accuracy of the SMA-score needs to be verified in replicative studies: if confirmed, its use could be crucial for the routine prognostic assessment, also in presymptomatic patients. Funding: Telethon Italia (grant #GGP12116).
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Affiliation(s)
- Emanuela Abiusi
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università cattolica del Sacro Cuore, Roma, Italy
| | - Paola Infante
- Center For Life Nano Science@Sapienza, Istituto Italiano di Tecnologia; Department of Molecular Medicine, Università degli Studi di Roma "La Sapienza", Roma, Italy, Roma, Italy
| | - Cinzia Cagnoli
- Clinical and Experimental Epileptology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy, Roma, Italy
| | | | - Marika Pane
- Pediatric Neurology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore, Rome, Italy.,Centro Clinico Nemo, Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore, Roma, Italy
| | - Giorgia Coratti
- Centro Clinico Nemo, Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore, Roma, Italy
| | - Maria Carmela Pera
- Centro Clinico Nemo, Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore, Roma, Italy
| | - Adele D'Amico
- Unit of Neuromuscular and Neurodegenerative Disorders, Dept. Neurosciences, Bambino Gesu' Children's Hospital IRCCS, Roma, Italy
| | - Federica Diano
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università cattolica del Sacro Cuore, Roma, Italy
| | - Agnese Novelli
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università cattolica del Sacro Cuore, Roma, Italy
| | - Serena Spartano
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università cattolica del Sacro Cuore, Roma, Italy
| | - Stefania Fiori
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università cattolica del Sacro Cuore, Roma, Italy
| | - Giovanni Baranello
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Isabella Moroni
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Maria Barbara Pasanisi
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Krizia Pocino
- Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Loredana Le Pera
- Bioenergetics and Molecular Biotechnologies (IBIOM), CNR-Institute of Biomembranes, Bari, Italy.,CNR-Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
| | - Davide D'Amico
- Amazentis SA, EPFL Innovation Park, Losanne, Switzerland
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Disorders, Dept. Neurosciences, Bambino Gesu' Children's Hospital IRCCS, Roma, Italy
| | - Francesco Ria
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Roma, Italy.,Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
| | - Claudio Bruno
- Center of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Denise Locatelli
- Clinical and Experimental Epileptology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy, Roma, Italy
| | - Enrico Silvio Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Dept. Neurosciences, Bambino Gesu' Children's Hospital IRCCS, Roma, Italy
| | - Lucia Ovidia Morandi
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eugenio Mercuri
- Pediatric Neurology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore, Rome, Italy.,Centro Clinico Nemo, Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore, Roma, Italy
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, Università degli Studi di Roma "La Sapienza", Roma, Italy.,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Francesco Danilo Tiziano
- Department of Life Sciences and Public Health, Section of Genomic Medicine, Università cattolica del Sacro Cuore, Roma, Italy.,Unit of Medical Genetics, Department of Laboratory science and Infectious Diseases, Fondazione Policlinico Universitario IRCCS "A. Gemelli", Rome, Italy
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14
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Dong X, Cheng Y, Qiao L, Wang X, Zeng C, Feng Y. Male-Biased gga-miR-2954 Regulates Myoblast Proliferation and Differentiation of Chicken Embryos by Targeting YY1. Genes (Basel) 2021; 12:1325. [PMID: 34573307 PMCID: PMC8470131 DOI: 10.3390/genes12091325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/25/2021] [Indexed: 02/02/2023] Open
Abstract
Previous studies have shown that gga-miR-2954 was highly expressed in the gonads and other tissues of male chickens, including muscle tissue. Yin Yang1 (YY1), which has functions in mammalian skeletal muscle development, was predicted to be a target gene of gga-miR-2954. The purpose of this study was to investigate whether gga-miR-2954 plays a role in skeletal muscle development by targeting YY1, and evaluate its function in the sexual dimorphism development of chicken muscle. Here, all the temporal and spatial expression profiles in chicken embryonic muscles showed that gga-miR-2954 is highly expressed in males and mainly localized in cytoplasm. Gga-miR-2954 exhibited upregulated expression of in vitro myoblast differentiation stages. Next, through the overexpression and loss-of-function experiments performed in chicken primary myoblasts, we found that gga-miR-2954 inhibited myoblast proliferation but promoted differentiation. During myogenesis, gga-miR-2954 could suppress the expression of YY1, which promoted myoblast proliferation and inhibited the process of myoblast cell differentiation into multinucleated myotubes. Overall, these findings reveal a novel role of gga-miR-2954 in skeletal muscle development through its function of the myoblast proliferation and differentiation by suppressing the expression of YY1. Moreover, gga-miR-2954 may contribute to the sex difference in chicken muscle development.
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Affiliation(s)
| | | | | | | | | | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (Y.C.); (L.Q.); (X.W.); (C.Z.)
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15
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Enhancement of myogenic differentiation and inhibition of rhabdomyosarcoma progression by miR-28-3p and miR-193a-5p regulated by SNAIL. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:888-904. [PMID: 34094709 PMCID: PMC8141673 DOI: 10.1016/j.omtn.2021.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/13/2021] [Indexed: 12/15/2022]
Abstract
Rhabdomyosarcoma (RMS) is a soft tissue mesenchymal tumor that affects mostly children and adolescents. It originates from the impaired myogenic differentiation of stem cells or early progenitors. SNAIL, a transcription factor that regulates epithelial-to-mesenchymal transition in tumors of epithelial origin, is also a key regulator of RMS growth, progression, and myogenic differentiation. Here, we demonstrate that the SNAIL-dependent microRNAs (miRNAs) miR-28-3p and miR-193a-5p are crucial regulators of RMS growth, differentiation, and progression. miR-28-3p and miR-193a-5p diminished proliferation and arrested RMS cells in G0/G1 phase in vitro. They induced the myogenic differentiation of both RMS cells and human myoblasts by upregulating myogenic factors. Furthermore, miR-28-3p and miR-193a-5p inhibited migration in a scratch assay, adhesion to endothelial cells, chemotaxis, and invasion toward SDF-1 and HGF and regulated angiogenic capabilities of the cells. Overexpression of miR-28-3p and miR-193a-5p induced formation of fibrotic structures and abnormal blood vessels in RMS xenografts in immunodeficient mice in vivo. Simultaneous overexpression of both miRNAs diminished tumor growth after subcutaneous implantation and inhibited the engraftment of RMS cells into bone marrow after intravenous injection in vivo. To conclude, we discovered novel SNAIL-dependent miRNAs that may become new therapeutic targets in RMS in the future.
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16
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Hicks JA, Liu HC. Centennial Review: Metabolic microRNA - shifting gears in the regulation of metabolic pathways in poultry. Poult Sci 2021; 100:100856. [PMID: 33652542 PMCID: PMC7936154 DOI: 10.1016/j.psj.2020.11.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 01/01/2023] Open
Abstract
Over 20 yr ago, a small noncoding class of RNA termed microRNA (miRNA) that was able to recognize sequences in mRNAs and inhibit their translation was discovered in Caenorhabditis elegans. In the intervening years, miRNA have been discovered in most eukaryotes and are now known to regulate the majority of protein-coding genes. It has been discovered that disruption of miRNA function often leads to the development of pathological conditions. One physiological system under extensive miRNA-mediated regulation is metabolism. Metabolism is one of the most dynamic of biological networks within multiple organs, including the liver, muscle, and adipose tissue, working in concert to respond to ever-changing nutritional cues and energy demands. Therefore, it is not surprising that miRNA regulate virtually all aspects of eukaryotic metabolism and have been linked to metabolic disorders, such as obesity, fatty liver diseases, and diabetes, just to name a few. Chickens, and birds in general, face their own unique metabolic challenges, particularly after hatching, when their metabolism must completely transform from using lipid-rich yolk to carbohydrate-rich feed as fuel in a very short period of time. Furthermore, commercial poultry breeds have undergone extensive selection over the last century for more desirable production traits, which has resulted in numerous metabolic consequences. Here, we review the current knowledge of miRNA-mediated regulation of metabolic development and function in chickens.
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Affiliation(s)
- Julie A Hicks
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Hsiao-Ching Liu
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA.
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Elliott JM, Rueckeis CA, Pan Y, Parrish TB, Walton DM, Linnstaedt SD. microRNA let-7i-5p mediates the relationship between muscle fat infiltration and neck pain disability following motor vehicle collision: a preliminary study. Sci Rep 2021; 11:3140. [PMID: 33542428 PMCID: PMC7862492 DOI: 10.1038/s41598-021-82734-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Persistent neck-pain disability (PNPD) is common following traumatic stress exposures such as motor vehicle collision (MVC). Substantial literature indicates that fat infiltration into neck muscle (MFI) is associated with post-MVC PNPD. However, little is known about the molecular mediators underlying this association. In the current study, we assessed whether microRNA expression signatures predict PNPD and whether microRNA mediate the relationship between neck MFI and PNPD. A nested cohort of 43 individuals from a longitudinal study of MVC survivors, who provided blood (PAXgene RNA) and underwent magnetic resonance imaging (MRI), were included in the current study. Peritraumatic microRNA expression levels were quantified via small RNA sequencing, neck MFI via MRI, and PNPD via the Neck Disability Index two-weeks, three-months, and twelve-months following MVC. Repeated measures regression models were used to assess the relationship between microRNA and PNPD and to perform mediation analyses. Seventeen microRNA predicted PNPD following MVC. One microRNA, let-7i-5p, mediated the relationship between neck MFI and PNPD. Peritraumatic blood-based microRNA expression levels predict PNPD following MVC and let-7i-5p might contribute to the underlying effects of neck MFI on persistent disability. In conclusion, additional studies are needed to validate this finding.
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Affiliation(s)
- James M Elliott
- Faculty of Medicine and Health, The Northern Sydney Local Health District, The Kolling Institute, The University of Sydney, St. Leonards, NSW, Australia
- Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cathleen A Rueckeis
- Institute for Trauma Recovery, University of North Carolina, Campus Box #7010, Chapel Hill, NC, 27599-7010, USA
| | - Yue Pan
- Institute for Trauma Recovery, University of North Carolina, Campus Box #7010, Chapel Hill, NC, 27599-7010, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Todd B Parrish
- Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Radiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David M Walton
- School of Physical Therapy, Western University, London, ON, Canada
| | - Sarah D Linnstaedt
- Institute for Trauma Recovery, University of North Carolina, Campus Box #7010, Chapel Hill, NC, 27599-7010, USA.
- Department of Anesthesiology, University of North Carolina, Chapel Hill, NC, USA.
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18
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Gao J, Ni X, Li H, Hayat F, Shi T, Gao Z. miR169 and PmRGL2 synergistically regulate the NF-Y complex to activate dormancy release in Japanese apricot (Prunus mume Sieb. et Zucc.). PLANT MOLECULAR BIOLOGY 2021; 105:83-97. [PMID: 32926248 DOI: 10.1007/s11103-020-01070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/28/2020] [Accepted: 09/06/2020] [Indexed: 06/11/2023]
Abstract
This study is the first to demonstrate that GA4-induced dormancy release is associated with the NF-Y complex, which interacts with gibberellin inhibitor RGL2 in Japanese apricot. Seasonal dormancy is not only vital for the survival in cold winter but also affects flowering of temperate fruit trees and the dormancy release depends on the accumulation of the cold temperatures (Chilling requirement-CR). To understand the mechanism of dormancy release in deciduous fruit crops, we compared miRNA sequencing data during the transition stage from paradormancy to dormancy release in the Japanese apricot and found that the miR169 family showed significant differentially up-regulated expression during dormancy induction and was down-regulated during the dormancy release periods. The 5' RACE assay and RT-qPCR validated its target gene NUCLEAR FACTOR-Y subunit A (NF-YA), which exhibited the opposite expression pattern. Further study showed that exogenous GA4 could inhibit the expression of the gibberellic acid (GA) signal transduction suppressor PmRGL2 (RGA-LIKE 2) and promote the expression of NF-Y. Moreover, the interaction between the NF-Y family and GA inhibitor PmRGL2 was verified by the yeast-two-hybrid (Y2H) system and a bimolecular fluorescence complementarity (BiFC) experiment. These results suggest that synergistic regulation of the NF-Y and PmRGL2 complex leads to the activation of dormancy release induced by GA4. These findings will help to elucidate the functional and regulatory roles of miR169 and NF-Y complex in seasonal bud dormancy induced by GA in Japanese apricot and provide new insights for the discovery of dormancy release mechanisms in woody plants.
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Affiliation(s)
- Jie Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaopeng Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hantao Li
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Faisal Hayat
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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19
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Choi SA, Koh EJ, Kim RN, Byun JW, Phi JH, Yang J, Wang KC, Park AK, Hwang DW, Lee JY, Kim SK. Extracellular vesicle-associated miR-135b and -135a regulate stemness in Group 4 medulloblastoma cells by targeting angiomotin-like 2. Cancer Cell Int 2020; 20:558. [PMID: 33292274 PMCID: PMC7678136 DOI: 10.1186/s12935-020-01645-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Background Extracellular vesicles (EVs) secreted by tumours, including exosomes, are important factors that regulate cell–cell interactions in oncogenesis. Although EV studies are ongoing, the biological understanding of EV-miRNAs derived from brain tumour spheroid-forming cells (BTSCs) of medulloblastoma is poor. Purposes We explored the specific cellular miRNAs and EV-miRNAs in medulloblastoma BTSCs to determine their potential biological function. Methods Bulk tumor cells (BTCs) and BTSCs were cultured under different conditions from medulloblastoma tissues (N = 10). Results Twenty-four miRNAs were simultaneously increased in both cells and EVs derived from BTSCs in comparison to BTCs. After inhibition of miR-135b or miR135a which were the most significantly increased in BTSCs, cell viability, self-renewal and stem cell marker expression decreased remarkably. Through integrated analysis of mRNAs and miRNAs data, we found that angiomotin-like 2 (AMOTL2), which was significantly decreased, was targeted by both miR-135b and miR-135a. STAT6 and GPX8 were targeted only by miR-135a. Importantly, low expression of AMOTL2 was significantly associated with overall poor survival in paediatric Group 3 and Group 4 medulloblastoma patients. Conclusion Our results indicated that inhibition of miR-135b or miR-135a leads to suppress stemness of BTSC through modulation of AMOTL2.
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Affiliation(s)
- Seung Ah Choi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Jung Koh
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Regional Emergency Medical Center, Seoul National University Hospital, Seoul, Korea
| | - Ryong Nam Kim
- Department of Biomedical Engineering, Seoul National University, Seoul, Korea
| | - Jung Woo Byun
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Hoon Phi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jeyul Yang
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Kyu-Chang Wang
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ae Kyung Park
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, Korea
| | - Do Won Hwang
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Yeoun Lee
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Anatomy, Neural Development and Anomaly Lab, Seoul National University College of Medicine, Seoul, Korea
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
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20
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Heier CR, Zhang A, Nguyen NY, Tully CB, Panigrahi A, Gordish-Dressman H, Pandey SN, Guglieri M, Ryan MM, Clemens PR, Thangarajh M, Webster R, Smith EC, Connolly AM, McDonald CM, Karachunski P, Tulinius M, Harper A, Mah JK, Fiorillo AA, Chen YW. Multi-Omics Identifies Circulating miRNA and Protein Biomarkers for Facioscapulohumeral Dystrophy. J Pers Med 2020; 10:jpm10040236. [PMID: 33228131 PMCID: PMC7711540 DOI: 10.3390/jpm10040236] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
The development of therapeutics for muscle diseases such as facioscapulohumeral dystrophy (FSHD) is impeded by a lack of objective, minimally invasive biomarkers. Here we identify circulating miRNAs and proteins that are dysregulated in early-onset FSHD patients to develop blood-based molecular biomarkers. Plasma samples from clinically characterized individuals with early-onset FSHD provide a discovery group and are compared to healthy control volunteers. Low-density quantitative polymerase chain reaction (PCR)-based arrays identify 19 candidate miRNAs, while mass spectrometry proteomic analysis identifies 13 candidate proteins. Bioinformatic analysis of chromatin immunoprecipitation (ChIP)-seq data shows that the FSHD-dysregulated DUX4 transcription factor binds to regulatory regions of several candidate miRNAs. This panel of miRNAs also shows ChIP signatures consistent with regulation by additional transcription factors which are up-regulated in FSHD (FOS, EGR1, MYC, and YY1). Validation studies in a separate group of patients with FSHD show consistent up-regulation of miR-100, miR-103, miR-146b, miR-29b, miR-34a, miR-454, miR-505, and miR-576. An increase in the expression of S100A8 protein, an inflammatory regulatory factor and subunit of calprotectin, is validated by Enzyme-Linked Immunosorbent Assay (ELISA). Bioinformatic analyses of proteomics and miRNA data further support a model of calprotectin and toll-like receptor 4 (TLR4) pathway dysregulation in FSHD. Moving forward, this panel of miRNAs, along with S100A8 and calprotectin, merit further investigation as monitoring and pharmacodynamic biomarkers for FSHD.
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Affiliation(s)
- Christopher R. Heier
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA; (H.G.-D.); (A.A.F.)
- Correspondence: (C.R.H.); (Y.-W.C.)
| | - Aiping Zhang
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA; (A.Z.); (N.Y.N.); (C.B.T.); (A.P.); (S.N.P.)
| | - Nhu Y Nguyen
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA; (A.Z.); (N.Y.N.); (C.B.T.); (A.P.); (S.N.P.)
| | - Christopher B. Tully
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA; (A.Z.); (N.Y.N.); (C.B.T.); (A.P.); (S.N.P.)
| | - Aswini Panigrahi
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA; (A.Z.); (N.Y.N.); (C.B.T.); (A.P.); (S.N.P.)
| | - Heather Gordish-Dressman
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA; (H.G.-D.); (A.A.F.)
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA; (A.Z.); (N.Y.N.); (C.B.T.); (A.P.); (S.N.P.)
| | - Sachchida Nand Pandey
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA; (A.Z.); (N.Y.N.); (C.B.T.); (A.P.); (S.N.P.)
| | | | - Monique M. Ryan
- The Royal Children’s Hospital, Melbourne University, Parkville, Victoria 3052, Australia;
| | - Paula R. Clemens
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA;
| | - Mathula Thangarajh
- Department of Neurology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA;
| | | | - Edward C. Smith
- Department of Pediatrics, Duke University Medical Center, Durham, NC 27705, USA;
| | - Anne M. Connolly
- Nationwide Children’s Hospital, The Ohio State University, Columbus, OH 43205, USA;
| | - Craig M. McDonald
- Department of Physical Medicine and Rehabilitation, University of California at Davis Medical Center, Sacramento, CA 95817, USA;
| | - Peter Karachunski
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Mar Tulinius
- Department of Pediatrics, Gothenburg University, Queen Silvia Children’s Hospital, 41685 Göteborg, Sweden;
| | - Amy Harper
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Jean K. Mah
- Deparment of Pediatrics and Clinical Neurosciences, Cumming School of Medicine, University of Calgary, T2N T3B, Calgary, AB 6A81N4, Canada;
| | - Alyson A. Fiorillo
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA; (H.G.-D.); (A.A.F.)
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA; (A.Z.); (N.Y.N.); (C.B.T.); (A.P.); (S.N.P.)
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA; (A.Z.); (N.Y.N.); (C.B.T.); (A.P.); (S.N.P.)
- Correspondence: (C.R.H.); (Y.-W.C.)
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Wu X, Ding M, Lin J. Three-microRNA expression signature predicts survival in triple-negative breast cancer. Oncol Lett 2019; 19:301-308. [PMID: 31897142 PMCID: PMC6923981 DOI: 10.3892/ol.2019.11118] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 10/23/2019] [Indexed: 12/15/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a specific type of breast cancer with poor overall survival (OS) time. Previous studies revealed that microRNAs (miRNAs/miRs) serve important roles in the pathogenesis, progression and prognosis of TNBC. The present study analyzed the miRNA expression and clinical data of patients with TNBC downloaded from The Cancer Genome Atlas. A total of 194 differentially expressed miRNAs were identified between TNBC and matched normal tissues using the cut-off criteria of P<0.05 and |log2 fold change|>2. Of these miRNAs, 65 were downregulated and 129 were upregulated. Using Kaplan-Meier survival analysis, a total of 77 miRNAs that were closely associated with OS time were identified (P<0.05). The intersection of the 77 miRNAs and 194 differentially expressed miRNAs revealed six miRNAs. Log-rank tests based on survival curves were performed and two miRNAs were eliminated. The prognostic value of the remaining four miRNAs was evaluated with a Cox proportional hazards model using multiple logistic regression with forward stepwise selection of variables. Three miRNAs (miR-21-3p, miR-659-5p and miR-200b-5p) were subsequently identified as independent risk factors associated with OS time in the model. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses revealed that the target genes of these three miRNAs were mainly involved in ‘cell protein metabolism’, ‘RNA transcriptional regulation’, ‘cell migration’, ‘MAPK signaling pathway’, ‘ErbB signaling pathway’, ‘prolactin signaling pathway’ and ‘adherens junctions’. Taken together, the results obtained in the present study suggested that the three-miRNA signature may serve as a prognostic biomarker for patients with TNBC.
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Affiliation(s)
- Xinquan Wu
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Mingji Ding
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Jianqin Lin
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
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22
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Robinson KA, Baker LA, Graham-Brown MPM, Watson EL. Skeletal muscle wasting in chronic kidney disease: the emerging role of microRNAs. Nephrol Dial Transplant 2019; 35:1469-1478. [DOI: 10.1093/ndt/gfz193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/27/2019] [Indexed: 12/17/2022] Open
Abstract
Abstract
Skeletal muscle wasting is a common complication of chronic kidney disease (CKD), characterized by the loss of muscle mass, strength and function, which significantly increases the risk of morbidity and mortality in this population. Numerous complications associated with declining renal function and lifestyle activate catabolic pathways and impair muscle regeneration, resulting in substantial protein wasting. Evidence suggests that increasing skeletal muscle mass improves outcomes in CKD, making this a clinically important research focus. Despite extensive research, the pathogenesis of skeletal muscle wasting is not completely understood. It is widely recognized that microRNAs (miRNAs), a family of short non-coding RNAs, are pivotal in the regulation of skeletal muscle homoeostasis, with significant roles in regulating muscle growth, regeneration and metabolism. The abnormal expression of miRNAs in skeletal muscle during disease has been well described in cellular and animal models of muscle atrophy, and in recent years, the involvement of miRNAs in the regulation of muscle atrophy in CKD has been demonstrated. As this exciting field evolves, there is emerging evidence for the involvement of miRNAs in a beneficial crosstalk system between skeletal muscle and other organs that may potentially limit the progression of CKD. In this article, we describe the pathophysiological mechanisms of muscle wasting and explore the contribution of miRNAs to the development of muscle wasting in CKD. We also discuss advances in our understanding of miRNAs in muscle–organ crosstalk and summarize miRNA-based therapeutics currently in clinical trials.
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Affiliation(s)
- Kate A Robinson
- Department of Infection Immunity and Inflammation, College of Life Sciences, University of Leicester, Leicester, UK
| | - Luke A Baker
- Department of Health Sciences, College of Life Sciences, George Davies Centre, University of Leicester, Leicester, UK
| | - Matthew P M Graham-Brown
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Cardiovascular Biomedical Research Centre, Glenfield Hospital Leicester, Leicester, UK
| | - Emma L Watson
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Cardiovascular Biomedical Research Centre, Glenfield Hospital Leicester, Leicester, UK
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23
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Mir BA, Islam R, Kalanon M, Russell AP, Foletta VC. MicroRNA suppression of stress-responsive NDRG2 during dexamethasone treatment in skeletal muscle cells. BMC Mol Cell Biol 2019; 20:12. [PMID: 31138100 PMCID: PMC6537443 DOI: 10.1186/s12860-019-0194-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 11/10/2022] Open
Abstract
Background MicroRNAs (miRNAs) are increasingly being identified as modulatory molecules for physiological and pathological processes in muscle. Here, we investigated whether miRNAs influenced the expression of the stress-responsive gene N-myc downstream-regulated gene 2 (Ndrg2) in skeletal muscle cells through the targeted degradation or translation inhibition of NDRG2 mRNA transcripts during basal or catabolic stress conditions. Results Three miRNAs, mmu-miR-23a-3p (miR-23a), mmu-miR-23b-3p (miR-23b) and mmu-miR-28-5p (miR-28), were identified using an in silico approach and confirmed to target the 3′ untranslated region of the mouse Ndrg2 gene through luciferase reporter assays. However, miR-23a, -23b or -28 overexpression had no influence on NDRG2 mRNA or protein levels up to 48 h post treatment in mouse C2C12 myotubes under basal conditions. Interestingly, a compensatory decrease in the endogenous levels of the miRNAs in response to each other’s overexpression was measured. Furthermore, dexamethasone, a catabolic stress agent that induces NDRG2 expression, decreased miR-23a and miR-23b endogenous levels at 24 h post treatment suggesting an interplay between these miRNAs and NDRG2 regulation under similar stress conditions. Accordingly, when overexpressed simultaneously, miR-23a, -23b and -28 attenuated the dexamethasone-induced increase of NDRG2 protein translation but did not affect Ndrg2 gene expression. Conclusion These findings highlight modulatory and co-regulatory roles for miR-23a, -23b and -28 and their novel regulation of NDRG2 during stress conditions in muscle. Electronic supplementary material The online version of this article (10.1186/s12860-019-0194-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bilal A Mir
- Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Science, Deakin University, Geelong, VIC, 3222, Australia
| | - Rabia Islam
- Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Science, Deakin University, Geelong, VIC, 3222, Australia
| | - Ming Kalanon
- Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Science, Deakin University, Geelong, VIC, 3222, Australia
| | - Aaron P Russell
- Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Science, Deakin University, Geelong, VIC, 3222, Australia
| | - Victoria C Foletta
- Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Science, Deakin University, Geelong, VIC, 3222, Australia.
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24
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Ma L, Zhou L, Quan S, Xu H, Yang J, Niu J. Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence. BMC PLANT BIOLOGY 2019; 19:192. [PMID: 31072362 PMCID: PMC6507046 DOI: 10.1186/s12870-019-1792-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/22/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND The objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (the first, fifth and ninth days of the late bloom stage), with 50 mg/L GA3 (calyx persistence treatment, C_1, C_5, C_9) or 500 mg/L PP333 (calyx abscission treatment, T_1, T_5, T_9), were collected and simultaneously conducted transcriptome and small RNA sequencing. RESULTS Through association analysis of transcriptome and small RNA sequencing, mRNA-miRNA network was conducted. Compared calyx persistence groups with calyx abscission groups during the same stage, 145, 56 and 150 mRNA-miRNA pairs were obtained in C_1 vs T_1, C_5 vs T_5 and C_9 vs T_9, respectively; When C_1 compared with C_5 and C_9, 90 and 506 mRNA-miRNA pairs were screened respectively, and 255 mRNA-miRNA pairs were obtained from the comparison between C_5 and C_9; When T_1 compared with the T_5 and T_9, respectively, 206 and 796 mRNA-miRNA pairs were obtained, and 383 mRNA-miRNA pairs were obtained from the comparison between T_5 and T_9. These mRNAs in miRNA-mRNA pairs were significantly enriched into the terpenoid backbone biosynthesis, photosynthesis - antenna proteins, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, zeatin biosynthesis and plant hormone signal transduction. In addition, we obtained some key genes from miRNA-mRNA pairs that may be associated with calyx abscission, including protein phosphatase 2C (psi-miR394a-HAB1), receptor-like protein kinase (psi-miR396a-5p-HERK1), cellulose synthase-like protein D3 (psi-miR827-CSLD3), beta-galactosidase (psi-miR858b-β-galactosidase), SPL-psi-miR156j/157d, abscisic acid 8'-hydroxylase 1 (psi-miR396a-5p-CYP707A1) and auxin response factor (psi-miR160a-3p-ARF6, psi-miR167d-ARF18, psi-miR167a-5p-ARF25), etc. CONCLUSION: By integrated analysis mRNA and miRNA, our study gives a better understanding of the important genes and regulation pathway related to calyx abscission in Korla fragrant pear. We have also established the network of miRNA-mRNA pairs to learn about precise regulation of miRNA on calyx abscission.
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Affiliation(s)
- Li Ma
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China
| | - Li Zhou
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China
| | - Shaowen Quan
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China
| | - Hang Xu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China
| | - Jieping Yang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China
| | - Jianxin Niu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China
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25
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Munk R, Martindale JL, Yang X, Yang JH, Grammatikakis I, Di Germanio C, Mitchell SJ, de Cabo R, Lehrmann E, Zhang Y, Becker KG, Raz V, Gorospe M, Abdelmohsen K, Panda AC. Loss of miR-451a enhances SPARC production during myogenesis. PLoS One 2019; 14:e0214301. [PMID: 30925184 PMCID: PMC6440632 DOI: 10.1371/journal.pone.0214301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/10/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that critically regulate gene expression. Their abundance and function have been linked to a range of physiologic and pathologic processes. In aged monkey muscle, miR-451a and miR-144-3p were far more abundant than in young monkey muscle. This observation led us to hypothesize that miR-451a and miR-144-3p may influence muscle homeostasis. To test if these conserved microRNAs were implicated in myogenesis, we investigated their function in the mouse myoblast line C2C12. The levels of both microRNAs declined with myogenesis; however, only overexpression of miR-451a, but not miR-144-3p, robustly impeded C2C12 differentiation, suggesting an inhibitory role for miR-451a in myogenesis. Further investigation of the regulatory influence of miR-451a identified as one of the major targets Sparc mRNA, which encodes a secreted protein acidic and rich in cysteine (SPARC) that functions in wound healing and cellular differentiation. In mouse myoblasts, miR-451a suppressed Sparc mRNA translation. Together, our findings indicate that miR-451a is downregulated in differentiated myoblasts and suggest that it decreases C2C12 differentiation at least in part by suppressing SPARC biosynthesis.
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Affiliation(s)
- Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Ioannis Grammatikakis
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Clara Di Germanio
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Sarah J Mitchell
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Elin Lehrmann
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kevin G Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Amaresh C Panda
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
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26
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Bian H, Zhou Y, Zhou D, Zhang Y, Shang D, Qi J. The latest progress on miR-374 and its functional implications in physiological and pathological processes. J Cell Mol Med 2019; 23:3063-3076. [PMID: 30772950 PMCID: PMC6484333 DOI: 10.1111/jcmm.14219] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/10/2019] [Accepted: 01/23/2019] [Indexed: 12/17/2022] Open
Abstract
Non‐coding RNAs (ncRNAs) have been emerging players in cell development, differentiation, proliferation and apoptosis. Based on their differences in length and structure, they are subdivided into several categories including long non‐coding RNAs (lncRNAs >200nt), stable non‐coding RNAs (60‐300nt), microRNAs (miRs or miRNAs, 18‐24nt), circular RNAs, piwi‐interacting RNAs (26‐31nt) and small interfering RNAs (about 21nt). Therein, miRNAs not only directly regulate gene expression through pairing of nucleotide bases between the miRNA sequence and a specific mRNA that leads to the translational repression or degradation of the target mRNA, but also indirectly affect the function of downstream genes through interactions with lncRNAs and circRNAs. The latest studies have highlighted their importance in physiological and pathological processes. MiR‐374 family member are located at the X‐chromosome inactivation center. In recent years, numerous researches have uncovered that miR‐374 family members play an indispensable regulatory role, such as in reproductive disorders, cell growth and differentiation, calcium handling in the kidney, various cancers and epilepsy. In this review, we mainly focus on the role of miR‐374 family members in multiple physiological and pathological processes. More specifically, we also summarize their promising potential as novel prognostic biomarkers and therapeutic targets from bench to bedside.
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Affiliation(s)
- Hongjun Bian
- Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Yi Zhou
- Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Dawei Zhou
- Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Yongsheng Zhang
- Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Deya Shang
- Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Jianni Qi
- Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
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27
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Faraldi M, Gomarasca M, Sansoni V, Perego S, Banfi G, Lombardi G. Normalization strategies differently affect circulating miRNA profile associated with the training status. Sci Rep 2019; 9:1584. [PMID: 30733582 PMCID: PMC6367481 DOI: 10.1038/s41598-019-38505-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/18/2018] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs are fine regulators of the whole-body adaptive response but their use as biomarkers is limited by the lack of standardized pre- and post-analytical procedures. This work aimed to compare different normalization approaches for RT-qPCR data analyses, in order to identify the most reliable and reproducible method to analyze circulating miRNA expression profiles in sedentary and highly-trained subjects. As the physically active status is known to affect miRNA expression, they could be effective biomarkers of the homeostatic response. Following RNA extraction from plasma, a panel of 179 miRNAs was assayed by RT-qPCR and quantified by applying different normalization strategies based on endogenous miRNAs and exogenous oligonucleotides. hsa-miR-320d was found as the most appropriate reference miRNA in reducing the technical variability among the experimental replicates and, hence, in highlighting the inter-cohorts differences. Our data showed an association between the physically active status and specific skeletal muscle- and bone-associated circulating miRNAs profiles, revealing that established epigenetic modifications affect the baseline physiological status of these tissues. Since different normalization strategies led to different outputs, in order to avoid misleading interpretation of data, we remark the importance of the accurate choice of the most reliable normalization method in every experimental setting.
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Affiliation(s)
- Martina Faraldi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy.
| | - Marta Gomarasca
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Veronica Sansoni
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Silvia Perego
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Giuseppe Banfi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy.,Vita-Salute San Raffaele University, Milano, Italy
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy.,Gdańsk University of Physical Education & Sport, Gdańsk, Poland
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28
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Li N, Zhang Y, Li HP, Han L, Yan XM, Li HB, Du W, Zhang JS, Yu QL. Differential expression of mRNA-miRNAs related to intramuscular fat content in the longissimus dorsi in Xinjiang brown cattle. PLoS One 2018; 13:e0206757. [PMID: 30412616 PMCID: PMC6226300 DOI: 10.1371/journal.pone.0206757] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/18/2018] [Indexed: 02/07/2023] Open
Abstract
In this study, we examined the role of mRNAs and miRNAs in variations in intramuscular fat content in the longissimus dorsi muscle in Xinjiang brown cattle. Two groups of Xinjiang brown cattle with extremely different intramuscular fat content in the longissimus dorsi were selected for combined of miRNA and mRNA analysis using an RNA-Seq. In total, 296 mRNAs and 362 miRNAs were significantly differentially expressed, including 155 newly predicted miRNAs, 275 significantly upregulated genes, 252 significantly upregulated miRNAs, 21 significantly downregulated genes and 110 significantly downregulated miRNAs. The combined miRNA and mRNA analysis identified 96 differentially expressed miRNAs and 27 differentially expressed mRNAs. In all, 47 upregulated miRNAs had a regulatory effect on 14 differentially downregulated target genes, and 49 downregulated miRNAs had a regulatory effect on 13 upregulated target genes. To verify the sequencing results, 10 differentially expressed genes (DEGs) and 10 differentially expressed miRNAs were selected for qRT-PCR. The qRT-PCR results confirmed the sequencing results. The results of this study shed light on the molecular regulation of bovine adipose tissue, which might help with the development of new strategies for improving meat quality and animal productivity in beef cattle to provide healthier meat products for consumers.
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Affiliation(s)
- Na Li
- Department of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Yang Zhang
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Hai-Peng Li
- Department of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling Han
- Department of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiang-Min Yan
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Hong-Bo Li
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Wei Du
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Jin-Shan Zhang
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Qun-Li Yu
- Department of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
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29
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Wang W, Chen J, Hui Y, Huang M, Yuan P. Down-regulation of miR-193a-3p promotes osteoblast differentiation through up-regulation of LGR4/ATF4 signaling. Biochem Biophys Res Commun 2018; 503:2186-2193. [DOI: 10.1016/j.bbrc.2018.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/01/2018] [Indexed: 12/14/2022]
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Lim JW, Wong CJ, Yao Z, Tawil R, van der Maarel SM, Miller DG, Tapscott SJ, Filippova GN. Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures. Hum Mol Genet 2018; 27:2644-2657. [PMID: 29741619 PMCID: PMC6048983 DOI: 10.1093/hmg/ddy173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/24/2018] [Accepted: 05/02/2018] [Indexed: 02/06/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4 macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defects mostly due to SMCHD1 mutation. Previous reports showed DUX4-induced gene expression changes as well as changes in microRNA expression in FSHD muscle cells. However, a genome wide analysis of small noncoding RNAs that might be regulated by DUX4 or by mutations in SMCHD1 has not been reported yet. Here, we identified several types of small noncoding RNAs including known microRNAs that are differentially expressed in FSHD2 muscle cells compared to control. Although fewer small RNAs were differentially expressed during muscle differentiation in FSHD2 cells compared to controls, most of the known myogenic microRNAs, such as miR1, miR133a and miR206 were induced in both FSHD2 and control muscle cells during differentiation. Our small RNA sequencing data analysis also revealed both DUX4- and SMCHD1-specific changes in FSHD2 muscle cells. Six FSHD2 microRNAs were affected by DUX4 overexpression in control myoblasts, whereas increased expression of tRNAs and 5S rRNAs in FSHD2 muscle cells was largely recapitulated in SMCHD1-depleted control myoblasts. Altogether, our studies suggest that the small noncoding RNA transcriptome changes in FSHD2 might be different from those in FSHD1 and that these differences may provide new diagnostic and therapeutic tools specific to FSHD2.
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Affiliation(s)
- Jong-Won Lim
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chao-Jen Wong
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Zizhen Yao
- MAT Department, Allen Brain Institute, Seattle, WA 98109, USA
| | - Rabi Tawil
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
| | | | - Daniel G Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98109, USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Galina N Filippova
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
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31
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Chodkowska KA, Ciecierska A, Majchrzak K, Ostaszewski P, Sadkowski T. Effect of β-hydroxy-β-methylbutyrate on miRNA expression in differentiating equine satellite cells exposed to hydrogen peroxide. GENES AND NUTRITION 2018; 13:10. [PMID: 29662554 PMCID: PMC5892041 DOI: 10.1186/s12263-018-0598-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 03/14/2018] [Indexed: 12/25/2022]
Abstract
Background Skeletal muscle injury activates satellite cells to initiate processes of proliferation, differentiation, and hypertrophy in order to regenerate muscle fibers. The number of microRNAs and their target genes are engaged in satellite cell activation. β-Hydroxy-β-methylbutyrate (HMB) is known to prevent exercise-induced muscle damage. The purpose of this study was to evaluate the effect of HMB on miRNA and relevant target gene expression in differentiating equine satellite cells exposed to H2O2. We hypothesized that HMB may regulate satellite cell activity, proliferation, and differentiation, hence attenuate the pathological processes induced during an in vitro model of H2O2-related injury by changing the expression of miRNAs. Methods Equine satellite cells (ESC) were isolated from the samples of skeletal muscle collected from young horses. ESC were treated with HMB (24 h) and then exposed to H2O2 (1 h). For the microRNA and gene expression assessment microarrays, technique was used. Identified miRNAs and genes were validated using real-time qPCR. Cell viability, oxidative stress, and cell damage were measured using colorimetric method and flow cytometry. Results Analysis of miRNA and gene profile in differentiating ESC pre-incubated with HMB and then exposed to H2O2 revealed difference in the expression of 27 miRNAs and 4740 genes, of which 344 were potential target genes for identified miRNAs. Special attention was focused on differentially expressed miRNAs and their target genes involved in processes related to skeletal muscle injury. Western blot analysis showed protein protection in HMB-pre-treated group compared to control. The viability test confirmed that HMB enhanced cell survival after the hydrogen peroxide exposition. Conclusions Our results suggest that ESC pre-incubated with HMB and exposed to H2O2 could affect expression on miRNA levels responsible for skeletal muscle development, cell proliferation and differentiation, and activation of tissue repair after injury. Enrichment analyses for targeted genes revealed that a large group of genes was associated with the regulation of signaling pathways crucial for muscle tissue development, protein metabolism, muscle injury, and regeneration, as well as with oxidative stress response.
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Affiliation(s)
- Karolina A Chodkowska
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Anna Ciecierska
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Kinga Majchrzak
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Piotr Ostaszewski
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Tomasz Sadkowski
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
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Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls. Sci Rep 2018; 8:5609. [PMID: 29618798 PMCID: PMC5884852 DOI: 10.1038/s41598-018-23139-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/05/2018] [Indexed: 02/08/2023] Open
Abstract
Amyotrophic lateral sclerosis is a late-onset disorder primarily affecting motor neurons and leading to progressive and lethal skeletal muscle atrophy. Small RNAs, including microRNAs (miRNAs), can serve as important regulators of gene expression and can act both globally and in a tissue-/cell-type-specific manner. In muscle, miRNAs called myomiRs govern important processes and are deregulated in various disorders. Several myomiRs have shown promise for therapeutic use in cellular and animal models of ALS; however, the exact miRNA species differentially expressed in muscle tissue of ALS patients remain unknown. Following small RNA-Seq, we compared the expression of small RNAs in muscle tissue of ALS patients and healthy age-matched controls. The identified snoRNAs, mtRNAs and other small RNAs provide possible molecular links between insulin signaling and ALS. Furthermore, the identified miRNAs are predicted to target proteins that are involved in both normal processes and various muscle disorders and indicate muscle tissue is undergoing active reinnervation/compensatory attempts thus providing targets for further research and therapy development in ALS.
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33
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Breed-dependent microRNA expression in the primary culture of skeletal muscle cells subjected to myogenic differentiation. BMC Genomics 2018; 19:109. [PMID: 29390965 PMCID: PMC5793348 DOI: 10.1186/s12864-018-4492-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 01/23/2018] [Indexed: 02/07/2023] Open
Abstract
Background Skeletal muscle in livestock develops into meat, an important source of protein and other nutrients for human consumption. The muscle is largely composed of a fixed number of multinucleated myofibers determined during late gestation and remains constant postnatally. A population of postnatal muscle stem cells, called satellite cells, gives rise to myoblast cells that can fuse with the existing myofibers, thus increasing their size. This requires a delicate balance of transcription and growth factors and specific microRNA (miRNA) expressed by satellite cells and their supporting cells from the muscle stem cell niche. The role of transcription and growth factors in bovine myogenesis is well-characterized; however, very little is known about the miRNA activity during this process. We have hypothesized that the expression of miRNA can vary between primary cultures of skeletal muscle cells isolated from the semitendinosus muscles of different cattle breeds and subjected to myogenic differentiation. Results After a 6-day myogenic differentiation of cells isolated from the muscles of the examined cattle breeds, we found statistically significant differences in the number of myotubes between Hereford (HER)/Limousine (LIM) beef breeds and the Holstein-Friesian (HF) dairy breed (p ≤ 0.001). The microarray analysis revealed differences in the expression of 23 miRNA among the aforementioned primary cultures. On the basis of a functional analysis, we assigned 9 miRNA as molecules responsible for differentiation progression (miR-1, -128a, -133a, -133b, -139, -206, -222, -486, and -503). The target gene prediction and functional analysis revealed 59 miRNA-related genes belonging to the muscle organ development process. Conclusion The number of myotubes and the miRNA expression in the primary cultures of skeletal muscle cells derived from the semitendinosus muscles of the HER/LIM beef cattle breeds and the HF dairy breed vary when cells are subjected to myogenic differentiation. The net effect of the identified miRNA and their target gene action should be considered the result of the breed-dependent activity of satellite cells and muscle stem cell niche cells and their mutual interactions, which putatively can be engaged in the formation of a larger number of myotubes in beef cattle-related cells (HER/LIM) during in vitro myogenesis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4492-5) contains supplementary material, which is available to authorized users.
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Öztürk-Kaloglu D, Hercher D, Heher P, Posa-Markaryan K, Sperger S, Zimmermann A, Wolbank S, Redl H, Hacobian A. A Noninvasive In Vitro Monitoring System Reporting Skeletal Muscle Differentiation. Tissue Eng Part C Methods 2017; 23:1-11. [PMID: 27901409 DOI: 10.1089/ten.tec.2016.0366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Monitoring of cell differentiation is a crucial aspect of cell-based therapeutic strategies depending on tissue maturation. In this study, we have developed a noninvasive reporter system to trace murine skeletal muscle differentiation. Either a secreted bioluminescent reporter (Metridia luciferase) or a fluorescent reporter (green fluorescent protein [GFP]) was placed under the control of the truncated muscle creatine kinase (MCK) basal promoter enhanced by variable numbers of upstream MCK E-boxes. The engineered pE3MCK vector, coding a triple tandem of E-Boxes and the truncated MCK promoter, showed twentyfold higher levels of luciferase activation compared with a Cytomegalovirus (CMV) promoter. This newly developed reporter system allowed noninvasive monitoring of myogenic differentiation in a straining bioreactor. Additionally, binding sequences of endogenous microRNAs (miRNAs; seed sequences) that are known to be downregulated in myogenesis were ligated as complementary seed sequences into the reporter vector to reduce nonspecific signal background. The insertion of seed sequences improved the signal-to-noise ratio up to 25% compared with pE3MCK. Due to the highly specific, fast, and convenient expression analysis for cells undergoing myogenic differentiation, this reporter system provides a powerful tool for application in skeletal muscle tissue engineering.
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Affiliation(s)
- Deniz Öztürk-Kaloglu
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - David Hercher
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - Philipp Heher
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - Katja Posa-Markaryan
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - Simon Sperger
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - Alice Zimmermann
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - Susanne Wolbank
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - Heinz Redl
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
| | - Ara Hacobian
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology , Vienna, Austria
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Circulating MiRNAs as biomarkers of gait speed responses to aerobic exercise training in obese older adults. Aging (Albany NY) 2017; 9:900-913. [PMID: 28301325 PMCID: PMC5391238 DOI: 10.18632/aging.101199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/03/2017] [Indexed: 01/01/2023]
Abstract
Gait speed is a useful predictor of adverse outcomes, including incident mobility disability and mortality in older adults. While aerobic exercise training (AEX) is generally an effective therapy to improve gait speed, individual responses are highly variable. Circulating microRNAs (miRNAs) may contribute to inter-individual changes in gait speed with AEX. We examined whether plasma miRNAs are associated with gait speed changes (dGaitSp) in 33 obese older adults (age: 69.3±3.6 years, BMI: 34.0±3.1 kg/m2, 85% white, 73% women) who performed treadmill walking, 4 days/week for 5 months. Gait speed (baseline: 1.02±0.19 m/s; range of response: −0.2 to 0.35 m/s) was assessed using a 400 meter-fast-paced walk test. Using Nanostring technology, 120 out of 800 miRNAs were found to be abundantly expressed in plasma and 4 of these were significantly changed after AEX: miR-376a-5p increased, while miR-16-5p, miR-27a-3p, and miR-28-3p all decreased. In addition, baseline miR-181a-5p levels (r=-0.40, p=0.02) and percent changes in miR-92a-3p (r=-0.44, p=0.009) associated negatively with dGaitSp. Linear regression combined baseline miR-181a-5p and miR-92a-3p levels showed even stronger associations with dGaitSp (r=-0.48, p=0.005). These results suggest that circulating miR-181a-5p and miR-92a-3p may predict and/or regulate AEX-induced gait speed changes in obese older adults.
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Mok GF, Lozano-Velasco E, Münsterberg A. microRNAs in skeletal muscle development. Semin Cell Dev Biol 2017; 72:67-76. [PMID: 29102719 DOI: 10.1016/j.semcdb.2017.10.032] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/24/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022]
Abstract
A fundamental process during both embryo development and stem cell differentiation is the control of cell lineage determination. In developing skeletal muscle, many of the diffusible signaling molecules, transcription factors and more recently non-coding RNAs that contribute to this process have been identified. This has facilitated advances in our understanding of the molecular mechanisms underlying the control of cell fate choice. Here we will review the role of non-coding RNAs, in particular microRNAs (miRNAs), in embryonic muscle development and differentiation, and in satellite cells of adult muscle, which are essential for muscle growth and regeneration. Some of these short post-transcriptional regulators of gene expression are restricted to skeletal muscle, but their expression can also be more widespread. In addition, we discuss a few examples of long non-coding RNAs, which are numerous but much less well understood.
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Affiliation(s)
- Gi Fay Mok
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Estefania Lozano-Velasco
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrea Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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Wang W, Wang Y, Liu W, van Wijnen AJ. Regulation and biological roles of the multifaceted miRNA-23b (MIR23B). Gene 2017; 642:103-109. [PMID: 29101066 DOI: 10.1016/j.gene.2017.10.085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/31/2017] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are important short endogenous non-coding RNAs that have critical biological roles by acting as post-transcriptional regulators of gene expression. Chromosomal region 9q22.32 encodes the miR-23b/27b/24-1 cluster and produces miR-23b, which is a pleiotropic modulator in many developmental processes and pathological conditions. Expression of miR-23b is actively suppressed and induced in response to many different stimuli. We discuss the biological functions and transcriptional regulation of this multifaceted miRNA in different tumor types, during development, upon viral infection, as well as in various clinical disorders, immune responses, as well as cardiovascular and thyroid functions. The combined body of work suggests that miR-23b expression is modulated by a diverse array of stimuli in cells from different lineages and participates in multiple gene regulatory feedback loops. Elevation of miR-23b levels appears to instruct cells to limit their proliferative and migratory potential, while promoting the acquisition of specialized phenotypes or protection from invading viruses and parasites. In contrast, loss of miR-23b can deregulate normal tissue homeostasis by removing constraints on cell cycle progression and cell motility. Collectively, the findings on miR-23b indicate that it is a very potent post-transcriptional regulator of growth and differentiation during development, multiple cancers and other biological processes. Understanding the regulation and activity of miR-23b has significant diagnostic value in many biological disorders and may identify cellular pathways that are amenable to therapeutic intervention.
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Affiliation(s)
- Wei Wang
- Department of Orthopeadics, Pu Ai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China; Department of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuji Wang
- Department of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; Department of Orthopaedics, Changzhou No. 2 People's Hospital, Nanjing Medical University, 29 Xinglong Alley, Jiangsu, China
| | - Weijun Liu
- Department of Orthopeadics, Pu Ai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Andre J van Wijnen
- Department of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
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Pinto SK, Lamon S, Stephenson EJ, Kalanon M, Mikovic J, Koch LG, Britton SL, Hawley JA, Camera DM. Expression of microRNAs and target proteins in skeletal muscle of rats selectively bred for high and low running capacity. Am J Physiol Endocrinol Metab 2017; 313:E335-E343. [PMID: 28465283 PMCID: PMC6189633 DOI: 10.1152/ajpendo.00043.2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 01/21/2023]
Abstract
Impairments in mitochondrial function and substrate metabolism are implicated in the etiology of obesity and Type 2 diabetes. MicroRNAs (miRNAs) can degrade mRNA or repress protein translation and have been implicated in the development of such disorders. We used a contrasting rat model system of selectively bred high- (HCR) or low- (LCR) intrinsic running capacity with established differences in metabolic health to investigate the molecular mechanisms through which miRNAs regulate target proteins mediating mitochondrial function and substrate oxidation processes. Quantification of select miRNAs using the rat miFinder miRNA PCR array revealed differential expression of 15 skeletal muscles (musculus tibialis anterior) miRNAs between HCR and LCR rats (14 with higher expression in LCR; P < 0.05). Ingenuity Pathway Analysis predicted these altered miRNAs to collectively target multiple proteins implicated in mitochondrial dysfunction and energy substrate metabolism. Total protein abundance of citrate synthase (CS; miR-19 target) and voltage-dependent anion channel 1 (miR-7a target) were higher in HCR compared with LCR cohorts (~57 and ~26%, respectively; P < 0.05). A negative correlation was observed for miR-19a-3p and CS (r = 0.32, P = 0.015) protein expression. To determine whether miR-19a-3p can regulate CS in vitro, we performed luciferase reporter and transfection assays in C2C12 myotubes. MiR-19a-3p binding to the CS untranslated region did not change luciferase reporter activity; however, miR-19a-3p transfection decreased CS protein expression (∼70%; P < 0.05). The differential miRNA expression targeting proteins implicated in mitochondrial dysfunction and energy substrate metabolism may contribute to the molecular basis, mediating the divergent metabolic health profiles of LCR and HCR rats.
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Affiliation(s)
- Samuel K Pinto
- Centre for Exercise and Nutrition, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| | - Séverine Lamon
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University Geelong, Victoria, Australia
| | - Erin J Stephenson
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Ming Kalanon
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University Geelong, Victoria, Australia
| | - Jasmine Mikovic
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University Geelong, Victoria, Australia
| | - Lauren G Koch
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan; and
| | - Steven L Britton
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan; and
| | - John A Hawley
- Centre for Exercise and Nutrition, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Donny M Camera
- Centre for Exercise and Nutrition, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia;
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Integration of miRNA and mRNA expression profiles reveals microRNA-regulated networks during muscle wasting in cardiac cachexia. Sci Rep 2017; 7:6998. [PMID: 28765595 PMCID: PMC5539204 DOI: 10.1038/s41598-017-07236-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 06/28/2017] [Indexed: 12/28/2022] Open
Abstract
Cardiac cachexia (CC) is a common complication of heart failure (HF) associated with muscle wasting and poor patient prognosis. Although different mechanisms have been proposed to explain muscle wasting during CC, its pathogenesis is still not understood. Here, we described an integrative analysis between miRNA and mRNA expression profiles of muscle wasting during CC. Global gene expression profiling identified 1,281 genes and 19 miRNAs differentially expressed in muscle wasting during CC. Several of these deregulated genes are known or putative targets of the altered miRNAs, including miR-29a-3p, miR-29b-3p, miR-210-5p, miR-214, and miR-489. Gene ontology analysis on integrative mRNA/miRNA expression profiling data revealed miRNA interactions affecting genes that regulate extra-cellular matrix (ECM) organization, proteasome protein degradation, citric acid cycle and respiratory electron transport. We further identified 11 miRNAs, including miR-29a-3p and miR-29b-3p, which target 21 transcripts encoding the collagen proteins related to ECM organization. Integrative miRNA and mRNA global expression data allowed us to identify miRNA target genes involved in skeletal muscle wasting in CC. Our functional experiments in C2C12 cells confirmed that miR-29b down-regulates collagen genes and contributes to muscle cell atrophy. Collectively, our results suggest that key ECM-associated miRNAs and their target genes may contribute to CC in HF.
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Stankevicins L, Barat A, Dessen P, Vassetzky Y, de Moura Gallo CV. The microRNA-205-5p is correlated to metastatic potential of 21T series: A breast cancer progression model. PLoS One 2017; 12:e0173756. [PMID: 28346474 PMCID: PMC5367783 DOI: 10.1371/journal.pone.0173756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 02/27/2017] [Indexed: 12/02/2022] Open
Abstract
MicroRNA is a class of noncoding RNAs able to base pair with complementary messenger RNA sequences, inhibiting their expression. These regulatory molecules play important roles in key cellular processes including cell proliferation, differentiation and response to DNA damage; changes in miRNA expression are a common feature of human cancers. To gain insights into the mechanisms involved in breast cancer progression we conducted a microRNA global expression analysis on a 21T series of cell lines obtained from the same patient during different stages of breast cancer progression. These stages are represented by cell lines derived from normal epithelial (H16N2), atypical ductal hyperplasia (21PT), primary in situ ductal carcinoma (21NT) and pleural effusion of a lung metastasis (21MT-1 and 21MT-2). In a global microRNA expression analysis, miR-205-5p was the only miRNA to display an important downregulation in the metastatic cell lines (21MT-1; 21MT-2) when compared to the non-invasive cells (21PT and 21NT). The lower amounts of miR-205-5p found also correlated with high histological grades biopsies and with higher invasion rates in a Boyden chamber assay. This work pinpoints miR-205-5p as a potential player in breast tumor invasiveness.
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Affiliation(s)
- L. Stankevicins
- Departamento de Genética, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcantara Gomes, Rio de Janeiro, Brazil
- CNRS UMR 8126 «Signalisation, noyaux et innovations en cancérologie», Université Paris-Sud, Institut de Cancérologie Gustave-Roussy, Villejuif cedex, France
| | - A. Barat
- CNRS UMR 8126 «Signalisation, noyaux et innovations en cancérologie», Université Paris-Sud, Institut de Cancérologie Gustave-Roussy, Villejuif cedex, France
| | - P. Dessen
- Functional Genomics Unit, Institut de Cancérologie Gustave-Roussy, Villejuif, France
| | - Y. Vassetzky
- CNRS UMR 8126 «Signalisation, noyaux et innovations en cancérologie», Université Paris-Sud, Institut de Cancérologie Gustave-Roussy, Villejuif cedex, France
- N.K. Koltzov Institute of Developmental Biology RAS, Moscow, Russia
| | - C. V. de Moura Gallo
- Departamento de Genética, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcantara Gomes, Rio de Janeiro, Brazil
- * E-mail:
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Davegårdh C, Broholm C, Perfilyev A, Henriksen T, García-Calzón S, Peijs L, Hansen NS, Volkov P, Kjøbsted R, Wojtaszewski JFP, Pedersen M, Pedersen BK, Ballak DB, Dinarello CA, Heinhuis B, Joosten LAB, Nilsson E, Vaag A, Scheele C, Ling C. Abnormal epigenetic changes during differentiation of human skeletal muscle stem cells from obese subjects. BMC Med 2017; 15:39. [PMID: 28222718 PMCID: PMC5320752 DOI: 10.1186/s12916-017-0792-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/11/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Human skeletal muscle stem cells are important for muscle regeneration. However, the combined genome-wide DNA methylation and expression changes taking place during adult myogenesis have not been described in detail and novel myogenic factors may be discovered. Additionally, obesity is associated with low relative muscle mass and diminished metabolism. Epigenetic alterations taking place during myogenesis might contribute to these defects. METHODS We used Infinium HumanMethylation450 BeadChip Kit (Illumina) and HumanHT-12 Expression BeadChip (Illumina) to analyze genome-wide DNA methylation and transcription before versus after differentiation of primary human myoblasts from 14 non-obese and 14 obese individuals. Functional follow-up experiments were performed using siRNA mediated gene silencing in primary human myoblasts and a transgenic mouse model. RESULTS We observed genome-wide changes in DNA methylation and expression patterns during differentiation of primary human muscle stem cells (myoblasts). We identified epigenetic and transcriptional changes of myogenic transcription factors (MYOD1, MYOG, MYF5, MYF6, PAX7, MEF2A, MEF2C, and MEF2D), cell cycle regulators, metabolic enzymes and genes previously not linked to myogenesis, including IL32, metallothioneins, and pregnancy-specific beta-1-glycoproteins. Functional studies demonstrated IL-32 as a novel target that regulates human myogenesis, insulin sensitivity and ATP levels in muscle cells. Furthermore, IL32 transgenic mice had reduced insulin response and muscle weight. Remarkably, approximately 3.7 times more methylation changes (147,161 versus 39,572) were observed during differentiation of myoblasts from obese versus non-obese subjects. In accordance, DNMT1 expression increased during myogenesis only in obese subjects. Interestingly, numerous genes implicated in metabolic diseases and epigenetic regulation showed differential methylation and expression during differentiation only in obese subjects. CONCLUSIONS Our study identifies IL-32 as a novel myogenic regulator, provides a comprehensive map of the dynamic epigenome during differentiation of human muscle stem cells and reveals abnormal epigenetic changes in obesity.
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Affiliation(s)
- Cajsa Davegårdh
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Christa Broholm
- Department of Endocrinology, Rigshospitalet, Copenhagen, 2100, Denmark
| | - Alexander Perfilyev
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Tora Henriksen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sonia García-Calzón
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Lone Peijs
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Petr Volkov
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Rasmus Kjøbsted
- Department of Exercise and Sports Sciences, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen F P Wojtaszewski
- Department of Exercise and Sports Sciences, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dov B Ballak
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA.,Department of Medicine, University of Colorado, Aurora, CO, 80045, USA
| | - Charles A Dinarello
- Department of Medicine, University of Colorado, Aurora, CO, 80045, USA.,Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bas Heinhuis
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Emma Nilsson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, 2100, Denmark.,Early Clinical Development, Translational Medical Unit, AstraZeneca, Mölndal, 431 83, Sweden
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden.
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Saada YB, Dib C, Lipinski M, Vassetzky YS. Genome- and Cell-Based Strategies in Therapy of Muscular Dystrophies. BIOCHEMISTRY (MOSCOW) 2017; 81:678-90. [PMID: 27449614 DOI: 10.1134/s000629791607004x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Muscular dystrophies are a group of heterogeneous genetic disorders characterized by progressive loss of skeletal muscle mass. Depending on the muscular dystrophy, the muscle weakness varies in degree of severity. The majority of myopathies are due to genetic events leading to a loss of function of key genes involved in muscle function. Although there is until now no curative treatment to stop the progression of most myopathies, a significant number of experimental gene- and cell-based strategies and approaches have been and are being tested in vitro and in animal models, aiming to restore gene function. Genome editing using programmable endonucleases is a powerful tool for modifying target genome sequences and has been extensively used over the last decade to correct in vitro genetic defects of many single-gene diseases. By inducing double-strand breaks (DSBs), the engineered endonucleases specifically target chosen sequences. These DSBs are spontaneously repaired either by homologous recombination in the presence of a sequence template, or by nonhomologous-end joining error prone repair. In this review, we highlight recent developments and challenges for genome-editing based strategies that hold great promise for muscular dystrophies and regenerative medicine.
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Affiliation(s)
- Y Bou Saada
- UMR 8126, CNRS, Université Paris-Sud, Université Paris Saclay, Institut de Cancérologie Gustave-Roussy, Villejuif, F-94805, France.
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43
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Sjögren RJO, Lindgren Niss MHL, Krook A. Skeletal Muscle microRNAs: Roles in Differentiation, Disease and Exercise. RESEARCH AND PERSPECTIVES IN ENDOCRINE INTERACTIONS 2017. [DOI: 10.1007/978-3-319-72790-5_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Hua W, Zhang M, Wang Y, Yu L, Zhao T, Qiu X, Wang L. Mechanical stretch regulates microRNA expression profile via NF-κB activation in C2C12 myoblasts. Mol Med Rep 2016; 14:5084-5092. [PMID: 27840929 PMCID: PMC5355701 DOI: 10.3892/mmr.2016.5907] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 09/23/2016] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs/miRs) and nuclear factor (NF)-κB activation are involved in mechanical stretch-induced skeletal muscle regeneration. However, there are a small number of miRNAs that have been reported to be associated with NF‑κB activation during mechanical stretch-induced myogenesis. In the present study, C2C12 myoblasts underwent cyclic mechanical stretch in vitro, to explore the relationship between miRNA expression and NF‑κB activation during stretch-mediated myoblast proliferation. The results revealed that 10% deformation, 0.125 Hz cyclic mechanical stretch could promote myoblast proliferation. The miRNA expression profile was subsequently altered; miR‑500, ‑1934, ‑31, ‑378, ‑331 and ‑5097 were downregulated, whereas miR‑1941 was upregulated. These miRNAs were all involved in stretch‑mediated myoblast proliferation. Notably, the expression of these miRNAs was reversed following treatment of 0.125 Hz mechanically stretched C2C12 cells with NF‑κB inhibitors, which was accompanied by C2C12 cell growth suppression. Therefore, the present study is the first, to the best of our knowledge, to demonstrate that the NF‑κB‑dependent miRNA profile is associated with mechanical stretch-induced myoblast proliferation.
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Affiliation(s)
- Wenxi Hua
- Department of Anatomy, Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangzhou, Guangdong 510515, P.R. China
| | - Mahui Zhang
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yongkui Wang
- Department of Anatomy, Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangzhou, Guangdong 510515, P.R. China
| | - Lei Yu
- Department of Anatomy, Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangzhou, Guangdong 510515, P.R. China
| | - Tingting Zhao
- Department of Anatomy, Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangzhou, Guangdong 510515, P.R. China
| | - Xiaozhong Qiu
- Department of Anatomy, Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangzhou, Guangdong 510515, P.R. China
| | - Leyu Wang
- Department of Anatomy, Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangzhou, Guangdong 510515, P.R. China
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MicroRNA-17-92 regulates myoblast proliferation and differentiation by targeting the ENH1/Id1 signaling axis. Cell Death Differ 2016; 23:1658-69. [PMID: 27315298 PMCID: PMC5041193 DOI: 10.1038/cdd.2016.56] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 05/19/2015] [Accepted: 05/20/2016] [Indexed: 12/21/2022] Open
Abstract
Myogenesis is an important biological process that occurs during both skeletal muscle regeneration and postnatal growth. Growing evidence points to the critical role of microRNAs (miRNAs) in myogenesis. Our analysis of miRNA expression patterns reveal that miRNAs of miR-17-92 cluster are dramatically downregulated in C2C12 cells after myogenesis stimulation, are strongly induced in mouse skeletal muscle after injury and decrease steadily thereafter and are downregulated with age in skeletal muscle during mouse and porcine postnatal growth. However, their roles in muscle developmental processes remain elusive. We show that the miR-17-92 cluster promotes mouse myoblast proliferation but inhibits myotube formation. miR-17, -20a and -92a target the actin-associated protein enigma homolog 1 (ENH1). The silencing of ENH1 increased the nuclear accumulation of the inhibitor of differentiation 1 (Id1) and represses myogenic differentiation. Furthermore, the injection of adenovirus expressing miR-20a into the tibialia anterior muscle downregulates ENH1 and delays regeneration. In addition, the downregulation of miR-17-92 during myogenesis is transcriptionally regulated by E2F1. Overall, our results reveal a E2F1/miR-17-92/ENH1/Id1 regulatory axis during myogenesis.
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Sheng X, Wang L, Ni H, Wang L, Qi X, Xing S, Guo Y. Comparative Analyses between Skeletal Muscle miRNAomes from Large White and Min Pigs Revealed MicroRNAs Associated with Postnatal Muscle Hypertrophy. PLoS One 2016; 11:e0156780. [PMID: 27253583 PMCID: PMC4890935 DOI: 10.1371/journal.pone.0156780] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/19/2016] [Indexed: 01/15/2023] Open
Abstract
The molecular mechanism regulated by microRNAs (miRNAs) that underlies postnatal hypertrophy of skeletal muscle is complex and remains unclear. Here, the miRNAomes of longissimus dorsi muscle collected at five postnatal stages (60, 120, 150, 180, and 210 days after birth) from Large White (commercial breed) and Min pigs (indigenous breed of China) were analyzed by Illumina sequencing. We identified 734 miRNAs comprising 308 annotated miRNAs and 426 novel miRNAs, of which 307 could be considered pig-specific. Comparative analysis between two breeds suggested that 60 and 120 days after birth were important stages for skeletal muscle hypertrophy and intramuscular fat accumulation. A total of 263 miRNAs were significantly differentially expressed between two breeds at one or more developmental stages. In addition, the differentially expressed miRNAs between every two adjacent developmental stages in each breed were determined. Notably, ssc-miR-204 was significantly more highly expressed in Min pig skeletal muscle at all postnatal stages compared with its expression in Large White pig skeletal muscle. Based on gene ontology and KEGG pathway analyses of its predicted target genes, we concluded that ssc-miR-204 may exert an impact on postnatal hypertrophy of skeletal muscle by regulating myoblast proliferation. The results of this study will help in elucidating the mechanism underlying postnatal hypertrophy of skeletal muscle modulated by miRNAs, which could provide valuable information for improvement of pork quality and human myopathy.
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Affiliation(s)
- Xihui Sheng
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, 102206, China
| | - Ligang Wang
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hemin Ni
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, 102206, China
| | - Lixian Wang
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaolong Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, 102206, China
| | - Shuhan Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, 102206, China
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Ozuemba B, Masilamani TJ, Loiselle JJ, Koenderink B, Vanderbeck KA, Knee J, Larivière C, Sutherland LC. Co- and post-transcriptional regulation of Rbm5 and Rbm10 in mouse cells as evidenced by tissue-specific, developmental and disease-associated variation of splice variant and protein expression levels. Gene 2016; 580:26-36. [PMID: 26784654 DOI: 10.1016/j.gene.2015.12.070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/31/2015] [Indexed: 01/09/2023]
Abstract
BACKGROUND Expression and function of the two RNA binding proteins and regulators of alternative splicing, RBM5 and RBM10, have largely been studied in human tissue and cell lines. The objective of the study described herein was to examine their expression in mouse tissue, in order to lay the framework for comprehensive functional studies using mouse models. METHODS All RNA variants of Rbm5 and Rbm10 were examined in a range of normal primary mouse tissues. RNA and protein were examined in differentiating C2C12 myoblasts and in denervated and dystonin-deficient mouse skeletal muscle. RESULTS All Rbm5 and Rbm10 variants examined were expressed in all mouse tissues and cell lines. In general, Rbm5 and Rbm10 RNA expression was higher in brain than in skin. RNA expression levels were more varied between cardiac and skeletal muscle, depending on the splice variant: for instance, Rbm10v1 RNA was higher in skeletal than cardiac muscle, whereas Rbm10v3 RNA was higher in cardiac than skeletal muscle. In mouse brain, cardiac and skeletal muscle, RNA encoding an approximately 17kDa potential paralogue of a small human RBM10 isoform was detected, and the protein observed in myoblasts and myotubes. Expression of Rbm5 and Rbm10 RNA remained constant during C2C12 myogenesis, but protein levels significantly decreased. In two muscle disease models, neither Rbm10 nor Rbm5 showed significant transcriptional changes, although significant specific alternative splicing changes of Rbm5 pre-mRNA were observed. Increased RBM10 protein levels were observed following denervation. CONCLUSIONS The varied co-transcriptional and post-transcriptional regulation aspects of Rbm5 and Rbm10 expression associated with mouse tissues, myogenesis and muscle disease states suggest that a mouse model would be an interesting and useful model in which to study comprehensive functional aspects of RBM5 and RBM10.
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Affiliation(s)
| | - Twinkle J Masilamani
- Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | - Julie J Loiselle
- Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | - Benjamin Koenderink
- AMRIC, Health Sciences North, 41 Ramsey Lake Road, Sudbury, ON, P3E 5J1, Canada
| | - Kaitlin A Vanderbeck
- School of Human Kinetics, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | - Jose Knee
- AMRIC, Health Sciences North, 41 Ramsey Lake Road, Sudbury, ON, P3E 5J1, Canada
| | - Céline Larivière
- Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada; School of Human Kinetics, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | - Leslie C Sutherland
- Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada; AMRIC, Health Sciences North, 41 Ramsey Lake Road, Sudbury, ON, P3E 5J1, Canada; Division of Medical Sciences, Northern Ontario School of Medicine, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada; Department of Chemistry and Biochemistry, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada; Department of Medicine, Division of Medical Oncology, University of Ottawa, Ottawa, ON, Canada.
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49
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Tian F, Han Y, Yan X, Zhong D, Yang G, Lei J, Li X, Wang X. Upregulation of microrna-451 increases the sensitivity of A549 cells to radiotherapy through enhancement of apoptosis. Thorac Cancer 2015; 7:226-31. [PMID: 27042226 PMCID: PMC4773304 DOI: 10.1111/1759-7714.12318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/27/2015] [Indexed: 01/21/2023] Open
Abstract
Background: As radioresistance of non‐small cell lung cancers (NSCLC) is one of the main causes of failure in radiotherapy, we examined whether micro ribonucleic acid (miR‐451) could function as a potential radiosensitizer of NSCLC and the related mechanism. Methods: Radioresistant NSCLC cell line A549 was transfected with pre‐miR‐451 or a scrambled control. The miR‐451 messenger RNA level, colony‐forming ability, apoptosis, and phosphatase and tensin homolog (PTEN) protein level of 549 cells were examined by real‐time polymerase chain reaction, clonogenic assay, flow cytometry analysis, and Western blot. Results: Upregulation of miR‐451 enhanced the suppressive effects of irradiation on the colony‐forming ability of A549 cells. The apoptosis and PTEN expression of A549 cells post‐irradiation were also enhanced by upregulation of miR‐451. Conclusions: Upregulation of miR‐451 sensitized radioresistant NSCLC A549 cells to irradiation through the enhancement of apoptosis. The activation of PTEN post‐irradiation was possibly correlated with the radiosensitization of A549 cells induced by miR‐451 overexpression.
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Affiliation(s)
- Feng Tian
- Department of Thoracic Surgery Tangdu Hospital the Forth Military Medical University Xi'an China
| | - Yong Han
- Department of Thoracic Surgery Tangdu Hospital the Forth Military Medical University Xi'an China
| | - Xiaolong Yan
- Department of Thoracic Surgery Tangdu Hospital the Forth Military Medical University Xi'an China
| | - Daixing Zhong
- Department of Thoracic Surgery Tangdu Hospital the Forth Military Medical University Xi'an China
| | - Guang Yang
- Department of Thoracic Surgery Tangdu Hospital the Forth Military Medical University Xi'an China
| | - Jie Lei
- Department of Thoracic Surgery Tangdu Hospital the Forth Military Medical University Xi'an China
| | - Xiaofei Li
- Department of Thoracic Surgery Tangdu Hospital the Forth Military Medical University Xi'an China
| | - Xiaoping Wang
- Department of Thoracic Surgery Tangdu Hospital the Forth Military Medical University Xi'an China
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50
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Režen T, Kovanda A, Eiken O, Mekjavič I, Rogelj B. Response to the letter to the editor by Kristensen MM, Helge JW and Dela F. Acta Physiol (Oxf) 2015. [PMID: 26198423 DOI: 10.1111/apha.12551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- T. Režen
- Biomedical Research Institute BRIS; Ljubljana Slovenia
| | - A. Kovanda
- Biomedical Research Institute BRIS; Ljubljana Slovenia
- Department of Biotechnology; Jozef Stefan Institute; Ljubljana Slovenia
| | - O. Eiken
- Department of Environmental Physiology; School of Technology and Health; Royal Institute of Technology; Solna Sweden
| | - I. Mekjavič
- Department of Automation, Biocybernetics and Robotics; Jozef Stefan Institute; Ljubljana Slovenia
| | - B. Rogelj
- Biomedical Research Institute BRIS; Ljubljana Slovenia
- Department of Biotechnology; Jozef Stefan Institute; Ljubljana Slovenia
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