1
|
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.
Collapse
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
| |
Collapse
|
2
|
Saini SK, Pérez‐Cremades D, Cheng HS, Kosmac K, Peterson CA, Li L, Tian L, Dong G, Wu KK, Bouverat B, Wohlgemuth SE, Ryan T, Sufit RL, Ferrucci L, McDermott MM, Leeuwenburgh C, Feinberg MW. Dysregulated Genes, MicroRNAs, Biological Pathways, and Gastrocnemius Muscle Fiber Types Associated With Progression of Peripheral Artery Disease: A Preliminary Analysis. J Am Heart Assoc 2022; 11:e023085. [PMID: 36300658 PMCID: PMC9673627 DOI: 10.1161/jaha.121.023085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/08/2022] [Indexed: 02/01/2023]
Abstract
Background Peripheral artery disease (PAD) is associated with gastrocnemius muscle abnormalities. However, the biological pathways associated with gastrocnemius muscle dysfunction and their associations with progression of PAD are largely unknown. This study characterized differential gene and microRNA (miRNA) expression in gastrocnemius biopsies from people without PAD compared with those with PAD. Participants with PAD included those with and without PAD progression. Methods and Results mRNA and miRNA sequencing were performed to identify differentially expressed genes, differentially expressed miRNAs, mRNA-miRNA interactions, and associated biological pathways for 3 sets of comparisons: (1) PAD progression (n=7) versus non-PAD (n=7); (2) PAD no progression (n=6) versus non-PAD; and (3) PAD progression versus PAD no progression. Immunohistochemistry was performed to determine gastrocnemius muscle fiber types and muscle fiber size. Differentially expressed genes and differentially expressed miRNAs were more abundant in the comparison of PAD progression versus non-PAD compared with PAD with versus without progression. Among the top significant cellular pathways in subjects with PAD progression were muscle contraction or development, transforming growth factor-beta, growth/differentiation factor, and activin signaling, inflammation, cellular senescence, and notch signaling. Subjects with PAD progression had increased frequency of smaller Type 2a gastrocnemius muscle fibers in exploratory analyses. Conclusions Humans with PAD progression exhibited greater differences in the number of gene and miRNA expression, biological pathways, and Type 2a muscle fiber size compared with those without PAD. Fewer differences were observed between people with PAD without progression and control patients without PAD. Further study is needed to confirm whether the identified transcripts may serve as potential biomarkers for diagnosis and progression of PAD.
Collapse
Affiliation(s)
- Sunil K. Saini
- All India Institute of Medical Sciences, Department of BiophysicsNew DelhiIndia
| | - Daniel Pérez‐Cremades
- Cardiovascular Division, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMA
- Department of PhysiologyUniversity of Valencia and INCLIVA Biomedical Research InstituteValenciaSpain
| | - Henry S. Cheng
- Cardiovascular Division, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMA
| | - Kate Kosmac
- Center for Muscle Biology, College of Health SciencesUniversity of KentuckyLexingtonKY
| | - Charlotte A Peterson
- Center for Muscle Biology, College of Health SciencesUniversity of KentuckyLexingtonKY
| | - Lingyu Li
- Department of Preventive Medicine, Northwestern University Feinberg School of MedicineChicagoIL
| | - Lu Tian
- Department of Health Research and Policy, Stanford UniversityStanfordCA
| | - Gengfu Dong
- Department of Applied Physiology & Kinesiology, University of FloridaGainesvilleFL
| | - Kevin K. Wu
- Department of Aging and Geriatric Research, University of Florida, Institute on AgingGainesvilleFL
| | - Brian Bouverat
- Department of Aging and Geriatric Research, University of Florida, Institute on AgingGainesvilleFL
| | - Stephanie E. Wohlgemuth
- Department of Aging and Geriatric Research, University of Florida, Institute on AgingGainesvilleFL
| | - Terence Ryan
- Department of Applied Physiology & Kinesiology, University of FloridaGainesvilleFL
| | - Robert L. Sufit
- Department of Medicine, Northwestern University Feinberg School of MedicineChicagoIL
| | - Luigi Ferrucci
- Division of Intramural Research, National Institute on AgingBaltimoreMD
| | - Mary M. McDermott
- Department of Preventive Medicine, Northwestern University Feinberg School of MedicineChicagoIL
- Department of Medicine, Northwestern University Feinberg School of MedicineChicagoIL
| | - Christiaan Leeuwenburgh
- Department of Aging and Geriatric Research, University of Florida, Institute on AgingGainesvilleFL
| | - Mark W. Feinberg
- Cardiovascular Division, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMA
| |
Collapse
|
3
|
Laghari AA, Suchal ZA, Avani R, Khan DA, Kabani AS, Nouman M, Enam SA. Prognostic Potential of MicroRNAs in Glioma Patients: A Meta-Analysis. ASIAN JOURNAL OF ONCOLOGY 2022. [DOI: 10.1055/s-0042-1744448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Abstract
Introduction MicroRNAs are a noncoding RNA involved in affecting several transcription and translation pathways. Their use has been discussed as potential predictors of several tumors. Their use as potential biomarker in glioma patients is still controversial. The purpose of this meta-analysis is to explore the possible role of such microRNAs in glioma patients.
Methods After an extensive literature search done on PubMed and Embase, 20 studies were chosen for our analyses with the 9 discussing 11 tumor promoting microRNAs and 11 studies discussing 11 tumor suppressing microRNAs. The data needed was extracted from these studies including the hazard ratio that was used as the effect size for the purpose of our analysis. The needed analysis was performed using Stata and Excel.
Results The pooled hazard ratio for our analysis with patients having a lower microRNA expression for tumor promoting microRNAs came to be 2.63 (p < 0.001), while the hazard ratio for patients with higher expression of tumor promoting microRNA was 2.47 (p < 0.001) with both results being statistically significant. However, as significant heterogeneity was observed a random effect model for analysis was used. Subgroup analysis was further performed using grade, cutoff value (mean or median), sample type (Serum or Blood), and Karnofsky performance score, all of them showing a high hazard ratio.
Conclusion Our results showed that both tumor inhibitory and promoting microRNA can be used as prognostic tool in glioma patients with a poorer prognosis associated with a lower expression in tumor suppressive and higher expression in tumor promoting microRNA, respectively. However, to support this, future studies on a much larger scale would be needed.
Collapse
Affiliation(s)
- Altaf Ali Laghari
- Division of Neurosurgery, Aga Khan University, Stadium Road, Karachi, Pakistan
| | | | - Rohan Avani
- Medical College, Aga Khan University, Karachi, Pakistan
| | | | | | - Muhammad Nouman
- Biological Sciences, Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Syed Ather Enam
- Department of Surgery, Aga Khan University, Stadium Road, Karachi, Pakistan
| |
Collapse
|
4
|
Nan YY, Zhang WJ, Huang DH, Li QY, Shi Y, Yang T, Liang XP, Xiao CY, Guo BL, Xiang Y. Evaluation of a five-gene signature associated with stromal infiltration for diffuse large B-cell lymphoma. World J Clin Cases 2021; 9:4585-4598. [PMID: 34222425 PMCID: PMC8223837 DOI: 10.12998/wjcc.v9.i18.4585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/26/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is a common non-Hodgkin lymphoma. The development of immunotherapy greatly improves the patient prognosis but there are some exceptions. Thus, screening for better biomarkers for prognostic evaluation could contribute to the treatment of DLBCL patients.
AIM To screen the novel mediators involved in the development of DLBCL.
METHODS The GSE60 dataset was applied to identify the differentially expressed genes (DEGs) in DLBCL, and the principal components analysis plot was used to determine the quality of the included samples. The protein-protein interactions were analyzed by the STRING tool. The key hub genes were entered into to the GEPIA database to determine their expressions in DLBCL. Furthermore, these hub gene alterations were analyzed in cBioportal. The UALCAN portal was employed to analyze the expression of the hub genes in different stages of DLBCL. The Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data Score was conducted to evaluate the correlation between the gene expression and tumor purity. The gene-gene correlation analysis was conducted in the GEPIA. The stromal score analysis was conducted in TIMER to confirm the correlation between the gene expression and infiltrated stromal cells. The correlation between the indicated genes and infiltration level of cancer-associated fibroblasts (CAFs) was also completed in TIMER with two methods, MCP-Counter and Tumor immune dysfunction and exclusion. The correlation between fibronectin (FN1) protein level and secreted protein acidic and cysteine-rich (SPARC) messenger ribonucleic acid expression was confirmed in the cBioportal.
RESULTS The top 20 DEGs in DLBCL were identified, and the principal components analysis plot confirmed the quality of the significant DEGs. The pairwise correlation coefficient analysis among all samples showed that these DEGs have a certain co-expression pattern. The DEGs were subjected to STRING to identify the hub genes, alpha-2-macroglobulin (A2M), cathepsin B (CTSB), FN1, matrix metallopeptidase 9 (MMP9), and SPARC. The five hub genes were confirmed to be overexpressed in DLBCL. The cBioportal portal detected these five hub genes that had gene alteration, including messenger ribonucleic acid high amplification and missense mutation, and the gene alteration percentages of A2M, FN1, CTSB, MMP9, and SPARC were 5%, 8%, 5%, 2.7%, and 5%, respectively. Furthermore, the five hub genes had a potential positive correlation with tumor stage. The correlation analysis between the five genes and tumor purity confirmed that the five genes were overexpressed in DLBCL and had a positive correlation with the development of DLBCL. More interestingly, the five genes had a significant correlation with the stromal infiltration scores. The correlation analysis between the fives genes and CAFs also showed a significant value, among which the top two genes, FN1 and SPARC, had a remarkable co-expression pattern.
CONCLUSION The top DEGs were identified, and the five hub genes were overexpressed in DLBCL. Furthermore, the gene alterations were confirmed and the positive correlation with tumor purity revealed the overexpression of the five genes and close association with the development of DLBCL. More interestingly, the five genes were positively correlated with stromal infiltration, especially in CAFs. The top two genes, FN1 and SPARC, showed a co-expression pattern, which indicates their potential as novel therapeutic targets for DLBCL.
Collapse
Affiliation(s)
- Ying-Yu Nan
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Wen-Jun Zhang
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - De-Hong Huang
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Qi-Ying Li
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yang Shi
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Tao Yang
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Xi-Ping Liang
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Chun-Yan Xiao
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Bing-Ling Guo
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Ying Xiang
- Department of Hematology, Chongqing University Cancer Hospital, Chongqing 400030, China
| |
Collapse
|
5
|
Lala-Tabbert N, AlSudais H, Marchildon F, Fu D, Wiper-Bergeron N. CCAAT/enhancer-binding protein beta promotes muscle stem cell quiescence through regulation of quiescence-associated genes. Stem Cells 2020; 39:345-357. [PMID: 33326659 DOI: 10.1002/stem.3319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022]
Abstract
Regeneration of skeletal muscle depends on resident muscle stem cells called satellite cells that in healthy, uninjured muscle remain quiescent (noncycling). After activation and expansion of satellite cells postinjury, satellite cell numbers return to uninjured levels and return to mitotic quiescence. Here, we show that the transcription factor CCAAT/enhancer-binding protein beta (C/EBPβ) is required to maintain quiescence of satellite cells in uninjured muscle. We show that C/EBPβ is expressed in quiescent satellite cells in vivo and upregulated in noncycling myoblasts in vitro. Loss of C/EBPβ in satellite cells promotes their premature exit from quiescence resulting in spontaneous activation and differentiation of the stem cell pool. Forced expression of C/EBPβ in myoblasts inhibits proliferation by upregulation of 28 quiescence-associated genes. Furthermore, we find that caveolin-1 is a direct transcriptional target of C/EBPβ and is required for cell cycle exit in muscle satellite cells expressing C/EBPβ. The induction of mitotic quiescence is considered necessary for the long-term maintenance of adult stem cell populations with dysregulation driving increased differentiation of progenitors and depletion of the stem cell pool. Our findings place C/EBPβ as an important transcriptional regulator of muscle satellite cell quiescence.
Collapse
Affiliation(s)
- Neena Lala-Tabbert
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Hamood AlSudais
- Graduate Program in Cellular and Molecular Medicine, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - François Marchildon
- Graduate Program in Cellular and Molecular Medicine, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York, USA
| | - Dechen Fu
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, USA
| | - Nadine Wiper-Bergeron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
6
|
Nair VD, Ge Y, Li S, Pincas H, Jain N, Seenarine N, Amper MAS, Goodpaster BH, Walsh MJ, Coen PM, Sealfon SC. Sedentary and Trained Older Men Have Distinct Circulating Exosomal microRNA Profiles at Baseline and in Response to Acute Exercise. Front Physiol 2020; 11:605. [PMID: 32587527 PMCID: PMC7298138 DOI: 10.3389/fphys.2020.00605] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022] Open
Abstract
Exercise has multi-systemic benefits and attenuates the physiological impairments associated with aging. Emerging evidence suggests that circulating exosomes mediate some of the beneficial effects of exercise via the transfer of microRNAs between tissues. However, the impact of regular exercise and acute exercise on circulating exosomal microRNAs (exomiRs) in older populations remains unknown. In the present study, we analyzed circulating exomiR expression in endurance-trained elderly men (n = 5) and age-matched sedentary males (n = 5) at baseline (Pre), immediately after a forty minute bout of aerobic exercise on a cycle ergometer (Post), and three hours after this acute exercise (3hPost). Following the isolation and enrichment of exosomes from plasma, exosome-enriched preparations were characterized and exomiR levels were determined by sequencing. The effect of regular exercise on circulating exomiRs was assessed by comparing the baseline expression levels in the trained and sedentary groups. The effect of acute exercise was determined by comparing baseline and post-training expression levels in each group. Regular exercise resulted in significantly increased baseline expression of three exomiRs (miR-486-5p, miR-215-5p, miR-941) and decreased expression of one exomiR (miR-151b). Acute exercise altered circulating exomiR expression in both groups. However, exomiRs regulated by acute exercise in the trained group (7 miRNAs at Post and 8 at 3hPost) were distinct from those in the sedentary group (9 at Post and 4 at 3hPost). Pathway analysis prediction and reported target validation experiments revealed that the majority of exercise-regulated exomiRs are targeting genes that are related to IGF-1 signaling, a pathway involved in exercise-induced muscle and cardiac hypertrophy. The immediately post-acute exercise exomiR signature in the trained group correlates with activation of IGF-1 signaling, whereas in the sedentary group it is associated with inhibition of IGF-1 signaling. While further validation is needed, including measurements of IGF-1/IGF-1 signaling in blood or skeletal muscle, our results suggest that training status may counteract age-related anabolic resistance by modulating circulating exomiR profiles both at baseline and in response to acute exercise.
Collapse
Affiliation(s)
- Venugopalan D. Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Side Li
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nimisha Jain
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nitish Seenarine
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mary Anne S. Amper
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bret H. Goodpaster
- Translational Research Institute, AdventHealth, Orlando, FL, United States
| | - Martin J. Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Paul M. Coen
- Translational Research Institute, AdventHealth, Orlando, FL, United States
| | - Stuart C. Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
7
|
Sannicandro AJ, McDonagh B, Goljanek-Whysall K. MicroRNAs as potential therapeutic targets for muscle wasting during cancer cachexia. Curr Opin Clin Nutr Metab Care 2020; 23:157-163. [PMID: 32073414 DOI: 10.1097/mco.0000000000000645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Muscle wasting in cancer cachexia remains an unmet clinical need due to lack of effective therapies associated with the complexity of the disease. Here, we discuss microRNAs, robust regulators of the expression of multiple genes, only recently characterized in cancer cachexia in humans and their therapeutic potential for muscle wasting. RECENT FINDINGS Changes in microRNAs in muscle of cancer patients have been demonstrated for the first time and these are associated with dysregulated signalling networks during muscle wasting. These data, together with studies in animal models, indicate that microRNAs are attractive therapeutic candidates for maintaining muscle mass, both during and following cancer treatment ultimately improving patient outcomes. SUMMARY Cancer cachexia is a complex metabolic condition associated with muscle wasting. Maintenance of muscle mass in cancer patients can improve their response to therapy and prognosis. microRNAs, which can act as oncogenes or tumour suppressors, are also dysregulated in muscle of cachexia patients. Studies in animal models of muscle wasting have demonstrated that microRNAs regulate muscle mass and strength. With more microRNA-based therapeutics in clinical trials and first RNA drugs approved, microRNAs present an attractive novel therapeutic avenue for maintaining muscle homeostasis in cachexia patients to improve their prognosis.
Collapse
Affiliation(s)
- Anthony J Sannicandro
- Discipline of Physiology, School of Medicine, National University of Ireland, Galway, Ireland
| | - Brian McDonagh
- Discipline of Physiology, School of Medicine, National University of Ireland, Galway, Ireland
| | - Katarzyna Goljanek-Whysall
- Discipline of Physiology, School of Medicine, National University of Ireland, Galway, Ireland
- Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| |
Collapse
|
8
|
Pandey PR, Yang JH, Tsitsipatis D, Panda AC, Noh JH, Kim KM, Munk R, Nicholson T, Hanniford D, Argibay D, Yang X, Martindale JL, Chang MW, Jones SW, Hernando E, Sen P, De S, Abdelmohsen K, Gorospe M. circSamd4 represses myogenic transcriptional activity of PUR proteins. Nucleic Acids Res 2020; 48:3789-3805. [PMID: 31980816 PMCID: PMC7144931 DOI: 10.1093/nar/gkaa035] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 02/02/2023] Open
Abstract
By interacting with proteins and nucleic acids, the vast family of mammalian circRNAs is proposed to influence many biological processes. Here, RNA sequencing analysis of circRNAs differentially expressed during myogenesis revealed that circSamd4 expression increased robustly in mouse C2C12 myoblasts differentiating into myotubes. Moreover, silencing circSamd4, which is conserved between human and mouse, delayed myogenesis and lowered the expression of myogenic markers in cultured myoblasts from both species. Affinity pulldown followed by mass spectrometry revealed that circSamd4 associated with PURA and PURB, two repressors of myogenesis that inhibit transcription of the myosin heavy chain (MHC) protein family. Supporting the hypothesis that circSamd4 might complex with PUR proteins and thereby prevent their interaction with DNA, silencing circSamd4 enhanced the association of PUR proteins with the Mhc promoter, while overexpressing circSamd4 interfered with the binding of PUR proteins to the Mhc promoter. These effects were abrogated when using a mutant circSamd4 lacking the PUR binding site. Our results indicate that the association of PUR proteins with circSamd4 enhances myogenesis by contributing to the derepression of MHC transcription.
Collapse
Affiliation(s)
- Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, Republic of Korea
| | - Kyoung Mi Kim
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Thomas Nicholson
- Institute of Inflammation and Ageing, MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK
| | - Douglas Hanniford
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Diana Argibay
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ming-Wen Chang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Simon W Jones
- Institute of Inflammation and Ageing, MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK
| | - Eva Hernando
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| |
Collapse
|
9
|
Du Q, de la Morena MT, van Oers NSC. The Genetics and Epigenetics of 22q11.2 Deletion Syndrome. Front Genet 2020; 10:1365. [PMID: 32117416 PMCID: PMC7016268 DOI: 10.3389/fgene.2019.01365] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
Chromosome 22q11.2 deletion syndrome (22q11.2del) is a complex, multi-organ disorder noted for its varying severity and penetrance among those affected. The clinical problems comprise congenital malformations; cardiac problems including outflow tract defects, hypoplasia of the thymus, hypoparathyroidism, and/or dysmorphic facial features. Additional clinical issues that can appear over time are autoimmunity, renal insufficiency, developmental delay, malignancy and neurological manifestations such as schizophrenia. The majority of individuals with 22q11.2del have a 3 Mb deletion of DNA on chromosome 22, leading to a haploinsufficiency of ~106 genes, which comprise coding RNAs, noncoding RNAs, and pseudogenes. The consequent haploinsufficiency of many of the coding genes are well described, including the key roles of T-box Transcription Factor 1 (TBX1) and DiGeorge Critical Region 8 (DGCR8) in the clinical phenotypes. However, the haploinsufficiency of these genes alone cannot account for the tremendous variation in the severity and penetrance of the clinical complications among those affected. Recent RNA and DNA sequencing approaches are uncovering novel genetic and epigenetic differences among 22q11.2del patients that can influence disease severity. In this review, the role of coding and non-coding genes, including microRNAs (miRNA) and long noncoding RNAs (lncRNAs), will be discussed in relation to their bearing on 22q11.2del with an emphasis on TBX1.
Collapse
Affiliation(s)
- Qiumei Du
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - M. Teresa de la Morena
- Department of Pediatrics, The University of Washington and Seattle Children’s Hospital, Seattle, WA, United States
| | - Nicolai S. C. van Oers
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| |
Collapse
|