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Wang J, Ren W, Sun Z, Han Z, Zeng Y, Meng J, Yao X. Comparative transcriptome analysis of slow-twitch and fast-twitch muscles in Kazakh horses. Meat Sci 2024; 216:109582. [PMID: 38991479 DOI: 10.1016/j.meatsci.2024.109582] [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: 05/21/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024]
Abstract
This study conducted a thorough analysis of the myofiber type composition in the extensor digitorum longus muscle (EDL) and soleus muscle (SOL) of Kazakh horses, across different genders (male and female). The results showed significant differences in myofiber type composition between EDL and SOL, with a higher proportion of Type I fibers in SOL muscles and a greater prevalence of Type II fibers in EDL muscles. Additionally, the myofiber diameter in Kazakh horses was relatively small, potentially related to the tenderness and edible quality of their muscles. Using high-throughput sequencing technology, we constructed 32 cDNA sequencing libraries and obtained high-quality read data. Gene expression analysis revealed 278 and 372 differentially expressed genes (DEGs) in EDL and SOL muscles, respectively, including genes related to muscle contraction, metabolism, and development. Intersection analysis of DEGs between genders showed that 60 DEGs were significantly different in both male and female horses. GO annotation and KEGG analysis further elucidated the roles of these DEGs in muscle structure, function, and cellular signaling. Protein-protein interaction (PPI) network analysis and identification of hub genes provided new insights into the molecular mechanisms underlying muscle growth and development. Finally, the reliability of the DEGs data was validated through quantitative real-time PCR (qRT-PCR). This study not only enhances our understanding of the biological characteristics of horse muscles but also provides potential molecular targets for improving horse muscle performance and health.
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Affiliation(s)
- Jianwen Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China
| | - Wanlu Ren
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zhiwen Sun
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zixiang Han
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yaqi Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China
| | - Jun Meng
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China.
| | - Xinkui Yao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China.
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Song H, Tian X, He L, Liu D, Li J, Mei Z, Zhou T, Liu C, He J, Jia X, Yang Z, Yan C, Han Y. CREG1 deficiency impaired myoblast differentiation and skeletal muscle regeneration. J Cachexia Sarcopenia Muscle 2024; 15:587-602. [PMID: 38272853 PMCID: PMC10995283 DOI: 10.1002/jcsm.13427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND CREG1 (cellular repressor of E1A-stimulated genes 1) is a protein involved in cellular differentiation and homeostasis regulation. However, its role in skeletal muscle satellite cells differentiation and muscle regeneration is poorly understood. This study aimed to investigate the role of CREG1 in myogenesis and muscle regeneration. METHODS RNA sequencing data (GSE8479) was analysed from the Gene Expression Omnibus database (GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi). We generated Creg1 knockdown and skeletal muscle satellite cells specific Creg1 overexpression mice mediated by adeno-associated virus serotype 9 (AAV9), skeletal muscle mature myofibre Creg1 knockout mice (myoblast/Creg1MKO), and control mice Creg1flox/flox (Creg1fl/fl) as in vivo models. The mice were injected into tibialis anterior (TA) muscle with 100 μL of 10 μM cardiotoxin to establish a muscle regeneration model. Creg1fl/fl and Creg1MKO mice were treated with AAV-sh-C-Cbl (2 × 1010 genomic copies/mouse) to silence C-Cbl in the TA muscle. 293T and C2C12 cells were transfected with plasmids using lipofectamine RNAi MAX in vitro. Mass spectrometry analyses and RNA sequencing transcriptomic assay were performed. RESULTS We analysed the transcriptional profiles of the skeletal muscle biopsies from healthy older (N = 25) and younger (N = 26) adult men and women in GSE8479 database, and the results showed that Creg1 was associated with human sarcopenia. We found that Creg1 knockdown mice regenerated less newly formed fibres in response to cardiotoxin injection (~30% reduction, P < 0.01); however, muscle satellite cells specific Creg1 overexpression mice regenerated more newly formed fibres (~20% increase, P < 0.05). AMPKa1 is known as a key mediator in the muscle regeneration process. Our results revealed that CREG1 deficiency inhibited AMPKa1 signalling through C-CBL E3-ubiquitin ligase-mediated AMPKa1 degradation (P < 0.01). C-CBL-mediated AMPKa1 ubiquitination was attributed to the K48-linked polyubiquitination of AMPKa1 at K396 and that the modification played an important role in the regulation of AMPKa1 protein stability. We also found that Creg1MKO mice regenerated less newly formed fibres compared with Creg1fl/fl mice (~30% reduction, P < 0.01). RNA-seq analysis showed that CREG1 deletion in impaired muscles led to the upregulation of inflammation and DKK3 expression. The TA muscles of Creg1MKO mice were injected with AAV-vector or AAV-shC-Cbl, silencing C-CBL (P < 0.01) in the skeletal muscles of Creg1MKO mice significantly improved muscle regeneration induced by CTX injury (P < 0.01). CONCLUSIONS Our findings suggest that CREG1 may be a potential therapeutic target for skeletal muscle regeneration.
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Affiliation(s)
- Haixu Song
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Xiaoxiang Tian
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Lianqi He
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Dan Liu
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Jiayin Li
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Zhu Mei
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Ting Zhou
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Chunying Liu
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Jiaqi He
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Xiaodong Jia
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Zheming Yang
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Chenghui Yan
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
| | - Yaling Han
- Department of Cardiology, Cardiovascular Research Institute, State Key Laboratory of Frigid Zone Cardiovascular DiseaseGeneral Hospital of Northern Theater CommandShenyangChina
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Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development. Animals (Basel) 2021; 11:ani11082311. [PMID: 34438768 PMCID: PMC8388485 DOI: 10.3390/ani11082311] [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: 07/02/2021] [Revised: 07/29/2021] [Accepted: 08/04/2021] [Indexed: 12/25/2022] Open
Abstract
The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA-Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co-expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA-mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS-00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT-PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle.
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Koutnik AP, Poff AM, Ward NP, DeBlasi JM, Soliven MA, Romero MA, Roberson PA, Fox CD, Roberts MD, D'Agostino DP. Ketone Bodies Attenuate Wasting in Models of Atrophy. J Cachexia Sarcopenia Muscle 2020; 11:973-996. [PMID: 32239651 PMCID: PMC7432582 DOI: 10.1002/jcsm.12554] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/18/2020] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Cancer Anorexia Cachexia Syndrome (CACS) is a distinct atrophy disease negatively influencing multiple aspects of clinical care and patient quality of life. Although it directly causes 20% of all cancer-related deaths, there are currently no model systems that encompass the entire multifaceted syndrome, nor are there any effective therapeutic treatments. METHODS A novel model of systemic metastasis was evaluated for the comprehensive CACS (metastasis, skeletal muscle and adipose tissue wasting, inflammation, anorexia, anemia, elevated protein breakdown, hypoalbuminemia, and metabolic derangement) in both males and females. Ex vivo skeletal muscle analysis was utilized to determine ubiquitin proteasome degradation pathway activation. A novel ketone diester (R/S 1,3-Butanediol Acetoacetate Diester) was assessed in multifaceted catabolic environments to determine anti-atrophy efficacy. RESULTS Here, we show that the VM-M3 mouse model of systemic metastasis demonstrates a novel, immunocompetent, logistically feasible, repeatable phenotype with progressive tumor growth, spontaneous metastatic spread, and the full multifaceted CACS with sex dimorphisms across tissue wasting. We also demonstrate that the ubiquitin proteasome degradation pathway was significantly upregulated in association with reduced insulin-like growth factor-1/insulin and increased FOXO3a activation, but not tumor necrosis factor-α-induced nuclear factor-kappa B activation, driving skeletal muscle atrophy. Additionally, we show that R/S 1,3-Butanediol Acetoacetate Diester administration shifted systemic metabolism, attenuated tumor burden indices, reduced atrophy/catabolism and mitigated comorbid symptoms in both CACS and cancer-independent atrophy environments. CONCLUSIONS Our findings suggest the ketone diester attenuates multifactorial CACS skeletal muscle atrophy and inflammation-induced catabolism, demonstrating anti-catabolic effects of ketone bodies in multifactorial atrophy.
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Affiliation(s)
- Andrew P. Koutnik
- Department of Molecular Pharmacology and PhysiologyMorsani College of Medicine, University of South FloridaTampaFLUSA
| | - Angela M. Poff
- Department of Molecular Pharmacology and PhysiologyMorsani College of Medicine, University of South FloridaTampaFLUSA
| | - Nathan P. Ward
- Department of Cancer PhysiologyMoffitt Cancer Center, H. Lee Moffitt Cancer Center and Research InstituteTampaFLUSA
| | - Janine M. DeBlasi
- Department of Molecular Pharmacology and PhysiologyMorsani College of Medicine, University of South FloridaTampaFLUSA
| | - Maricel A. Soliven
- Department of Molecular Pharmacology and PhysiologyMorsani College of Medicine, University of South FloridaTampaFLUSA
| | | | | | - Carl D. Fox
- School of KinesiologyAuburn UniversityAuburnALUSA
| | | | - Dominic P. D'Agostino
- Department of Molecular Pharmacology and PhysiologyMorsani College of Medicine, University of South FloridaTampaFLUSA
- Institute for Human and Machine CognitionOcalaFLUSA
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Sun H, Sui Z, Wang D, Ba H, Zhao H, Zhang L, Li C. Identification of interactive molecules between antler stem cells and dermal papilla cells using an in vitro co-culture system. J Mol Histol 2019; 51:15-31. [DOI: 10.1007/s10735-019-09853-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/30/2019] [Indexed: 12/25/2022]
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González-Prendes R, Quintanilla R, Mármol-Sánchez E, Pena RN, Ballester M, Cardoso TF, Manunza A, Casellas J, Cánovas Á, Díaz I, Noguera JL, Castelló A, Mercadé A, Amills M. Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles. BMC Genomics 2019; 20:170. [PMID: 30832586 PMCID: PMC6399881 DOI: 10.1186/s12864-019-5557-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression and the genetic determinism of IMF traits in the porcine gluteus medius (GM) and longissimus dorsi (LD) muscles. RESULTS A comparative analysis of the mRNA expression profiles of the pig GM and LD muscles in 16 Duroc pigs with available microarray mRNA expression measurements revealed the existence of 106 differentially expressed probes (fold-change > 1.5 and q-value < 0.05). Amongst the genes displaying the most significant differential expression, several loci belonging to the Hox transcription factor family were either upregulated (HOXA9, HOXA10, HOXB6, HOXB7 and TBX1) or downregulated (ARX) in the GM muscle. Differences in the expression of genes with key roles in carbohydrate and lipid metabolism (e.g. FABP3, ORMDL1 and SLC37A1) were also detected. By performing a GWAS for IMF content and composition traits recorded in the LD and GM muscles of 350 Duroc pigs, we identified the existence of one region on SSC14 (110-114 Mb) displaying significant associations with C18:0, C18:1(n-7), saturated and unsaturated fatty acid contents in both GM and LD muscles. Moreover, we detected several genome-wide significant associations that were not consistently found in both muscles. Further studies should be performed to confirm whether these associations are muscle-specific. Finally, the performance of an eQTL scan for 74 genes, located within GM QTL regions and with available microarray measurements of gene expression, made possible to identify 14 cis-eQTL regulating the expression of 14 loci, and six of them were confirmed by RNA-Seq. CONCLUSIONS We have detected significant differences in the mRNA expression patterns of the porcine LD and GM muscles, evidencing that the transcriptomic profile of the skeletal muscle tissue is affected by anatomical, metabolic and functional factors. A highly significant association with IMF composition on SSC14 was replicated in both muscles, highlighting the existence of a common genetic determinism, but we also observed the existence of a few associations whose magnitude and significance varied between LD and GM muscles.
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Affiliation(s)
- Rayner González-Prendes
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Emilio Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramona N. Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, 25198 Lleida, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, DF 70.040-020 Brazil
| | - Arianna Manunza
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joaquim Casellas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 Canada
| | - Isabel Díaz
- Institute for Research and Technology in Food and Agriculture (IRTA), Tecnologia dels Aliments, 17121 Monells, Spain
| | - José Luis Noguera
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Mercadé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Motohashi N, Uezumi A, Asakura A, Ikemoto-Uezumi M, Mori S, Mizunoe Y, Takashima R, Miyagoe-Suzuki Y, Takeda S, Shigemoto K. Tbx1 regulates inherited metabolic and myogenic abilities of progenitor cells derived from slow- and fast-type muscle. Cell Death Differ 2018; 26:1024-1036. [PMID: 30154444 DOI: 10.1038/s41418-018-0186-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/18/2018] [Accepted: 07/27/2018] [Indexed: 11/09/2022] Open
Abstract
Skeletal muscle is divided into slow- and fast-type muscles, which possess distinct contractile and metabolic properties. Myogenic progenitors associated with each muscle fiber type are known to intrinsically commit to specific muscle fiber lineage during embryonic development. However, it is still unclear whether the functionality of postnatal adult myogenic cells is attributable to the muscle fiber in which they reside, and whether the characteristics of myogenic cells derived from slow- and fast-type fibers can be distinguished at the genetic level. In this study, we isolated adult satellite cells from slow- and fast-type muscle individually and observed that satellite cells from each type of muscle generated myotubes expressing myosin heavy chain isoforms similar to their original muscle, and showed different metabolic features. Notably, we discovered that slow muscle-derived cells had low potential to differentiate but high potential to self-renew compared with fast muscle-derived cells. Additionally, cell transplantation experiments of slow muscle-derived cells into fast-type muscle revealed that slow muscle-derived cells could better contribute to myofiber formation and satellite cell constitution than fast muscle-derived cells, suggesting that the recipient muscle fiber type may not affect the predetermined abilities of myogenic cells. Gene expression analyses identified T-box transcriptional factor Tbx1 as a highly expressed gene in fast muscle-derived myoblasts. Gain- and loss-of-function experiments revealed that Tbx1 modulated muscle fiber types and oxidative metabolism in myotubes, and that Tbx1 stimulated myoblast differentiation, but did not regulate myogenic cell self-renewal. Our data suggest that metabolic and myogenic properties of myogenic progenitor cells vary depending on the type of muscle from which they originate, and that Tbx1 expression partially explains the functional differences of myogenic cells derived from fast-type and slow-type muscles.
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Affiliation(s)
- Norio Motohashi
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan. .,Stem Cell Institute, Paul and Sheila Wellstone Muscular Dystrophy Center, Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
| | - Akiyoshi Uezumi
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Atsushi Asakura
- Stem Cell Institute, Paul and Sheila Wellstone Muscular Dystrophy Center, Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Madoka Ikemoto-Uezumi
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Shuuichi Mori
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Yuhei Mizunoe
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Rumi Takashima
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Yuko Miyagoe-Suzuki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan
| | - Kazuhiro Shigemoto
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
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Zoupa M, Xavier GM, Bryan S, Theologidis I, Arno M, Cobourne MT. Gene expression profiling in the developing secondary palate in the absence of Tbx1 function. BMC Genomics 2018; 19:429. [PMID: 29866044 PMCID: PMC5987606 DOI: 10.1186/s12864-018-4782-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/11/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Microdeletion of chromosome 22q11 is associated with significant developmental anomalies, including disruption of the cardiac outflow tract, thymic/parathyroid aplasia and cleft palate. Amongst the genes within this region, TBX1 is a major candidate for many of these developmental defects. Targeted deletion of Tbx1 in the mouse has provided significant insight into the function of this transcription factor during early development of the cardiac and pharyngeal systems. However, less is known about its role during palatogenesis. To assess the influence of Tbx1 function on gene expression profile within the developing palate we performed a microarray screen using total RNA isolated from the secondary palate of E13.5 mouse embryos wild type, heterozygous and mutant for Tbx1. RESULTS Expression-level filtering and statistical analysis revealed a total of 577 genes differentially expressed across genotypes. Data were clustered into 3 groups based on comparison between genotypes. Group A was composed of differentially expressed genes in mutant compared to wild type (n = 89); Group B included differentially expressed genes in heterozygous compared to wild type (n = 400) and Group C included differentially expressed genes in mutant compared to heterozygous (n = 88). High-throughput quantitative real-time PCR (RT-PCR) confirmed a total of 27 genes significantly changed between wild type and mutant; and 27 genes between heterozygote and mutant. Amongst these, the majority were present in both groups A and C (26 genes). Associations existed with hypertrophic cardiomyopathy, cardiac muscle contraction, dilated cardiomyopathy, focal adhesion, tight junction and calcium signalling pathways. No significant differences in gene expression were found between wild type and heterozygous palatal shelves. CONCLUSIONS Significant differences in gene expression profile within the secondary palate of wild type and mutant embryos is consistent with a primary role for Tbx1 during palatogenesis.
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Affiliation(s)
- Maria Zoupa
- Centre for Craniofacial Development and Regeneration, King's College London Dental Institute, Floor 27, Guy's Tower, London, SE1 9RT, UK
| | - Guilherme Machado Xavier
- Centre for Craniofacial Development and Regeneration, King's College London Dental Institute, Floor 27, Guy's Tower, London, SE1 9RT, UK.,Department of Orthodontics, King's College London Dental Institute, London, UK
| | - Stephanie Bryan
- Department of Orthodontics, King's College London Dental Institute, London, UK
| | - Ioannis Theologidis
- Division of Development and Gene Expression, Institute of Molecular Biology and BiotechnologyFoundation for Research & Technology, Crete, Greece
| | - Matthew Arno
- Genomics Centre, King's College London, London, UK
| | - Martyn T Cobourne
- Centre for Craniofacial Development and Regeneration, King's College London Dental Institute, Floor 27, Guy's Tower, London, SE1 9RT, UK. .,Department of Orthodontics, King's College London Dental Institute, London, UK.
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Baribault C, Ehrlich KC, Ponnaluri VKC, Pradhan S, Lacey M, Ehrlich M. Developmentally linked human DNA hypermethylation is associated with down-modulation, repression, and upregulation of transcription. Epigenetics 2018; 13:275-289. [PMID: 29498561 PMCID: PMC5997157 DOI: 10.1080/15592294.2018.1445900] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA methylation can affect tissue-specific gene transcription in ways that are difficult to discern from studies focused on genome-wide analyses of differentially methylated regions (DMRs). To elucidate the variety of associations between differentiation-related DNA hypermethylation and transcription, we used available epigenomic and transcriptomic profiles from 38 human cell/tissue types to focus on such relationships in 94 genes linked to hypermethylated DMRs in myoblasts (Mb). For 19 of the genes, promoter-region hypermethylation in Mb (and often a few heterologous cell types) was associated with gene repression but, importantly, DNA hypermethylation was absent in many other repressed samples. In another 24 genes, DNA hypermethylation overlapped cryptic enhancers or super-enhancers and correlated with down-modulated, but not silenced, gene expression. However, such methylation was absent, surprisingly, in both non-expressing samples and highly expressing samples. This suggests that some genes need DMR hypermethylation to help repress cryptic enhancer chromatin only when they are actively transcribed. For another 11 genes, we found an association between intergenic hypermethylated DMRs and positive expression of the gene in Mb. DNA hypermethylation/transcription correlations similar to those of Mb were evident sometimes in diverse tissues, such as aorta and brain. Our findings have implications for the possible involvement of methylated DNA in Duchenne's muscular dystrophy, congenital heart malformations, and cancer. This epigenomic analysis suggests that DNA methylation is not simply the inevitable consequence of changes in gene expression but, instead, is often an active agent for fine-tuning transcription in association with development.
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Affiliation(s)
- Carl Baribault
- a Tulane Cancer Center , Tulane University Health Sciences Center , New Orleans , LA 70112 , USA.,b Department of Mathematics , Tulane University , New Orleans , LA 70118 , USA
| | - Kenneth C Ehrlich
- c Center for Bioinformatics and Genomics , Tulane University Health Sciences Center , New Orleans , LA 70112 , USA
| | | | | | - Michelle Lacey
- b Department of Mathematics , Tulane University , New Orleans , LA 70118 , USA
| | - Melanie Ehrlich
- a Tulane Cancer Center , Tulane University Health Sciences Center , New Orleans , LA 70112 , USA.,c Center for Bioinformatics and Genomics , Tulane University Health Sciences Center , New Orleans , LA 70112 , USA.,e Hayward Genetics Center Tulane University Health Sciences Center , New Orleans , LA 70112 , USA
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Yu B, Kiechl S, Qi D, Wang X, Song Y, Weger S, Mayr A, Le Bras A, Karamariti E, Zhang Z, Barco Barrantes ID, Niehrs C, Schett G, Hu Y, Wang W, Willeit J, Qu A, Xu Q. A Cytokine-Like Protein Dickkopf-Related Protein 3 Is Atheroprotective. Circulation 2017; 136:1022-1036. [PMID: 28674110 PMCID: PMC5598907 DOI: 10.1161/circulationaha.117.027690] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/06/2017] [Indexed: 12/28/2022]
Abstract
Supplemental Digital Content is available in the text. Background: Dickkopf-related protein 3 (DKK3) is a secreted protein that is involved in the regulation of cardiac remodeling and vascular smooth muscle cell differentiation, but little is known about its role in atherosclerosis. Methods: We tested the hypothesis that DKK3 is atheroprotective using both epidemiological and experimental approaches. Blood DKK3 levels were measured in the Bruneck Study in 2000 (n=684) and then in 2005 (n=574). DKK3-deficient mice were crossed with apolipoprotein E-/- mice to evaluate atherosclerosis development and vessel injury-induced neointimal formation. Endothelial cell migration and the underlying mechanisms were studied using in vitro cell culture models. Results: In the prospective population-based Bruneck Study, the level of plasma DKK3 was inversely related to carotid artery intima-media thickness and 5-year progression of carotid atherosclerosis independently from standard risk factors for atherosclerosis. Experimentally, we analyzed the area of atherosclerotic lesions, femoral artery injury-induced reendothelialization, and neointima formation in both DKK3-/-/apolipoprotein E-/- and DKK3+/+/apolipoprotein E-/- mice. It was demonstrated that DKK3 deficiency accelerated atherosclerosis and delayed reendothelialization with consequently exacerbated neointima formation. To explore the underlying mechanisms, we performed transwell and scratch migration assays using cultured human endothelial cells, which exhibited a significant induction in cell migration in response to DKK3 stimulation. This DKK3-induced migration activated ROR2 and DVL1, activated Rac1 GTPases, and upregulated JNK and c-jun phosphorylation in endothelial cells. Knockdown of the ROR2 receptor using specific siRNA or transfection of a dominant-negative form of Rac1 in endothelial cells markedly inhibited cell migration and downstream JNK and c-jun phosphorylation. Conclusions: This study provides the evidence for a role of DKK3 in the protection against atherosclerosis involving endothelial migration and repair, with great therapeutic potential implications against atherosclerosis.
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Affiliation(s)
- Baoqi Yu
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Stefan Kiechl
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Dan Qi
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Xiaocong Wang
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Yanting Song
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Siegfried Weger
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Agnes Mayr
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Alexandra Le Bras
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Eirini Karamariti
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Zhongyi Zhang
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Ivan Del Barco Barrantes
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Christof Niehrs
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Georg Schett
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Yanhua Hu
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Wen Wang
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Johann Willeit
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Aijuan Qu
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
| | - Qingbo Xu
- From Cardiovascular Division, King's College London British Heart Foundation Centre, London, United Kingdom (B.Y., X.W., A.L.B., E.K., Z.Z., Y.H., Q.X.); Department of Neurology, Medical University of Innsbruck, Austria (S.K., J.W.); Department of Physiology and Pathophysiology, Capital Medical University, Beijing, China (D.Q., Y.S., A.Q.); Department of Internal and Laboratory Medicine, Bruneck Hospital, Italy (S.W., A.M.); Division of Molecular Embryology, German Cancer Research Center (DKFZ) Heidelberg Germany and Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, Heidelberg, Germany (I.d.B.B., C.N.); Institute of Molecular Biology, Mainz, Germany (C.N.); Department of Internal Medicine, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Germany (G.S.); The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Qilu Hospital, Shandong University, Jinan, China (Y.H., Q.X.); and Institute of Bioengineering, Queen Mary University of London, United Kingdom (W.W.)
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The induction of antigen-specific CTL by in situ Ad-REIC gene therapy. Gene Ther 2016; 23:408-14. [PMID: 26836118 DOI: 10.1038/gt.2016.7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/17/2015] [Accepted: 01/20/2016] [Indexed: 01/03/2023]
Abstract
An adenovirus vector carrying the human Reduced Expression in Immortalized Cell (REIC)/Dkk-3 gene (Ad-REIC) mediates simultaneous induction of cancer-selective apoptosis and augmentation of anticancer immunity. In our preclinical and clinical studies, in situ Ad-REIC gene therapy showed remarkable direct and indirect antitumor effects to realize therapeutic cancer vaccines. We herein aimed to confirm the induction of tumor-associated antigen-specific cytotoxic T lymphocytes (CTLs) by Ad-REIC. Using an ovalbumin (OVA), a tumor-associated antigen, expressing E.G7 tumor-bearing mouse model, we investigated the induction and expansion of OVA-specific CTLs responsible for indirect, systemic effects of Ad-REIC. The intratumoral administration of Ad-REIC mediated clear antitumor effects with the accumulation of OVA-specific CTLs in the tumor tissues and spleen. The CD86-positive dendritic cells (DCs) were upregulated in the tumor draining lymph nodes of Ad-REIC-treated mice. In a dual tumor-bearing mouse model in the left and right back, Ad-REIC injection in one side significantly suppressed the tumor growth on both sides and significant infiltration of OVA-specific CTLs into non-injected tumor was also detected. Consequently, in situ Ad-REIC gene therapy is expected to realize a new-generation cancer vaccine via anticancer immune activation with DC and tumor antigen-specific CTL expansion.
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Chandra S, Baribault C, Lacey M, Ehrlich M. Myogenic differential methylation: diverse associations with chromatin structure. BIOLOGY 2014; 3:426-51. [PMID: 24949935 PMCID: PMC4085616 DOI: 10.3390/biology3020426] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/21/2014] [Accepted: 05/21/2014] [Indexed: 11/16/2022]
Abstract
Employing a new algorithm for identifying differentially methylated regions (DMRs) from reduced representation bisulfite sequencing profiles, we identified 1972 hypermethylated and 3250 hypomethylated myogenic DMRs in a comparison of myoblasts (Mb) and myotubes (Mt) with 16 types of nonmuscle cell cultures. DMRs co-localized with a variety of chromatin structures, as deduced from ENCODE whole-genome profiles. Myogenic hypomethylation was highly associated with both weak and strong enhancer-type chromatin, while hypermethylation was infrequently associated with enhancer-type chromatin. Both myogenic hypermethylation and hypomethylation often overlapped weak transcription-type chromatin and Polycomb-repressed-type chromatin. For representative genes, we illustrate relationships between DNA methylation, the local chromatin state, DNaseI hypersensitivity, and gene expression. For example, MARVELD2 exhibited myogenic hypermethylation in transcription-type chromatin that overlapped a silenced promoter in Mb and Mt while TEAD4 had myogenic hypomethylation in intronic subregions displaying enhancer-type or transcription-type chromatin in these cells. For LSP1, alternative promoter usage and active promoter-type chromatin were linked to highly specific myogenic or lymphogenic hypomethylated DMRs. Lastly, despite its myogenesis-associated expression, TBX15 had multiple hypermethylated myogenic DMRs framing its promoter region. This could help explain why TBX15 was previously reported to be underexpressed and, unexpectedly, its promoter undermethylated in placentas exhibiting vascular intrauterine growth restriction.
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Affiliation(s)
- Sruti Chandra
- Center for Bioinformatics and Genomics, New Orleans, LA 70112, USA.
| | - Carl Baribault
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA.
| | - Michelle Lacey
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA.
| | - Melanie Ehrlich
- Center for Bioinformatics and Genomics, New Orleans, LA 70112, USA.
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Mustafina LJ, Naumov VA, Cieszczyk P, Popov DV, Lyubaeva EV, Kostryukova ES, Fedotovskaya ON, Druzhevskaya AM, Astratenkova IV, Glotov AS, Alexeev DG, Mustafina MM, Egorova ES, Maciejewska-Karłowska A, Larin AK, Generozov EV, Nurullin RE, Jastrzębski Z, Kulemin NA, Ospanova EA, Pavlenko AV, Sawczuk M, Akimov EB, Danilushkina AA, Zmijewski P, Vinogradova OL, Govorun VM, Ahmetov II. AGTR2 gene polymorphism is associated with muscle fibre composition, athletic status and aerobic performance. Exp Physiol 2014; 99:1042-52. [PMID: 24887114 DOI: 10.1113/expphysiol.2014.079335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Muscle fibre type is a heritable trait and can partly predict athletic success. It has been proposed that polymorphisms of genes involved in the regulation of muscle fibre characteristics may predispose the muscle precursor cells of a given individual to be predominantly fast or slow. In the present study, we examined the association between 15 candidate gene polymorphisms and muscle fibre type composition of the vastus lateralis muscle in 55 physically active, healthy men. We found that rs11091046 C allele carriers of the angiotensin II type 2 receptor gene (AGTR2; involved in skeletal muscle development, metabolism and circulatory homeostasis) had a significantly higher percentage of slow-twitch fibres than A allele carriers [54.2 (11.1) versus 45.2 (10.2)%; P = 0.003]. These data indicate that 15.2% of the variation in muscle fibre composition of the vastus lateralis muscle can be explained by the AGTR2 genotype. Next, we investigated the frequencies of the AGTR2 alleles in 2178 Caucasian athletes and 1220 control subjects. The frequency of the AGTR2 C allele was significantly higher in male and female endurance athletes compared with power athletes (males, 62.7 versus 51.7%, P = 0.0038; females, 56.6 versus 48.1%, P = 0.0169) and control subjects (males, 62.7 versus 51.0%, P = 0.0006; elite female athletes, 65.1 versus 55.2%, P = 0.0488). Furthermore, the frequency of the AGTR2 A allele was significantly over-represented in female power athletes (51.9%) in comparison to control subjects (44.8%, P = 0.0069). We also found that relative maximal oxygen consumption was significantly greater in male endurance athletes with the AGTR2 C allele compared with AGTR2 A allele carriers [n = 28; 62.3 (4.4) versus 57.4 (6.0) ml min(-1) kg(-1); P = 0.0197]. Taken together, these results demonstrate that the AGTR2 gene C allele is associated with an increased proportion of slow-twitch muscle fibres, endurance athlete status and aerobic performance, while the A allele is associated with a higher percentage of fast-twitch fibres and power-oriented disciplines.
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Affiliation(s)
- Leysan J Mustafina
- Sport Technology Research Centre, Volga Region State Academy of Physical Culture, Sport and Tourism, Kazan, Russia Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia
| | | | - Pawel Cieszczyk
- Department of Tourism and Recreation, Academy of Physical Education and Sport, Gdansk, Poland Department of Physical Culture and Health Promotion, University of Szczecin, Szczecin, Poland
| | - Daniil V Popov
- Laboratory of Exercise Physiology, SSC RF Institute for Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina V Lyubaeva
- Laboratory of Exercise Physiology, SSC RF Institute for Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | - Olga N Fedotovskaya
- Sports Genetics Laboratory, St Petersburg Research Institute of Physical Culture, St Petersburg, Russia
| | - Anastasiya M Druzhevskaya
- Sports Genetics Laboratory, St Petersburg Research Institute of Physical Culture, St Petersburg, Russia
| | - Irina V Astratenkova
- Sports Genetics Laboratory, St Petersburg Research Institute of Physical Culture, St Petersburg, Russia
| | | | - Dmitry G Alexeev
- Research Institute for Physical-Chemical Medicine, Moscow, Russia
| | | | - Emiliya S Egorova
- Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia
| | | | - Andrey K Larin
- Research Institute for Physical-Chemical Medicine, Moscow, Russia
| | | | - Ruslan E Nurullin
- Sport Technology Research Centre, Volga Region State Academy of Physical Culture, Sport and Tourism, Kazan, Russia
| | - Zbigniew Jastrzębski
- Department of Tourism and Recreation, Academy of Physical Education and Sport, Gdansk, Poland
| | | | - Elena A Ospanova
- Research Institute for Physical-Chemical Medicine, Moscow, Russia
| | | | - Marek Sawczuk
- Department of Physical Culture and Health Promotion, University of Szczecin, Szczecin, Poland
| | - Egor B Akimov
- Centre for Sports Innovation Technologies and National Teams of the Moscow Department of Physical Culture and Sport, Moscow, Russia
| | - Anna A Danilushkina
- Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia
| | - Piotr Zmijewski
- Department of Physiology, Institute of Sport, Warsaw, Poland
| | - Olga L Vinogradova
- Laboratory of Exercise Physiology, SSC RF Institute for Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Vadim M Govorun
- Research Institute for Physical-Chemical Medicine, Moscow, Russia
| | - Ildus I Ahmetov
- Sport Technology Research Centre, Volga Region State Academy of Physical Culture, Sport and Tourism, Kazan, Russia Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia Research Institute for Physical-Chemical Medicine, Moscow, Russia Sports Genetics Laboratory, St Petersburg Research Institute of Physical Culture, St Petersburg, Russia
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15
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Post-exercise impact of ingested whey protein hydrolysate on gene expression profiles in rat skeletal muscle: activation of extracellular signal-regulated kinase 1/2 and hypoxia-inducible factor-1α. Br J Nutr 2014; 111:2067-78. [DOI: 10.1017/s0007114514000233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have previously shown that whey protein hydrolysate (WPH) causes a greater increase in muscle protein synthesis than does a mixture of amino acids that is identical in amino acid composition. The present study was conducted to investigate the effect of WPH on gene expression. Male Sprague–Dawley rats subjected to a 2 h swimming exercise were administered either a carbohydrate–amino acid diet or a carbohydrate–WPH diet immediately after exercise. At 1 h after exercise, epitrochlearis muscle mRNA was sampled and subjected to DNA microarray analysis. We found that ingestion of WPH altered 189 genes after considering the false discovery rate. Among the up-regulated genes, eight Gene Ontology (GO) terms were enriched, which included key elements such as Cd24, Ccl2, Ccl7 and Cxcl1 involved in muscle repair after exercise. In contrast, nine GO terms were enriched in gene sets that were down-regulated by the ingestion of WPH, and these GO terms fell into two clusters, ‘regulation of ATPase activity’ and ‘immune response’. Furthermore, we found that WPH activated two upstream proteins, extracellular signal-regulated kinase 1/2 (ERK1/2) and hypoxia-inducible factor-1α (HIF-1α), which might act as key factors for regulating gene expression. These results suggest that ingestion of WPH, compared with ingestion of a mixture of amino acids with an identical amino acid composition, induces greater changes in the post-exercise gene expression profile via activation of the proteins ERK1/2 and HIF-1α.
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16
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Zhang Y, Han Q, Li C, Li W, Fan H, Xing Q, Yan B. Genetic analysis of the TBX1 gene promoter in indirect inguinal hernia. Gene 2013; 535:290-3. [PMID: 24295890 DOI: 10.1016/j.gene.2013.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 10/31/2013] [Accepted: 11/03/2013] [Indexed: 12/22/2022]
Abstract
Inguinal hernia is a common disease, most cases of which are indirect inguinal hernia (IIH). Genetic factors play an important role for inguinal hernia. Increased incidences of inguinal hernia have been reported in patients with 22q11.2 microdeletion syndrome, which is mainly caused by TBX1 gene mutations. Thus, we hypothesized that altered TBX1 gene expression may contribute to IIH development. In this study, the human TBX1 gene promoter was genetically analyzed in children with IIH (n=100) and ethnic-matched controls (n=167). Functions of DNA sequence variants (DSVs) within the TBX1 gene promoter were examined in cultured human fibroblast cells. The results showed that two heterozygous DSVs were found, both of which were single nucleotide polymorphisms. One DSV, g.4248 C>T (rs41298629), was identified in a 2-year-old boy with right-sided IIH, but not in all controls, which significantly decreased TBX1 gene promoter activity. Another DSV, g.4199 C>T (rs41260844), was found in both IIH patients and controls with similar frequencies (P>0.05), which did not affect TBX1 gene promoter activity. Collectively, our data suggested that the DSV within the TBX1 gene promoter may change TBX1 level, contributing to IIH development as a rare risk factor. Underlying molecular mechanisms need to be established.
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Affiliation(s)
- Yu Zhang
- Division of General Surgery, Jining Medical University Affiliated Hospital, Jining Medical University, Jining, Shandong 272029, China
| | - Qingluan Han
- Division of General Surgery, Jining Medical University Affiliated Hospital, Jining Medical University, Jining, Shandong 272029, China
| | - Chunyu Li
- Division of Electrocardiogram, Jining Medical University Affiliated Hospital, Jining Medical University, Jining, Shandong 272029, China
| | - Wei Li
- Division of General Surgery, Jining Medical University Affiliated Hospital, Jining Medical University, Jining, Shandong 272029, China
| | - Hongjin Fan
- Division of General Surgery, Jining Medical University Affiliated Hospital, Jining Medical University, Jining, Shandong 272029, China
| | - Qining Xing
- Division of General Surgery, Jining Medical University Affiliated Hospital, Jining Medical University, Jining, Shandong 272029, China
| | - Bo Yan
- Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Jining Medical University Affiliated Hospital, Jining Medical University, Jining, Shandong 272029, China.
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17
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Karamariti E, Margariti A, Winkler B, Wang X, Hong X, Baban D, Ragoussis J, Huang Y, Han JDJ, Wong MM, Sag CM, Shah AM, Hu Y, Xu Q. Smooth muscle cells differentiated from reprogrammed embryonic lung fibroblasts through DKK3 signaling are potent for tissue engineering of vascular grafts. Circ Res 2013; 112:1433-43. [PMID: 23529184 DOI: 10.1161/circresaha.111.300415] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RATIONALE Smooth muscle cells (SMCs) are a key component of tissue-engineered vessels. However, the sources by which they can be isolated are limited. OBJECTIVE We hypothesized that a large number of SMCs could be obtained by direct reprogramming of fibroblasts, that is, direct differentiation of specific cell lineages before the cells reaching the pluripotent state. METHODS AND RESULTS We designed a combined protocol of reprogramming and differentiation of human neonatal lung fibroblasts. Four reprogramming factors (OCT4, SOX2, KLF4, and cMYC) were overexpressed in fibroblasts under reprogramming conditions for 4 days with cells defined as partially-induced pluripotent stem (PiPS) cells. PiPS cells did not form tumors in vivo after subcutaneous transplantation in severe combined immunodeficiency mice and differentiated into SMCs when seeded on collagen IV and maintained in differentiation media. PiPS-SMCs expressed a panel of SMC markers at mRNA and protein levels. Furthermore, the gene dickkopf 3 was found to be involved in the mechanism of PiPS-SMC differentiation. It was revealed that dickkopf 3 transcriptionally regulated SM22 by potentiation of Wnt signaling and interaction with Kremen1. Finally, PiPS-SMCs repopulated decellularized vessel grafts and ultimately gave rise to functional tissue-engineered vessels when combined with previously established PiPS-endothelial cells, leading to increased survival of severe combined immunodeficiency mice after transplantation of the vessel as a vascular graft. CONCLUSIONS We developed a protocol to generate SMCs from PiPS cells through a dickkopf 3 signaling pathway, useful for generating tissue-engineered vessels. These findings provide a new insight into the mechanisms of SMC differentiation with vast therapeutic potential.
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Affiliation(s)
- Eirini Karamariti
- Cardiovascular Division, British Heart Foundation Centre, King's College London, UK
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18
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Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M. Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics 2013; 8:317-32. [PMID: 23417056 PMCID: PMC3669123 DOI: 10.4161/epi.23989] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 12/31/2022] Open
Abstract
Myogenic cell cultures derived from muscle biopsies are excellent models for human cell differentiation. We report the first comprehensive analysis of myogenesis-specific DNA hyper- and hypo-methylation throughout the genome for human muscle progenitor cells (both myoblasts and myotubes) and skeletal muscle tissue vs. 30 non-muscle samples using reduced representation bisulfite sequencing. We also focused on four genes with extensive hyper- or hypo-methylation in the muscle lineage (PAX3, TBX1, MYH7B/MIR499 and OBSCN) to compare DNA methylation, DNaseI hypersensitivity, histone modification, and CTCF binding profiles. We found that myogenic hypermethylation was strongly associated with homeobox or T-box genes and muscle hypomethylation with contractile fiber genes. Nonetheless, there was no simple relationship between differential gene expression and myogenic differential methylation, rather only for subsets of these genes, such as contractile fiber genes. Skeletal muscle retained ~30% of the hypomethylated sites but only ~3% of hypermethylated sites seen in myogenic progenitor cells. By enzymatic assays, skeletal muscle was 2-fold enriched globally in genomic 5-hydroxymethylcytosine (5-hmC) vs. myoblasts or myotubes and was the only sample type enriched in 5-hmC at tested myogenic hypermethylated sites in PAX3/CCDC140 andTBX1. TET1 and TET2 RNAs, which are involved in generation of 5-hmC and DNA demethylation, were strongly upregulated in myoblasts and myotubes. Our findings implicate de novo methylation predominantly before the myoblast stage and demethylation before and after the myotube stage in control of transcription and co-transcriptional RNA processing. They also suggest that, in muscle, TET1 or TET2 are involved in active demethylation and in formation of stable 5-hmC residues.
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MESH Headings
- 5-Methylcytosine/analogs & derivatives
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- CCCTC-Binding Factor
- Cardiac Myosins/genetics
- Cardiac Myosins/metabolism
- Case-Control Studies
- Cell Lineage/genetics
- Child
- Cytosine/analogs & derivatives
- Cytosine/metabolism
- DNA Methylation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Developmental
- Genes, Homeobox
- Genome, Human
- Guanine Nucleotide Exchange Factors/genetics
- Guanine Nucleotide Exchange Factors/metabolism
- Histones/metabolism
- Humans
- Infant, Newborn
- Male
- Middle Aged
- Mixed Function Oxygenases
- Muscle Development/genetics
- Muscle Fibers, Skeletal/metabolism
- Muscle Proteins/genetics
- Muscle Proteins/metabolism
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Myoblasts/metabolism
- Myosin Heavy Chains/genetics
- Myosin Heavy Chains/metabolism
- PAX3 Transcription Factor
- Paired Box Transcription Factors/genetics
- Paired Box Transcription Factors/metabolism
- Protein Serine-Threonine Kinases
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Repressor Proteins/metabolism
- Rho Guanine Nucleotide Exchange Factors
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
- Transcription, Genetic
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Affiliation(s)
- Koji Tsumagari
- Program in Human Genetics and Tulane Cancer Center; Tulane Health Sciences Center; New Orleans, LA USA
| | - Carl Baribault
- Tulane Cancer Center and Department of Mathematics; Tulane Health Sciences Center and Tulane University; New Orleans, LA USA
| | | | | | - Jason Gertz
- HudsonAlpha Institute for Biotechnology; Huntsville, AL USA
| | | | - Melody Badoo
- Department of Pathology and Tulane Cancer Center; Tulane Health Sciences Center; New Orleans, LA USA
| | - Charlene M. Crain
- Center for Stem Cell Research and Regenerative Medicine; Tulane Health Sciences Center; New Orleans, LA USA
| | - Lingyun Song
- Institute for Genome Sciences & Policy; Duke University; Durham, NC USA
| | | | | | - Michelle Lacey
- Tulane Cancer Center and Department of Mathematics; Tulane Health Sciences Center and Tulane University; New Orleans, LA USA
| | - Melanie Ehrlich
- Program in Human Genetics; Tulane Cancer Center and Center for Bioinformatics and Genomics; Tulane Health Sciences Center; New Orleans, LA USA
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19
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Hudson NJ, Lyons RE, Reverter A, Greenwood PL, Dalrymple BP. Inferring the in vivo cellular program of developing bovine skeletal muscle from expression data. Gene Expr Patterns 2013; 13:109-25. [PMID: 23419240 DOI: 10.1016/j.gep.2013.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 02/04/2013] [Accepted: 02/06/2013] [Indexed: 12/01/2022]
Abstract
We outline an in vivo cellular program of bovine longissimus muscle development inferred from expression data from 60 days post conception to 3months postnatal. Analytic challenges included changes in cellular composition, ambiguous 'diagnostic' markers of cell type and contrasts between cattle human and mouse myogenesis. Nevertheless, the expression profiles of the myosin isoforms support slow and fast muscle fibres emanating from primary and secondary myogenesis respectively, while expression of the prenatal myosin subunits is down regulated prior to birth. Of the canonical pro-myogenic transcription factors (TF), MYF6 and MYF5 are negatively co-expressed, with MYF6 displaying higher expression in the post-natal samples and MYF5, MYOG, HES6 and PAX7 displaying higher expression in early development. A set of TFs (SIX1, EYA2 and DACH2) considered important in undifferentiated murine cells were equally abundant in differentiated bovine cells. An examination of mammalian regulators of fibre composition, muscle mass and muscle metabolism, underscored the roles of PPARGC1A, TGFβ signalling and the NHR4 Nuclear Hormone Receptors on bovine muscle development. Enriched among the most variably expressed genes from the entire data set were molecules regulating mitochondrial metabolism of carbohydrate (PDK4), fat (UCP3), protein (AGXT2L1) and high energy phosphate (CKMT2). The dramatic increase in the expression of these transcripts, which may enable the peri-natal transition to metabolic independence critical for new-born herbivores, provides surprising evidence for substantial developmental remodelling of muscle mitochondria and reflects changes in nutrient availability. Overall, despite differences in size, metabolism and physiology, the muscle structural subunit expression program appears very similar in ruminants, rodents and humans.
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Affiliation(s)
- Nicholas J Hudson
- Computational and Systems Biology Group, CSIRO Food Futures and CSIRO Animal, Food and Health Sciences, 306 Carmody Road, St. Lucia, QLD 4072, Australia.
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20
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Veeck J, Dahl E. Targeting the Wnt pathway in cancer: the emerging role of Dickkopf-3. Biochim Biophys Acta Rev Cancer 2011; 1825:18-28. [PMID: 21982838 DOI: 10.1016/j.bbcan.2011.09.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/16/2011] [Accepted: 09/16/2011] [Indexed: 11/19/2022]
Abstract
Aberrant activation of the Wnt signaling pathway is a major trait of many human cancers. Due to its vast implications in tumorigenesis and progression, the Wnt pathway has attracted considerable attention at several molecular levels, also with respect to developing novel cancer therapeutics. Indeed, research in Wnt biology has recently provided numerous clues, and evidence is accumulating that the secreted Wnt antagonist Dickkopf-related protein 3 (Dkk-3) and its regulators may constitute interesting therapeutic targets in the most important human cancers. Based on the currently available literature, we here review the knowledge on the biological role of Dkk-3 as an antagonist of the Wnt signaling pathway, the involvement of Dkk-3 in several stages of tumor development, the genetic and epigenetic mechanisms disrupting DKK3 gene function in cancerous cells, and the potential clinical value of Dkk-3 expression/DKK3 promoter methylation as a biomarker and molecular target in cancer diseases. In conclusion, Dkk-3 rapidly emerges as a key player in human cancer with auspicious tumor suppressive capacities, most of all affecting apoptosis and proliferation. Its gene expression is frequently downregulated by promoter methylation in almost any solid and hematological tumor entity. Clinically, evidence is accumulating of Dkk-3 being both a potential tumor biomarker and effective anti-cancer agent. Although further research is needed, re-establishing Dkk-3 expression in cancer cells holds promise as novel targeted molecular tumor therapy.
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Affiliation(s)
- Jürgen Veeck
- Division of Medical Oncology, Department of Internal Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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21
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Nierobisz LS, Sporer KRB, Strasburg GM, Reed KM, Velleman SG, Ashwell CM, Felts JV, Mozdziak PE. Differential expression of genes characterizing myofibre phenotype. Anim Genet 2011; 43:298-308. [DOI: 10.1111/j.1365-2052.2011.02249.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Liao B, Xu Y. Exercise improves skeletal muscle insulin resistance without reduced basal mTOR/S6K1 signaling in rats fed a high-fat diet. Eur J Appl Physiol 2011; 111:2743-52. [PMID: 21404070 DOI: 10.1007/s00421-011-1892-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 02/25/2011] [Indexed: 11/26/2022]
Abstract
Exercise improves high-fat diet (HFD)-induced skeletal muscle insulin resistance, but the mechanism is unresolved. This study aims to explore whether the improvement in response to exercise is associated with mTOR/S6K1 signaling and whether the signaling changes are muscle-specific. Male SD rats (150-180 g) were used for this study. After the experimental period, 6 weeks of exercise improved HFD-impaired intraperitoneal glucose tolerance and insulin-stimulated 2-deoxyglucose uptake in soleus (SOL) and extensor digitorum longus (EDL) muscles. Furthermore, 6 weeks of the HFD resulted in a reduced type I fiber ratio of SOL, an increased type I ratio of EDL, and a reduced fiber size of EDL, whereas exercise increased type I fiber ratio of SOL as well as type I fiber cross-sectional areas of EDL. However, the HFD had a main effect on basal cytosolic phosphorylation of S6K1 on Thr(389) content in SOL, which was also influenced by a significant interaction between the diet and exercise in EDL. Exercise had no direct effect on the basal phosphorylation of Akt on Ser(473), mTOR on Ser(2448), S6K1 on Thr(389) content in SOL. On the contrary, exercise prevented HFD-induced decrease in basal phosphorylation of S6K1 on Thr(389) content in EDL. These results indicate that 6 weeks of HFD and exercise lead to alterations in fiber type shift, fiber size, and basal phosphorylation of S6K1 on Thr(389) content in a muscle-specific pattern. Exercise prevents HFD-induced skeletal muscle insulin resistance, which is not associated with a reduced basal phosphorylation of mTOR/S6K1 alteration in the muscles.
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Affiliation(s)
- Bagen Liao
- Department of Sports Medicine, Guangzhou Sports University, Guangzhou Dadao 1268, Guangzhou, 510076, China.
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