1
|
Nejad FM, Mohammadabadi M, Roudbari Z, Gorji AE, Sadkowski T. Network visualization of genes involved in skeletal muscle myogenesis in livestock animals. BMC Genomics 2024; 25:294. [PMID: 38504177 PMCID: PMC10953195 DOI: 10.1186/s12864-024-10196-3] [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: 12/28/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Muscle growth post-birth relies on muscle fiber number and size. Myofibre number, metabolic and contractile capacities are established pre-birth during prenatal myogenesis. The aim of this study was to identify genes involved in skeletal muscle development in cattle, sheep, and pigs - livestock. RESULTS The cattle analysis showed significant differences in 5043 genes during the 135-280 dpc period. In sheep, 444 genes differed significantly during the 70-120 dpc period. Pigs had 905 significantly different genes for the 63-91 dpc period.The biological processes and KEGG pathway enrichment results in each species individually indicated that DEGs in cattle were significantly enriched in regulation of cell proliferation, cell division, focal adhesion, ECM-receptor interaction, and signaling pathways (PI3K-Akt, PPAR, MAPK, AMPK, Ras, Rap1); in sheep - positive regulation of fibroblast proliferation, negative regulation of endothelial cell proliferation, focal adhesion, ECM-receptor interaction, insulin resistance, and signaling pathways (PI3K-Akt, HIF-1, prolactin, Rap1, PPAR); in pigs - regulation of striated muscle tissue development, collagen fibril organization, positive regulation of insulin secretion, focal adhesion, ECM-receptor interaction, and signaling pathways (PPAR, FoxO, HIF-1, AMPK). Among the DEGs common for studied animal species, 45 common genes were identified. Based on these, a protein-protein interaction network was created and three significant modules critical for skeletal muscle myogenesis were found, with the most significant module A containing four recognized hub genes - EGFR, VEGFA, CDH1, and CAV1. Using the miRWALK and TF2DNA databases, miRNAs (bta-miR-2374 and bta-miR-744) and transcription factors (CEBPB, KLF15, RELA, ZNF143, ZBTB48, and REST) associated with hub genes were detected. Analysis of GO term and KEGG pathways showed that such processes are related to myogenesis and associated with module A: positive regulation of MAP kinase activity, vascular endothelial growth factor receptor, insulin-like growth factor binding, focal adhesion, and signaling pathways (PI3K-Akt, HIF-1, Rap1, Ras, MAPK). CONCLUSIONS The identified genes, common to the prenatal developmental period of skeletal muscle in livestock, are critical for later muscle development, including its growth by hypertrophy. They regulate valuable economic characteristics. Enhancing and breeding animals according to the recognized genes seems essential for breeders to achieve superior gains in high-quality muscle mass.
Collapse
Affiliation(s)
- Fatemeh Mohammadi Nejad
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammadreza Mohammadabadi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Zahra Roudbari
- Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran.
| | - Abdolvahab Ebrahimpour Gorji
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | - Tomasz Sadkowski
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland.
| |
Collapse
|
2
|
Gui LK, Liu HJ, Jin LJ, Peng XC. Krüpple-like factors in cardiomyopathy: emerging player and therapeutic opportunities. Front Cardiovasc Med 2024; 11:1342173. [PMID: 38516000 PMCID: PMC10955087 DOI: 10.3389/fcvm.2024.1342173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/23/2024] [Indexed: 03/23/2024] Open
Abstract
Cardiomyopathy, a heterogeneous pathological condition characterized by changes in cardiac structure or function, represents a significant risk factor for the prevalence and mortality of cardiovascular disease (CVD). Research conducted over the years has led to the modification of definition and classification of cardiomyopathy. Herein, we reviewed seven of the most common types of cardiomyopathies, including Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC), diabetic cardiomyopathy, Dilated Cardiomyopathy (DCM), desmin-associated cardiomyopathy, Hypertrophic Cardiomyopathy (HCM), Ischemic Cardiomyopathy (ICM), and obesity cardiomyopathy, focusing on their definitions, epidemiology, and influencing factors. Cardiomyopathies manifest in various ways ranging from microscopic alterations in cardiomyocytes, to tissue hypoperfusion, cardiac failure, and arrhythmias caused by electrical conduction abnormalities. As pleiotropic Transcription Factors (TFs), the Krüppel-Like Factors (KLFs), a family of zinc finger proteins, are involved in regulating the setting and development of cardiomyopathies, and play critical roles in associated biological processes, including Oxidative Stress (OS), inflammatory reactions, myocardial hypertrophy and fibrosis, and cellular autophagy and apoptosis, particularly in diabetic cardiomyopathy. However, research into KLFs in cardiomyopathy is still in its early stages, and the pathophysiologic mechanisms of some KLF members in various types of cardiomyopathies remain unclear. This article reviews the roles and recent research advances in KLFs, specifically those targeting and regulating several cardiomyopathy-associated processes.
Collapse
Affiliation(s)
- Le-Kun Gui
- Department of Cardiology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- School of Medicine, Yangtze University, Jingzhou, Hubei, China
| | - Huang-Jun Liu
- Department of Cardiology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Li-Jun Jin
- Department of Cardiology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Xiao-Chun Peng
- Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China
- Laboratory of Oncology, School of Basic Medicine, Center for Molecular Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China
| |
Collapse
|
3
|
Neshan M, Tsilimigras DI, Han X, Zhu H, Pawlik TM. Molecular Mechanisms of Cachexia: A Review. Cells 2024; 13:252. [PMID: 38334644 PMCID: PMC10854699 DOI: 10.3390/cells13030252] [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: 12/19/2023] [Revised: 01/18/2024] [Accepted: 01/28/2024] [Indexed: 02/10/2024] Open
Abstract
Cachexia is a condition characterized by substantial loss of body weight resulting from the depletion of skeletal muscle and adipose tissue. A considerable fraction of patients with advanced cancer, particularly those who have been diagnosed with pancreatic or gastric cancer, lung cancer, prostate cancer, colon cancer, breast cancer, or leukemias, are impacted by this condition. This syndrome manifests at all stages of cancer and is associated with an unfavorable prognosis. It heightens the susceptibility to surgical complications, chemotherapy toxicity, functional impairments, breathing difficulties, and fatigue. The early detection of patients with cancer cachexia has the potential to enhance both their quality of life and overall survival rates. Regarding this matter, blood biomarkers, although helpful, possess certain limitations and do not exhibit universal application. Additionally, the available treatment options for cachexia are currently limited, and there is a lack of comprehensive understanding of the underlying molecular pathways associated with this condition. Thus, this review aims to provide an overview of molecular mechanisms associated with cachexia and potential therapeutic targets for the development of effective treatments for this devastating condition.
Collapse
Affiliation(s)
- Mahdi Neshan
- Department of General Surgery, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd 8915887857, Iran;
| | - Diamantis I. Tsilimigras
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH 43210, USA; (D.I.T.); (X.H.); (H.Z.)
| | - Xu Han
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH 43210, USA; (D.I.T.); (X.H.); (H.Z.)
| | - Hua Zhu
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH 43210, USA; (D.I.T.); (X.H.); (H.Z.)
| | - Timothy M. Pawlik
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH 43210, USA; (D.I.T.); (X.H.); (H.Z.)
| |
Collapse
|
4
|
Li J, Chen Z, Bai Y, Wei Y, Guo D, Liu Z, Niu Y, Shi B, Zhang X, Cai Y, Zhao Z, Hu J, Wang J, Liu X, Li S, Zhao F. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. Int J Mol Sci 2023; 25:158. [PMID: 38203329 PMCID: PMC10779322 DOI: 10.3390/ijms25010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | | | | | | | | |
Collapse
|
5
|
Wang R, Zhong J, Pan X, Su Z, Xu Y, Zhang M, Chen X, Chen N, Yu T, Zhou Q. A novel intronic circular RNA circFGFR1 int2 up-regulates FGFR1 by recruiting transcriptional activators P65/FUS and suppressing miR-4687-5p to promote prostate cancer progression. J Transl Med 2023; 21:840. [PMID: 37993879 PMCID: PMC10664560 DOI: 10.1186/s12967-023-04718-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
Fibroblast growth factor receptor 1 (FGFR1) is a core component of the FGFs/FGFR pathway that activates multiple signalling pathways, including ERK1/2, PI3K/AKT, PLCγ, and NF-κB. Aberrant expression of FGFR1 due to gene amplification, chromosome rearrangement, point mutation, and epigenetic deregulations, have been reported in various cancers. FGFR1 overexpression has also been reported in prostate cancer (PCa), but the underlining mechanisms are not clear. Here we report a novel circular RNA, circFGFR1int2, derived from intron 2 of FGFR1 gene, which is overexpressed in PCa and associated with tumor progression. Importantly, we show that circFGFR1int2 facilitates FGFR1 transcription by recruiting transcription activators P65/FUS and by interacting with FGFR1 promoter. Moreover, we show that circFGFR1int2 suppresses post-transcriptional inhibitory effects of miR-4687-5p on FGFR1 mRNA. These mechanisms synergistically promote PCa cell growth, migration, and invasion. Overexpression of circFGFR1int2 is significantly correlated with higher tumor grade, Gleason score, and PSA level, and is a significant unfavorable prognosticator for CRPC-free survival (CFS) (RR = 3.277, 95% confidence interval: 1.192-9.009; P = 0.021). These findings unravelled novel mechanisms controlling FGFR1 gene expression by intronic circRNA and its potential clinicopathological utility as a diagnostic or therapeutic target.
Collapse
Affiliation(s)
- Ruyue Wang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinjing Zhong
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiuyi Pan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhengzheng Su
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunyi Xu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengni Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xueqin Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ni Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ting Yu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qiao Zhou
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
6
|
Gao S, Huang S, Zhang Y, Fang G, Liu Y, Zhang C, Li Y, Du J. The transcriptional regulator KLF15 is necessary for myoblast differentiation and muscle regeneration by activating FKBP5. J Biol Chem 2023; 299:105226. [PMID: 37673339 PMCID: PMC10622842 DOI: 10.1016/j.jbc.2023.105226] [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: 03/28/2023] [Revised: 08/18/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023] Open
Abstract
Successful muscle regeneration following injury is essential for functional homeostasis of skeletal muscles. Krüppel-like factor 15 (KLF15) is a metabolic transcriptional regulator in the muscles. However, little is known regarding its function in muscle regeneration. Here, we examined microarray datasets from the Gene Expression Omnibus database, which indicated downregulated KLF15 in muscles from patients with various muscle diseases. Additionally, we found that Klf15 knockout (Klf15KO) impaired muscle regeneration following injury in mice. Furthermore, KLF15 expression was robustly induced during myoblast differentiation. Myoblasts with KLF15 deficiency showed a marked reduction in their fusion capacity. Unbiased transcriptome analysis of muscles on day 7 postinjury revealed downregulated genes involved in cell differentiation and metabolic processes in Klf15KO muscles. The FK506-binding protein 51 (FKBP5), a positive regulator of myoblast differentiation, was ranked as one of the most strongly downregulated genes in the Klf15KO group. A mechanistic search revealed that KLF15 binds directly to the promoter region of FKBP5 and activates FKBP5 expression. Local delivery of FKBP5 rescued the impaired muscle regeneration in Klf15KO mice. Our findings reveal a positive regulatory role of KLF15 in myoblast differentiation and muscle regeneration by activating FKBP5 expression. KLF15 signaling may be a novel therapeutic target for muscle disorders associated with injuries or diseases.
Collapse
Affiliation(s)
- Shijuan Gao
- Collaborative Innovation Centre for Cardiovascular Disorders, The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Shan Huang
- Collaborative Innovation Centre for Cardiovascular Disorders, The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yanhong Zhang
- Collaborative Innovation Centre for Cardiovascular Disorders, The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Guangming Fang
- Collaborative Innovation Centre for Cardiovascular Disorders, The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yan Liu
- Collaborative Innovation Centre for Cardiovascular Disorders, The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Congcong Zhang
- Collaborative Innovation Centre for Cardiovascular Disorders, The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
| | - Yulin Li
- Collaborative Innovation Centre for Cardiovascular Disorders, The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
| | - Jie Du
- Collaborative Innovation Centre for Cardiovascular Disorders, The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
| |
Collapse
|
7
|
Dasgupta A, Gibbard DF, Schmitt RE, Arneson-Wissink PC, Ducharme AM, Bruinsma ES, Hawse JR, Jatoi A, Doles JD. A TGF-β/KLF10 signaling axis regulates atrophy-associated genes to induce muscle wasting in pancreatic cancer. Proc Natl Acad Sci U S A 2023; 120:e2215095120. [PMID: 37585460 PMCID: PMC10462925 DOI: 10.1073/pnas.2215095120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 06/14/2023] [Indexed: 08/18/2023] Open
Abstract
Cancer cachexia, and its associated complications, represent a large and currently untreatable roadblock to effective cancer management. Many potential therapies have been proposed and tested-including appetite stimulants, targeted cytokine blockers, and nutritional supplementation-yet highly effective therapies are lacking. Innovative approaches to treating cancer cachexia are needed. Members of the Kruppel-like factor (KLF) family play wide-ranging and important roles in the development, maintenance, and metabolism of skeletal muscle. Within the KLF family, we identified KLF10 upregulation in a multitude of wasting contexts-including in pancreatic, lung, and colon cancer mouse models as well as in human patients. We subsequently interrogated loss-of-function of KLF10 as a potential strategy to mitigate cancer associated muscle wasting. In vivo studies leveraging orthotopic implantation of pancreas cancer cells into wild-type and KLF10 KO mice revealed significant preservation of lean mass and robust suppression of pro-atrophy muscle-specific ubiquitin ligases Trim63 and Fbxo32, as well as other factors implicated in atrophy, calcium signaling, and autophagy. Bioinformatics analyses identified Transforming growth factor beta (TGF-β), a known inducer of KLF10 and cachexia promoting factor, as a key upstream regulator of KLF10. We provide direct in vivo evidence that KLF10 KO mice are resistant to the atrophic effects of TGF-β. ChIP-based binding studies demonstrated direct binding to Trim63, a known wasting-associated atrogene. Taken together, we report a critical role for the TGF-β/KLF10 axis in the etiology of pancreatic cancer-associated muscle wasting and highlight the utility of targeting KLF10 as a strategy to prevent muscle wasting and limit cancer-associated cachexia.
Collapse
Affiliation(s)
- Aneesha Dasgupta
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN55905
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN46202
- Indiana Center for Musculoskeletal Health, Indianapolis, IN46202
- Tumor Microenvironment & Metastasis Program, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN46202
| | - Daniel F. Gibbard
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN55905
| | - Rebecca E. Schmitt
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN55905
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN46202
- Indiana Center for Musculoskeletal Health, Indianapolis, IN46202
- Tumor Microenvironment & Metastasis Program, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN46202
| | - Paige C. Arneson-Wissink
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN55905
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN55905
| | | | | | - John R. Hawse
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN55905
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN55905
| | - Aminah Jatoi
- Department of Oncology, Mayo Clinic, Rochester, MN55905
| | - Jason D. Doles
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN55905
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN46202
- Indiana Center for Musculoskeletal Health, Indianapolis, IN46202
- Tumor Microenvironment & Metastasis Program, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN46202
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN55905
| |
Collapse
|
8
|
Ling X, Wang Q, Zhang J, Zhang G. Genome-Wide Analysis of the KLF Gene Family in Chicken: Characterization and Expression Profile. Animals (Basel) 2023; 13:ani13091429. [PMID: 37174466 PMCID: PMC10177326 DOI: 10.3390/ani13091429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/08/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
The kruppel-like factor (KLF) gene family is a group of transcription factors containing highly conserved zinc-finger motifs, which play a crucial role in cell proliferation and differentiation. Chicken has been widely used as a model animal for analyzing gene function, however, little is known about the function of the KLF gene family in chickens. In this study, we performed genome-wide studies of chicken KLF genes and analyzed their biological and expression characteristics. We identified 13 KLF genes from chickens. Our phylogenetic, motif, and conserved domain analyses indicate that the KLF gene family has remained conserved through evolution. Synteny analysis showed the collinear relationship among KLFs, which indicated that they had related biomolecular functions. Interaction network analysis revealed that KLFs worked with 20 genes in biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that KLF2 was involved in Apelin and Forkhead Box O (FOXO) signaling pathways. Moreover, qPCR showed that 13 KLF genes were expressed in the nine selected tissues and displayed various gene expression patterns in chickens. RNA-seq showed that KLF3 and KLF10 genes were differentially expressed in the normal and high-fat diet fed groups, and KLF4, KLF5, KLF6, KLF7, KLF9, KLF12, and KLF13 genes were differentially expressed between undifferentiated and differentiated chicken preadipocytes. Besides, RNA-seq also showed that KLF genes displayed different expression patterns in muscle at 11 and 16 embryonic days old, and in 1-day-old chickens. These results indicated that the KLF genes were involved in the development of muscle and fat in chickens. Our findings provide some valuable reference points for the subsequent study of the function of KLF genes.
Collapse
Affiliation(s)
- Xuanze Ling
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Qifan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Jin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| |
Collapse
|
9
|
Inhibition of Klf10 Attenuates Oxidative Stress-Induced Senescence of Chondrocytes via Modulating Mitophagy. Molecules 2023; 28:molecules28030924. [PMID: 36770589 PMCID: PMC9921806 DOI: 10.3390/molecules28030924] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/24/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Osteoarthritis (OA) is the most prevalent degenerative joint disease in the elderly. Accumulation of evidence has suggested that chondrocyte senescence plays a significant role in OA development. Here, we show that Krüppel-like factor 10 (Klf10), also named TGFβ inducible early gene-1 (TIEG1), is involved in the pathology of chondrocyte senescence. Knocking down the Klf10 in chondrocytes attenuated the tert-butyl hydroperoxide (TBHP)-induced senescence, inhibited generation of reactive oxygen species (ROS), and maintained mitochondrial homeostasis by activating mitophagy. These findings suggested that knocking down Klf10 inhibited senescence-related changes in chondrocytes and improved cartilage homeostasis, indicating that Klf10 may be a therapeutic target for protecting cartilage against OA.
Collapse
|
10
|
Milton CI, Selfe J, Aladowicz E, Man SYK, Bernauer C, Missiaglia E, Walters ZS, Gatz SA, Kelsey A, Generali M, Box G, Valenti M, de Haven‐Brandon A, Galiwango D, Hayes A, Clarke M, Izquierdo E, Gonzalez De Castro D, Raynaud FI, Kirkin V, Shipley JM. FGF7-FGFR2 autocrine signaling increases growth and chemoresistance of fusion-positive rhabdomyosarcomas. Mol Oncol 2022; 16:1272-1289. [PMID: 34850536 PMCID: PMC8936514 DOI: 10.1002/1878-0261.13145] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/30/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
Rhabdomyosarcomas are aggressive pediatric soft-tissue sarcomas and include high-risk PAX3-FOXO1 fusion-gene-positive cases. Fibroblast growth factor receptor 4 (FGFR4) is known to contribute to rhabdomyosarcoma progression; here, we sought to investigate the involvement and potential for therapeutic targeting of other FGFRs in this disease. Cell-based screening of FGFR inhibitors with potential for clinical repurposing (NVP-BGJ398, nintedanib, dovitinib, and ponatinib) revealed greater sensitivity of fusion-gene-positive versus fusion-gene-negative rhabdomyosarcoma cell lines and was shown to be correlated with high expression of FGFR2 and its specific ligand, FGF7. Furthermore, patient samples exhibit higher mRNA levels of FGFR2 and FGF7 in fusion-gene-positive versus fusion-gene-negative rhabdomyosarcomas. Sustained intracellular mitogen-activated protein kinase (MAPK) activity and FGF7 secretion into culture media during serum starvation of PAX3-FOXO1 rhabdomyosarcoma cells together with decreased cell viability after genetic silencing of FGFR2 or FGF7 was in keeping with a novel FGF7-FGFR2 autocrine loop. FGFR inhibition with NVP-BGJ398 reduced viability and was synergistic with SN38, the active metabolite of irinotecan. In vivo, NVP-BGJ398 abrogated xenograft growth and warrants further investigation in combination with irinotecan as a therapeutic strategy for fusion-gene-positive rhabdomyosarcomas.
Collapse
Affiliation(s)
- Christopher I. Milton
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
- Present address:
Signal Transduction and Molecular Pharmacology TeamCancer Research UK Cancer Therapeutics UnitThe Institute of Cancer ResearchSuttonUK
| | - Joanna Selfe
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Ewa Aladowicz
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Stella Y. K. Man
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Carolina Bernauer
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Edoardo Missiaglia
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
- Present address:
Department of Molecular PathologyCentre Hospitalier Universitaire VaudoisLausanneSwitzerland
| | - Zoë S. Walters
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
- Present address:
Translational Epigenomics TeamHuman Development and HealthFaculty of MedicineSouthampton General HospitalUK
| | - Susanne A. Gatz
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
- Present address:
Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Anna Kelsey
- Department of Paediatric HistopathologyManchester University NHS Foundation TrustRoyal Manchester Children’s HospitalUK
| | - Melanie Generali
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
- Present address:
Center for Therapy Development and Good Manufacturing PracticeInstitute for Regenerative Medicine (IREM)University of ZurichSwitzerland
| | - Gary Box
- Cancer Pharmacology and Stress Response TeamDivision of Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Melanie Valenti
- Cancer Pharmacology and Stress Response TeamDivision of Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Alexis de Haven‐Brandon
- Cancer Pharmacology and Stress Response TeamDivision of Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - David Galiwango
- Drug Metabolism and Pharmacokinetics TeamDivision of Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Angela Hayes
- Drug Metabolism and Pharmacokinetics TeamDivision of Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Matthew Clarke
- Glioma TeamDivision of Molecular PathologyThe Institute of Cancer ResearchLondonUK
| | - Elisa Izquierdo
- Glioma TeamDivision of Molecular PathologyThe Institute of Cancer ResearchLondonUK
| | - David Gonzalez De Castro
- Molecular HaematologyDivision of Molecular PathologyThe Institute of Cancer ResearchLondonUK
- Present address:
School of MedicineDentistry and Biomedical sciencesQueens University BelfastUK
| | - Florence I. Raynaud
- Drug Metabolism and Pharmacokinetics TeamDivision of Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Vladimir Kirkin
- Cancer Pharmacology and Stress Response TeamDivision of Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Janet M. Shipley
- Sarcoma Molecular Pathology TeamDivisions of Molecular Pathology and Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| |
Collapse
|
11
|
Wang S, Zha X, Ruan S, Yao S, Zhang X. Kruppel like factor 10 up-regulates PDZ and LIM domain containing protein 2 via nuclear factor kappa-B pathway to inhibit proliferation and inflammatory of fibroblastoid synovial cell in rheumatoid arthritis. Bioengineered 2021; 13:1779-1790. [PMID: 34713769 PMCID: PMC8805881 DOI: 10.1080/21655979.2021.1995992] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease caused by synovitis. Two genes, KLF10 (Kruppel like factor 10) and PDZ and LIM domain containing protein 2 (PDLIM2), play key roles in cell inflammation and proliferation. However, the specific roles of the two on inflammation and proliferation of RA-fibroblastoid synovial cell (RA-FLS) have not been reported so far. RT-qPCR and Western blot detected the expressions of PDLIM2 and KLF10 in Human Rheumatoid arthritis FLSs (HFLSs-RA). Cell transfection techniques overexpressed PDLIM2 and KLF10 or inhibited the expression of KLF10. JAPAR database predicted the binding sites of PDLIM2 and KLF10, and the binding between the two was detected and verified using luciferase reporter genes and ChIP. Subsequently, CCK-8 technology, TUNEL staining, Western blot, wound healing and ELISA detected proliferation-related indicators, migration-related indications and inflammation-related indicators. Finally, western blot was used to detect the expression of NF-κB pathway-related proteins to further explore the mechanism.The expression of PDLIM2 was decreased in HFLSs-RA. Overexpression of PDLIM2 inhibited proliferation, migration and inflammation in HFLSs-RA. KLF10 can transcriptionally activate PDLIM2. Interfering with KLF10 reversed the inhibition effects of PDLIM2 overexpression on the proliferation, migration and inflammation, which was possibly through the NF-κB pathway. Overall, KLF10 can up-regulate PDLIM2 by regulating the NF-κB pathway to inhibit inflammation and proliferation of HFLSs-RA.
Collapse
Affiliation(s)
- Shan Wang
- Rheumatology and immunology department, The First people's Hospital of Hefei, The Third Affiliated Hospital of Anhui Medical University. Hefei, 230061, Anhui, China
| | - Xuwen Zha
- Rheumatology and immunology department, The First people's Hospital of Hefei, The Third Affiliated Hospital of Anhui Medical University. Hefei, 230061, Anhui, China
| | - Shengting Ruan
- Rheumatology and immunology department, The First people's Hospital of Hefei, The Third Affiliated Hospital of Anhui Medical University. Hefei, 230061, Anhui, China
| | - Shoulin Yao
- Rheumatology and immunology department, The First people's Hospital of Hefei, The Third Affiliated Hospital of Anhui Medical University. Hefei, 230061, Anhui, China
| | - Xiaoyu Zhang
- Rheumatology and immunology department, The First people's Hospital of Hefei, The Third Affiliated Hospital of Anhui Medical University. Hefei, 230061, Anhui, China
| |
Collapse
|
12
|
miR-21-5p Regulates the Proliferation and Differentiation of Skeletal Muscle Satellite Cells by Targeting KLF3 in Chicken. Genes (Basel) 2021; 12:genes12060814. [PMID: 34073601 PMCID: PMC8227323 DOI: 10.3390/genes12060814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
The proliferation and differentiation of skeletal muscle satellite cells (SMSCs) play an important role in the development of skeletal muscle. Our previous sequencing data showed that miR-21-5p is one of the most abundant miRNAs in chicken skeletal muscle. Therefore, in this study, the spatiotemporal expression of miR-21-5p and its effects on skeletal muscle development of chickens were explored using in vitro cultured SMSCs as a model. The results in this study showed that miR-21-5p was highly expressed in the skeletal muscle of chickens. The overexpression of miR-21-5p promoted the proliferation of SMSCs as evidenced by increased cell viability, increased cell number in the proliferative phase, and increased mRNA and protein expression of proliferation markers including PCNA, CDK2, and CCND1. Moreover, it was revealed that miR-21-5p promotes the formation of myotubes by modulating the expression of myogenic markers including MyoG, MyoD, and MyHC, whereas knockdown of miR-21-5p showed the opposite result. Gene prediction and dual fluorescence analysis confirmed that KLF3 was one of the direct target genes of miR-21-5p. We confirmed that, contrary to the function of miR-21-5p, KLF3 plays a negative role in the proliferation and differentiation of SMSCs. Si-KLF3 promotes cell number and proliferation activity, as well as the cell differentiation processes. Our results demonstrated that miR-21-5p promotes the proliferation and differentiation of SMSCs by targeting KLF3. Collectively, the results obtained in this study laid a foundation for exploring the mechanism through which miR-21-5p regulates SMSCs.
Collapse
|
13
|
Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals. Animals (Basel) 2021; 11:ani11030835. [PMID: 33809500 PMCID: PMC7999090 DOI: 10.3390/ani11030835] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Skeletal muscle mass is an important economic trait, and muscle development and growth is a crucial factor to supply enough meat for human consumption. Thus, understanding (candidate) genes regulating skeletal muscle development is crucial for understanding molecular genetic regulation of muscle growth and can be benefit the meat industry toward the goal of increasing meat yields. During the past years, significant progress has been made for understanding these mechanisms, and thus, we decided to write a comprehensive review covering regulators and (candidate) genes crucial for muscle development and growth in farm animals. Detection of these genes and factors increases our understanding of muscle growth and development and is a great help for breeders to satisfy demands for meat production on a global scale. Abstract Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.
Collapse
|
14
|
Kang T, Xing W, Xi Y, Chen K, Zhan M, Tang X, Wang Y, Zhang R, Lei M. MiR-543 regulates myoblast proliferation and differentiation of C2C12 cells by targeting KLF6. J Cell Biochem 2020; 121:4827-4837. [PMID: 32348593 DOI: 10.1002/jcb.29710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/12/2020] [Indexed: 12/17/2022]
Abstract
MicroRNA-543 (miR-543) has been found to play a suppressive role in various human cancers in many studies, whereas the specific functions of miR-543 in muscle development remain poorly understood. Here, we found that the expression of miR-543 was high in skeletal muscle and increased during the differentiation of C2C12 cells. Overexpression of miR-543 repressed C2C12 cell proliferation and promoted differentiation, while knockdown of miR-543 expression produced the opposite results. During myogenesis, we predicted and verified that Krüppel-like factor 6 (KLF6), a suppressor of multiple tumor cells, was a target gene of miR-543. Then, miR-543 was found to specifically target KLF6 and repress its expression. Besides this, knockdown of KLF6 promoted the differentiation but inhibited the proliferation of C2C12 cells. Si-KLF6 can rescue the influence of miR-543 inhibitor on C2C12 cell differentiation. Our results indicate a new regulatory mechanism of miR-543 on KLF6 expression and suggest the possibility of using the miR-543/KLF6 pathway as a potential target for studying myogenesis.
Collapse
Affiliation(s)
- Tingting Kang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenkai Xing
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu Xi
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kun Chen
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mengsi Zhan
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoyin Tang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yueying Wang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ruirui Zhang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Minggang Lei
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
15
|
The Potential Effects of Curcumin on Pulmonary Fibroblasts of Idiopathic Pulmonary Fibrosis (IPF)-Approaching with Next-Generation Sequencing and Bioinformatics. Molecules 2020; 25:molecules25225458. [PMID: 33233354 PMCID: PMC7700625 DOI: 10.3390/molecules25225458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial lung disease. Currently, therapeutic options are limited for this fatal disease. Curcumin, with its pleiotropic effects, has been studied for its potential therapeutic utilities in various diseases, including pulmonary fibrosis. However, the detailed mechanisms have not been studied comprehensively. We conducted a next-generation sequencing and bioinformatics study to investigate changes in the profiles of mRNA and microRNA after curcumin treatment in IPF fibroblasts. We identified 23 downregulated and 8 upregulated protein-coding genes in curcumin-treated IPF fibroblasts. Using STRING and IPA, we identified that suppression of cell cycle progression was the main cellular function associated with these differentially expressed genes. We also identified 13 downregulated and 57 upregulated microRNAs in curcumin-treated IPF fibroblasts. Further analysis identified a potential microRNA-mediated gene expression alteration in curcumin-treated IPF fibroblasts, namely, downregulated hsa-miR-6724-5p and upregulated KLF10. Therefore, curcumin might decrease the level of hsa-miR-6724-5p, leading to increased KLF10 expression, resulting in cell cycle arrest in curcumin-treated IPF fibroblasts. In conclusion, our findings might support the potential role of curcumin in the treatment of IPF, but further in-depth study is warranted to confirm our findings.
Collapse
|
16
|
Nilsson E, Benrick A, Kokosar M, Krook A, Lindgren E, Källman T, Martis MM, Højlund K, Ling C, Stener-Victorin E. Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome. J Clin Endocrinol Metab 2018; 103:4465-4477. [PMID: 30113663 DOI: 10.1210/jc.2018-00935] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 07/27/2018] [Indexed: 02/13/2023]
Abstract
CONTEXT Insulin resistance in skeletal muscle is a major risk factor for the development of type 2 diabetes in women with polycystic ovary syndrome (PCOS). Despite this, the mechanisms underlying insulin resistance in PCOS are largely unknown. OBJECTIVE To investigate the genome-wide DNA methylation and gene expression patterns in skeletal muscle from women with PCOS and controls and relate them to phenotypic variations. DESIGN/PARTICIPANTS In a case-control study, skeletal muscle biopsies from women with PCOS (n = 17) and age-, weight-, and body mass index‒matched controls (n = 14) were analyzed by array-based DNA methylation and mRNA expression profiling. RESULTS Eighty-five unique transcripts were differentially expressed in muscle from women with PCOS vs controls, including DYRK1A, SYNPO2, SCP2, and NAMPT. Furthermore, women with PCOS had reduced expression of genes involved in immune system pathways. Two CpG sites showed differential DNA methylation after correction for multiple testing. However, an mRNA expression of ∼30% of the differentially expressed genes correlated with DNA methylation levels of CpG sites in or near the gene. Functional follow-up studies demonstrated that KLF10 is under transcriptional control of insulin, where insulin promotes glycogen accumulation in myotubes of human muscle cells. Testosterone downregulates the expression levels of COL1A1 and MAP2K6. CONCLUSION PCOS is associated with aberrant skeletal muscle gene expression with dysregulated pathways. Furthermore, we identified specific changes in muscle DNA methylation that may affect gene expression. This study showed that women with PCOS have epigenetic and transcriptional changes in skeletal muscle that, in part, can explain the metabolic abnormalities seen in these women.
Collapse
Affiliation(s)
- Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Anna Benrick
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- School of Health and Education, University of Skövde, Skövde, Sweden
| | - Milana Kokosar
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Krook
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Eva Lindgren
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Källman
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Mihaela M Martis
- National Bioinformatics Infrastructure Sweden, Division of Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Kurt Højlund
- Department of Endocrinology, Odense University, Odense C, Denmark
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | | |
Collapse
|
17
|
Lee EJ, Kim M, Kim YD, Chung MJ, Elfadl A, Ulah HMA, Park D, Lee S, Park HS, Kim TH, Hwang D, Jeong KS. Establishment of stably expandable induced myogenic stem cells by four transcription factors. Cell Death Dis 2018; 9:1092. [PMID: 30361642 PMCID: PMC6202407 DOI: 10.1038/s41419-018-1114-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/04/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022]
Abstract
Life-long regeneration of healthy muscle by cell transplantation is an ideal therapy for patients with degenerative muscle diseases. Yet, obtaining muscle stem cells from patients is very limited due to their exhaustion in disease condition. Thus, development of a method to obtain healthy myogenic stem cells is required. Here, we showed that the four transcription factors, Six1, Eya1, Esrrb, and Pax3, converts fibroblasts into induced myogenic stem cells (iMSCs). The iMSCs showed effective differentiation into multinucleated myotubes and also higher proliferation capacity than muscle derived stem cells both in vitro and in vivo. The iMSCs do not lose their proliferation capacity though the passaging number is increased. We further isolated CD106-negative and α7-integrin-positive iMSCs (sort-iMSCs) showing higher myogenic differentiation capacity than iMSCs. Moreover, genome-wide transcriptomic analysis of iMSCs and sort-iMSCs, followed by network analysis, revealed the genes and signaling pathways associated with enhanced proliferation and differentiation capacity of iMSCs and sort-iMSCs, respectively. The stably expandable iMSCs provide a new source for drug screening and muscle regenerative therapy for muscle wasting disease.
Collapse
Affiliation(s)
- Eun-Joo Lee
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Minhyung Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Yong Deuk Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.,Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Myung-Jin Chung
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.,Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ahmed Elfadl
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.,Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - H M Arif Ulah
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.,Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dongsu Park
- Department of Molecular Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Center for Skeletal Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sunray Lee
- Cell Engineering for Origin Research Center 45-13, Ujeongguk-ro, Jongno-gu, Seoul, 03150, Republic of Korea
| | - Hyun-Sook Park
- Cell Engineering for Origin Research Center 45-13, Ujeongguk-ro, Jongno-gu, Seoul, 03150, Republic of Korea
| | - Tae-Hwan Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Daehee Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.,Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea.,Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Kyu-Shik Jeong
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea.
| |
Collapse
|
18
|
Gong W, Zhu G, Li J, Yang X. LncRNA MALAT1 promotes the apoptosis and oxidative stress of human lens epithelial cells via p38MAPK pathway in diabetic cataract. Diabetes Res Clin Pract 2018; 144:314-321. [PMID: 29936249 DOI: 10.1016/j.diabres.2018.06.020] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 06/08/2018] [Accepted: 06/19/2018] [Indexed: 11/21/2022]
Abstract
BACKGROUND LncRNAs are involved in various biological processes and disorders. We aimed to investigate the role of lncRNA MALAT1 deregulation in the pathogenic mechanism of diabetic cataract (DC). METHODS The expression of MALAT1 in the tissues and cells was detected by qRT-PCR. The levels of SP1, p38 and apoptosis-related protein were assessed by Western blot assay. Chromatin immunoprecipitation assay and Dual luciferase assay were performed to evaluate the relationship between SP1 and MALAT1. The viability and apoptosis of human lens epithelial cells (HLECs) were analyzed by MTT assay and flow cytometry. The levels of malonyldialdehyde (MDA), superoxide dismutase (SOD) and phospholipid hydroperoxide glutathione peroxidase (GSH-Px) were used to examine the level of oxidative stress. RESULTS MALAT1 not only was aberrantly expressed in DC anterior lens capsule tissues and high glucose (HG)-treated HLECs, but also were up-regulated by HG to promote the apoptosis and oxidative stress of HLECs. HG induced the up-regulation of MALAT1 via SP1 binding MALAT1 promoter regions in HLECs. Moreover, p38 was up-regulated in HG-treated HLECs, and knockdown of p38 reversed the effect of MALAT1 over-expression on HLECs. CONCLUSION HG induced the up-regulation of MALAT1 in HLECs via SP1 binding SP1 binding MALAT1, which promoted the apoptosis and oxidative stress of HLECs through the activation of p38MAPK signaling pathway.
Collapse
Affiliation(s)
- Weifeng Gong
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Guangyue Zhu
- Department of Ophthalmology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Li
- Department of Ophthalmology, The Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xin Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| |
Collapse
|
19
|
Zhou L, Xu DY, Sha WG, Shen L, Lu GY. Long non-coding RNA MALAT1 interacts with transcription factor Foxo1 to regulate SIRT1 transcription in high glucose-induced HK-2 cells injury. Biochem Biophys Res Commun 2018; 503:849-855. [DOI: 10.1016/j.bbrc.2018.06.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/17/2018] [Indexed: 10/28/2022]
|
20
|
The regulation of skeletal muscle fiber-type composition by betaine is associated with NFATc1/MyoD. J Mol Med (Berl) 2018; 96:685-700. [PMID: 29876588 DOI: 10.1007/s00109-018-1657-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/03/2023]
Abstract
Increasing evidence indicates that muscular dysfunction or alterations in skeletal muscle fiber-type composition not only are involved in muscle metabolism and function but also can limit functional capacity. Therefore, understanding the mechanisms regulating key events during skeletal myogenesis is necessary. Betaine is a naturally occurring component of commonly eaten foods. Here, we showed that 10 mM betaine supplementation in vitro significantly repressed myoblast proliferation and enhanced myoblast differentiation. This effect can be mediated by regulation of miR-29b-3p. Further analysis showed that betaine supplementation in vitro regulated skeletal muscle fiber-type composition through the induction of NFATc1 and the negative regulation of MyoD expression. Furthermore, mice fed with 10 mM betaine in water for 133 days showed no impairment in overall health. Consistently, betaine supplementation increased muscle mass, promoted muscle formation, and modulated the ratio of fiber types in skeletal muscle in vivo. These findings shed light on the diverse biological functions of betaine and indicate that betaine supplementation may lead to new therapies for diseases such as muscular dystrophy or other diseases related to muscle dysfunction. KEY MESSAGES: Betaine supplementation inhibits proliferation and promotes differentiation of C2C12 myoblasts. Betaine supplementation regulates fast to slow muscle fiber-type conversion and is associated with NFATc1/MyoD. Betaine supplementation enhances skeletal myogenesis in vivo. Betaine supplementation does not impair health of mice.
Collapse
|
21
|
Jia X, Min L, Zhu S, Zhang S, Huang X. Loss of sonic hedgehog gene leads to muscle development disorder and megaesophagus in mice. FASEB J 2018; 32:5703-5715. [DOI: 10.1096/fj.201701581r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Xueting Jia
- Department of GastroenterologyNational Clinical Research Center for Digestive Diseases, Beijing Digestive Disease CenterBeijing Key Laboratory for Precancerous Lesion of Digestive Diseases
- Department of StomatologyBeijing Friendship Hospital, Capital Medical UniversityBeijingChina
| | - Li Min
- Department of GastroenterologyNational Clinical Research Center for Digestive Diseases, Beijing Digestive Disease CenterBeijing Key Laboratory for Precancerous Lesion of Digestive Diseases
| | - Shengtao Zhu
- Department of GastroenterologyNational Clinical Research Center for Digestive Diseases, Beijing Digestive Disease CenterBeijing Key Laboratory for Precancerous Lesion of Digestive Diseases
| | - Shutian Zhang
- Department of GastroenterologyNational Clinical Research Center for Digestive Diseases, Beijing Digestive Disease CenterBeijing Key Laboratory for Precancerous Lesion of Digestive Diseases
| | - Xiaofeng Huang
- Department of StomatologyBeijing Friendship Hospital, Capital Medical UniversityBeijingChina
| |
Collapse
|
22
|
DiMario JX. KLF10 Gene Expression Modulates Fibrosis in Dystrophic Skeletal Muscle. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1263-1275. [PMID: 29458012 DOI: 10.1016/j.ajpath.2018.01.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 01/22/2018] [Accepted: 01/30/2018] [Indexed: 02/06/2023]
Abstract
Dystrophic skeletal muscle is characterized by fibrotic accumulation of extracellular matrix components that compromise muscle structure, function, and capacity for regeneration. Tissue fibrosis is often initiated and sustained through transforming growth factor-β (TGF-β) signaling, and Krüppel-like factor 10 (KLF10) is an immediate early gene that is transcriptionally activated in response to TGF-β signaling. It encodes a transcriptional regulator that mediates the effects of TGF-β signaling in a variety of cell types. This report presents results of investigation of the effects of loss of KLF10 gene expression in wild-type and dystrophic (mdx) skeletal muscle. On the basis of RT-PCR, Western blot, and histological analyses of mouse tibialis anterior and diaphragm muscles, collagen type I (Col1a1) and fibronectin gene expression and protein deposition were increased in KLF10-/- mice, contributing to increased fibrosis. KLF10-/- mice displayed increased expression of genes encoding SMAD2, SMAD3, and SMAD7, particularly in diaphragm muscle. SMAD4 gene expression was unchanged. Expression of the extracellular matrix remodeling genes, MMP2 and TIMP1, was also increased in KLF10-deficient mouse muscle. Histological analyses and assays of hydroxyproline content indicated that the loss of KLF10 increased fibrosis. Dystrophic KLF10-null mice also had reduced grip strength. The effects of loss of KLF10 gene expression were most pronounced in dystrophic diaphragm muscle, suggesting that KLF10 moderates the fibrotic effects of TGF-β signaling in chronically damaged regenerating muscle.
Collapse
Affiliation(s)
- Joseph X DiMario
- Department of Cell Biology and Anatomy, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, Illinois.
| |
Collapse
|
23
|
Cavanaugh E, DiMario JX. Sp3 controls fibroblast growth factor receptor 4 gene activity during myogenic differentiation. Gene 2017; 617:24-31. [PMID: 28359915 DOI: 10.1016/j.gene.2017.03.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/20/2016] [Accepted: 03/25/2017] [Indexed: 11/17/2022]
Abstract
Fibroblast growth factor/fibroblast growth factor receptor (FGF/FGFR) signaling is a critical component in the regulation of myoblast proliferation and differentiation. The transient FGFR4 gene expression during the transition from proliferating myoblasts to differentiated myotubes indicates that FGFR4 regulates this critical phase of myogenesis. The Specificity Protein (SP) family of transcription factors controls FGFR family member gene activity. We sought to determine if members of the Sp family regulate mouse FGFR4 gene activity during myogenic differentiation. RT-PCR and western blot analysis of FGFR4 mRNA and protein revealed transient expression over 72h, with peak expression between 24 and 36h after addition of differentiation medium to C2C12 myogenic cultures. Sp3 also displayed a transient expression pattern with peak expression occurring after 6h of differentiation. We cloned a 1527bp fragment of the mouse FGFR4 promoter into a luciferase reporter. This FGFR4 promoter contains eight putative Sp binding sites and directed luciferase gene activity comparable to native FGFR4 expression. Overexpression of Sp1 and Sp3 showed that Sp1 repressed FGFR4 gene activity, and Sp3 activated FGFR4 gene activity during myogenic differentiation. Mutational analyses of multiple Sp binding sites within the FGFR4 promoter revealed that three of these sites were transcriptionally active. Electromobility shift assays and chromatin immunoprecipitation of the area containing the activator sites showed that Sp3 bound to this promoter location.
Collapse
Affiliation(s)
- Eric Cavanaugh
- School of Graduate and Postdoctoral Studies and Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, Illinois 60064, United States
| | - Joseph X DiMario
- School of Graduate and Postdoctoral Studies and Chicago Medical School, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, Illinois 60064, United States.
| |
Collapse
|
24
|
Hu Q, Li S, Chen C, Zhu M, Chen Y, Zhao Z. 17β-Estradiol treatment drives Sp1 to upregulate MALAT-1 expression and epigenetically affects physiological processes in U2OS cells. Mol Med Rep 2017; 15:1335-1342. [DOI: 10.3892/mmr.2017.6115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/16/2016] [Indexed: 11/05/2022] Open
|
25
|
Hayashi S, Manabe I, Suzuki Y, Relaix F, Oishi Y. Klf5 regulates muscle differentiation by directly targeting muscle-specific genes in cooperation with MyoD in mice. eLife 2016; 5. [PMID: 27743478 PMCID: PMC5074804 DOI: 10.7554/elife.17462] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/13/2016] [Indexed: 12/18/2022] Open
Abstract
Krüppel-like factor 5 (Klf5) is a zinc-finger transcription factor that controls various biological processes, including cell proliferation and differentiation. We show that Klf5 is also an essential mediator of skeletal muscle regeneration and myogenic differentiation. During muscle regeneration after injury (cardiotoxin injection), Klf5 was induced in the nuclei of differentiating myoblasts and newly formed myofibers expressing myogenin in vivo. Satellite cell-specific Klf5 deletion severely impaired muscle regeneration, and myotube formation was suppressed in Klf5-deleted cultured C2C12 myoblasts and satellite cells. Klf5 knockdown suppressed induction of muscle differentiation-related genes, including myogenin. Klf5 ChIP-seq revealed that Klf5 binding overlaps that of MyoD and Mef2, and Klf5 physically associates with both MyoD and Mef2. In addition, MyoD recruitment was greatly reduced in the absence of Klf5. These results indicate that Klf5 is an essential regulator of skeletal muscle differentiation, acting in concert with myogenic transcription factors such as MyoD and Mef2.
Collapse
Affiliation(s)
- Shinichiro Hayashi
- Department of Cellular and Molecular Medicine, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ichiro Manabe
- Department of Aging Research, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yumi Suzuki
- Department of Cellular and Molecular Medicine, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Yumiko Oishi
- Department of Cellular and Molecular Medicine, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
26
|
Li S, Wang Q, Qiang Q, Shan H, Shi M, Chen B, Zhao S, Yuan L. Sp1-mediated transcriptional regulation of MALAT1 plays a critical role in tumor. J Cancer Res Clin Oncol 2015; 141:1909-20. [PMID: 25773124 DOI: 10.1007/s00432-015-1951-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 03/05/2015] [Indexed: 12/18/2022]
Abstract
BACKGROUND MALAT1 was discovered as a prognostic marker for lung cancer metastasis and has been found upregulated in many types of tumor, but its transcriptional regulation mechanism in tumors remains unclear. METHODS A deletion analysis of MALAT1 promoter region was performed to find the cis elements that were critical for the transcriptional activation of MALAT1 gene. Reporter gene assays were employed to analyze the effect of Sp1 on the promoter activity of MALAT1 gene. The binding activity of Sp1 with the promoter of MALAT1 gene was examined by EMSA and ChIP assay. Effects of Sp1 on regulation of MALAT1 were analyzed by RNA interference in vitro and in vivo mouse model. RESULTS By means of luciferase assay, Sp1 was found to activate the promoter of the human MALAT1 gene. The binding of Sp1 to this region was also detected by electrophoretic mobility shift and chromatin immunoprecipitation assays. Sp1 knockdown also decreased the MALAT1 and inhibited A549 lung cancer cells' growth and invasion in vitro. Furthermore, knockdown of Sp1 also mimicked the inhibition of MALAT1 in A549 lung cancer cells' growth and metastasis in vivo. CONCLUSIONS Taken together, our data suggest that upregulation of MALAT1 was mediated by the transcription factor Sp1 in A549 lung cancer cells, and Sp1 could be therapeutic target for cancer.
Collapse
Affiliation(s)
- Shufeng Li
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China.
| | - Qiwei Wang
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China
| | - Qian Qiang
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China
| | - Haitao Shan
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China
| | - Minke Shi
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Baojun Chen
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Sheng Zhao
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China
| | - Liudi Yuan
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China
| |
Collapse
|
27
|
Yang X, Koltes JE, Park CA, Chen D, Reecy JM. Gene co-expression network analysis provides novel insights into myostatin regulation at three different mouse developmental timepoints. PLoS One 2015; 10:e0117607. [PMID: 25695797 PMCID: PMC4335066 DOI: 10.1371/journal.pone.0117607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/29/2014] [Indexed: 12/03/2022] Open
Abstract
Myostatin (Mstn) knockout mice exhibit large increases in skeletal muscle mass. However, relatively few of the genes that mediate or modify MSTN effects are known. In this study, we performed co-expression network analysis using whole transcriptome microarray data from MSTN-null and wild-type mice to identify genes involved in important biological processes and pathways related to skeletal muscle and adipose development. Genes differentially expressed between wild-type and MSTN-null mice were further analyzed for shared DNA motifs using DREME. Differentially expressed genes were identified at 13.5 d.p.c. during primary myogenesis and at d35 during postnatal muscle development, but not at 17.5 d.p.c. during secondary myogenesis. In total, 283 and 2034 genes were differentially expressed at 13.5 d.p.c. and d35, respectively. Over-represented transcription factor binding sites in differentially expressed genes included SMAD3, SP1, ZFP187, and PLAGL1. The use of regulatory (RIF) and phenotypic (PIF) impact factor and differential hubbing co-expression analyses identified both known and potentially novel regulators of skeletal muscle growth, including Apobec2, Atp2a2, and Mmp13 at d35 and Sox2, Tmsb4x, and Vdac1 at 13.5 d.p.c. Among the genes with the highest PIF scores were many fiber type specifying genes. The use of RIF, PIF, and differential hubbing analyses identified both known and potentially novel regulators of muscle development. These results provide new details of how MSTN may mediate transcriptional regulation as well as insight into novel regulators of MSTN signal transduction that merit further study regarding their physiological roles in muscle and adipose development.
Collapse
Affiliation(s)
- Xuerong Yang
- Animal Nutrition Institute, Sichuan Agricultural University, Ya’an, Sichuan, China
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Carissa A. Park
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Daiwen Chen
- Animal Nutrition Institute, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| |
Collapse
|
28
|
Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle. BMC Genomics 2015; 16:50. [PMID: 25651817 PMCID: PMC4328970 DOI: 10.1186/s12864-015-1238-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 01/12/2023] Open
Abstract
Background Domestication of the wild pig has led to obese and lean phenotype breeds, and evolutionary genome research has sought to identify the regulatory mechanisms underlying this phenotypic diversity. However, revealing the molecular mechanisms underlying muscle phenotype variation based on differentially expressed genes has proved to be difficult. To characterize the mechanisms regulating muscle phenotype variation under artificial selection, we aimed to provide an integrated view of genome organization by weighted gene coexpression network analysis. Results Our analysis was based on 20 publicly available next-generation sequencing datasets of lean and obese pig muscle generated from 10 developmental stages. The evolution of the constructed coexpression modules was examined using the genome resequencing data of 37 domestic pigs and 11 wild boars. Our results showed the regulation of muscle development might be more complex than had been previously acknowledged, and is regulated by the coordinated action of muscle, nerve and immunity related genes. Breed-specific modules that regulated muscle phenotype divergence were identified, and hundreds of hub genes with major roles in muscle development were determined to be responsible for key functional distinctions between breeds. Our evolutionary analysis showed that the role of changes in the coding sequence under positive selection in muscle phenotype divergence was minor. Conclusions Muscle phenotype divergence was found to be regulated by the divergence of coexpression network modules under artificial selection, and not by changes in the coding sequence of genes. Our results present multiple lines of evidence suggesting links between modules and muscle phenotypes, and provide insights into the molecular bases of genome organization in muscle development and phenotype variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1238-5) contains supplementary material, which is available to authorized users.
Collapse
|
29
|
Ghandhi SA, Ponnaiya B, Panigrahi SK, Hopkins KM, Cui Q, Hei TK, Amundson SA, Lieberman HB. RAD9 deficiency enhances radiation induced bystander DNA damage and transcriptomal response. Radiat Oncol 2014; 9:206. [PMID: 25234738 PMCID: PMC4261775 DOI: 10.1186/1748-717x-9-206] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Radiation induced bystander effects are an important component of the overall response of cells to irradiation and are associated with human health risks. The mechanism responsible includes intra-cellular and inter-cellular signaling by which the bystander response is propagated. However, details of the signaling mechanism are not well defined. METHODS We measured the bystander response of Mrad9+/+ and Mrad9-/- mouse embryonic stem cells, as well as human H1299 cells with inherent or RNA interference-mediated reduced RAD9 levels after exposure to 1 Gy α particles, by scoring chromosomal aberrations and micronuclei formation, respectively. In addition, we used microarray gene expression analyses to profile the transcriptome of directly irradiated and bystander H1299 cells. RESULTS We demonstrated that Mrad9 null enhances chromatid aberration frequency induced by radiation in bystander mouse embryonic stem cells. In addition, we found that H1299 cells with reduced RAD9 protein levels showed a higher frequency of radiation induced bystander micronuclei formation, compared with parental cells containing inherent levels of RAD9. The enhanced bystander response in human cells was associated with a unique transcriptomic profile. In unirradiated cells, RAD9 reduction broadly affected stress response pathways at the mRNA level; there was reduction in transcript levels corresponding to genes encoding multiple members of the UVA-MAPK and p38MAPK families, such as STAT1 and PARP1, suggesting that these signaling mechanisms may not function optimally when RAD9 is reduced. Using network analysis, we found that differential activation of the SP1 and NUPR1 transcriptional regulators was predicted in directly irradiated and bystander H1299 cells. Transcription factor prediction analysis also implied that HIF1α (Hypoxia induced factor 1 alpha) activation by protein stabilization in irradiated cells could be a negative predictor of the bystander response, suggesting that local hypoxic stress experienced by cells directly exposed to radiation may influence whether or not they will elicit a bystander response in neighboring cells.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Howard B Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
| |
Collapse
|
30
|
Óvilo C, Benítez R, Fernández A, Núñez Y, Ayuso M, Fernández AI, Rodríguez C, Isabel B, Rey AI, López-Bote C, Silió L. Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics. BMC Genomics 2014; 15:413. [PMID: 24885501 PMCID: PMC4070551 DOI: 10.1186/1471-2164-15-413] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/27/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in piglets of both genetic types, in order to identify genes, pathways and regulatory factors responsible for their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DU×IB) were generated. Piglets (14 from each genetic type) were slaughtered at weaning (28 days) and longissimus dorsi was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays. RESULTS Loin muscle chemical composition showed significant differences between genetic types in intramuscular fat content (6.1% vs. 4.3% in IB and DUxIB animals, respectively, P = 0.009) and in saturated (P = 0.019) and monounsaturated fatty acid proportions (P = 0.044). The statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR < 0.10), 102 upregulated in IB and 154 upregulated in DU×IB. Transcript differences were validated for a subset of DE genes by qPCR. We observed alteration in biological functions related to extracellular matrix function and organization, cellular adhesion, muscle growth, lipid metabolism and proteolysis. Candidate genes with known effects on muscle growth were found among the DE genes upregulated in DU×IB. Genes related to lipid metabolism and proteolysis were found among those upregulated in IB. Regulatory factors (RF) potentially involved in the expression differences were identified by calculating the regulatory impact factors. Twenty-nine RF were found, some of them with known relationship with tissue development (MSTN, SIX4, IRX3), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these RF and DE genes show relevant differences between genetic types. CONCLUSION These results provide valuable information about genetic mechanisms determining the phenotypic differences on growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. Transcription factors and regulatory mechanisms are proposed for these altered biological functions.
Collapse
Affiliation(s)
- Cristina Óvilo
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Rita Benítez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Almudena Fernández
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Yolanda Núñez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Miriam Ayuso
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | | | - Carmen Rodríguez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Beatriz Isabel
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - Ana Isabel Rey
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | | | - Luis Silió
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| |
Collapse
|
31
|
Wang J, Chen T, Feng F, Wei H, Pang W, Yang G, Shen QW. KLF15 regulates slow myosin heavy chain expression through NFATc1 in C2C12 myotubes. Biochem Biophys Res Commun 2014; 446:1231-6. [DOI: 10.1016/j.bbrc.2014.03.091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 03/19/2014] [Indexed: 10/25/2022]
|