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Yoon JH, Kim S. Learning gene networks under SNP perturbation using SNP and allele-specific expression data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563661. [PMID: 37961468 PMCID: PMC10634764 DOI: 10.1101/2023.10.23.563661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Allele-specific expression quantification from RNA-seq reads provides opportunities to study the control of gene regulatory networks by cis-acting and trans-acting genetic variants. Many existing methods performed a single-gene and single-SNP association analysis to identify expression quantitative trait loci (eQTLs), and placed the eQTLs against known gene networks for functional interpretation. Instead, we view eQTL data as a capture of the effects of perturbation of gene regulatory system by a large number of genetic variants and reconstruct a gene network perturbed by eQTLs. We introduce a statistical framework called CiTruss for simultaneously learning a gene network and cis-acting and trans-acting eQTLs that perturb this network, given population allele-specific expression and SNP data. CiTruss uses a multi-level conditional Gaussian graphical model to model trans-acting eQTLs perturbing the expression of both alleles in gene network at the top level and cis-acting eQTLs perturbing the expression of each allele at the bottom level. We derive a transformation of this model that allows efficient learning for large-scale human data. Our analysis of the GTEx and LG×SM advanced intercross line mouse data for multiple tissue types with CiTruss provides new insights into genetics of gene regulation. CiTruss revealed that gene networks consist of local subnetworks over proximally located genes and global subnetworks over genes scattered across genome, and that several aspects of gene regulation by eQTLs such as the impact of genetic diversity, pleiotropy, tissue-specific gene regulation, and local and long-range linkage disequilibrium among eQTLs can be explained through these local and global subnetworks.
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Affiliation(s)
- Jun Ho Yoon
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States of America
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Dual Role of YY1 in HPV Life Cycle and Cervical Cancer Development. Int J Mol Sci 2022; 23:ijms23073453. [PMID: 35408813 PMCID: PMC8998550 DOI: 10.3390/ijms23073453] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/27/2023] Open
Abstract
Human papillomaviruses (HPVs) are considered to be key etiological agents responsible for the induction and development of cervical cancer. However, it has been suggested that HPV infection alone may not be sufficient to promote cervical carcinogenesis, and other unknown factors might be required to establish the disease. One of the suggested proteins whose deregulation has been linked with oncogenesis is transcription factor Yin Yang 1 (YY1). YY1 is a multifunctional protein that is involved not only in the regulation of gene transcription and protein modification, but can also control important cell signaling pathways, such as cell growth, development, differentiation, and apoptosis. Vital functions of YY1 also indicate that the protein could be involved in tumorigenesis. The overexpression of this protein has been observed in different tumors, and its level has been correlated with poor prognoses of many types of cancers. YY1 can also regulate the transcription of viral genes. It has been documented that YY1 can bind to the HPV long control region and regulate the expression of viral oncogenes E6 and E7; however, its role in the HPV life cycle and cervical cancer development is different. In this review, we explore the role of YY1 in regulating the expression of cellular and viral genes and subsequently investigate how these changes inadvertently contribute toward the development of cervical malignancy.
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Ju X, Liu Y, Shan Y, Ji G, Zhang M, Tu Y, Zou J, Chen X, Geng Z, Shu J. Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens. Sci Rep 2021; 11:20861. [PMID: 34675224 PMCID: PMC8531282 DOI: 10.1038/s41598-021-00176-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
SART and PMM are mainly composed of oxidative myofibers and glycolytic myofibers, respectively, and myofiber types profoundly influence postnatal muscle growth and meat quality. SART and PMM are composed of lncRNAs and circRNAs that participate in myofiber type regulation. To elucidate the regulatory mechanism of myofiber type, lncRNA and circRNA sequencing was used to systematically compare the transcriptomes of the SART and PMM of Chinese female Qingyuan partridge chickens at their marketing age. The luminance value (L*), redness value (a*), average diameter, cross-sectional area, and density difference between the PMM and SART were significant (p < 0.05). ATPase staining results showed that PMMs were all darkly stained and belonged to the glycolytic type, and the proportion of oxidative myofibers in SART was 81.7%. A total of 5 420 lncRNAs were identified, of which 365 were differentially expressed in the SART compared with the PMM (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and KEGG pathways (p < 0.05), including striated muscle cell differentiation, regulation of cell proliferation, regulation of muscle cell differentiation, myoblast differentiation, regulation of myoblast differentiation, and MAPK signaling pathway. Pathways and coexpression network analyses suggested that XR_003077811.1, XR_003072304.1, XR_001465942.2, XR_001465741.2, XR_001470487.1, XR_003077673.1 and XR_003074785.1 played important roles in regulating oxidative myofibers by TBX3, QKI, MYBPC1, CALM2, and PPARGC1A expression. A total of 10 487 circRNAs were identified, of which 305 circRNAs were differentially expressed in the SART compared with the PMM (p < 0.05). Functional enrichment analysis showed that differentially expressed circRNAs were involved in host gene expression and were enriched in the AMPK, calcium signaling pathway, FoxO signaling pathway, p53 signaling pathway, and cellular senescence. Novel_circ_004282 and novel_circ_002121 played important roles in regulating oxidative myofibers by PPP3CA and NFATC1 expression. Using lncRNA-miRNA/circRNA-miRNA integrated analysis, we identified many candidate interaction networks that might affect muscle fiber performance. Important lncRNA-miRNA-mRNA networks, such as lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A, regulate oxidative myofibers. This study reveals that lncXR_003077811.1, lncXR_003072304.1, lncXR_001465942.2, lncXR_001465741.2, lncXR_001470487.1, lncXR_003077673.1, XR_003074785.1, novel_circ_004282 and novel_circ_002121 might regulate oxidative myofibers. The lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A pathway might regulate oxidative myofibers. All these findings provide rich resources for further in-depth research on the regulatory mechanism of lncRNAs and circRNAs in myofibers.
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Affiliation(s)
- Xiaojun Ju
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yifan Liu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, Jiangsu, China
| | - Yanju Shan
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, Jiangsu, China
| | - Gaige Ji
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, Jiangsu, China
| | - Ming Zhang
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, Jiangsu, China
| | - Yunjie Tu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, Jiangsu, China
| | - Jianmin Zou
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, Jiangsu, China
| | - Xingyong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Jingting Shu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, Jiangsu, China.
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Dong X, Cheng Y, Qiao L, Wang X, Zeng C, Feng Y. Male-Biased gga-miR-2954 Regulates Myoblast Proliferation and Differentiation of Chicken Embryos by Targeting YY1. Genes (Basel) 2021; 12:genes12091325. [PMID: 34573307 PMCID: PMC8470131 DOI: 10.3390/genes12091325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/25/2021] [Indexed: 02/02/2023] Open
Abstract
Previous studies have shown that gga-miR-2954 was highly expressed in the gonads and other tissues of male chickens, including muscle tissue. Yin Yang1 (YY1), which has functions in mammalian skeletal muscle development, was predicted to be a target gene of gga-miR-2954. The purpose of this study was to investigate whether gga-miR-2954 plays a role in skeletal muscle development by targeting YY1, and evaluate its function in the sexual dimorphism development of chicken muscle. Here, all the temporal and spatial expression profiles in chicken embryonic muscles showed that gga-miR-2954 is highly expressed in males and mainly localized in cytoplasm. Gga-miR-2954 exhibited upregulated expression of in vitro myoblast differentiation stages. Next, through the overexpression and loss-of-function experiments performed in chicken primary myoblasts, we found that gga-miR-2954 inhibited myoblast proliferation but promoted differentiation. During myogenesis, gga-miR-2954 could suppress the expression of YY1, which promoted myoblast proliferation and inhibited the process of myoblast cell differentiation into multinucleated myotubes. Overall, these findings reveal a novel role of gga-miR-2954 in skeletal muscle development through its function of the myoblast proliferation and differentiation by suppressing the expression of YY1. Moreover, gga-miR-2954 may contribute to the sex difference in chicken muscle development.
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Lang M, Ou D, Liu Z, Li Y, Zhang X, Zhang F. LncRNA MHRT Promotes Cardiac Fibrosis via miR-3185 Pathway Following Myocardial Infarction. Int Heart J 2021; 62:891-899. [PMID: 34334583 DOI: 10.1536/ihj.20-298] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Long-chain noncoding RNA (lncRNA) is a new class of molecular regulators in heart development and disease. However, the role of specific lncRNA in cardiac fibrosis remains to be fully explored. This study aimed to investigate the role and potential mechanism of lncRNA MHRT in myocardial fibrosis after myocardial infarction (MI).Cardiac fibroblasts (CFs) were isolated from a mouse model of MI. The expression levels of MHRT and miR-3185 in the hearts of MI and CFs mice treated with transforming growth factor beta 1 (TGF-β1) were analyzed by qRT-PCR. The collagen expression was assessed using qRT-PCR and Western blot. Cell proliferation was assessed by performing MTT and EdU assays. The direct interaction between lncRNA and miRNA was analyzed by luciferase assay, RNA-binding protein immunoprecipitation (RIP) assay, and RNA pull-down assay.The expression levels of MHRT were raised in MI and CFs mice treated with TGF-β1. Overexpression of MHRT promoted collagen production and CF proliferation, while silencing of MHRT showed the opposite effect. MiR-3185 was a target gene of MHRT. In addition, overexpression of MHRT reduced the expression levels of miR-3185, and siMHRT reversed the inhibitory effect of TGF-β1 on the expression of miR-3185. Overexpression of miR-3185 inhibited the upregulation of Col I and Col III induced by TGF-β1.MHRT promoted cardiac fibrosis after MI through miR-3185 and increased myocardial collagen deposition and promoted myocardial fibrosis.
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Affiliation(s)
- Mingjian Lang
- Department of Cardiovascular Medicine, Chengdu Fifth People's Hospital
| | - Dengke Ou
- Department of Cardiovascular Medicine, Chengdu Fifth People's Hospital
| | - Zhaohui Liu
- Department of Cardiovascular Medicine, Chengdu Fifth People's Hospital
| | - Yong Li
- Department of Cardiovascular Medicine, Chengdu Fifth People's Hospital
| | - Xiaohua Zhang
- Department of Cardiovascular Medicine, Chengdu Fifth People's Hospital
| | - Fuping Zhang
- Department of Day Surgery Ward, Chengdu Fifth People's Hospital
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Iqbal A, Ping J, Ali S, Zhen G, Juan L, Kang JZ, Ziyi P, Huixian L, Zhihui Z. Role of microRNAs in myogenesis and their effects on meat quality in pig - A review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1873-1884. [PMID: 32819078 PMCID: PMC7649413 DOI: 10.5713/ajas.20.0324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/02/2020] [Accepted: 08/16/2020] [Indexed: 02/02/2023]
Abstract
The demand for food is increasing day by day because of the increasing global population. Therefore, meat, the easiest and largely available source of protein, needs to be produced in large amounts with good quality. The pork industry is a significant shareholder in fulfilling the global meat demands. Notably, myogenesis- development of muscles during embryogenesis- is a complex mechanism which culminates in meat production. But the molecular mechanisms which govern the myogenesis are less known. The involvement of miRNAs in myogenesis and meat quality, which depends on factors such as myofiber composition and intramuscular fat contents which determine the meat color, flavor, juiciness, and water holding capacity, are being extrapolated to increase both the quantity and quality of pork. Various kinds of microRNAs (miRNAs), miR-1, miR-21, miR22, miR-27, miR-34, miR-127, miR-133, miR-143, miR-155, miR-199, miR-206, miR-208, miR-378, and miR-432 play important roles in pig skeletal muscle development. Further, the quality of meat also depends upon myofiber which is developed through the expression of different kinds of miRNAs at different stages. This review will focus on the mechanism of myogenesis, the role of miRNAs in myogenesis, and meat quality with a focus on the pig.
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Affiliation(s)
- Ambreen Iqbal
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Jiang Ping
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Shaokat Ali
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Gao Zhen
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Liu Juan
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Jin Zi Kang
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Pan Ziyi
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Lu Huixian
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Zhao Zhihui
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
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Marceca GP, Nigita G, Calore F, Croce CM. MicroRNAs in Skeletal Muscle and Hints on Their Potential Role in Muscle Wasting During Cancer Cachexia. Front Oncol 2020; 10:607196. [PMID: 33330108 PMCID: PMC7732629 DOI: 10.3389/fonc.2020.607196] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer-associated cachexia is a heterogeneous, multifactorial syndrome characterized by systemic inflammation, unintentional weight loss, and profound alteration in body composition. The main feature of cancer cachexia is represented by the loss of skeletal muscle tissue, which may or may not be accompanied by significant adipose tissue wasting. Such phenotypic alteration occurs as the result of concomitant increased myofibril breakdown and reduced muscle protein synthesis, actively contributing to fatigue, worsening of quality of life, and refractoriness to chemotherapy. According to the classical view, this condition is primarily triggered by interactions between specific tumor-induced pro-inflammatory cytokines and their cognate receptors expressed on the myocyte membrane. This causes a shift in gene expression of muscle cells, eventually leading to a pronounced catabolic condition and cell death. More recent studies, however, have shown the involvement of regulatory non-coding RNAs in the outbreak of cancer cachexia. In particular, the role exerted by microRNAs is being widely addressed, and several mechanistic studies are in progress. In this review, we discuss the most recent findings concerning the role of microRNAs in triggering or exacerbating muscle wasting in cancer cachexia, while mentioning about possible roles played by long non-coding RNAs and ADAR-mediated miRNA modifications.
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Affiliation(s)
- Gioacchino P Marceca
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Federica Calore
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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Singh GB, Cowan DB, Wang DZ. Tiny Regulators of Massive Tissue: MicroRNAs in Skeletal Muscle Development, Myopathies, and Cancer Cachexia. Front Oncol 2020; 10:598964. [PMID: 33330096 PMCID: PMC7719840 DOI: 10.3389/fonc.2020.598964] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscles are the largest tissues in our body and the physiological function of muscle is essential to every aspect of life. The regulation of development, homeostasis, and metabolism is critical for the proper functioning of skeletal muscle. Consequently, understanding the processes involved in the regulation of myogenesis is of great interest. Non-coding RNAs especially microRNAs (miRNAs) are important regulators of gene expression and function. MiRNAs are small (~22 nucleotides long) noncoding RNAs known to negatively regulate target gene expression post-transcriptionally and are abundantly expressed in skeletal muscle. Gain- and loss-of function studies have revealed important roles of this class of small molecules in muscle biology and disease. In this review, we summarize the latest research that explores the role of miRNAs in skeletal muscle development, gene expression, and function as well as in muscle disorders like sarcopenia and Duchenne muscular dystrophy (DMD). Continuing with the theme of the current review series, we also briefly discuss the role of miRNAs in cancer cachexia.
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Affiliation(s)
- Gurinder Bir Singh
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Douglas B Cowan
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
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9
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Kaur M, Kumar A, Siddaraju NK, Fairoze MN, Chhabra P, Ahlawat S, Vijh RK, Yadav A, Arora R. Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits. Sci Rep 2020; 10:16332. [PMID: 33004825 PMCID: PMC7529745 DOI: 10.1038/s41598-020-73071-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
The study presents the miRNA profiles of two Indian sheep populations with divergent carcass and muscle traits. The RNA sequencing of longissimus thoracis muscles from the two populations revealed a total of 400 known miRNAs. Myomirs or miRNAs specific to skeletal muscles identified in our data included oar-miR-1, oar-miR-133b, oar-miR-206 and oar-miR-486. Comparison of the two populations led to identification of 100 differentially expressed miRNAs (p < 0.05). A total of 45 miRNAs exhibited a log2 fold change of ≥ ( ±) 3.0. Gene Ontology analysis revealed cell proliferation, epithelial to mesenchymal transition, apoptosis, immune response and cell differentiation as the most significant functions of the differentially expressed miRNAs. The differential expression of some miRNAs was validated by qRT-PCR analysis. Enriched pathways included metabolism of proteins and lipids, PI3K-Akt, EGFR and cellular response to stress. The microRNA-gene interaction network revealed miR-21, miR-155, miR-143, miR-221 and miR-23a as the nodal miRNAs, with multiple targets. MicroRNA-21 formed the focal point of the network with 42 interactions. The hub miRNAs identified in our study form putative regulatory candidates for future research on meat quality traits in Indian sheep. Our results provide insight into the biological pathways and regulatory molecules implicated in muscling traits of sheep.
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Affiliation(s)
- Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.,Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.,Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | | | | | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Anita Yadav
- Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
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Hernández-Hernández O, Ávila-Avilés RD, Hernández-Hernández JM. Chromatin Landscape During Skeletal Muscle Differentiation. Front Genet 2020; 11:578712. [PMID: 33193700 PMCID: PMC7530293 DOI: 10.3389/fgene.2020.578712] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/31/2020] [Indexed: 12/02/2022] Open
Abstract
Cellular commitment and differentiation involve highly coordinated mechanisms by which tissue-specific genes are activated while others are repressed. These mechanisms rely on the activity of specific transcription factors, chromatin remodeling enzymes, and higher-order chromatin organization in order to modulate transcriptional regulation on multiple cellular contexts. Tissue-specific transcription factors are key mediators of cell fate specification with the ability to reprogram cell types into different lineages. A classic example of a master transcription factor is the muscle specific factor MyoD, which belongs to the family of myogenic regulatory factors (MRFs). MRFs regulate cell fate determination and terminal differentiation of the myogenic precursors in a multistep process that eventually culminate with formation of muscle fibers. This developmental progression involves the activation and proliferation of muscle stem cells, commitment, and cell cycle exit and fusion of mononucleated myoblast to generate myotubes and myofibers. Although the epigenetics of muscle regeneration has been extensively addressed and discussed over the recent years, the influence of higher-order chromatin organization in skeletal muscle regeneration is still a field of development. In this review, we will focus on the epigenetic mechanisms modulating muscle gene expression and on the incipient work that addresses three-dimensional genome architecture and its influence in cell fate determination and differentiation to achieve skeletal myogenesis. We will visit known alterations of genome organization mediated by chromosomal fusions giving rise to novel regulatory landscapes, enhancing oncogenic activation in muscle, such as alveolar rhabdomyosarcomas (ARMS).
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Affiliation(s)
- Oscar Hernández-Hernández
- Laboratory of Genomic Medicine, Department of Genetics, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Rodolfo Daniel Ávila-Avilés
- Laboratory of Epigenetics of Skeletal Muscle Regeneration, Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
| | - J Manuel Hernández-Hernández
- Laboratory of Epigenetics of Skeletal Muscle Regeneration, Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
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The YY1/miR-548t-5p/CXCL11 signaling axis regulates cell proliferation and metastasis in human pancreatic cancer. Cell Death Dis 2020; 11:294. [PMID: 32341359 PMCID: PMC7186231 DOI: 10.1038/s41419-020-2475-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/18/2023]
Abstract
Pancreatic cancer (PC) is a malignant tumor with a poor prognosis and high mortality. However, the biological role of miR-548t-5p in PC has not been reported. In this study, we found that miR-548t-5p expression was significantly decreased in PC tissues compared with adjacent tissues, and that low miR-548t-5p expression was associated with malignant PC behavior. In addition, high miR-548t-5p expression inhibited the proliferation, migration, and invasion of PC cell lines. Regarding the molecular mechanism, the luciferase reporter gene, chromatin immunoprecipitation (ChIP), and functional recovery assays revealed that YY1 binds to the miR-548t-5p promoter and positively regulates the expression and function of miR-548t-5p. miR-548t-5p also directly regulates CXCL11 to inhibit its expression. A high level of CXCL11 was associated with worse Tumor Node Metastasis (TNM) staging in patients with PC, enhancing proliferation and metastasis in PC cells. Our study shows that the YY1/miR-548t-5p/CXCL11 axis plays an important role in PC and provides a new potential candidate for the treatment of PC.
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Wang Y, Zhang L, Pang Y, Song L, Shang H, Li Z, Liu Q, Zhang Y, Wang X, Li Q, Zhang Q, Liu C, Li F. MicroRNA-29 family inhibits rhabdomyosarcoma formation and progression by regulating GEFT function. Am J Transl Res 2020; 12:1136-1154. [PMID: 32269740 PMCID: PMC7137044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/13/2020] [Indexed: 06/11/2023]
Abstract
The microRNA-29 family, which contains mir-29a, mir-29b, and mir-29c, can promote or resist the development of several types of tumors. However, its role in rhabdomyosarcoma (RMS) has not been determined. In this work, we detected the expression of mir-29a/b/c in RMS. Results showed that the tissues and cell lines in RMS were significantly lower than those in muscle and human skeletal muscle cells, and that these cell lines could also inhibit the proliferation, migration, and invasion and induce apoptosis of RMS cells. Dual-luciferase reporter assay and RNA immunoprecipitation verified the direct binding site between mir-29a/b/c and GEFT. Under the combined actions of mir-29a/b/c and GEFT, the former weakened the promoting effect of GEFT on RMS cells. Finally, mir-29a inhibited the tumorigenesis of subcutaneous xenografts in nude mice and inhibited the mRNA and protein expression levels of GEFT in transplanted tumors. These findings proved that mir-29 inhibits the occurrence of RMS and may be a potential molecular target.
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Affiliation(s)
- Yang Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Liang Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
- Department of Anesthesiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730, China
| | - Yuweng Pang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Lingxie Song
- Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical UniversityBeijing 100020, China
| | - Hao Shang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Zhenzhen Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Qianqian Liu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Yangyang Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Xiaomeng Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Qianru Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Qiaochu Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Chunxia Liu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
| | - Feng Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi 832002, China
- Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical UniversityBeijing 100020, China
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13
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Gasparini P, Ferrari A, Casanova M, Limido F, Massimino M, Sozzi G, Fortunato O. MiRNAs as Players in Rhabdomyosarcoma Development. Int J Mol Sci 2019; 20:ijms20225818. [PMID: 31752446 PMCID: PMC6888285 DOI: 10.3390/ijms20225818] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
Rhabdomyosarcoma (RMS), the most common soft tissue sarcoma of childhood and adolescence, is a rare but aggressive malignancy that originates from immature mesenchymal cells committed to skeletal muscle differentiation. Although RMS is, generally, responsive to the modern multimodal therapeutic approaches, the prognosis of RMS depends on multiple variables and for some patients the outcome remains dismal. Further comprehension of the molecular and cellular biology of RMS would lead to identification of novel therapeutic targets. MicroRNAs (miRNAs) are small non-coding RNAs proved to function as key regulators of skeletal muscle cell fate determination and to play important roles in RMS pathogenesis. The purpose of this review is to better delineate the role of miRNAs as a biomarkers or functional leaders in RMS development, so to possibly elucidate some of RMS molecular mechanisms and potentially therapeutically target them to improve clinical management of pediatric RMS.
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Affiliation(s)
- Patrizia Gasparini
- Tumor Genomics Unit, Department of Research; Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy;
- Correspondence: (O.F.); (P.G.); Tel.: +39-02-2390-3775 (O.F. & P.G.); Fax: +39-02-2390-2928 (O.F. & P.G.)
| | - Andrea Ferrari
- Pediatric Oncology Unit; Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (A.F.); (M.C.); (F.L.); (M.M.)
| | - Michela Casanova
- Pediatric Oncology Unit; Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (A.F.); (M.C.); (F.L.); (M.M.)
| | - Francesca Limido
- Pediatric Oncology Unit; Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (A.F.); (M.C.); (F.L.); (M.M.)
| | - Maura Massimino
- Pediatric Oncology Unit; Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (A.F.); (M.C.); (F.L.); (M.M.)
| | - Gabriella Sozzi
- Tumor Genomics Unit, Department of Research; Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy;
| | - Orazio Fortunato
- Tumor Genomics Unit, Department of Research; Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy;
- Correspondence: (O.F.); (P.G.); Tel.: +39-02-2390-3775 (O.F. & P.G.); Fax: +39-02-2390-2928 (O.F. & P.G.)
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14
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Mechanism and Functions of Identified miRNAs in Poultry Skeletal Muscle Development – A Review. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2019-0049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract
Development of the skeletal muscle goes through several complex processes regulated by numerous genetic factors. Although much efforts have been made to understand the mechanisms involved in increased muscle yield, little work is done about the miRNAs and candidate genes that are involved in the skeletal muscle development in poultry. Comprehensive research of candidate genes and single nucleotide related to poultry muscle growth is yet to be experimentally unraveled. However, over a few periods, studies in miRNA have disclosed that they actively participate in muscle formation, differentiation, and determination in poultry. Specifically, miR-1, miR-133, and miR-206 influence tissue development, and they are highly expressed in the skeletal muscles. Candidate genes such as CEBPB, MUSTN1, MSTN, IGF1, FOXO3, mTOR, and NFKB1, have also been identified to express in the poultry skeletal muscles development. However, further researches, analysis, and comprehensive studies should be made on the various miRNAs and gene regulatory factors that influence the skeletal muscle development in poultry. The objective of this review is to summarize recent knowledge in miRNAs and their mode of action as well as transcription and candidate genes identified to regulate poultry skeletal muscle development.
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15
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Chen L, Guo T, Yu Y, Sun Y, Yu G, Cheng L. Heat shock cognate protein 70 promotes the differentiation of C2C12 myoblast and targets Yin Yang 1. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:551. [PMID: 31807532 DOI: 10.21037/atm.2019.09.88] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background Heat shock cognate protein 70 (HSC70) is a constitutively expressed molecular chaperone protein which can maintain the structure and function of the protein. HSC70 is engaged in a variety of physiological processes, yet its role during skeletal muscle differentiation is still unclear. Methods C2C12 cells were obtained and cultured. During differentiation, the expression of HSC70 was evaluated by RT-PCR. To determine the function of HSC70 during C2C12 myoblast differentiation, myotube transfection of siR-HSC70 was performed with Lipofectamine 2000 Reagent. Western blot was used to measure the expression of Yin Yang 1 (YY1) after down-regulating HSC70. To further assess if YY1 mediates the pro-differentiation effect of HSC70, a plasmid of YY1 overexpression was used to increase the expression of YY1 in the presence of siR-HSC70-2. The formation of myotubes was visualized by immunofluorescent staining, while the expression levels of MyoD and MyoG were evaluated by RT-PCR. Results In this study, we found that HSC70 was up-regulated during C2C12 myoblast differentiation. Knockdown of HSC70 not only inhibited the C2C12 myoblast differentiation but also reduced the expression of MyoD and MyoG. When YY1 protein was over-expressed, it could restore the differentiation in cells with HSC70 knockdown or inhibition. Conclusions Collectively, this study demonstrates that HSC70 is involved in the regulation of C2C12 myoblast differentiation via YY1 and may serve as a potential target for a therapeutic strategy to prevent muscle atrophy.
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Affiliation(s)
- Lei Chen
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Tao Guo
- Department of Orthopedics, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Yan Yu
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Yeqing Sun
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Guangrong Yu
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Liming Cheng
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration, Ministry of Education of the People's Republic of China, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
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16
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Bonnet S, Boucherat O, Paulin R, Wu D, Hindmarch CCT, Archer SL, Song R, Moore JB, Provencher S, Zhang L, Uchida S. Clinical value of non-coding RNAs in cardiovascular, pulmonary, and muscle diseases. Am J Physiol Cell Physiol 2019; 318:C1-C28. [PMID: 31483703 DOI: 10.1152/ajpcell.00078.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although a majority of the mammalian genome is transcribed to RNA, mounting evidence indicates that only a minor proportion of these transcriptional products are actually translated into proteins. Since the discovery of the first non-coding RNA (ncRNA) in the 1980s, the field has gone on to recognize ncRNAs as important molecular regulators of RNA activity and protein function, knowledge of which has stimulated the expansion of a scientific field that quests to understand the role of ncRNAs in cellular physiology, tissue homeostasis, and human disease. Although our knowledge of these molecules has significantly improved over the years, we have limited understanding of their precise functions, protein interacting partners, and tissue-specific activities. Adding to this complexity, it remains unknown exactly how many ncRNAs there are in existence. The increased use of high-throughput transcriptomics techniques has rapidly expanded the list of ncRNAs, which now includes classical ncRNAs (e.g., ribosomal RNAs and transfer RNAs), microRNAs, and long ncRNAs. In addition, splicing by-products of protein-coding genes and ncRNAs, so-called circular RNAs, are now being investigated. Because there is substantial heterogeneity in the functions of ncRNAs, we have summarized the present state of knowledge regarding the functions of ncRNAs in heart, lungs, and skeletal muscle. This review highlights the pathophysiologic relevance of these ncRNAs in the context of human cardiovascular, pulmonary, and muscle diseases.
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Affiliation(s)
- Sébastien Bonnet
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Olivier Boucherat
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Roxane Paulin
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Danchen Wu
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Charles C T Hindmarch
- Queen's Cardiopulmonary Unit, Translational Institute of Medicine, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Stephen L Archer
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Rui Song
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California
| | - Joseph B Moore
- Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky.,The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Steeve Provencher
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Lubo Zhang
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California
| | - Shizuka Uchida
- Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky.,The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, Kentucky.,Cardiovascular Innovation Institute, University of Louisville, Louisville, Kentucky
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17
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Jacques M, Hiam D, Craig J, Barrès R, Eynon N, Voisin S. Epigenetic changes in healthy human skeletal muscle following exercise- a systematic review. Epigenetics 2019; 14:633-648. [PMID: 31046576 PMCID: PMC6557592 DOI: 10.1080/15592294.2019.1614416] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/16/2019] [Accepted: 04/26/2019] [Indexed: 12/20/2022] Open
Abstract
Exercise training is continually challenging whole-body homeostasis, leading to improvements in performance and health. Adaptations to exercise training are complex and are influenced by both environmental and genetic factors. Epigenetic factors regulate gene expression in a tissue-specific manner and constitute a link between the genotype and the environment. Moreover, epigenetic factors are emerging as potential biomarkers that could predict the response to exercise training. This systematic review aimed to identify epigenetic changes that have been reported in skeletal muscle following exercise training in healthy populations. A literature search of five databases (PUBMED, MEDLINE, CINHAL, SCOPUS and SportDiscuss) was conducted in November 2018. Articles were included if they examined epigenetic modifications (DNA methylation, histone modifications and non-coding RNAs) in skeletal muscle, following either an acute bout of exercise, an exercise intervention in a pre/post design, or a case/control type of study. Twenty-two studies met the inclusion criteria. Several epigenetic markers including DNA methylation of genes known to be differentially expressed after exercise and myomiRs were reported to be modified after exercise. Several epigenetic marks were identified to be altered in response to exercise, with potential influence on skeletal muscle metabolism. However, whether these epigenetic marks play a role in the physiological impact of exercise is unclear. Exercise epigenetics is still a very young research field, and it is expected that in the future the causality of such changes will be elucidated via the utilization of emerging experimental models able to target the epigenome.
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Affiliation(s)
- Macsue Jacques
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Danielle Hiam
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Jeffrey Craig
- Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
- Environmental & Genetic Epidemiology Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
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18
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Xu M, Chen X, Chen D, Yu B, Li M, He J, Huang Z. Regulation of skeletal myogenesis by microRNAs. J Cell Physiol 2019; 235:87-104. [DOI: 10.1002/jcp.28986] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/31/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Meng Xu
- Key Laboratory for Animal Disease‐Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition Sichuan Agricultural University Chengdu Sichuan China
| | - Xiaoling Chen
- Key Laboratory for Animal Disease‐Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition Sichuan Agricultural University Chengdu Sichuan China
| | - Daiwen Chen
- Key Laboratory for Animal Disease‐Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition Sichuan Agricultural University Chengdu Sichuan China
| | - Bing Yu
- Key Laboratory for Animal Disease‐Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition Sichuan Agricultural University Chengdu Sichuan China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology Sichuan Agricultural University Chengdu Sichuan China
| | - Jun He
- Key Laboratory for Animal Disease‐Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition Sichuan Agricultural University Chengdu Sichuan China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease‐Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition Sichuan Agricultural University Chengdu Sichuan China
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19
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Li X, Qin M, Huang J, Ma J, Hu X. Clinical significance of miRNA‑1 and its potential target gene network in lung squamous cell carcinoma. Mol Med Rep 2019; 19:5063-5078. [PMID: 31059033 PMCID: PMC6522896 DOI: 10.3892/mmr.2019.10171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 09/21/2019] [Indexed: 11/25/2022] Open
Abstract
Previous studies demonstrated that miRNA-1 (miR-1) is downregulated in certain human cancer and serves a crucial role in the progression of cancer. However, there are only a few previous studies examining the association between miR-1 and lung squamous cell carcinoma (LUSC) and the regulatory mechanism of miR-1 in LUSC remains unclear. Therefore, the present study investigated the clinical significance and determined the potential molecular mechanism of miR-1 in LUSC. The expression of miR-1 and its clinical significance in LUSC was examined by conducting a meta-analysis of 12 studies using Stata 14, MetaDiSc1.4 and SPSS version 23. In addition, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the potential target genes of miR-1 gathered from Gene Expression Omnibus and ArrayExpress. Meta-analysis demonstrated that miR-1 was significantly downregulated in LUSC [standardized mean difference: −1.44; 95% confidence interval (CI): −2.08, −0.81], and the area under the curve was 0.9096 (Q*=0.8416) with sensitivity of 0.71 (95% CI: 0.66, 0.76) and specificity of 0.88 (95% CI: 0.86, 0.90). The pooled positive likelihood ratio and negative likelihood ratio were 4.93 (95% CI: 2.54, 9.55) and 0.24 (95% CI: 0.10, 0.54), respectively. Bioinformatics analysis demonstrated that miR-1 may be involved in the progression of LUSC via the ‘cell cycle’, ‘p53 signaling pathway’, ‘Fanconi anemia pathway’, ‘homologous recombination’, ‘glycine, serine and threonine metabolism’ and ‘oocyte meiosis’. In summary, miR-1 was significantly downregulated in LUSC, suggesting a novel and promising non-invasive biomarker for diagnosing LUSC, and miR-1 was involved in LUSC progression via a number of significant pathways.
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Affiliation(s)
- Xiaojiao Li
- Department of Positron Emission Tomography‑Computed Tomography, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Meijiao Qin
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jiacheng Huang
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jie Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiaohua Hu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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20
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Chen F, Zhou J, Li Y, Zhao Y, Yuan J, Cao Y, Wang L, Zhang Z, Zhang B, Wang CC, Cheung TH, Wu Z, Wong CCL, Sun H, Wang H. YY1 regulates skeletal muscle regeneration through controlling metabolic reprogramming of satellite cells. EMBO J 2019; 38:embj.201899727. [PMID: 30979776 DOI: 10.15252/embj.201899727] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 02/04/2023] Open
Abstract
Skeletal muscle satellite cells (SCs) are adult muscle stem cells responsible for muscle regeneration after acute or chronic injuries. The lineage progression of quiescent SC toward activation, proliferation, and differentiation during the regeneration is orchestrated by cascades of transcription factors (TFs). Here, we elucidate the function of TF Yin Yang1 (YY1) in muscle regeneration. Muscle-specific deletion of YY1 in embryonic muscle progenitors leads to severe deformity of diaphragm muscle formation, thus neonatal death. Inducible deletion of YY1 in SC almost completely blocks the acute damage-induced muscle repair and exacerbates the chronic injury-induced dystrophic phenotype. Examination of SC revealed that YY1 loss results in cell-autonomous defect in activation and proliferation. Mechanistic search revealed that YY1 binds and represses mitochondrial gene expression. Simultaneously, it also stabilizes Hif1α protein and activates Hif1α-mediated glycolytic genes to facilitate a metabolic reprogramming toward glycolysis which is needed for SC proliferation. Altogether, our findings have identified YY1 as a key regulator of SC metabolic reprogramming through its dual roles in modulating both mitochondrial and glycolytic pathways.
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Affiliation(s)
- Fengyuan Chen
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yang Cao
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Lijun Wang
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Zongkang Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynecology, Li Ka Shing Institute of Health Sciences, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Tom H Cheung
- The State Key Lab in Molecular Neuroscience, Division of Life Science, Center for Stem Cell Research and Center for Systems Biology and Human Diseases, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhenguo Wu
- The State Key Lab in Molecular Neuroscience, Division of Life Science, Center for Stem Cell Research and Center for Systems Biology and Human Diseases, The Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
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21
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Hays E, Bonavida B. YY1 regulates cancer cell immune resistance by modulating PD-L1 expression. Drug Resist Updat 2019; 43:10-28. [PMID: 31005030 DOI: 10.1016/j.drup.2019.04.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 02/08/2023]
Abstract
Recent advances in the treatment of various cancers have resulted in the adaptation of several novel immunotherapeutic strategies. Notably, the recent intervention through immune checkpoint inhibitors has resulted in significant clinical responses and prolongation of survival in patients with several therapy-resistant cancers (melanoma, lung, bladder, etc.). This intervention was mediated by various antibodies directed against inhibitory receptors expressed on cytotoxic T-cells or against corresponding ligands expressed on tumor cells and other cells in the tumor microenvironment (TME). However, the clinical responses were only observed in a subset of the treated patients; it was not clear why the remaining patients did not respond to checkpoint inhibitor therapies. One hypothesis stated that the levels of PD-L1 expression correlated with poor clinical responses to cell-mediated anti-tumor immunotherapy. Hence, exploring the underlying mechanisms that regulate PD-L1 expression on tumor cells is one approach to target such mechanisms to reduce PD-L1 expression and, therefore, sensitize the resistant tumor cells to respond to PD-1/PD-L1 antibody treatments. Various investigations revealed that the overexpression of the transcription factor Yin Yang 1 (YY1) in most cancers is involved in the regulation of tumor cells' resistance to cell-mediated immunotherapies. We, therefore, hypothesized that the role of YY1 in cancer immune resistance may be correlated with PD-L1 overexpression on cancer cells. This hypothesis was investigated and analysis of the reported literature revealed that several signaling crosstalk pathways exist between the regulations of both YY1 and PD-L1 expressions. Such pathways include p53, miR34a, STAT3, NF-kB, PI3K/AKT/mTOR, c-Myc, and COX-2. Noteworthy, many clinical and pre-clinical drugs have been utilized to target these above pathways in various cancers independent of their roles in the regulation of PD-L1 expression. Therefore, the direct inhibition of YY1 and/or the use of the above targeted drugs in combination with checkpoint inhibitors should result in enhancing the cell-mediated anti-tumor cell response and also reverse the resistance observed with the use of checkpoint inhibitors alone.
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Affiliation(s)
- Emily Hays
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, United States
| | - Benjamin Bonavida
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, United States.
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22
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Cui S, Li L, Mubarokah SN, Meech R. Wnt/β‐catenin signaling induces the myomiRs miR‐133b and miR‐206 to suppress Pax7 and induce the myogenic differentiation program. J Cell Biochem 2019; 120:12740-12751. [DOI: 10.1002/jcb.28542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Shuang Cui
- Department of Clinical Pharmacology, College of Medicine and Public Health Flinders University Bedford Park South Australia Australia
- Department of Physiology Shandong University School of Medicine Jinan Shandong China
| | - Liang Li
- Department of Biochemistry Flinders University, College of Medicine and Public Health Bedford Park South Australia Australia
- Department of Biochemistry University of Adelaide Adelaide South Australia Australia
| | - Siti Nurul Mubarokah
- Department of Clinical Pharmacology, College of Medicine and Public Health Flinders University Bedford Park South Australia Australia
| | - Robyn Meech
- Department of Clinical Pharmacology, College of Medicine and Public Health Flinders University Bedford Park South Australia Australia
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23
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miR-1260b, mediated by YY1, activates KIT signaling by targeting SOCS6 to regulate cell proliferation and apoptosis in NSCLC. Cell Death Dis 2019; 10:112. [PMID: 30737371 PMCID: PMC6368632 DOI: 10.1038/s41419-019-1390-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/03/2019] [Accepted: 01/21/2019] [Indexed: 01/16/2023]
Abstract
Non-small cell lung cancer (NSCLC) is one of the most common aggressive malignancies. miRNAs have been identified as important biomarkers and regulators of NSCLC. However, the functional contributions of miR-1260b to NSCLC cell proliferation and apoptosis have not been studied. In this study, miR-1260b was upregulated in NSCLC plasma, tissues, and cell lines, and its high expression was correlated with tumor size and progression. Functionally, miR-1260b overexpression promoted cell proliferation and cell cycle, conversely inhibited cell apoptosis and senescence. Mechanically, miR-1260b negatively regulated SOCS6 by directly binding to its 3′-UTR. Furthermore, miR-1260b-mediated suppression of SOCS6 activated KIT signaling. Moreover, YY1 was an upstream regulator of miR-1260b. This study is the first to illustrate that miR-1260b, mediated by YY1, activates KIT signaling by targeting SOCS6 to regulate NSCLC cell proliferation and apoptosis, and is a potential biomarker and therapeutic target for NSCLC. In sum, our work provides new insights into the molecular mechanisms of NSCLC involved in cell proliferation and apoptosis.
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Riuzzi F, Sorci G, Arcuri C, Giambanco I, Bellezza I, Minelli A, Donato R. Cellular and molecular mechanisms of sarcopenia: the S100B perspective. J Cachexia Sarcopenia Muscle 2018; 9:1255-1268. [PMID: 30499235 PMCID: PMC6351675 DOI: 10.1002/jcsm.12363] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022] Open
Abstract
Primary sarcopenia is a condition of reduced skeletal muscle mass and strength, reduced agility, and increased fatigability and risk of bone fractures characteristic of aged, otherwise healthy people. The pathogenesis of primary sarcopenia is not completely understood. Herein, we review the essentials of the cellular and molecular mechanisms of skeletal mass maintenance; the alterations of myofiber metabolism and deranged properties of muscle satellite cells (the adult stem cells of skeletal muscles) that underpin the pathophysiology of primary sarcopenia; the role of the Ca2+ -sensor protein, S100B, as an intracellular factor and an extracellular signal regulating cell functions; and the functional role of S100B in muscle tissue. Lastly, building on recent results pointing to S100B as to a molecular determinant of myoblast-brown adipocyte transition, we propose S100B as a transducer of the deleterious effects of accumulation of reactive oxygen species in myoblasts and, potentially, myofibers concurring to the pathophysiology of sarcopenia.
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Affiliation(s)
- Francesca Riuzzi
- Department of Experimental Medicine, University of Perugia, Perugia, 06132, Italy.,Interuniversity Institute of Myology
| | - Guglielmo Sorci
- Department of Experimental Medicine, University of Perugia, Perugia, 06132, Italy.,Interuniversity Institute of Myology
| | - Cataldo Arcuri
- Department of Experimental Medicine, University of Perugia, Perugia, 06132, Italy.,Interuniversity Institute of Myology
| | - Ileana Giambanco
- Department of Experimental Medicine, University of Perugia, Perugia, 06132, Italy.,Interuniversity Institute of Myology
| | - Ilaria Bellezza
- Department of Experimental Medicine, University of Perugia, Perugia, 06132, Italy
| | - Alba Minelli
- Department of Experimental Medicine, University of Perugia, Perugia, 06132, Italy
| | - Rosario Donato
- Department of Experimental Medicine, University of Perugia, Perugia, 06132, Italy.,Interuniversity Institute of Myology.,Centro Universitario di Ricerca sulla Genomica Funzionale, University of Perugia, Perugia, 06132, Italy
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25
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Inhibition of the JNK/MAPK signaling pathway by myogenesis-associated miRNAs is required for skeletal muscle development. Cell Death Differ 2018; 25:1581-1597. [PMID: 29449644 PMCID: PMC6143622 DOI: 10.1038/s41418-018-0063-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 12/24/2017] [Accepted: 01/04/2018] [Indexed: 12/16/2022] Open
Abstract
Skeletal muscle differentiation is controlled by multiple cell signaling pathways, however, the JNK/MAPK signaling pathway dominating this process has not been fully elucidated. Here, we report that the JNK/MAPK pathway was significantly downregulated in the late stages of myogenesis, and in contrast to P38/MAPK pathway, it negatively regulated skeletal muscle differentiation. Based on the PAR-CLIP-seq analysis, we identified six elevated miRNAs (miR-1a-3p, miR-133a-3p, miR-133b-3p, miR-206-3p, miR-128-3p, miR-351-5p), namely myogenesis-associated miRNAs (mamiRs), negatively controlled the JNK/MAPK pathway by repressing multiple factors for the phosphorylation of the JNK/MAPK pathway, including MEKK1, MEKK2, MKK7, and c-Jun but not JNK protein itself, and as a result, expression of transcriptional factor MyoD and mamiRs were further promoted. Our study revealed a novel double-negative feedback regulatory pattern of cell-specific miRNAs by targeting phosphorylation kinase signaling cascade responsible for skeletal muscle development.
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26
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Breed-dependent microRNA expression in the primary culture of skeletal muscle cells subjected to myogenic differentiation. BMC Genomics 2018; 19:109. [PMID: 29390965 PMCID: PMC5793348 DOI: 10.1186/s12864-018-4492-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 01/23/2018] [Indexed: 02/07/2023] Open
Abstract
Background Skeletal muscle in livestock develops into meat, an important source of protein and other nutrients for human consumption. The muscle is largely composed of a fixed number of multinucleated myofibers determined during late gestation and remains constant postnatally. A population of postnatal muscle stem cells, called satellite cells, gives rise to myoblast cells that can fuse with the existing myofibers, thus increasing their size. This requires a delicate balance of transcription and growth factors and specific microRNA (miRNA) expressed by satellite cells and their supporting cells from the muscle stem cell niche. The role of transcription and growth factors in bovine myogenesis is well-characterized; however, very little is known about the miRNA activity during this process. We have hypothesized that the expression of miRNA can vary between primary cultures of skeletal muscle cells isolated from the semitendinosus muscles of different cattle breeds and subjected to myogenic differentiation. Results After a 6-day myogenic differentiation of cells isolated from the muscles of the examined cattle breeds, we found statistically significant differences in the number of myotubes between Hereford (HER)/Limousine (LIM) beef breeds and the Holstein-Friesian (HF) dairy breed (p ≤ 0.001). The microarray analysis revealed differences in the expression of 23 miRNA among the aforementioned primary cultures. On the basis of a functional analysis, we assigned 9 miRNA as molecules responsible for differentiation progression (miR-1, -128a, -133a, -133b, -139, -206, -222, -486, and -503). The target gene prediction and functional analysis revealed 59 miRNA-related genes belonging to the muscle organ development process. Conclusion The number of myotubes and the miRNA expression in the primary cultures of skeletal muscle cells derived from the semitendinosus muscles of the HER/LIM beef cattle breeds and the HF dairy breed vary when cells are subjected to myogenic differentiation. The net effect of the identified miRNA and their target gene action should be considered the result of the breed-dependent activity of satellite cells and muscle stem cell niche cells and their mutual interactions, which putatively can be engaged in the formation of a larger number of myotubes in beef cattle-related cells (HER/LIM) during in vitro myogenesis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4492-5) contains supplementary material, which is available to authorized users.
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27
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Bonavida B. Linking Autophagy and the Dysregulated NFκB/ SNAIL/YY1/RKIP/PTEN Loop in Cancer: Therapeutic Implications. Crit Rev Oncog 2018; 23:307-320. [PMID: 30311562 PMCID: PMC6370039 DOI: 10.1615/critrevoncog.2018027212] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The role of autophagy in the pathogenesis of various cancers has been well documented in many reports. Autophagy in cancer cells regulates cell proliferation, viability, invasion, epithelial-to-mesenchymal transition (EMT), metastasis, and responses to chemotherapeutic and immunotherapeutic treatment strategies. These manifestations are the result of various regulatory gene products that govern autophagic, biochemical, and molecular mechanisms. In several human cancer cell models, the presence of a dysregulated circuit-namely, NFκB/SNAIL/YY1/RKIP/PTEN-that plays a major role in the regulation of tumor cell unique characteristics just listed for autophagy-regulated activities. Accordingly, the autophagic mechanism and the dysregulated circuit in cancer cells share many of the same properties and activities. Thus, it has been hypothesized that there must exist a biochemical/molecular link between the two. The present review describes the link and the association of each gene product of the dysregulated circuit with the autophagic mechanism and delineates the presence of crosstalk. Crosstalk between autophagy and the dysregulated circuit is significant and has important implications in the development of targeted therapies aimed at either autophagy or the dysregulated gene products in cancer cells.
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Affiliation(s)
- Benjamin Bonavida
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90025-1747,
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28
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Mok GF, Lozano-Velasco E, Münsterberg A. microRNAs in skeletal muscle development. Semin Cell Dev Biol 2017; 72:67-76. [PMID: 29102719 DOI: 10.1016/j.semcdb.2017.10.032] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/24/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022]
Abstract
A fundamental process during both embryo development and stem cell differentiation is the control of cell lineage determination. In developing skeletal muscle, many of the diffusible signaling molecules, transcription factors and more recently non-coding RNAs that contribute to this process have been identified. This has facilitated advances in our understanding of the molecular mechanisms underlying the control of cell fate choice. Here we will review the role of non-coding RNAs, in particular microRNAs (miRNAs), in embryonic muscle development and differentiation, and in satellite cells of adult muscle, which are essential for muscle growth and regeneration. Some of these short post-transcriptional regulators of gene expression are restricted to skeletal muscle, but their expression can also be more widespread. In addition, we discuss a few examples of long non-coding RNAs, which are numerous but much less well understood.
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Affiliation(s)
- Gi Fay Mok
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Estefania Lozano-Velasco
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrea Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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29
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Yang C, Zhang JJ, Peng YP, Zhu Y, Yin LD, Wei JS, Gao WT, Jiang KR, Miao Y. A Yin-Yang 1/miR-30a regulatory circuit modulates autophagy in pancreatic cancer cells. J Transl Med 2017; 15:211. [PMID: 29052509 PMCID: PMC5649049 DOI: 10.1186/s12967-017-1308-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022] Open
Abstract
Background Autophagy is a highly regulated biological process that mediates the degradation of intracellular components. It is required for tumor cell metabolism and homeostasis. Yin-Yang 1 (YY1) has been reported to be involved in autophagy in several carcinomas. However, its role in autophagy in pancreatic cancer, one of the deadliest human malignancies, is unknown. Here, we investigated the function of YY1 in pancreatic cancer cells autophagy and its mechanisms of action. Methods The activity of cells undergoing autophagy was assessed using transmission electron microscopy, immunofluorescence, and Western blotting. A luciferase activity assay, real-time quantitative polymerase chain reaction (RT-qPCR), and chromatin immunoprecipitation (ChIP) were also used to identify putative downstream targets of YY1. Results YY1 was confirmed to regulate autophagy in pancreatic cancer cells. It was found to directly regulate the expression of miR-30a, a known modulator of autophagy-associated genes. Furthermore, overexpression of miR-30a attenuated the pro-autophagic effects of YY1. Conclusions Cumulatively, our data suggest that miR-30a acts in a feedback loop to modulate the pro-autophagic activities of YY1. Thus, autophagy in pancreatic cancer cells may be regulated, in part, by a tightly coordinated YY1/miR-30a regulatory circuit. These findings provide a potential druggable target for the development of treatments for pancreatic cancer.
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Affiliation(s)
- Chuang Yang
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Jing-Jing Zhang
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Yun-Peng Peng
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Yi Zhu
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Ling-Di Yin
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Ji-Shu Wei
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Wen-Tao Gao
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Kui-Rong Jiang
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Yi Miao
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China. .,Pancreas Institute, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People's Republic of China.
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30
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Morozzi G, Beccafico S, Bianchi R, Riuzzi F, Bellezza I, Giambanco I, Arcuri C, Minelli A, Donato R. Oxidative stress-induced S100B accumulation converts myoblasts into brown adipocytes via an NF-κB/YY1/miR-133 axis and NF-κB/YY1/BMP-7 axis. Cell Death Differ 2017; 24:2077-2088. [PMID: 28885620 DOI: 10.1038/cdd.2017.132] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/20/2017] [Accepted: 07/03/2017] [Indexed: 12/17/2022] Open
Abstract
Muscles of sarcopenic people show hypotrophic myofibers and infiltration with adipose and, at later stages, fibrotic tissue. The origin of infiltrating adipocytes resides in fibro-adipogenic precursors and nonmyogenic mesenchymal progenitor cells, and in satellite cells, the adult stem cells of skeletal muscles. Myoblasts and brown adipocytes share a common Myf5+ progenitor cell: the cell fate depends on levels of bone morphogenetic protein 7 (BMP-7), a TGF-β family member. S100B, a Ca2+-binding protein of the EF-hand type, is expressed at relatively high levels in myoblasts from sarcopenic humans and exerts anti-myogenic effects via NF-κB-dependent inhibition of MyoD, a myogenic transcription factor acting upstream of the essential myogenic factor, myogenin. Adipogenesis requires high levels of ROS, and myoblasts of sarcopenic subjects show elevated ROS levels. Here we show that: (1) ROS overproduction in myoblasts results in upregulation of S100B levels via NF-κB activation; and (2) ROS/NF-κB-induced accumulation of S100B causes myoblast transition into brown adipocytes. S100B activates an NF-κB/Ying Yang 1 axis that negatively regulates the promyogenic and anti-adipogenic miR-133 with resultant accumulation of the brown adipogenic transcription regulator, PRDM-16. S100B also upregulates BMP-7 via NF-κB/Ying Yang 1 with resultant BMP-7 autocrine activity. Interestingly, myoblasts from sarcopenic humans show features of brown adipocytes. We also show that S100B levels and NF-κB activity are elevated in brown adipocytes obtained by culturing myoblasts in adipocyte differentiation medium and that S100B knockdown or NF-κB inhibition in myoblast-derived brown adipocytes reconverts them into fusion-competent myoblasts. At last, interstitial cells and, unexpectedly, a subpopulation of myofibers in muscles of geriatric but not young mice co-express S100B and the brown adipocyte marker, uncoupling protein-1. These results suggest that S100B is an important intracellular molecular signal regulating Myf5+ progenitor cell differentiation into fusion-competent myoblasts or brown adipocytes depending on its levels.
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Affiliation(s)
- Giulio Morozzi
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy
| | - Sara Beccafico
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy.,Istituto Interuniversitario di Miologia, Perugia, Italy
| | - Roberta Bianchi
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy
| | - Francesca Riuzzi
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy.,Istituto Interuniversitario di Miologia, Perugia, Italy
| | - Ilaria Bellezza
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy
| | - Ileana Giambanco
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy
| | - Cataldo Arcuri
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy
| | - Alba Minelli
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy
| | - Rosario Donato
- Department of Experimental Medicine, Istituto Interuniversitario di Miologia, Perugia Medical School, University of Perugia, Perugia, Italy.,Istituto Interuniversitario di Miologia, Perugia, Italy.,Centro Universitario per la Ricerca sulla Genomica Funzionale, Piazza Lucio Severi 1, Perugia 06132, Italy
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31
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Xue J, Xue J, Zhang J, Li D, Jiang L. miR-130b-3p/301b-3p negatively regulated Rb1cc1 expression on myogenic differentiation of chicken primary myoblasts. Biotechnol Lett 2017; 39:1611-1619. [PMID: 28721582 DOI: 10.1007/s10529-017-2400-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/10/2017] [Indexed: 01/13/2023]
Abstract
OBJECTIVES To explore the roles of miR-130b-3p and miR-301b-3p which may regulate Rb1-inducible coiled-coil 1 (Rb1cc1) expression during myogenic differentiation of chicken primary myoblasts. RESULTS After 4 days of myogenic differentiation, myotubes appeared and after 6 days the cells fused to each other and expression of MyHC could be detected by immunofluorescence staining. TargetScan and RNAhybrid 2.2 showed miR-130b-3p and miR-301b-3p were well complementary with the target site of Rb1cc1 3'-untranslated region (3'-UTR). Using the dual-luciferase assay, we found miR-130b-3p and miR-301b-3p could inhibit Rb1cc1 expression by binding to its 3'-UTR. Real-time PCR showed Rb1cc1 mRNA expression level was almost reciprocal to that of miR-130b-3p or miR-301b-3p during myogenic differentiation. Furthermore, over-expression of miR-130b-3p or miR-301b-3p down-regulated the expression levels of Rb1cc1, myoblast determination protein, myogenin and myosin heavy chain. CONCLUSIONS miR-130b-3p or miR-301b-3p negatively regulate Rb1cc1 expression to affect myogenic differentiation.
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Affiliation(s)
- Jian Xue
- College of Animal Husbandry & Veterinary, Jinzhou Medical University, No. 48, Section 5, Renmin Street, Guta District, Jinzhou City, 121001, Liaoning Province, People's Republic of China.
| | - Jingwen Xue
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Ji Zhang
- College of Food Science and Engineering, Jinzhou Medical University, Jinzhou City, 121001, People's Republic of China
| | - Dan Li
- College of Animal Husbandry & Veterinary, Jinzhou Medical University, No. 48, Section 5, Renmin Street, Guta District, Jinzhou City, 121001, Liaoning Province, People's Republic of China
| | - Lei Jiang
- College of Animal Husbandry & Veterinary, Jinzhou Medical University, No. 48, Section 5, Renmin Street, Guta District, Jinzhou City, 121001, Liaoning Province, People's Republic of China
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32
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Zhou J, Zhang S, Wang H, Sun H. LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells. Nucleic Acids Res 2017; 45:e108. [PMID: 28379566 PMCID: PMC5499579 DOI: 10.1093/nar/gkx232] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/27/2017] [Indexed: 02/01/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are key regulators of diverse cellular processes. Recent advances in high-throughput sequencing have allowed for an unprecedented discovery of novel lncRNAs. To identify functional lncRNAs from thousands of candidates for further functional validation is still a challenging task. Here, we present a novel computational framework, lncFunNet (lncRNA Functional inference through integrated Network) that integrates ChIP-seq, CLIP-seq and RNA-seq data to predict, prioritize and annotate lncRNA functions. In mouse embryonic stem cells (mESCs), using lncFunNet we not only recovered most of the functional lncRNAs known to maintain mESC pluripotency but also predicted a plethora of novel functional lncRNAs. Similarly, in mouse myoblast C2C12 cells, applying lncFunNet led to prediction of reservoirs of functional lncRNAs in both proliferating myoblasts (MBs) and differentiating myotubes (MTs). Further analyses demonstrated that these lncRNAs are frequently bound by key transcription factors, interact with miRNAs and constitute key nodes in biological network motifs. Further experimentations validated their dynamic expression profiles and functionality during myoblast differentiation. Collectively, our studies demonstrate the use of lncFunNet to annotate and identify functional lncRNAs in a given biological system.
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Affiliation(s)
- Jiajian Zhou
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Suyang Zhang
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Hao Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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33
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Koltai E, Bori Z, Chabert C, Dubouchaud H, Naito H, Machida S, Davies KJ, Murlasits Z, Fry AC, Boldogh I, Radak Z. SIRT1 may play a crucial role in overload-induced hypertrophy of skeletal muscle. J Physiol 2017; 595:3361-3376. [PMID: 28251652 PMCID: PMC5451718 DOI: 10.1113/jp273774] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 02/23/2017] [Indexed: 01/08/2023] Open
Abstract
KEY POINTS Silent mating type information regulation 2 homologue 1 (SIRT1) activity and content increased significantly in overload-induced hypertrophy. SIRT1-mediated signalling through Akt, the endothelial nitric oxide synthase mediated pathway, regulates anabolic process in the hypertrophy of skeletal muscle. The regulation of catabolic signalling via forkhead box O 1 and protein ubiquitination is SIRT1 dependent. Overload-induced changes in microRNA levels regulate SIRT1 and insulin-like growth factor 1 signalling. ABSTRACT Significant skeletal muscle mass guarantees functional wellbeing and is important for high level performance in many sports. Although the molecular mechanism for skeletal muscle hypertrophy has been well studied, it still is not completely understood. In the present study, we used a functional overload model to induce plantaris muscle hypertrophy by surgically removing the soleus and gastrocnemius muscles in rats. Two weeks of muscle ablation resulted in a 40% increase in muscle mass, which was associated with a significant increase in silent mating type information regulation 2 homologue 1 (SIRT1) content and activity (P < 0.001). SIRT1-regulated Akt, endothelial nitric oxide synthase and GLUT4 levels were also induced in hypertrophied muscles, and SIRT1 levels correlated with muscle mass, paired box protein 7 (Pax7), proliferating cell nuclear antigen (PCNA) and nicotinamide phosphoribosyltransferase (Nampt) levels. Alternatively, decreased forkhead box O 1 (FOXO1) and increased K48 polyubiquitination also suggest that SIRT1 could be involved in the catabolic process of hypertrophy. Furthermore, increased levels of K63 and muscle RING finger 2 (MuRF2) protein could also be important enhancers of muscle mass. We report here that the levels of miR1 and miR133a decrease in hypertrophy and negatively correlate with muscle mass, SIRT1 and Nampt levels. Our results reveal a strong correlation between SIRT1 levels and activity, SIRT1-regulated pathways and overload-induced hypertrophy. These findings, along with the well-known regulatory roles that SIRT1 plays in modulating both anabolic and catabolic pathways, allow us to propose the hypothesis that SIRT1 may actually play a crucial causal role in overload-induced hypertrophy of skeletal muscle. This hypothesis will now require rigorous direct and functional testing.
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Affiliation(s)
- Erika Koltai
- Research Institute of Sport Science, University of Physical Education, Budapest, Hungary
| | - Zoltán Bori
- Research Institute of Sport Science, University of Physical Education, Budapest, Hungary
| | - Clovis Chabert
- Université Joseph Fourier, Laboratoire de Bioénergétique Fondamentale et Appliquée, Grenoble Cedex, 0938041, France
| | - Hervé Dubouchaud
- Université Joseph Fourier, Laboratoire de Bioénergétique Fondamentale et Appliquée, Grenoble Cedex, 0938041, France
| | - Hisashi Naito
- Department of Exercise Physiology, Graduate School of Health and Sports Science & Medicine, Juntendo University, Japan
| | - Shuichi Machida
- Department of Exercise Physiology, Graduate School of Health and Sports Science & Medicine, Juntendo University, Japan
| | - Kelvin Ja Davies
- Ethel Percy Andrus Gerontology Centre of the Leonard Davis School of Gerontology; and Division of Molecular & Computational Biology, Department of Biological Sciences, of the Dornsife College of Letters, Arts, and Sciences, the University of Southern California, Los Angeles, CA, 90089-0191, USA
| | | | - Andrew C Fry
- Osness Human Performance Laboratories, Department of Health, Sport, and Exercise Sciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Zsolt Radak
- Research Institute of Sport Science, University of Physical Education, Budapest, Hungary.,Institute of Sport Sciences and Physical Education, University of Pecs, Pecs, Hungary
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34
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Bianchi M, Renzini A, Adamo S, Moresi V. Coordinated Actions of MicroRNAs with other Epigenetic Factors Regulate Skeletal Muscle Development and Adaptation. Int J Mol Sci 2017; 18:E840. [PMID: 28420141 PMCID: PMC5412424 DOI: 10.3390/ijms18040840] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/04/2017] [Accepted: 04/13/2017] [Indexed: 01/01/2023] Open
Abstract
Epigenetics plays a pivotal role in regulating gene expression in development, in response to cellular stress or in disease states, in virtually all cell types. MicroRNAs (miRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate gene expression. miRNAs were discovered in 1993 and have been extensively studied ever since. They can be expressed in a tissue-specific manner and play a crucial role in tissue development and many biological processes. miRNAs are responsible for changes in the cell epigenome because of their ability to modulate gene expression post-transcriptionally. Recently, numerous studies have shown that miRNAs and other epigenetic factors can regulate each other or cooperate in regulating several biological processes. On the one hand, the expression of some miRNAs is silenced by DNA methylation, and histone modifications have been demonstrated to modulate miRNA expression in many cell types or disease states. On the other hand, miRNAs can directly target epigenetic factors, such as DNA methyltransferases or histone deacetylases, thus regulating chromatin structure. Moreover, several studies have reported coordinated actions between miRNAs and other epigenetic mechanisms to reinforce the regulation of gene expression. This paper reviews multiple interactions between miRNAs and epigenetic factors in skeletal muscle development and in response to stimuli or disease.
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Affiliation(s)
- Marzia Bianchi
- DAHFMO Unit of Histology and Medical Embryology, Interuniversity Institute of Myology, Sapienza University of Rome, Via Antonio Scarpa 14, 00161 Rome, Italy.
| | - Alessandra Renzini
- DAHFMO Unit of Histology and Medical Embryology, Interuniversity Institute of Myology, Sapienza University of Rome, Via Antonio Scarpa 14, 00161 Rome, Italy.
| | - Sergio Adamo
- DAHFMO Unit of Histology and Medical Embryology, Interuniversity Institute of Myology, Sapienza University of Rome, Via Antonio Scarpa 14, 00161 Rome, Italy.
| | - Viviana Moresi
- DAHFMO Unit of Histology and Medical Embryology, Interuniversity Institute of Myology, Sapienza University of Rome, Via Antonio Scarpa 14, 00161 Rome, Italy.
- Laboratory of Cardiovascular Endocrinology, IRCCS San Raffaele Pisana, 00166 Rome, Italy.
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35
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Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity. Cell Discov 2017; 3:17002. [PMID: 28326190 PMCID: PMC5348715 DOI: 10.1038/celldisc.2017.2] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/29/2016] [Indexed: 12/21/2022] Open
Abstract
Malat1 is one of the most abundant long non-coding RNAs in various cell types; its exact cellular function is still a matter of intense investigation. In this study we characterized the function of Malat1 in skeletal muscle cells and muscle regeneration. Utilizing both in vitro and in vivo assays, we demonstrate that Malat1 has a role in regulating gene expression during myogenic differentiation of myoblast cells. Specifically, we found that knockdown of Malat1 accelerates the myogenic differentiation in cultured cells. Consistently, Malat1 knockout mice display enhanced muscle regeneration after injury and deletion of Malat1 in dystrophic mdx mice also improves the muscle regeneration. Mechanistically, in the proliferating myoblasts, Malat1 recruits Suv39h1 to MyoD-binding loci, causing trimethylation of histone 3 lysine 9 (H3K9me3), which suppresses the target gene expression. Upon differentiation, the pro-myogenic miR-181a is increased and targets the nuclear Malat1 transcripts for degradation through Ago2-dependent nuclear RNA-induced silencing complex machinery; the Malat1 decrease subsequently leads to the destabilization of Suv39h1/HP1β/HDAC1-repressive complex and displacement by a Set7-containing activating complex, which allows MyoD trans-activation to occur. Together, our findings identify a regulatory axis of miR-181a-Malat1-MyoD/Suv39h1 in myogenesis and uncover a previously unknown molecular mechanism of Malat1 action in gene regulation.
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36
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Gonçalves TJ, Armand AS. Non-coding RNAs in skeletal muscle regeneration. Noncoding RNA Res 2017; 2:56-67. [PMID: 30159421 PMCID: PMC6096429 DOI: 10.1016/j.ncrna.2017.03.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 01/09/2023] Open
Abstract
Following injury, skeletal muscles can regenerate from muscle specific stem cells, called satellite cells. Quiescent in uninjured muscles, satellite cells become activated, proliferate and differentiate into myotubes. Muscle regeneration occurs following distinct main overlapping phases, including inflammation, regeneration and maturation of the regenerated myofibers. Each step of muscle regeneration is orchestrated through complex signaling networks and gene regulatory networks, leading to the expression of specific set of genes in each concerned cell type. Apart from the well-established transcriptional mechanisms involving the myogenic regulatory factors of the MyoD family, increasing data indicate that each step of muscle regeneration is controlled by a wide range of non-coding RNAs. In this review, we discuss the role of two classes of non-coding RNAs (microRNAs and long non-coding RNAs) in the inflammatory, regeneration and maturation steps of muscle regeneration.
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Affiliation(s)
- Tristan J.M. Gonçalves
- Institut Necker-Enfants Malades, Inserm, U1151, 14 rue Maria Helena Vieira Da Silva, CS 61431, Paris, F-75014, France
- INSERM UMRS 1124, 45 rue des Saints-Pères, F-75270 Paris cedex 06, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Anne-Sophie Armand
- Institut Necker-Enfants Malades, Inserm, U1151, 14 rue Maria Helena Vieira Da Silva, CS 61431, Paris, F-75014, France
- INSERM UMRS 1124, 45 rue des Saints-Pères, F-75270 Paris cedex 06, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Amirouche A, Jahnke VE, Lunde JA, Koulmann N, Freyssenet DG, Jasmin BJ. Muscle-specific microRNA-206 targets multiple components in dystrophic skeletal muscle representing beneficial adaptations. Am J Physiol Cell Physiol 2017; 312:C209-C221. [DOI: 10.1152/ajpcell.00185.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/06/2016] [Accepted: 12/21/2016] [Indexed: 01/31/2023]
Abstract
Over the last several years, converging lines of evidence have indicated that miR-206 plays a pivotal role in promoting muscle differentiation and regeneration, thereby potentially impacting positively on the progression of neuromuscular disorders, including Duchenne muscular dystrophy (DMD). Despite several studies showing the regulatory function of miR-206 on target mRNAs in skeletal muscle cells, the effects of overexpression of miR-206 in dystrophic muscles remain to be established. Here, we found that miR-206 overexpression in mdx mouse muscles simultaneously targets multiple mRNAs and proteins implicated in satellite cell differentiation, muscle regeneration, and at the neuromuscular junction. Overexpression of miR-206 also increased the levels of several muscle-specific mRNAs/proteins, while enhancing utrophin A expression at the sarcolemma. Finally, we also observed that the increased expression of miR-206 in dystrophin-deficient mouse muscle decreased the production of proinflammatory cytokines and infiltration of macrophages. Taken together, our results show that miR-206 acts as a pleiotropic regulator that targets multiple key mRNAs and proteins expected to provide beneficial adaptations in dystrophic muscle, thus highlighting its therapeutic potential for DMD.
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Affiliation(s)
- Adel Amirouche
- Laboratoire Interuniversitaire de Biologie de la Motricité, Université de Saint Etienne, Université de Lyon, Lyon, France
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; and
| | - Vanessa E. Jahnke
- Laboratoire Interuniversitaire de Biologie de la Motricité, Université de Saint Etienne, Université de Lyon, Lyon, France
| | - John A. Lunde
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; and
| | - Nathalie Koulmann
- Institut de Recherche Biomédicale des Armées, Département Environnements Opérationnels, Bretigny-sur-Orge, France
| | - Damien G. Freyssenet
- Laboratoire Interuniversitaire de Biologie de la Motricité, Université de Saint Etienne, Université de Lyon, Lyon, France
| | - Bernard J. Jasmin
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; and
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Wang M, Liu C, Su Y, Zhang K, Zhang Y, Chen M, Ge M, Gu L, Lu T, Li N, Yu Z, Meng Q. miRNA-34c inhibits myoblasts proliferation by targeting YY1. Cell Cycle 2017; 16:1661-1672. [PMID: 28125315 DOI: 10.1080/15384101.2017.1281479] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
miRNAs are increasingly being implicated as key regulators of cell proliferation, apoptosis, and differentiation. miRNA-34c appears to play a crucial role in cancer pathogenesis wherein it exerts its effect as a tumor suppressor. However, the role of miR-34c in myoblast proliferation remains poorly understood. Here, we found that overexpression miR-34c inhibited myoblasts proliferation by reducing the protein and mRNA expression of cell cycle genes. In contrast, blocking the function of miR-34c promoted myoblasts proliferation and increased the protein and mRNA expression of cell cycle genes. Moreover, miR-34c directly targeted YY1 and inhibited its expression. Similar to overexpression miR-34c, knockdown of YY1 by siRNA suppressed myoblasts proliferation. Our study provides novel evidence for a role of miR-34c in inhibiting myoblasts proliferation by repressing YY1. Thus, miR-34c has the potential to be used to enhance skeletal muscle development and regeneration.
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Affiliation(s)
- Meng Wang
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Chuncheng Liu
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Yang Su
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Kuo Zhang
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Yuying Zhang
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Min Chen
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Mengxu Ge
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Lijie Gu
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Tianyu Lu
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Ning Li
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Zhengquan Yu
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
| | - Qingyong Meng
- a The State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University , Beijing , China
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Bracken CP, Scott HS, Goodall GJ. A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet 2016; 17:719-732. [DOI: 10.1038/nrg.2016.134] [Citation(s) in RCA: 468] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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E2F1-miR-20a-5p/20b-5p auto-regulatory feedback loop involved in myoblast proliferation and differentiation. Sci Rep 2016; 6:27904. [PMID: 27282946 PMCID: PMC4901305 DOI: 10.1038/srep27904] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/26/2016] [Indexed: 02/06/2023] Open
Abstract
miR-17 family microRNAs (miRNAs) are crucial for embryo development, however, their role in muscle development is still unclear. miR-20a-5p and miR-20b-5p belong to the miR-17 family and are transcribed from the miR-17~92 and miR-106a~363 clusters respectively. In this study, we found that miR-20a-5p and miR-20b-5p promoted myoblast differentiation and repressed myoblast proliferation by directly binding the 3' UTR of E2F transcription factor 1 (E2F1) mRNA. E2F1 is an important transcriptional factor for organism's normal development. Overexpression of E2F1 in myoblasts promoted myoblast proliferation and inhibited myoblast differentiation. Conversely, E2F1 inhibition induced myoblast differentiation and repressed myoblast proliferation. Moreover, E2F1 can bind directly to promoters of the miR-17~92 and miR-106a~363 clusters and activate their transcription, and E2F1 protein expression is correlated with the expression of pri-miR-17~92 and pri-miR-106a~363 during myoblast differentiation. These results suggested an auto-regulatory feedback loop between E2F1 and miR-20a-5p/20b-5p, and indicated that miR-20a-5p, miR-20b-5p and E2F1 are involved in myoblast proliferation and differentiation through the auto-regulation between E2F1 and miR-20a-5p/20b-5p. These findings provide new insight into the mechanism of muscle differentiation, and further shed light on the understanding of muscle development and muscle diseases.
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41
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42
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Coda DM, Lingua MF, Morena D, Foglizzo V, Bersani F, Ala U, Ponzetto C, Taulli R. SMYD1 and G6PD modulation are critical events for miR-206-mediated differentiation of rhabdomyosarcoma. Cell Cycle 2016; 14:1389-402. [PMID: 25644430 DOI: 10.1080/15384101.2015.1005993] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Rhadomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. RMS cells resemble fetal myoblasts but are unable to complete myogenic differentiation. In previous work we showed that miR-206, which is low in RMS, when induced in RMS cells promotes the resumption of differentiation by modulating more than 700 genes. To better define the pathways involved in the conversion of RMS cells into their differentiated counterpart, we focused on 2 miR-206 effectors emerged from the microarray analysis, SMYD1 and G6PD. SMYD1, one of the most highly upregulated genes, is a H3K4 histone methyltransferase. Here we show that SMYD1 silencing does not interfere with the proliferative block or with the loss anchorage independence imposed by miR-206, but severely impairs differentiation of ERMS, ARMS, and myogenic cells. Thus SMYD1 is essential for the activation of muscle genes. Conversely, among the downregulated genes, we found G6PD, the enzyme catalyzing the rate-limiting step of the pentose phosphate shunt. In this work, we confirmed that G6PD is a direct target of miR-206. Moreover, we showed that G6PD silencing in ERMS cells impairs proliferation and soft agar growth. However, G6PD overexpression does not interfere with the pro-differentiating effect of miR-206, suggesting that G6PD downmodulation contributes to - but is not an absolute requirement for - the tumor suppressive potential of miR-206. Targeting cancer metabolism may enhance differentiation. However, therapeutic inhibition of G6PD is encumbered by side effects. As an alternative, we used DCA in combination with miR-206 to increase the flux of pyruvate into the mitochondrion by reactivating PDH. DCA enhanced the inhibition of RMS cell growth induced by miR-206, and sustained it upon miR-206 de-induction. Altogether these results link miR-206 to epigenetic and metabolic reprogramming, and suggest that it may be worth combining differentiation-inducing with metabolism-directed approaches.
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Key Words
- DCA, Dichloroacetate
- DHEA, Dehydroepiandrosterone
- G6PD, Glucose 6 Phosphate Dehydrogenase
- HMT, Histone MethylTransferase
- MREs, MicroRNA Responsive Elements
- MRFs, Myogenic Regulatory Factors
- PDH, Pyruvate Dehydrogenase
- PDK, Pyruvate Dehydrogenase Kinase
- PPP, Pentose Phosphate Pathway
- RMS, Rhabdomyosarcoma
- Rhabdomyosarcoma
- SMYD1, SET and MYND domain-containing protein 1
- TCA cycle, TriCarboxylic Acid cycle
- differentiation therapy
- metabolism and cancer
- miR-206
- myomiRs, muscle-specific microRNAs
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Sun K, Zhou L, Zhao Y, Wang H, Sun H. Genome-wide RNA-seq and ChIP-seq reveal Linc-YY1 function in regulating YY1/PRC2 activity during skeletal myogenesis. GENOMICS DATA 2016; 7:247-9. [PMID: 26981420 PMCID: PMC4778671 DOI: 10.1016/j.gdata.2016.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 01/30/2016] [Accepted: 01/31/2016] [Indexed: 11/25/2022]
Abstract
Little is known how lincRNAs are involved in skeletal myogenesis. Here we describe the discovery and functional annotation of Linc-YY1, a novel lincRNA originating from the promoter of the transcription factor (TF) Yin Yang 1 (YY1). Starting from whole transcriptome shotgun sequencing (a.k.a. RNA-seq) data from muscle C2C12 cells, a series of bioinformatics analysis was applied towards the identification of hundreds of high-confidence novel lincRNAs. Genome-wide approaches were then employed to demonstrate that Linc-YY1 functions to promote myogenesis through associating with YY1 and regulating YY1/PRC2 transcriptional activity in trans. Here we describe the details of the ChIP-seq, RNA-seq experiments, and data analysis procedures associated with the study published by Zhou and colleagues in the Nature Communications Journal in 2015 Zhou et al. (2015) [1]. The data was deposited on NCBI's Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE74049.
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Affiliation(s)
- Kun Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Liang Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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44
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Muscle-specific microRNAs in skeletal muscle development. Dev Biol 2016; 410:1-13. [DOI: 10.1016/j.ydbio.2015.12.013] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 01/19/2023]
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45
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Zhou L, Sun K, Zhao Y, Zhang S, Wang X, Li Y, Lu L, Chen X, Chen F, Bao X, Zhu X, Wang L, Tang LY, Esteban MA, Wang CC, Jauch R, Sun H, Wang H. Linc-YY1 promotes myogenic differentiation and muscle regeneration through an interaction with the transcription factor YY1. Nat Commun 2015; 6:10026. [PMID: 26658965 DOI: 10.1038/ncomms10026] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/28/2015] [Indexed: 12/22/2022] Open
Abstract
Little is known how lincRNAs are involved in skeletal myogenesis. Here we describe the discovery of Linc-YY1 from the promoter of the transcription factor (TF) Yin Yang 1 (YY1) gene. We demonstrate that Linc-YY1 is dynamically regulated during myogenesis in vitro and in vivo. Gain or loss of function of Linc-YY1 in C2C12 myoblasts or muscle satellite cells alters myogenic differentiation and in injured muscles has an impact on the course of regeneration. Linc-YY1 interacts with YY1 through its middle domain, to evict YY1/Polycomb repressive complex (PRC2) from target promoters, thus activating the gene expression in trans. In addition, Linc-YY1 also regulates PRC2-independent function of YY1. Finally, we identify a human Linc-YY1 orthologue with conserved function and show that many human and mouse TF genes are associated with lincRNAs that may modulate their activity. Altogether, we show that Linc-YY1 regulates skeletal myogenesis and uncover a previously unappreciated mechanism of gene regulation by lincRNA.
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Affiliation(s)
- Liang Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kun Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Suyang Zhang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Xuecong Wang
- Genome Regulation Laboratory, Drug Discovery Pipeline, Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Yuying Li
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Leina Lu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaona Chen
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Fengyuan Chen
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Xichen Bao
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Xihua Zhu
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Lijun Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ling-Yin Tang
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Miguel A Esteban
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Chi-Chiu Wang
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Hao Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Orthopedics and Traumatology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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46
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A PCR-Based Method to Construct Lentiviral Vector Expressing Double Tough Decoy for miRNA Inhibition. PLoS One 2015; 10:e0143864. [PMID: 26624995 PMCID: PMC4666662 DOI: 10.1371/journal.pone.0143864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/09/2015] [Indexed: 01/12/2023] Open
Abstract
DNA vector-encoded Tough Decoy (TuD) miRNA inhibitor is attracting increased attention due to its high efficiency in miRNA suppression. The current methods used to construct TuD vectors are based on synthesizing long oligonucleotides (~90 mer), which have been costly and problematic because of mutations during synthesis. In this study, we report a PCR-based method for the generation of double Tough Decoy (dTuD) vector in which only two sets of shorter oligonucleotides (< 60 mer) were used. Different approaches were employed to test the inhibitory potency of dTuDs. We demonstrated that dTuD is the most efficient method in miRNA inhibition in vitro and in vivo. Using this method, a mini dTuD library against 88 human miRNAs was constructed and used for a high-throughput screening (HTS) of AP-1 pathway-related miRNAs. Seven miRNAs (miR-18b-5p, -101-3p, -148b-3p, -130b-3p, -186-3p, -187-3p and -1324) were identified as candidates involved in AP-1 pathway regulation. This novel method allows for an accurate and cost-effective generation of dTuD miRNA inhibitor, providing a powerful tool for efficient miRNA suppression in vitro and in vivo.
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47
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Sun K, Lu L, Wang H, Sun H. Genome-wide profiling of YY1 binding sites during skeletal myogenesis. GENOMICS DATA 2015; 2:89-91. [PMID: 26484078 PMCID: PMC4535464 DOI: 10.1016/j.gdata.2014.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 11/01/2022]
Abstract
Skeletal muscle differentiation is regulated by a network of transcription factors, epigenetic regulators and noncoding RNAs. We have recently performed ChIP-seq experiments to explore the genome-wide binding of transcription factor YY1 in skeletal muscle cells. Our results identified thousands of YY1 binding peaks, underscoring its multifaceted functions in muscle cells. In particular, we identified a very high proportion of YY1 binding peaks residing in the intergenic regions, which led to the discovery of some novel lincRNAs under YY1 regulation. Here we describe the details of the ChIP-seq experiments and data analysis procedures associated with the study published by Lu et al. in the EMBO Journal in 2013 [1].
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Affiliation(s)
- Kun Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Leina Lu
- Department of Obstetrics and Gynaecology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Huating Wang
- Department of Obstetrics and Gynaecology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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48
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Zhao G, Li Q, Wang A, Jiao J. YY1 regulates melanoma tumorigenesis through a miR-9 ~ RYBP axis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:66. [PMID: 26104682 PMCID: PMC4511530 DOI: 10.1186/s13046-015-0177-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/27/2015] [Indexed: 12/22/2022]
Abstract
Background The Yin Yang 1 (YY1) transcription factor has been identified to target a plethora of potential target genes, which are important for cell proliferation and differentiation. Although the role that YY1 plays in different human types of cancer has been reported, its biological and mechanistic significance in melanoma has not been well defined. Methods Quantitative RT-PCR analysis was used to determine whether aberrant YY1 and miR-9 expression occurred in melanoma, compared with benign nevi and normal tissue controls. Furthermore, the transcriptional regulation of YY1 on miR-9 expression was assessed by using quantitative ChIP-PCR assay. Subsequently, the effects of YY1 and miR-9 on proliferation, cell cycle, migration and invasion of melanoma cells were detected using CCK-8, flow cytometric analysis, wound healing and transwell invasion assays, respectively. Finally, the post-transcriptional regulation of miR-9 on RYBP was analyzed using luciferase reporter and immunoblot analysis. Results Elevated YY1 levels were observed in patients with melanoma, compared with benign nevi and normal tissue controls, and the increased YY1 was associated with melanoma metastasis state and tumor stage. Furthermore, YY1 negatively regulated miR-9 transcription. Silencing of YY1 inhibited proliferation, cell cycle progression, migration and invasion in melanoma cells, while ectopic of miR-9 did the same. Additionally, RYBP was shown to be a direct target of miR-9 through binding to its 3′ UTR, thus forming a YY1 ~ miR-9 ~ RYBP axis. Conclusions These results identify a novel YY1 ~ miR-9 ~ RYBP axis involved in melanoma tumorigenesis and reinforce the idea that regulatory circuitries involving miRNAs and TFs are prevalent mechanisms.
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Affiliation(s)
- Guowei Zhao
- Department of Dermatology, The Central Hospital of Zibo City, Zibo, 255036, Shandong Province, China.
| | - Qiang Li
- Oncology Department, The Foruth People's Hospital of Zibo City, Zibo, 255067, Shandong Province, China.
| | - Aiqin Wang
- Department of Dermatology, The Central Hospital of Zibo City, Zibo, 255036, Shandong Province, China.
| | - Jian Jiao
- Department of Dermatology, Qilu Hospital Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.
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Wang AM, Huang TT, Hsu KW, Huang KH, Fang WL, Yang MH, Lo SS, Chi CW, Lin JJ, Yeh TS. Yin Yang 1 is a target of microRNA-34 family and contributes to gastric carcinogenesis. Oncotarget 2015; 5:5002-16. [PMID: 24970812 PMCID: PMC4148117 DOI: 10.18632/oncotarget.2073] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer is the second leading cause of cancer-related death worldwide. Herein, we investigated the role of transcription factor Yin Yang 1 (YY1), a multi-functional protein, in tumorigenesis of gastric cancer cells. Results showed that YY1 contributed to gastric carcinogenesis of SC-M1 cells including growth, viability, and abilities of colony formation, migration, invasion, and tumorsphere formation. Levels of pluripotency genes CD44, Oct4, SOX-2, and Nanog were also up-regulated by YY1 in SC-M1 cells. Additionally, the 3'-untranslated region (3'-UTR) of YY1 mRNA was the target of microRNA-34 (miR-34) family consisting of miR-34a, miR-34b, and miR-34c. Overexpression of miR-34 family suppressed carcinogenesis through down-regulation of YY1 in NUGC-3 gastric cancer cells scarcely expressing miR-34 family. Alternatively, knockdown of miR-34 family promoted tumorigenesis via up-regulation of YY1 in SC-M1 and AZ521 gastric cancer cells with higher levels of miR-34 family. The miR-34 family also affected tumorsphere ultra-structure and inhibited the xenografted tumor growth as well as lung metastasis of SC-M1 cells through YY1. Expressions of miR-34a and miR-34c in gastric cancer tissues of patients were lower than those in normal tissues. Taken together, these results suggest that miR-34 family-YY1 axis plays an important role in the control of gastric carcinogenesis.
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Affiliation(s)
- An-Ming Wang
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei , Taiwan. Department of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei , Taiwan
| | - Tzu-Ting Huang
- Department of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei , Taiwan. Department and Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei , Taiwan. These authors contributed equally to this work
| | - Kai-Wen Hsu
- Department of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei , Taiwan. These authors contributed equally to this work
| | - Kuo-Hung Huang
- Department of Surgery, Taipei Veterans General Hospital, Taipei , Taiwan. Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei , Taiwan. These authors contributed equally to this work
| | - Wen-Liang Fang
- Department of Surgery, Taipei Veterans General Hospital, Taipei , Taiwan. Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei , Taiwan. These authors contributed equally to this work
| | - Muh-Hwa Yang
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei , Taiwan
| | - Su-Shun Lo
- Department of Medicine, School of Medicine, National Yang-Ming University, Taipei , Taiwan. Department of Surgery, National Yang-Ming University Hospital, Yi-Lan, Taiwan
| | - Chin-Wen Chi
- Department and Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei , Taiwan. Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei , Taiwan
| | - Jing-Jer Lin
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei , Taiwan. Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tien-Shun Yeh
- Department of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei , Taiwan. Genome Research Center, National Yang-Ming University, Taipei , Taiwan. Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
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Abstract
In recent years, long noncoding RNAs (lncRNAs) have emerged as an important class of regulators of gene expression. lncRNAs exhibit several distinctive features that confer unique regulatory functions, including exquisite cell- and tissue-specific expression and the capacity to transduce higher-order spatial information. Here we review evidence showing that lncRNAs exert critical functions in adult tissue stem cells, including skin, brain, and muscle, as well as in developmental patterning and pluripotency. We highlight new approaches for ascribing lncRNA functions and discuss mammalian dosage compensation as a classic example of an lncRNA network coupled to stem cell differentiation.
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Affiliation(s)
- Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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