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Li M, Li Y, Wang Z, Cui F, Yang F, Wang H, Shi Q, Huang X. microRNA-mRNA expression profiles in the skeletal muscle of myotonic dystrophy type 1. Neurol Res 2024; 46:613-625. [PMID: 38810890 DOI: 10.1080/01616412.2024.2339102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/30/2024] [Indexed: 05/31/2024]
Abstract
OBJECTIVES Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy in adults, yet there are currently no disease-modifying treatments. Disrupted miRNA expressions may lead to dysregulation of target mRNAs and dysfunction involved in DM1 pathogenic mechanism. METHODS We used microarray platforms to examine the miRNA/mRNA expression profiles in skeletal muscle biopsies derived from DM1 patients and matched controls. Bioinformatics analysis and dual-luciferase reporter assay were conducted to provide insight into miRNA-mRNA regulatory networks altered in DM1. RESULTS Twenty-three differentially expressed miRNAs and 135 differentially expressed genes were identified. qPCR confirmed that miR-3201, myogenic factor 5 (MYF5), myogenic differentiation 1 (MYOD1), CUGBP, Elav-like family member 1 (CELF1), and CELF2 were significantly up-regulated, while miR-196a, miR-200c, and miR-146a were significantly down-regulated. Enriched functions and pathways such as multicellular organismal development, RNA splicing, cell differentiation, and spliceosome are relevant to DM1. The miRNA-mRNA interaction network revealed that miR-182, miR-30c-2, and miR-200c were the critical nodes that potentially interacted with hub genes. Luciferase reporter assay confirmed the direct interaction between miR-196a and CELF2. CONCLUSION Those results implied that the observed miRNA/mRNA dysregulation could contribute to specific functions and pathways related to DM1 pathogenesis, highlighting the dysfunction of miR-196a and CELF2.
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Affiliation(s)
- Mao Li
- Department of Neurology of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yifan Li
- Geriatric Neurological Department of the Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Zhanjun Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Fang Cui
- Department of Neurology of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fei Yang
- Department of Neurology of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hongfen Wang
- Department of Neurology of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qiang Shi
- Department of Neurology of the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xusheng Huang
- Department of Neurology of the First Medical Center, Chinese PLA General Hospital, Beijing, China
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2
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Yun J, Huang X, Liu C, Shi M, Li W, Niu J, Cai C, Yang Y, Gao P, Guo X, Li B, Lu C, Cao G. Genome-wide analysis of circular RNA-mediated ceRNA regulation in porcine skeletal muscle development. BMC Genomics 2023; 24:196. [PMID: 37046223 PMCID: PMC10099641 DOI: 10.1186/s12864-023-09284-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND As a diverse and abundant class of endogenous RNAs, circular RNAs (circRNAs) participate in various biological processes including cell proliferation and apoptosis. Nevertheless, few researchers have investigated the role of circRNAs in muscle development in cultivated pigs. RESULTS In this study, we used RNA-seq to construct circRNA expression profiles in skeletal muscle of Jinfen White pigs at the age of 1, 90, and 180 days. Among the 16,990 identified circRNAs, 584 circRNAs were differentially expressed. Moreover, the enrichment analysis of DE circRNA host genes showed that they were mainly involved in muscle contraction, muscle organ development and muscle system processes, as well as AMPK and cAMP-related signal pathways. We also constructed a circRNA-miRNA-mRNA co-expression network to find key circRNAs which many involved in the regulation of porcine skeletal muscle development through the competitive endogenous RNA (ceRNA) mechanism. It is noteworthy that circ_0018595/miR-1343/PGM1 axis may play a regulatory role in the development of porcine skeletal muscle. CONCLUSIONS This study identified the circRNAs and present the circRNA expression profile in the development of pigs, revealed that DE circRNA host genes participate in different cell fates and enriched the porcine ceRNA network. Thus, this work will become a valuable resource for further in-depth study of the regulatory mechanism of circRNA in the development of porcine skeletal muscle.
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Affiliation(s)
- Jiale Yun
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaoyu Huang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chang Liu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Mingyue Shi
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Wenxia Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Jin Niu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chunbo Cai
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Yang Yang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaohong Guo
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China.
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China.
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3
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Kong L, Fang Y, Du M, Wang Y, He H, Liu Z. Gαi2 regulates the adult myogenesis of masticatory muscle satellite cells. J Cell Mol Med 2023; 27:1239-1249. [PMID: 36977201 PMCID: PMC10148056 DOI: 10.1111/jcmm.17726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/22/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Although similar to trunk and limb skeletal muscles, masticatory muscles are believed as unique in both developmental origins and myogenesis. Gαi2 has been demonstrated to promote muscle hypertrophy and muscle satellite cell differentiation in limb muscles. However, the effect of Gαi2 on masticatory muscles is still unexplored. This study aimed to identify the role of Gαi2 in the proliferation and differentiation of masticatory muscle satellite cells, further exploring the metabolic mechanism of masticatory muscles. The proliferation rate, myotube size, fusion index of masticatory muscle satellite cells and Pax7, Myf5, MyoD, Tcf21 and Musculin expressions were significantly decreased by Gαi2 knockdown, while in cells infected with AdV4-Gαi2, the proliferation rate, myotube size, fusion index and Tbx1 expression were significantly increased. Masticatory muscle satellite cells also displayed phenotype transformation as Gαi2 changed. In addition, Gαi2 altered myosin heavy chain (MyHC) isoforms of myotubes with less MyHC-2A expression in siGαi2 group and more MyHC-slow expression in AdV4-Gαi2 group. In conclusion, Gαi2 could positively affect the adult myogenesis of masticatory muscle satellite cells and maintain the superiority of MyHC-slow. Masticatory muscle satellite cells may have their unique Gαi2-regulated myogenic transcriptional networks, although they may share some common characteristics with trunk and limb muscles.
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Affiliation(s)
- Lin Kong
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yi Fang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Kunming Medical University School and Hospital of Stomatology, Kunming, China
- Yunnan Key Laboratory of Stomatology, Kunming, China
| | - Mingyuan Du
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Orthodontics, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yunlong Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Orthodontics, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hong He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Orthodontics, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhijian Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Orthodontics, School and Hospital of Stomatology, Wuhan University, Wuhan, China
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4
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Raza SHA, Liang C, Guohua W, Pant SD, Mohammedsaleh ZM, Shater AF, Alotaibi MA, Khan R, Schreurs N, Cheng G, Mei C, Zan L. Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis. Front Vet Sci 2021; 8:794628. [PMID: 34966817 PMCID: PMC8710720 DOI: 10.3389/fvets.2021.794628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/22/2021] [Indexed: 01/17/2023] Open
Abstract
Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 18 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 17 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 17 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.
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Affiliation(s)
| | - Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wang Guohua
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Sameer D Pant
- School of Animal & Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Zuhair M Mohammedsaleh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Abdullah F Shater
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetic, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Nicola Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, China
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Ka HI, Seo H, Choi Y, Kim J, Cho M, Choi SY, Park S, Han S, An J, Chung HS, Yang Y, Kim MJ. Loss of splicing factor IK impairs normal skeletal muscle development. BMC Biol 2021; 19:44. [PMID: 33789631 PMCID: PMC8015194 DOI: 10.1186/s12915-021-00980-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND IK is a splicing factor that promotes spliceosome activation and contributes to pre-mRNA splicing. Although the molecular mechanism of IK has been previously reported in vitro, the physiological role of IK has not been fully understood in any animal model. Here, we generate an ik knock-out (KO) zebrafish using the CRISPR/Cas9 system to investigate the physiological roles of IK in vivo. RESULTS The ik KO embryos display severe pleiotropic phenotypes, implying an essential role of IK in embryonic development in vertebrates. RNA-seq analysis reveals downregulation of genes involved in skeletal muscle differentiation in ik KO embryos, and there exist genes having improper pre-mRNA splicing among downregulated genes. The ik KO embryos display impaired neuromuscular junction (NMJ) and fast-twitch muscle development. Depletion of ik reduces myod1 expression and upregulates pax7a, preventing normal fast muscle development in a non-cell-autonomous manner. Moreover, when differentiation is induced in IK-depleted C2C12 myoblasts, myoblasts show a reduced ability to form myotubes. However, inhibition of IK does not influence either muscle cell proliferation or apoptosis in zebrafish and C2C12 cells. CONCLUSION This study provides that the splicing factor IK contributes to normal skeletal muscle development in vivo and myogenic differentiation in vitro.
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Affiliation(s)
- Hye In Ka
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea.,Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Hyemin Seo
- Howard Hughes Medical Institute and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Youngsook Choi
- Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Joohee Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Mina Cho
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Sujeong Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Sora Han
- Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Jinsu An
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - Hak Suk Chung
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - Young Yang
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea. .,Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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6
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Chen X, Sun Y, Zhang T, Roepstorff P, Yang F. Comprehensive Analysis of the Proteome and PTMomes of C2C12 Myoblasts Reveals that Sialylation Plays a Role in the Differentiation of Skeletal Muscle Cells. J Proteome Res 2020; 20:222-235. [PMID: 33216553 DOI: 10.1021/acs.jproteome.0c00353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The C2C12 myoblast is a model that has been used extensively to study the process of skeletal muscle differentiation. Proteomics has advanced our understanding of skeletal muscle biology and also the differentiation process of skeletal muscle cells. However, there is still no comprehensive analysis of C2C12 myoblast proteomes, which is important for the understanding of key drivers for the differentiation of skeletal muscle cells. Here, we conducted multidimensional proteome profiling to get a comprehensive analysis of proteomes and PTMomes of C2C12 myoblasts with a TiSH strategy. A total of 8313 protein groups were identified, including 7827 protein groups from nonmodified peptides, 3803 phosphoproteins, and 977 formerly sialylated N-linked glycoproteins. Integrated analysis of proteomic and PTMomic data showed that almost all of the kinases and transcription factors in the muscle cell differentiation pathway were phosphorylated. Further analysis indicated that sialylation might play a role in the differentiation of C2C12 myoblasts. Further functional analysis demonstrated that C2C12 myoblasts showed a decreased level of sialylation during skeletal muscle cell differentiation. Inhibition of sialylation with the sialyltransferase inhibitor 3Fax-Neu5Ac resulted in the lower expression of MHC and suppression of myoblast fusion. In all, these results indicate that sialylation has an effect on the differentiation of skeletal muscle cells.
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Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Yaping Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Tingting Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100149, China
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7
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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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