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Li C, Xu J, Zhang Y, Ding Y, Zhou X, Su Z, Qu C, Liang J, Han Y, Wang D, Shi Y, Li CJ, Liu GE, Kang X. Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle. J Anim Sci 2024; 102:skae357. [PMID: 39565284 PMCID: PMC11641427 DOI: 10.1093/jas/skae357] [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: 01/29/2024] [Accepted: 11/19/2024] [Indexed: 11/21/2024] Open
Abstract
Intramuscular fat content is one of the most important factors affecting beef quality. However, the role of alternative polyadenylation (APA) in intramuscular fat deposition remains unclear. We compared APA events in muscle samples from high and low intramuscular fat (IMF) cattle, based on RNA-seq data. A total of 363 significant APAs were identified. Notably, the number of shortened 3'UTR events exceeded the number of lengthened 3'UTR events, and genes associated with shortened 3'UTR events were enriched in fatty acid metabolism-related pathways. Most APA events had alternative 3'UTR (aUTR) lengths of 200 to 300 bp. As the 3'UTR lengthened, the aUTR also lengthened (R2 = 0.79). These findings indicate that genes with longer 3'UTRs are more likely to be regulated by APA in the muscle of cattle with high IMF. To determine whether the identified APA events drove alterations in the expression of fat deposition-related genes, we analyzed the relationship between APA events and differentially expressed genes and identified several genes critical for fat deposition (e.g., PFKL and SLC1A5). Since miRNAs usually bind to the 3'UTR region of protein-coding genes and affect gene expression, we constructed an miRNA-APA network to detect several key miRNAs that may regulate fat deposition. We identified 10 important miRNAs that affect changes in IMF content, which may be gained (gained miRNA-binding sites) or lost (lost miRNA-binding sites) owing to 187 differential APA events. Our study characterized the APA profiles of cattle with high and low intramuscular fat content and provided further insights into the relationship between APA, miRNA, and fat deposition.
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Affiliation(s)
- Chenglong Li
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Junjie Xu
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yanfeng Zhang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yanling Ding
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Xiaonan Zhou
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Zonghua Su
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Chang Qu
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Jiahao Liang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yurun Han
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Dingxiang Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yuangang Shi
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Xiaolong Kang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China
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Li J, Chen Z, Bai Y, Wei Y, Guo D, Liu Z, Niu Y, Shi B, Zhang X, Cai Y, Zhao Z, Hu J, Wang J, Liu X, Li S, Zhao F. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. Int J Mol Sci 2023; 25:158. [PMID: 38203329 PMCID: PMC10779322 DOI: 10.3390/ijms25010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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3
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Nguyen MT, Dash R, Jeong K, Lee W. Role of Actin-Binding Proteins in Skeletal Myogenesis. Cells 2023; 12:2523. [PMID: 37947600 PMCID: PMC10650911 DOI: 10.3390/cells12212523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Maintenance of skeletal muscle quantity and quality is essential to ensure various vital functions of the body. Muscle homeostasis is regulated by multiple cytoskeletal proteins and myogenic transcriptional programs responding to endogenous and exogenous signals influencing cell structure and function. Since actin is an essential component in cytoskeleton dynamics, actin-binding proteins (ABPs) have been recognized as crucial players in skeletal muscle health and diseases. Hence, dysregulation of ABPs leads to muscle atrophy characterized by loss of mass, strength, quality, and capacity for regeneration. This comprehensive review summarizes the recent studies that have unveiled the role of ABPs in actin cytoskeletal dynamics, with a particular focus on skeletal myogenesis and diseases. This provides insight into the molecular mechanisms that regulate skeletal myogenesis via ABPs as well as research avenues to identify potential therapeutic targets. Moreover, this review explores the implications of non-coding RNAs (ncRNAs) targeting ABPs in skeletal myogenesis and disorders based on recent achievements in ncRNA research. The studies presented here will enhance our understanding of the functional significance of ABPs and mechanotransduction-derived myogenic regulatory mechanisms. Furthermore, revealing how ncRNAs regulate ABPs will allow diverse therapeutic approaches for skeletal muscle disorders to be developed.
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Affiliation(s)
- Mai Thi Nguyen
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea;
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Republic of Korea
| | - Kyuho Jeong
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
| | - Wan Lee
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
- Channelopathy Research Center, Dongguk University College of Medicine, 32 Dongguk-ro, Ilsan Dong-gu, Goyang 10326, Republic of Korea
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Chen B, Wang Y, Hou D, Zhang Y, Zhang B, Niu Y, Ji H, Tian Y, Liu X, Kang X, Cai H, Li Z. Transcriptome-Based Identification of the Muscle Tissue-Specific Expression Gene CKM and Its Regulation of Proliferation, Apoptosis and Differentiation in Chicken Primary Myoblasts. Animals (Basel) 2023; 13:2316. [PMID: 37508090 PMCID: PMC10376263 DOI: 10.3390/ani13142316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Skeletal muscle is an essential tissue in meat-producing animals, and meat-producing traits have been a hot topic in chicken genetic breeding research. Current research shows that creatine kinase M-type-like (CKM) is one of the most abundant proteins in skeletal muscle and plays an important role in the growth and development of skeletal muscle, but its role in the development of chicken skeletal muscle is still unclear. Via RNA sequencing (RNA-seq), we found that CKM was highly expressed in chicken breast muscle tissue. In this study, the expression profile of CKM was examined by quantitative real-time PCR (qPCR), and overexpression and RNA interference techniques were used to explore the functions of CKM in the proliferation, apoptosis and differentiation of chicken primary myoblasts (CPMs). It was shown that CKM was specifically highly expressed in breast muscle and leg muscle and was highly expressed in stage 16 embryonic muscle, while CKM inhibited proliferation, promoted the apoptosis and differentiation of CPMs and was involved in regulating chicken myogenesis. Transcriptome sequencing was used to identify genes that were differentially expressed in CPMs after CKM disruption, and bioinformatics analysis showed that CKM was involved in regulating chicken myogenesis. In summary, CKM plays an important role in skeletal muscle development during chicken growth and development.
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Affiliation(s)
- Bingjie Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Dan Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yushi Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Bochun Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Haigang Ji
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450001, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450001, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450001, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Zhengzhou 450001, China
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He J, Zhu Q, Han P, Zhou T, Li J, Wang X, Cheng J. Transcriptomic Networks Reveal the Tissue-Specific Cold Shock Responses in Japanese Flounder ( Paralichthys olivaceus). BIOLOGY 2023; 12:784. [PMID: 37372069 DOI: 10.3390/biology12060784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Low temperature is among the important factors affecting the distribution, survival, growth, and physiology of aquatic animals. In this study, coordinated transcriptomic responses to 10 °C acute cold stress were investigated in the gills, hearts, livers, and spleens of Japanese flounder (Paralichthys olivaceus), an important aquaculture species in east Asia. Histological examination suggested different levels of injury among P. olivaceus tissues after cold shock, mainly in the gills and livers. Based on transcriptome and weighted gene coexpression network analysis, 10 tissue-specific cold responsive modules (CRMs) were identified, revealing a cascade of cellular responses to cold stress. Specifically, five upregulated CRMs were enriched with induced differentially expressed genes (DEGs), mainly corresponding to the functions of "extracellular matrix", "cytoskeleton", and "oxidoreductase activity", indicating the induced cellular response to cold shock. The "cell cycle/division" and "DNA complex" functions were enriched in the downregulated CRMs for all four tissues, which comprised inhibited DEGs, suggesting that even with tissue-specific responses, cold shock may induce severely disrupted cellular functions in all tissues, reducing aquaculture productivity. Therefore, our results revealed the tissue-specific regulation of the cellular response to low-temperature stress, which warrants further investigation and provides more comprehensive insights for the conservation and cultivation of P. olivaceus in cold water.
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Affiliation(s)
- Jiayi He
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
| | - Qing Zhu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
| | - Ping Han
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
| | - Tianyu Zhou
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
| | - Juyan Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, 169 Qixingnan Road, Ningbo 315832, China
| | - Jie Cheng
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao 266237, China
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Zhang J, Sheng H, Pan C, Wang S, Yang M, Hu C, Wei D, Wang Y, Ma Y. Identification of key genes in bovine muscle development by co-expression analysis. PeerJ 2023; 11:e15093. [PMID: 37070092 PMCID: PMC10105563 DOI: 10.7717/peerj.15093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/27/2023] [Indexed: 04/19/2023] Open
Abstract
Background Skeletal muscle is not only an important tissue involved in exercise and metabolism, but also an important part of livestock and poultry meat products. Its growth and development determines the output and quality of meat to a certain extent, and has an important impact on the economic benefits of animal husbandry. Skeletal muscle development is a complex regulatory network process, and its molecular mechanism needs to be further studied. Method We used a weighted co-expression network (WGCNA) and single gene set enrichment analysis (GSEA) to study the RNA-seq data set of bovine tissue differential expression analysis, and the core genes and functional enrichment pathways closely related to muscle tissue development were screened. Finally, the accuracy of the analysis results was verified by tissue expression profile detection and bovine skeletal muscle satellite cell differentiation model in vitro (BSMSCs). Results In this study, Atp2a1, Tmod4, Lmod3, Ryr1 and Mybpc2 were identified as marker genes in muscle tissue, which are mainly involved in glycolysis/gluconeogenesis, AMPK pathway and insulin pathway. The assay results showed that these five genes were highly expressed in muscle tissue and positively correlated with the differentiation of bovine BSMSCs. Conclusions In this study, several muscle tissue characteristic genes were excavated, which may play an important role in muscle development and provide new insights for bovine molecular genetic breeding.
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Affiliation(s)
| | | | | | | | | | | | | | - Yachun Wang
- China Agricultural University, Beijing, China
| | - Yun Ma
- Ningxia University, Yinchuan, China
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Fisher G, Mackels L, Markati T, Sarkozy A, Ochala J, Jungbluth H, Ramdas S, Servais L. Early clinical and pre-clinical therapy development in Nemaline myopathy. Expert Opin Ther Targets 2022; 26:853-867. [PMID: 36524401 DOI: 10.1080/14728222.2022.2157258] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Nemaline myopathies (NM) represent a group of clinically and genetically heterogeneous congenital muscle disorders with the common denominator of nemaline rods on muscle biopsy. NEB and ACTA1 are the most common causative genes. Currently, available treatments are supportive. AREAS COVERED We explored experimental treatments for NM, identifying at least eleven mainly pre-clinical approaches utilizing murine and/or human muscle cells. These approaches target either i) the causative gene or associated genes implicated in the same pathway; ii) pathophysiologically relevant biochemical mechanisms such as calcium/myosin regulation of muscle contraction; iii) myogenesis; iv) other therapies that improve or optimize muscle function more generally; v) and/or combinations of the above. The scope and efficiency of these attempts is diverse, ranging from gene-specific effects to those widely applicable to all NM-associated genes. EXPERT OPINION The wide range of experimental therapies currently under consideration for NM is promising. Potential translation into clinical use requires consideration of additional factors such as the potential muscle type specificity as well as the possibility of gene expression remodeling. Challenges in clinical translation include the rarity and heterogeneity of genotypes, phenotypes, and disease trajectories, as well as the lack of longitudinal natural history data and validated outcomes and biomarkers.
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Affiliation(s)
- Gemma Fisher
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Laurane Mackels
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK.,Neuromuscular Reference Center, University and University Hospital of Liège, Liège, Belgium
| | - Theodora Markati
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Anna Sarkozy
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Hospital, Institute of Child Health, London, UK
| | - Julien Ochala
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heinz Jungbluth
- Department of Paediatric Neurology - Neuromuscular Service, Evelina Children's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK.,Randall Centre for Cell and Molecular Biophysics, Muscle Signalling Section, Faculty of Life Sciences and Medicine (FoLSM), King's College London, London, UK
| | - Sithara Ramdas
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK.,Department of Paediatric Neurology, John Radcliffe Hospital, Oxford, UK
| | - Laurent Servais
- MDUK Neuromuscular Centre, Department of Paediatrics, University of Oxford, Oxford, UK.,Neuromuscular Reference Center, University and University Hospital of Liège, Liège, Belgium
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Liu Z, Zhang G, Chen J, Tong J, Wang H, Chen J, Yang D, Hu J. G-CSF promotes the viability and angiogenesis of injured liver via direct effects on the liver cells. Mol Biol Rep 2022; 49:8715-8725. [PMID: 35781603 PMCID: PMC9463201 DOI: 10.1007/s11033-022-07715-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022]
Abstract
Background Presently, liver transplantation is the only treatment strategy for liver failure (LF). Although granulocyte-colony stimulating factor (G-CSF) exhibits protective functions in LF, it is not clear whether it directly affects the liver cells. Methods and Results We established an injured liver cell model and observed that G-CSF treatment promoted cell viability and enhanced Ki67 and VEGF-A expression. Thereafter, human umbilical vein endothelial cells (HUVECs) were cultured in a conditioned medium collected from the G-CSF-treated injured liver cells. HUVECs’ proliferation and tubule formation were promoted. Furthermore, in an injured liver mouse model, confirmed via haematoxylin–eosin staining, we evaluated serum alanine aminotransferase activity, Ki67 expression, and microvessel density (MVD). G-CSF treatment significantly relieved liver injury, upregulated Ki67 expression, and enhanced MVD in the injured mouse liver tissue. Additionally, AKT and ERK signal targets were explored, and it was demonstrated that the effects of G-CSF on injured liver cells were mediated through the AKT and ERK signalling pathways. Conclusions G-CSF promotes injured liver viability and angiogenesis by directly affecting injured liver cells via the AKT and ERK signalling pathways. These findings improve our understanding of the role of G-CSF in recovery from LF. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07715-4.
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Affiliation(s)
- Zifeng Liu
- Medical School of Chinese PLA, Beijing, China.,Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Guiling Zhang
- Department of Pathology, Chengwu People's Hospital, Heze, China
| | - Jing Chen
- Medical School of Chinese PLA, Beijing, China.,Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jingjing Tong
- Medical School of Chinese PLA, Beijing, China.,Department of Infectious Diseases, Beijing Jishuitan, Beijing, China
| | - Hongmin Wang
- Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China.,Peking University 302 Clinical Medical School, Beijing, China
| | - Jing Chen
- Medical School of Chinese PLA, Beijing, China
| | - Dong Yang
- Oncology Department, Affiliated Hospital of Jining Medical University, Jining, China
| | - Jinhua Hu
- Medical School of Chinese PLA, Beijing, China. .,Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China. .,Peking University 302 Clinical Medical School, Beijing, China.
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Hou X, Wang L, Zhao F, Liu X, Gao H, Shi L, Yan H, Wang L, Zhang L. Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds. Animals (Basel) 2021; 11:ani11113169. [PMID: 34827901 PMCID: PMC8614396 DOI: 10.3390/ani11113169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Variation exists in muscle-related traits, such as muscle growth and meat quality, between obese and lean pigs. In this study, the transcriptome profiles of skeletal muscle between Beijing Blackand Yorkshire pigs were characterized to explore the molecular mechanism underlying skeletal muscle-relatedtraits. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that differentially expressed mRNAs, lncRNAs, and circRNAs involved in skeletal muscle development and fatty acid metabolism played a key role in the determination of muscle-related traits between different pig breeds. These results provide candidate genes responsible for muscle phenotypic variation and are valuable for pig breeding. Abstract RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.
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Involvement of DPY19L3 in Myogenic Differentiation of C2C12 Myoblasts. Molecules 2021; 26:molecules26185685. [PMID: 34577156 PMCID: PMC8467457 DOI: 10.3390/molecules26185685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
DPY19L3 has been identified as a C-mannosyltransferase for thrombospondin type-1 repeat domain-containing proteins. In this study, we focused on the role of DPY19L3 in the myogenic differentiation of C2C12 mouse myoblast cells. We carried out DPY19L3 gene depletion using the CRISPR/Cas9 system. The result showed that these DPY19L3-knockout cells could not be induced for differentiation. Moreover, the phosphorylation levels of MEK/ERK and p70S6K were suppressed in the DPY19L3-knockout cells compared with that of parent cells, suggesting that the protein(s) that is(are) DPY19L3-mediated C-mannosylated and regulate(s) MEK/ERK or p70S6K signaling is(are) required for the differentiation.
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Yang BG, Yuan Y, Zhou DK, Ma YH, Mahrous KF, Wang SZ, He YM, Duan XH, Zhang WY, E G. Genome-wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development. Anim Genet 2021; 52:550-555. [PMID: 34029388 DOI: 10.1111/age.13092] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 12/25/2022]
Abstract
As one of the best-known commercial goat breeds in the world, Boer goat has undergone long-term artificial selection for nearly 100 years, and its excellent growth rate and meat production performance have attracted considerable worldwide attention. Herein, we used single nucleotide polymorphisms (SNPs) called from the whole-genome sequencing data of 46 Australian Boer goats to detect polymorphisms and identify genomic regions related to muscle development in comparison with those of 81 non-specialized meat goat individuals from Europe, Africa, and Asia. A total of 13 795 202 SNPs were identified, and the whole-genome selective signal screen with a π ratio of nucleotide diversity (πcase /πcontrol ) and pairwise fixation index (FST ) was analyzed. Finally, we identified 1741 candidate selective windows based on the top 5% threshold of both parameters; here, 449 candidate genes were only found in 727 of these regions. A total of 433 genes out of the 449 genes obtained were annotated to 2729 gene ontology terms, of which 51 were directly linked to muscle development (e.g., muscle organ development, muscle cell differentiation) by 30 candidate genes (e.g., JAK2, KCNQ1, PDE5A, PDLIM5, TBX5). In addition, 246 signaling pathways were annotated by 178 genes, and two pathways related to muscle contraction, including vascular smooth muscle contraction (ADCY7, PRKCB, PLA2G4E, ROCK2) and cardiac muscle contraction (CACNA2D3, CASQ2, COX6B1), were identified. The results could improve the current understanding of the genetic effects of artificial selection on the muscle development of goat. More importantly, this study provides valuable candidate genes for future breeding of goats.
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Affiliation(s)
- B-G Yang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Y Yuan
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - D-K Zhou
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Y-H Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - K-F Mahrous
- Division of Genetic Engineering and Biotechnology Research Cell, Biology Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - S-Z Wang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Y-M He
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - X-H Duan
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - W-Y Zhang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Guangxin E
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
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