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Nourisa J, Passemiers A, Shakeri F, Omidi M, Helmholz H, Raimondi D, Moreau Y, Tomforde S, Schlüter H, Luthringer-Feyerabend B, Cyron CJ, Aydin RC, Willumeit-Römer R, Zeller-Plumhoff B. Gene regulatory network analysis identifies MYL1, MDH2, GLS, and TRIM28 as the principal proteins in the response of mesenchymal stem cells to Mg 2+ ions. Comput Struct Biotechnol J 2024; 23:1773-1785. [PMID: 38689715 PMCID: PMC11058716 DOI: 10.1016/j.csbj.2024.04.033] [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: 12/15/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
Magnesium (Mg)-based implants have emerged as a promising alternative for orthopedic applications, owing to their bioactive properties and biodegradability. As the implants degrade, Mg2+ ions are released, influencing all surrounding cell types, especially mesenchymal stem cells (MSCs). MSCs are vital for bone tissue regeneration, therefore, it is essential to understand their molecular response to Mg2+ ions in order to maximize the potential of Mg-based biomaterials. In this study, we conducted a gene regulatory network (GRN) analysis to examine the molecular responses of MSCs to Mg2+ ions. We used time-series proteomics data collected at 11 time points across a 21-day period for the GRN construction. We studied the impact of Mg2+ ions on the resulting networks and identified the key proteins and protein interactions affected by the application of Mg2+ ions. Our analysis highlights MYL1, MDH2, GLS, and TRIM28 as the primary targets of Mg2+ ions in the response of MSCs during 1-21 days phase. Our results also identify MDH2-MYL1, MDH2-RPS26, TRIM28-AK1, TRIM28-SOD2, and GLS-AK1 as the critical protein relationships affected by Mg2+ ions. By offering a comprehensive understanding of the regulatory role of Mg2+ ions on MSCs, our study contributes valuable insights into the molecular response of MSCs to Mg-based materials, thereby facilitating the development of innovative therapeutic strategies for orthopedic applications.
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Affiliation(s)
- Jalil Nourisa
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
| | | | - Farhad Shakeri
- Institute of Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Maryam Omidi
- Institute of Clinical Chemistry/Central Laboratories, University Medical Center Hamburg, Hamburg, Germany
| | - Heike Helmholz
- Institute of Metallic Biomaterials, Helmholtz Zentrum Hereon, Geesthacht, Germany
| | | | | | - Sven Tomforde
- Department of Computer Science, Intelligent Systems, University of Kiel, Kiel, Germany
| | - Hartmuth Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, University of Hamburg, Hamburg, Germany
| | | | - Christian J. Cyron
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
- Institute for Continuum and Material Mechanics, Hamburg University of Technology, Hamburg, Germany
| | - Roland C. Aydin
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
- Institute for Continuum and Material Mechanics, Hamburg University of Technology, Hamburg, Germany
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Renaux A, Terwagne C, Cochez M, Tiddi I, Nowé A, Lenaerts T. A knowledge graph approach to predict and interpret disease-causing gene interactions. BMC Bioinformatics 2023; 24:324. [PMID: 37644440 PMCID: PMC10463539 DOI: 10.1186/s12859-023-05451-5] [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: 06/07/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Understanding the impact of gene interactions on disease phenotypes is increasingly recognised as a crucial aspect of genetic disease research. This trend is reflected by the growing amount of clinical research on oligogenic diseases, where disease manifestations are influenced by combinations of variants on a few specific genes. Although statistical machine-learning methods have been developed to identify relevant genetic variant or gene combinations associated with oligogenic diseases, they rely on abstract features and black-box models, posing challenges to interpretability for medical experts and impeding their ability to comprehend and validate predictions. In this work, we present a novel, interpretable predictive approach based on a knowledge graph that not only provides accurate predictions of disease-causing gene interactions but also offers explanations for these results. RESULTS We introduce BOCK, a knowledge graph constructed to explore disease-causing genetic interactions, integrating curated information on oligogenic diseases from clinical cases with relevant biomedical networks and ontologies. Using this graph, we developed a novel predictive framework based on heterogenous paths connecting gene pairs. This method trains an interpretable decision set model that not only accurately predicts pathogenic gene interactions, but also unveils the patterns associated with these diseases. A unique aspect of our approach is its ability to offer, along with each positive prediction, explanations in the form of subgraphs, revealing the specific entities and relationships that led to each pathogenic prediction. CONCLUSION Our method, built with interpretability in mind, leverages heterogenous path information in knowledge graphs to predict pathogenic gene interactions and generate meaningful explanations. This not only broadens our understanding of the molecular mechanisms underlying oligogenic diseases, but also presents a novel application of knowledge graphs in creating more transparent and insightful predictors for genetic research.
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Affiliation(s)
- Alexandre Renaux
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Chloé Terwagne
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Michael Cochez
- Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Discovery Lab, Elsevier, Amsterdam, The Netherlands
| | - Ilaria Tiddi
- Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
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Zhong D, Huang K, Zhang L, Cai Y, Li H, Liu Q, Shi D, Li H, Jiang Y. Circ2388 regulates myogenesis and muscle regeneration. Cell Tissue Res 2023; 393:149-161. [PMID: 37221302 DOI: 10.1007/s00441-023-03787-1] [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: 10/14/2022] [Accepted: 05/11/2023] [Indexed: 05/25/2023]
Abstract
The formation of skeletal muscle is a complex process that is coordinated by many regulatory factors, such as myogenic factors and noncoding RNAs. Numerous studies have proved that circRNA is an indispensable part of muscle development. However, little is known about circRNAs in bovine myogenesis. In this study, we discovered a novel circRNA, circ2388, formed by reverse splicing of the fourth and fifth exons of the MYL1 gene. The expression of circ2388 was different between fetal and adult cattle muscle. This circRNA is 99% homologous between cattle and buffalo and is localized in the cytoplasm. Thoroughly, we proved that circ2388 had no effect on cattle and buffalo myoblast proliferation but promotes myoblast differentiation and myotube fusion. Furthermore, circ2388 in vivo stimulated skeletal muscle regeneration in mouse muscle injury model. Taken together, our findings suggest that circ2388 promotes myoblast differentiation and promotes the recovery and regeneration of damaged muscles.
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Affiliation(s)
- Dandan Zhong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Xianyang, Yangling, Shaanxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
| | - Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
| | - Liyin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Xianyang, Yangling, Shaanxi, China
| | - Huiren Li
- Animal Husbandry Station of Chongzuo City, 532200, Chongzuo, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225, Foshan, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Xianyang, Yangling, Shaanxi, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Xianyang, Yangling, Shaanxi, China
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Sun Y, Zhu B, Ling S, Yan B, Wang X, Jia S, Martyniuk CJ, Zhang W, Yang L, Zhou B. Decabromodiphenyl Ethane Mainly Affected the Muscle Contraction and Reproductive Endocrine System in Female Adult Zebrafish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:470-479. [PMID: 34919388 DOI: 10.1021/acs.est.1c06679] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The novel brominated flame retardant decabromodiphenyl ethane (DBDPE) has become a widespread environmental pollutant. However, the target tissue and toxicity of DBDPE are still not clear. In the current study, female zebrafish were exposed to 1 and 100 nM DBDPE for 28 days. Chemical analysis revealed that DBDPE tended to accumulate in the brain other than the liver and gonad. Subsequently, tandem mass tag-based quantitative proteomics and parallel reaction monitoring verification were performed to screen the differentially expressed proteins in the brain. Bioinformatics analysis revealed that DBDPE mainly affected the biological process related to muscle contraction and estrogenic response. Therefore, the neurotoxicity and reproductive disruptions were validated via multilevel toxicological endpoints. Specifically, locomotor behavioral changes proved the potency of neurotoxicity, which may be caused by disturbance of muscular proteins and calcium homeostasis; decreases of sex hormone levels and transcriptional changes of genes related to the hypothalamic-pituitary-gonad-liver axis confirmed reproductive disruptions upon DBDPE exposure. In summary, our results suggested that DBDPE primarily accumulated in the brain and evoked neurotoxicity and reproductive disruptions in female zebrafish. These findings can provide important clues for a further mechanism study and risk assessment of DBDPE.
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Affiliation(s)
- Yumiao Sun
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Biran Zhu
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Siyuan Ling
- Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Biao Yan
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiulin Wang
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuzhao Jia
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611 United States
| | - Wei Zhang
- Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lihua Yang
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Bingsheng Zhou
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Metikala S, Casie Chetty S, Sumanas S. Single-cell transcriptome analysis of the zebrafish embryonic trunk. PLoS One 2021; 16:e0254024. [PMID: 34234366 PMCID: PMC8263256 DOI: 10.1371/journal.pone.0254024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/17/2021] [Indexed: 11/27/2022] Open
Abstract
During embryonic development, cells differentiate into a variety of distinct cell types and subtypes with diverse transcriptional profiles. To date, transcriptomic signatures of different cell lineages that arise during development have been only partially characterized. Here we used single-cell RNA-seq to perform transcriptomic analysis of over 20,000 cells disaggregated from the trunk region of zebrafish embryos at the 30 hpf stage. Transcriptional signatures of 27 different cell types and subtypes were identified and annotated during this analysis. This dataset will be a useful resource for many researchers in the fields of developmental and cellular biology and facilitate the understanding of molecular mechanisms that regulate cell lineage choices during development.
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Affiliation(s)
- Sanjeeva Metikala
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, Tampa, FL, United States of America
| | - Satish Casie Chetty
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Molecular and Developmental Biology Graduate Program, University of Cincinnati, Cincinnati, OH, United States of America
| | - Saulius Sumanas
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, Tampa, FL, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
- * E-mail:
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6
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Yuan R, Zhang J, Wang Y, Zhu X, Hu S, Zeng J, Liang F, Tang Q, Chen Y, Chen L, Zhu W, Li M, Mo D. Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle. DNA Res 2021; 28:6261936. [PMID: 34009337 PMCID: PMC8154859 DOI: 10.1093/dnares/dsab003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Myofibres (primary and secondary myofibre) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibres to secondary myofibres in pigs, we conducted an integrative three-dimensional structure of genome and transcriptomic characterization of longissimus dorsi muscle of pig from primary myofibre formation stage [embryonic Day 35 (E35)] to secondary myofibre formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains are changed intradomain interactions (D-scores) and 2,730 genes with differential promoter–enhancer interactions and (or) enhancer activity from E35 to E80. The alterations of genome architecture were found to correlate with expression of genes that play significant roles in neuromuscular junction, embryonic morphogenesis, skeletal muscle development or metabolism, typically, NEFL, MuSK, SLN, Mef2D and GCK. Significantly, Sox6 and MATN2 play important roles in the process of primary to secondary myofibres formation and increase the regulatory potential score and genes expression in it. In brief, we reveal the genomic reorganization from E35 to E80 and construct genome-wide high-resolution interaction maps that provide a resource for studying long-range control of gene expression from E35 to E80.
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Affiliation(s)
- Renqiang Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xingxing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jianhua Zeng
- Guangdong YIHAO Food Co., Ltd, Guangzhou 510620, China
| | - Feng Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Luxi Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wei Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
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7
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Xu Y, Xu F, Lv Y, Wang S, Li J, Zhou C, Jiang J, Xie B, He F. A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients. Sci Rep 2021; 11:6374. [PMID: 33737696 PMCID: PMC7973582 DOI: 10.1038/s41598-021-86048-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most malignant cancers with poor prognosis worldwide. Emerging evidence indicates that competing endogenous RNAs (ceRNAs) are involved in various diseases, however, the regulatory mechanisms of ceRNAs underlying HNSCC remain unclear. In this study, we retrieved differentially expressed long non-coding RNAs (DElncRNAs), messenger RNAs (DEmRNAs) and microRANs (DEmiRNAs) from The Cancer Genome Atlas database and constructed a ceRNA-based risk model in HNSCC by integrated bioinformatics approaches. Functional enrichment analyses showed that DEmRNAs might be involved in extracellular matrix related biological processes, and protein–protein interaction network further selected out prognostic genes, including MYL1 and ACTN2. Importantly, co-expressed RNAs identified by weighted co-expression gene network analysis constructed the ceRNA networks. Moreover, AC114730.3, AC136375.3, LAT and RYR3 were highly correlated to overall survival of HNSCC by Kaplan–Meier method and univariate Cox regression analysis, which were subsequently implemented multivariate Cox regression analysis to build the risk model. Our study provides a deeper understanding of ceRNAs on the regulatory mechanisms, which will facilitate the expansion of the roles on the ceRNAs in the tumorigenesis, development and treatment of HNSCC.
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Affiliation(s)
- Yuzi Xu
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Fengqin Xu
- The First Affiliated Hospital of Kangda College of Nanjing Medical University, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, 222000, Jiangsu, People's Republic of China
| | - Yiming Lv
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, People's Republic of China
| | - Siyuan Wang
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Jia Li
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Chuan Zhou
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Jimin Jiang
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Binbin Xie
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3# East Qingchun Road, Hangzhou, 310016, Zhejiang, People's Republic of China.
| | - Fuming He
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China.
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8
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Chen Z, Li XY, Guo P, Wang DL. MYBPC2 and MYL1 as Significant Gene Markers for Rhabdomyosarcoma. Technol Cancer Res Treat 2021; 20:1533033820979669. [PMID: 33499774 PMCID: PMC7844451 DOI: 10.1177/1533033820979669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Rhabdomyosarcoma is the most common soft tissue tumor in children. Rhabdomyosarcoma commonly results in pain and bleeding caused by tumor compression and is prone to early metastasis and recurrence, which can seriously affect the therapeutic outcomes and long-term prognosis. Up to 37.7% of rhabdomyosarcomas may metastasize. Therefore, the molecular mechanisms underlying rhabdomyosarcoma must be explored to identify an effective target for its early diagnosis and specific treatment. METHODS A dataset of 18 rhabdomyosarcoma tissue samples and 6 healthy skeletal muscle samples was downloaded. Differentially expressed genes between rhabdomyosarcoma and healthy tissue samples were identified by GEO2R. Kyoto Encyclopedia of Genes and Genomes and gene ontology pathway enrichment analyses were performed. A protein-protein interaction network was constructed, and hub genes were identified. Expression and survival analyses of hub genes were performed. Additionally, 30 patients with rhabdomyosarcoma were recruited, and overall survival information and samples were collected. Reverse transcription quantitative real-time polymerase chain reaction assays were performed to verify the expression of MYBPC2 and MYL1 in rhabdomyosarcoma tumor tissues. The Kaplan-Meier method was used to explore overall survival based on our clinical data. RESULTS In total, 164 genes were up-regulated and 394 were down-regulated in rhabdomyosarcoma tumor tissues. Gene ontology analysis revealed that variations were predominantly enriched in the cell cycle, muscle contraction, muscle system processes, cytoskeleton, nucleotide binding, and cytoskeletal protein binding. The protein-protein interaction network revealed 3274 edges, and 441 nodes were constructed. Ten hub genes were identified; of these, MYBPC2 and MYL1 were significantly up-regulated in rhabdomyosarcoma. Compared with the healthy group, patients with rhabdomyosarcoma exhibiting high expression of MYBPC2 and MYL1 exhibited significantly worse overall survival. CONCLUSIONS We found differentially expressed genes between rhabdomyosarcoma and healthy tissue samples. MYBPC2 and MYL1 may be involved in the pathogenesis of rhabdomyosarcoma and therefore deserve further exploration.
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Affiliation(s)
- Zihang Chen
- General Surgery Department, Hangzhou Fuyang District First People's Hospital, Hangzhou, People's Republic of China
| | - Xing-Yu Li
- School of Basic Medicine, Peking University, Beijing, People's Republic of China
| | - Peng Guo
- Department of Orthopedics, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Dong-Lai Wang
- Department of Orthopedics, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
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9
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Elnour IE, Wang X, Zhansaya T, Akhatayeva Z, Khan R, Cheng J, Hung Y, Lan X, Lei C, Chen H. Circular RNA circMYL1 Inhibit Proliferation and Promote Differentiation of Myoblasts by Sponging miR-2400. Cells 2021; 10:cells10010176. [PMID: 33467116 PMCID: PMC7830797 DOI: 10.3390/cells10010176] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/08/2021] [Accepted: 01/14/2021] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of endogenous non-coding RNAs (ncRNAs) involved in regulating skeletal muscle development by sponging miRNAs. In this study, we found that the circMYL1 expression was down-regulated during myoblast proliferation, while gradually up-regulated in myoblast differentiation. The potential role of circMYL1 was identified in the proliferation of bovine myoblast through mRNA and protein expression of proliferation marker genes (PCNA, CyclinD1, and CDK2), cell counting kit-8 assay, flow cytometry analysis, and 5-ethynyl 2′-deoxyuridine (EdU) assay. Analysis of the expression of differentiation marker genes (MyoD, MyoG, and MYH2) and immunofluorescence of Myosin heavy chain (MyHC) was used to assess cell differentiation. The proliferation analysis revealed that circMYL1 inhibited the proliferation of bovine primary myoblast. Furthermore, the differentiation analysis demonstrated that circMYL1 promoted the differentiation of bovine primary myoblast. The luciferase screening and RNA immunoprecipitation (RIP) assays found that circMYL1 could have interaction with miR-2400. Additionally, we demonstrated that miR-2400 promoted proliferation and inhibited differentiation of bovine primary myoblast, while circMYL1 may eliminate the effects of miR-2400, as showed by rescue experiments. Together, our results revealed that a novel circular RNA of circMYL1 could inhibit proliferation and promote differentiation of myoblast by sponging miR-2400.
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Affiliation(s)
- Ibrahim Elsaeid Elnour
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
- Faculty of Veterinary Science, University of Nyala, Nyala 155, Sudan
| | - Xiaogang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
| | - Toremurat Zhansaya
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
| | - Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
| | - Rajwali Khan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
| | - Jie Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
| | - Yongzhen Hung
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (I.E.E.); (X.W.); (T.Z.); (Z.A.); (R.K.); (J.C.); (Y.H.); (X.L.); (C.L.)
- Correspondence: ; Tel.: +86-029-87092102; Fax: +86-029-87092164
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10
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Liu R, Liu X, Bai X, Xiao C, Dong Y. Identification and Characterization of circRNA in Longissimus Dorsi of Different Breeds of Cattle. Front Genet 2020; 11:565085. [PMID: 33324445 PMCID: PMC7726199 DOI: 10.3389/fgene.2020.565085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/27/2020] [Indexed: 01/16/2023] Open
Abstract
Shandong black cattle is a new breed of cattle that is developed by applying modern biotechnology, such as somatic cloning, and conventional breeding methods to Luxi cattle. It is very important to study the function and regulatory mechanism of circRNAs in muscle differentiation among different breeds to improve meat quality and meat production performance and to provide new ideas for beef cattle meat quality improvements and new breed development. Therefore, the goal of this study was to sequence and identify circRNAs in muscle tissues of different breeds of cattle. We used RNA-seq to identify circRNAs in the muscles of two breeds of cattle (Shandong black and Luxi). We identified 14,640 circRNAs and found 655 differentially expressed circRNAs. We also analyzed the classification and characteristics of circRNAs in muscle tissue. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used on the parental genes of circRNAs. They were mainly involved in a variety of biological processes, such as muscle fiber development, smooth muscle cell proliferation, bone system morphogenesis, tight junctions and the MAPK, AMPK, and mTOR signaling pathways. In addition, we used miRanda to predict the interactions between 14 circRNAs and 11 miRNAs. Based on the above assays, we identified circRNAs (circ0001048, circ0001103, circ0001159, circ0003719, circ0003424, circ0003721, circ0003720, circ0001519, circ0001530, circ0005011, circ0014518, circ0000181, circ0000190, circ0010558) that may play important roles in the regulation of muscle growth and development. Using real-time quantitative PCR, 14 circRNAs were randomly selected to verify the real circRNAs. Luciferase reporter gene system was used to verify the binding site of miR-1 in circ0014518. Our results provide more information about circRNAs regulating muscle development in different breeds of cattle and lay a solid foundation for future experiments.
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Affiliation(s)
- Ruili Liu
- Laboratory of Animal Physiology and Biochemistry, Animal Embryo Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
| | - Xianxun Liu
- Laboratory of Animal Physiology and Biochemistry, Animal Embryo Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
| | - Xuejin Bai
- Laboratory of Animal Physiology and Biochemistry, Animal Embryo Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
- Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
| | - Chaozhu Xiao
- Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
| | - Yajuan Dong
- Laboratory of Animal Physiology and Biochemistry, Animal Embryo Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
- Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
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11
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Ravenscroft G, Clayton JS, Faiz F, Sivadorai P, Milnes D, Cincotta R, Moon P, Kamien B, Edwards M, Delatycki M, Lamont PJ, Chan SH, Colley A, Ma A, Collins F, Hennington L, Zhao T, McGillivray G, Ghedia S, Chao K, O'Donnell-Luria A, Laing NG, Davis MR. Neurogenetic fetal akinesia and arthrogryposis: genetics, expanding genotype-phenotypes and functional genomics. J Med Genet 2020; 58:609-618. [PMID: 33060286 DOI: 10.1136/jmedgenet-2020-106901] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/16/2020] [Accepted: 07/05/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Fetal akinesia and arthrogryposis are clinically and genetically heterogeneous and have traditionally been refractive to genetic diagnosis. The widespread availability of affordable genome-wide sequencing has facilitated accurate genetic diagnosis and gene discovery in these conditions. METHODS We performed next generation sequencing (NGS) in 190 probands with a diagnosis of arthrogryposis multiplex congenita, distal arthrogryposis, fetal akinesia deformation sequence or multiple pterygium syndrome. This sequencing was a combination of bespoke neurogenetic disease gene panels and whole exome sequencing. Only class 4 and 5 variants were reported, except for two cases where the identified variants of unknown significance (VUS) are most likely to be causative for the observed phenotype. Co-segregation studies and confirmation of variants identified by NGS were performed where possible. Functional genomics was performed as required. RESULTS Of the 190 probands, 81 received an accurate genetic diagnosis. All except two of these cases harboured class 4 and/or 5 variants based on the American College of Medical Genetics and Genomics guidelines. We identified phenotypic expansions associated with CACNA1S, CHRNB1, GMPPB and STAC3. We describe a total of 50 novel variants, including a novel missense variant in the recently identified gene for arthrogryposis with brain malformations-SMPD4. CONCLUSIONS Comprehensive gene panels give a diagnosis for a substantial proportion (42%) of fetal akinesia and arthrogryposis cases, even in an unselected cohort. Recently identified genes account for a relatively large proportion, 32%, of the diagnoses. Diagnostic-research collaboration was critical to the diagnosis and variant interpretation in many cases, facilitated genotype-phenotype expansions and reclassified VUS through functional genomics.
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Affiliation(s)
- Gina Ravenscroft
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia .,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Joshua S Clayton
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Fathimath Faiz
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Padma Sivadorai
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Rob Cincotta
- Maternal and Fetal Medicine, Mater Mothers' Hospital, Brisbane, Queensland, Australia
| | - Phillip Moon
- Department of Obstetrics, Redland Hospital, Cleveland, Queensland, Australia
| | - Ben Kamien
- Genetic Services WA, Women and Newborn Heath Service, Subiaco, Western Australia, Australia.,Hunter Genetics, Hunter New England Health, New Lambton, New South Wales, Australia
| | - Matthew Edwards
- Hunter Genetics, Hunter New England Health, New Lambton, New South Wales, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Phillipa J Lamont
- Neurology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Sophelia Hs Chan
- Paediatric Neurology Division, Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Alison Colley
- Clinical Genetics Services SWSLHD, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Alan Ma
- Department of Clinical Genetics, Children's Hospital Westmead, Sydney, New South Wales, Australia
| | - Felicity Collins
- Clinical Genetics Department, Western Sydney Genetics Program, Children's Hospitalat Westmead, Westmead, New South Wales, Australia
| | - Lucinda Hennington
- Mercy Health, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Austin Health, Melbourne, Victoria, Australia.,Alfred Health, Melbourne, Victoria, Australia
| | - Teresa Zhao
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sondhya Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Katherine Chao
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Anne O'Donnell-Luria
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia.,PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Mark R Davis
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
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12
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Beecroft SJ, Yau KS, Allcock RJN, Mina K, Gooding R, Faiz F, Atkinson VJ, Wise C, Sivadorai P, Trajanoski D, Kresoje N, Ong R, Duff RM, Cabrera-Serrano M, Nowak KJ, Pachter N, Ravenscroft G, Lamont PJ, Davis MR, Laing NG. Targeted gene panel use in 2249 neuromuscular patients: the Australasian referral center experience. Ann Clin Transl Neurol 2020; 7:353-362. [PMID: 32153140 PMCID: PMC7086001 DOI: 10.1002/acn3.51002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/28/2020] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Objective To develop, test, and iterate a comprehensive neuromuscular targeted gene panel in a national referral center. Methods We designed two iterations of a comprehensive targeted gene panel for neuromuscular disorders. Version 1 included 336 genes, which was increased to 464 genes in Version 2. Both panels used TargetSeqTM probe‐based hybridization for target enrichment followed by Ion Torrent sequencing. Targeted high‐coverage sequencing and analysis was performed on 2249 neurology patients from Australia and New Zealand (1054 Version 1, 1195 Version 2) from 2012 to 2015. No selection criteria were used other than referral from a suitable medical specialist (e.g., neurologist or clinical geneticist). Patients were classified into 15 clinical categories based on the clinical diagnosis from the referring clinician. Results Six hundred and sixty‐five patients received a genetic diagnosis (30%). Diagnosed patients were significantly younger that undiagnosed patients (26.4 and 32.5 years, respectively; P = 4.6326E‐9). The diagnostic success varied markedly between disease categories. Pathogenic variants in 10 genes explained 38% of the disease burden. Unexpected phenotypic expansions were discovered in multiple cases. Triage of unsolved cases for research exome testing led to the discovery of six new disease genes. Interpretation A comprehensive targeted diagnostic panel was an effective method for neuromuscular disease diagnosis within the context of an Australasian referral center. Use of smaller disease‐specific panels would have precluded diagnosis in many patients and increased cost. Analysis through a centralized laboratory facilitated detection of recurrent, but under‐recognized pathogenic variants.
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Affiliation(s)
- Sarah J Beecroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Kyle S Yau
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Richard J N Allcock
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kym Mina
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Rebecca Gooding
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Fathimath Faiz
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Vanessa J Atkinson
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Cheryl Wise
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Padma Sivadorai
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Daniel Trajanoski
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Nina Kresoje
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Royston Ong
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Rachael M Duff
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Macarena Cabrera-Serrano
- Department of Neurology, Hospital Universitario Virgen del Rocio, Instituto de Biomedicina de Sevilla, CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Kristen J Nowak
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia.,Public and Aboriginal Health Division, Department of Health, Office of Population Health Genomics, Perth, Western Australia, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Phillipa J Lamont
- Neurogenetic Unit, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia.,Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
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13
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Altered miRNA and mRNA Expression in Sika Deer Skeletal Muscle with Age. Genes (Basel) 2020; 11:genes11020172. [PMID: 32041309 PMCID: PMC7073773 DOI: 10.3390/genes11020172] [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: 01/09/2020] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022] Open
Abstract
Studies of the gene and miRNA expression profiles associated with the postnatal late growth, development, and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA sequencing (RNA-seq) and microRNA sequencing (miRNA-seq) analyses to determine the differentially expressed (DE) unigenes and miRNAs from skeletal muscle tissues at 1, 3, 5, and 10 years in sika deer. A total of 51,716 unigenes, 171 known miRNAs, and 60 novel miRNAs were identified based on four mRNA and small RNA libraries. A total of 2,044 unigenes and 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 1,946 unigenes and 4 miRNAs were differentially expressed between adult and adolescent sika deer, and 2,209 unigenes and 1 miRNAs were differentially expressed between aged and adult sika deer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DE unigenes and miRNA were mainly related to energy and substance metabolism, processes that are closely associate with the growth, development, and aging of skeletal muscle. We also constructed mRNA–mRNA and miRNA–mRNA interaction networks related to the growth, development, and aging of skeletal muscle. The results show that mRNA (Myh1, Myh2, Myh7, ACTN3, etc.) and miRNAs (miR-133a, miR-133c, miR-192, miR-151-3p, etc.) may play important roles in muscle growth and development, and mRNA (WWP1, DEK, UCP3, FUS, etc.) and miRNAs (miR-17-5p, miR-378b, miR-199a-5p, miR-7, etc.) may have key roles in muscle aging. In this study, we determined the dynamic miRNA and unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent miRNAs and unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth, and maintenance and will also provide valuable information for sika deer genetic breeding.
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14
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Leal-Gutiérrez JD, Elzo MA, Mateescu RG. Identification of eQTLs and sQTLs associated with meat quality in beef. BMC Genomics 2020; 21:104. [PMID: 32000679 PMCID: PMC6993519 DOI: 10.1186/s12864-020-6520-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/20/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Transcription has a substantial genetic control and genetic dissection of gene expression could help us understand the genetic architecture of complex phenotypes such as meat quality in cattle. The objectives of the present research were: 1) to perform eQTL and sQTL mapping analyses for meat quality traits in longissimus dorsi muscle; 2) to uncover genes whose expression is influenced by local or distant genetic variation; 3) to identify expression and splicing hot spots; and 4) to uncover genomic regions affecting the expression of multiple genes. RESULTS Eighty steers were selected for phenotyping, genotyping and RNA-seq evaluation. A panel of traits related to meat quality was recorded in longissimus dorsi muscle. Information on 112,042 SNPs and expression data on 8588 autosomal genes and 87,770 exons from 8467 genes were included in an expression and splicing quantitative trait loci (QTL) mapping (eQTL and sQTL, respectively). A gene, exon and isoform differential expression analysis previously carried out in this population identified 1352 genes, referred to as DEG, as explaining part of the variability associated with meat quality traits. The eQTL and sQTL mapping was performed using a linear regression model in the R package Matrix eQTL. Genotype and year of birth were included as fixed effects, and population structure was accounted for by including as a covariate the first PC from a PCA analysis on genotypic data. The identified QTLs were classified as cis or trans using 1 Mb as the maximum distance between the associated SNP and the gene being analyzed. A total of 8377 eQTLs were identified, including 75.6% trans, 10.4% cis, 12.5% DEG trans and 1.5% DEG cis; while 11,929 sQTLs were uncovered: 66.1% trans, 16.9% DEG trans, 14% cis and 3% DEG cis. Twenty-seven expression master regulators and 13 splicing master regulators were identified and were classified as membrane-associated or cytoskeletal proteins, transcription factors or DNA methylases. These genes could control the expression of other genes through cell signaling or by a direct transcriptional activation/repression mechanism. CONCLUSION In the present analysis, we show that eQTL and sQTL mapping makes possible positional identification of gene and isoform expression regulators.
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Affiliation(s)
| | - Mauricio A Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Raluca G Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
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15
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Blackburn DM, Lazure F, Corchado AH, Perkins TJ, Najafabadi HS, Soleimani VD. High-resolution genome-wide expression analysis of single myofibers using SMART-Seq. J Biol Chem 2019; 294:20097-20108. [PMID: 31753917 DOI: 10.1074/jbc.ra119.011506] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/15/2019] [Indexed: 12/26/2022] Open
Abstract
Skeletal muscle is a heterogeneous tissue. Individual myofibers that make up muscle tissue exhibit variation in their metabolic and contractile properties. Although biochemical and histological assays are available to study myofiber heterogeneity, efficient methods to analyze the whole transcriptome of individual myofibers are lacking. Here, we report on a single-myofiber RNA-sequencing (smfRNA-Seq) approach to analyze the whole transcriptome of individual myofibers by combining single-fiber isolation with Switching Mechanism at 5' end of RNA Template (SMART) technology. Using smfRNA-Seq, we first determined the genes that are expressed in the whole muscle, including in nonmyogenic cells. We also analyzed the differences in the transcriptome of myofibers from young and old mice to validate the effectiveness of this new method. Our results suggest that aging leads to significant changes in the expression of metabolic genes, such as Nos1, and structural genes, such as Myl1, in myofibers. We conclude that smfRNA-Seq is a powerful tool to study developmental, disease-related, and age-related changes in the gene expression profile of skeletal muscle.
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Affiliation(s)
- Darren M Blackburn
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada.,Molecular and Regenerative Medicine Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada.,Molecular and Regenerative Medicine Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Aldo H Corchado
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Theodore J Perkins
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada .,Molecular and Regenerative Medicine Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
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16
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Sitbon YH, Yadav S, Kazmierczak K, Szczesna-Cordary D. Insights into myosin regulatory and essential light chains: a focus on their roles in cardiac and skeletal muscle function, development and disease. J Muscle Res Cell Motil 2019; 41:313-327. [PMID: 31131433 DOI: 10.1007/s10974-019-09517-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/21/2019] [Indexed: 12/15/2022]
Abstract
The activity of cardiac and skeletal muscles depends upon the ATP-coupled actin-myosin interactions to execute the power stroke and muscle contraction. The goal of this review article is to provide insight into the function of myosin II, the molecular motor of the heart and skeletal muscles, with a special focus on the role of myosin II light chain (MLC) components. Specifically, we focus on the involvement of myosin regulatory (RLC) and essential (ELC) light chains in striated muscle development, isoform appearance and their function in normal and diseased muscle. We review the consequences of isoform switching and knockout of specific MLC isoforms on cardiac and skeletal muscle function in various animal models. Finally, we discuss how dysregulation of specific RLC/ELC isoforms can lead to cardiac and skeletal muscle diseases and summarize the effects of most studied mutations leading to cardiac or skeletal myopathies.
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Affiliation(s)
- Yoel H Sitbon
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL, 33136, USA
| | - Sunil Yadav
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL, 33136, USA
| | - Katarzyna Kazmierczak
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL, 33136, USA
| | - Danuta Szczesna-Cordary
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL, 33136, USA.
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17
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Ravenscroft G, Bryson-Richardson RJ, Nowak KJ, Laing NG. Recent advances in understanding congenital myopathies. F1000Res 2018; 7. [PMID: 30631434 PMCID: PMC6290972 DOI: 10.12688/f1000research.16422.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
By definition, congenital myopathy typically presents with skeletal muscle weakness and hypotonia at birth. Traditionally, congenital myopathy subtypes have been predominantly distinguished on the basis of the pathological hallmarks present on skeletal muscle biopsies. Many genes cause congenital myopathies when mutated, and a burst of new causative genes have been identified because of advances in gene sequencing technology. Recent discoveries include extending the disease phenotypes associated with previously identified genes and determining that genes formerly known to cause only dominant disease can also cause recessive disease. The more recently identified congenital myopathy genes account for only a small proportion of patients. Thus, the congenital myopathy genes remaining to be discovered are predicted to be extremely rare causes of disease, which greatly hampers their identification. Significant progress in the provision of molecular diagnoses brings important information and value to patients and their families, such as possible disease prognosis, better disease management, and informed reproductive choice, including carrier screening of parents. Additionally, from accurate genetic knowledge, rational treatment options can be hypothesised and subsequently evaluated
in vitro and in animal models. A wide range of potential congenital myopathy therapies have been investigated on the basis of improved understanding of disease pathomechanisms, and some therapies are in clinical trials. Although large hurdles remain, promise exists for translating treatment benefits from preclinical models to patients with congenital myopathy, including harnessing proven successes for other genetic diseases.
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Affiliation(s)
- Gianina Ravenscroft
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | | | - Kristen J Nowak
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,School of Biological Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia.,Office of Population Health Genomics, Western Australian Department of Health, East Perth, WA, Australia
| | - Nigel G Laing
- Centre for Medical Research, The University of Western Australia, Perth, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
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