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Tanaka T, Goto Y, Horie M, Masuda K, Shinno Y, Matsumoto Y, Okuma Y, Yoshida T, Horinouchi H, Motoi N, Yatabe Y, Watanabe S, Yamamoto N, Ohe Y. Whole Exome Sequencing of Thymoma Patients Exhibiting Exceptional Responses to Pemetrexed Monotherapy. Cancers (Basel) 2023; 15:4018. [PMID: 37627046 PMCID: PMC10452868 DOI: 10.3390/cancers15164018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Pemetrexed is used for the chemotherapy of advanced thymoma. Exceptional responses of thymoma to pemetrexed treatment are not frequently observed. The underlying genetic mechanism of the exceptional responses remains unclear. We used whole-exome sequencing to explore the specific genomic aberrations that lead to an extreme and durable response. METHODS Whole-exome sequencing using NovaSeq6000 (150 bp paired-end sequencing) was performed on nine formalin-fixed paraffin-embedded tissues from patients with advanced thymomas treated with pemetrexed (two exceptional responders and seven typical responders). RESULTS We identified 284 somatic single-nucleotide variants (SNVs; 272 missense, 8 missense/splice-site, 3 stop-gain, and 1 stop-gain/splice-site), 34 insertions and deletions (Indels; 33 frameshift and one splice region), and 21 copy number variations (CNVs; 15 gains and six losses). No difference in the number of SNVs variants and distribution of deleterious Indels was observed between the exceptional and typical responders. Interestingly, arm-level chromosomal CNVs (15 gains and six losses) were detected in four patients, including an exceptional responder. The highest number of arm-level CNVs was observed in an exceptional responder. CONCLUSION Exceptional responders to pemetrexed for metastatic thymomas may be characterized by arm-level CNVs. Further, whole-genome and RNA sequencing studies should be performed.
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Affiliation(s)
- Tomohiro Tanaka
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Medical & Dental Hospital, Niigata 951-8510, Japan
| | - Yasushi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Masafumi Horie
- Department of Molecular and Cellular Pathology, Kanazawa University, Kanazawa 920-8640, Japan
| | - Ken Masuda
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuki Shinno
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuji Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yusuke Okuma
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Tatsuya Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Noriko Motoi
- Department of Pathology, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Yasushi Yatabe
- Department of Pathology and Clinical Laboratory, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Shunichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Noboru Yamamoto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
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Kmietczyk V, Oelschläger J, Gupta P, Varma E, Hartl S, Furkel J, Konstandin M, Marx A, Loewenthal Z, Kamuf-Schenk V, Jürgensen L, Stroh C, Gorska A, Martin-Garrido A, Heineke J, Jakobi T, Frey N, Völkers M. Ythdf2 regulates cardiac remodeling through its mRNA target transcripts. J Mol Cell Cardiol 2023; 181:57-66. [PMID: 37315764 DOI: 10.1016/j.yjmcc.2023.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
m6A mRNA methylation controls cardiomyocyte function and increased overall m6A levels are a stereotyping finding in heart failure independent of the underlying etiology. However, it is largely unknown how the information is read by m6A reader proteins in heart failure. Here we show that the m6A reader protein Ythdf2 controls cardiac function and identified a novel mechanism how reader proteins control gene expression and cardiac function. Deletion of Ythdf2 in cardiomyocytes in vivo leads to mild cardiac hypertrophy, reduced heart function, and increased fibrosis during pressure overload as well as during aging. Similarly, in vitro the knockdown of Ythdf2 results in cardiomyocyte growth and remodeling. Mechanistically, we identified the eucaryotic elongation factor 2 as post-transcriptionally regulated by Ythdf2 using cell type specific Ribo-seq data. Our study expands our understanding on the regulatory functions of m6A methylation in cardiomyocytes and how cardiac function is controlled by the m6A reader protein Ythdf2.
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Affiliation(s)
- V Kmietczyk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - J Oelschläger
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - P Gupta
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - E Varma
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - S Hartl
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - J Furkel
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - M Konstandin
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - A Marx
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Z Loewenthal
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - V Kamuf-Schenk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - L Jürgensen
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - C Stroh
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - A Gorska
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - A Martin-Garrido
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University
| | - J Heineke
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University
| | - T Jakobi
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona, College of Medicine - Phoenix, Phoenix, USA
| | - N Frey
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - M Völkers
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.
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3
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Varma E, Burghaus J, Schwarzl T, Sekaran T, Gupta P, Górska AA, Hofmann C, Stroh C, Jürgensen L, Kamuf-Schenk V, Li X, Medert R, Leuschner F, Kmietczyk V, Freichel M, Katus HA, Hentze MW, Frey N, Völkers M. Translational control of Ybx1 expression regulates cardiac function in response to pressure overload in vivo. Basic Res Cardiol 2023; 118:25. [PMID: 37378715 PMCID: PMC10307726 DOI: 10.1007/s00395-023-00996-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/31/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
RNA-protein interactions are central to cardiac function, but how activity of individual RNA-binding protein is regulated through signaling cascades in cardiomyocytes during heart failure development is largely unknown. The mechanistic target of rapamycin kinase is a central signaling hub that controls mRNA translation in cardiomyocytes; however, a direct link between mTOR signaling and RNA-binding proteins in the heart has not been established. Integrative transcriptome and translatome analysis revealed mTOR dependent translational upregulation of the RNA binding protein Ybx1 during early pathological remodeling independent of mRNA levels. Ybx1 is necessary for pathological cardiomyocyte growth by regulating protein synthesis. To identify the molecular mechanisms how Ybx1 regulates cellular growth and protein synthesis, we identified mRNAs bound to Ybx1. We discovered that eucaryotic elongation factor 2 (Eef2) mRNA is bound to Ybx1, and its translation is upregulated during cardiac hypertrophy dependent on Ybx1 expression. Eef2 itself is sufficient to drive pathological growth by increasing global protein translation. Finally, Ybx1 depletion in vivo preserved heart function during pathological cardiac hypertrophy. Thus, activation of mTORC1 links pathological signaling cascades to altered gene expression regulation by activation of Ybx1 which in turn promotes translation through increased expression of Eef2.
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Affiliation(s)
- Eshita Varma
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Jana Burghaus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Thileepan Sekaran
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Parul Gupta
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Agnieszka A Górska
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Christoph Hofmann
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Claudia Stroh
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Verena Kamuf-Schenk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Xue Li
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Rebekka Medert
- Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
| | - Florian Leuschner
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Vivien Kmietczyk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Marc Freichel
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
- Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
| | - Hugo A Katus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Norbert Frey
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Mirko Völkers
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany.
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4
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Li X, Shen Y, Xu X, Guo G, Chen Y, Wei Q, Li H, He K, Liu C. Genomic and RNA-Seq profiling of patients with HFrEF unraveled OAS1 mutation and aggressive expression. Int J Cardiol 2023; 375:44-54. [PMID: 36414043 DOI: 10.1016/j.ijcard.2022.11.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Heart failure (HF) is a complex pathophysiological state characterized by inadequate delivery of blood and nutrients to the cardiac tissues. It is rarely curable and is commonly associated with a poor prognosis. In this study, we aimed to analyse exomic and RNA-Seq data from patients with HF to identify the key altered pathways in HF. METHODS Whole blood samples were collected from patients with HF and subjected to whole exome sequencing (WES) and RNA-Seq analysis. The gene expression and RNA-Seq data obtained were verified using gene chip analysis and RT-PCR. RESULTS Both exomic and RNA-Seq data confirmed the dysregulation of phosphorylation and immune signalling in patients with HF. Specifically, exomic analysis showed that TITIN, OBSCURIN, NOD2, CDH2, MAP3K5, and SLC17A4 mutations were associated with HF, and RNA-Seq revealed that S100A12, S100A8, S100A9, PFDN5, and TMCC2, were upregulated in patients with HF. Additionally, comparison between RNA-seq and WES data showed that OAS1 mutations are associated with HF. CONLCUSION Our findings indicated that patients with HF show an overall disruption of key phosphorylation and immune signalling pathways. Based on RNA-seq and WES, OAS1 mutations may be primarily responsible for these changes.
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Affiliation(s)
- Xin Li
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Beijing 100853, China
| | - Yanying Shen
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Xiang Xu
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Ge Guo
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Yibing Chen
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Qingxia Wei
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Hanlu Li
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Kunlun He
- Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Beijing 100853, China; Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China.
| | - Chunlei Liu
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Beijing 100853, China.
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5
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Hamledari H, Asghari P, Jayousi F, Aguirre A, Maaref Y, Barszczewski T, Ser T, Moore E, Wasserman W, Klein Geltink R, Teves S, Tibbits GF. Using human induced pluripotent stem cell-derived cardiomyocytes to understand the mechanisms driving cardiomyocyte maturation. Front Cardiovasc Med 2022; 9:967659. [PMID: 36061558 PMCID: PMC9429949 DOI: 10.3389/fcvm.2022.967659] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cardiovascular diseases are the leading cause of mortality and reduced quality of life globally. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide a personalized platform to study inherited heart diseases, drug-induced cardiac toxicity, and cardiac regenerative therapy. However, the immaturity of CMs obtained by current strategies is a major hurdle in utilizing hiPSC-CMs at their fullest potential. Here, the major findings and limitations of current maturation methodologies to enhance the utility of hiPSC-CMs in the battle against a major source of morbidity and mortality are reviewed. The most recent knowledge of the potential signaling pathways involved in the transition of fetal to adult CMs are assimilated. In particular, we take a deeper look on role of nutrient sensing signaling pathways and the potential role of cap-independent translation mediated by the modulation of mTOR pathway in the regulation of cardiac gap junctions and other yet to be identified aspects of CM maturation. Moreover, a relatively unexplored perspective on how our knowledge on the effects of preterm birth on cardiovascular development can be actually utilized to enhance the current understanding of CM maturation is examined. Furthermore, the interaction between the evolving neonatal human heart and brown adipose tissue as the major source of neonatal thermogenesis and its endocrine function on CM development is another discussed topic which is worthy of future investigation. Finally, the current knowledge regarding transcriptional mediators of CM maturation is still limited. The recent studies have produced the groundwork to better understand CM maturation in terms of providing some of the key factors involved in maturation and development of metrics for assessment of maturation which proves essential for future studies on in vitro PSC-CMs maturation.
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Affiliation(s)
- Homa Hamledari
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Parisa Asghari
- Department of Cellular and Physiological Sciences, University of British Colombia, Vancouver, BC, Canada
| | - Farah Jayousi
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Alejandro Aguirre
- Department of Medical Genetics, University of British Colombia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Yasaman Maaref
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Tiffany Barszczewski
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Terri Ser
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, BC, Canada
| | - Edwin Moore
- Department of Cellular and Physiological Sciences, University of British Colombia, Vancouver, BC, Canada
| | - Wyeth Wasserman
- Department of Medical Genetics, University of British Colombia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Ramon Klein Geltink
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, BC, Canada
| | - Sheila Teves
- Department of Biochemistry and Molecular Biology, University of British Colombia, Vancouver, BC, Canada
| | - Glen F. Tibbits
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
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Wang J, Li B, Yang X, Liang C, Raza SHA, Pan Y, Zhang K, Zan L. Integration of RNA-seq and ATAC-seq identifies muscle-regulated hub genes in cattle. Front Vet Sci 2022; 9:925590. [PMID: 36032309 PMCID: PMC9404375 DOI: 10.3389/fvets.2022.925590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
As the main product of livestock, muscle itself plays an irreplaceable role in maintaining animal body movement and regulating metabolism. Therefore, it is of great significance to explore its growth, development and regeneration to improve the meat yield and quality of livestock. In this study, we attempted to use RNA-seq and ATAC-seq techniques to identify differentially expressed genes (DEGs) specifically expressed in bovine skeletal muscle as potential candidates for studying the regulatory mechanisms of muscle development. Microarray data from 8 tissue samples were selected from the GEO database for analysis. First, we obtained gene modules related to each tissue through WGCNA analysis. Through Gene Ontology (GO) functional annotation, the module of lightyellow (MElightyellow) was closely related to muscle development, and 213 hub genes were screened as follow-up research targets. Further, the difference analysis showed that, except for PREB, all other candidate hub genes were up-regulated (muscle group vs. other-group). ATAC-seq analysis showed that muscle-specific accessible chromatin regions were mainly located in promoter of genes related to muscle structure development (GO:0061061), muscle cell development (GO:0055001) and muscle system process (GO:0003012), which were involved in cAMP, CGMP-PKG, MAPK, and other signaling pathways. Next, we integrated the results of RNA-seq and ATAC-seq analysis, and 54 of the 212 candidate hub genes were identified as key regulatory genes in skeletal muscle development. Finally, through motif analysis, 22 of the 54 key genes were found to be potential target genes of transcription factor MEF2C. Including CAPN3, ACTN2, MB, MYOM3, SRL, CKM, ALPK3, MAP3K20, UBE2G1, NEURL2, CAND2, DOT1L, HRC, MAMSTR, FSD2, LRRC2, LSMEM1, SLC29A2, FHL3, KLHL41, ATXN7L2, and PDRG1. This provides a potential reference for studying the molecular mechanism of skeletal muscle development in mammals.
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Affiliation(s)
- Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Bingzhi Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xinran Yang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | | | - Yueting Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- National Beef Cattle Improvement Center, Northwest A&F University, Xianyang, China
- *Correspondence: Linsen Zan
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7
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Li X, Zhang Y, Zhao Y, Zhou Y, Han Q, Yang Y, Zhang L, Shi L, Jin X, Zhang R, Gao H, Xue G, Li D, Zhang ZR, Lu Y, Yang B, Pan Z. Cullin-associated and neddylation-dissociated 1 protein (CAND1) governs cardiac hypertrophy and heart failure partially through regulating calcineurin degradation. Pharmacol Res 2022; 182:106284. [PMID: 35661710 DOI: 10.1016/j.phrs.2022.106284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/16/2022] [Accepted: 05/29/2022] [Indexed: 11/19/2022]
Abstract
Pathological cardiac hypertrophy is a process characterized by significant disturbance of protein turnover. Cullin-associated and Neddylation-dissociated 1 (CAND1) acts as a coordinator to modulate substrate protein degradation by promoting the formation of specific cullin-based ubiquitin ligase 3 complex in response to substrate accumulation, which thereby facilitate the maintaining of normal protein homeostasis. Accumulation of calcineurin is critical in the pathogenesis of cardiac hypertrophy and heart failure. However, whether CAND1 titrates the degradation of hypertrophy related protein eg. calcineurin and regulates cardiac hypertrophy remains unknown. Therefore, we aim to explore the role of CAND1 in cardiac hypertrophy and heart failure and the underlying molecular mechanism. Here, we found that the protein level of CAND1 was increased in cardiac tissues from heart failure (HF) patients and TAC mice, whereas the mRNA level did not change. CAND1-KO+/- aggravated TAC-induced cardiac hypertrophic phenotypes; in contrast, CAND1-Tg attenuated the maladaptive cardiac remodeling. At the molecular level, CAND1 overexpression downregulated, whereas CAND1-KO+/- or knockdown upregulated calcineurin expression at both in vivo and in vitro conditions. Mechanistically, CAND1 overexpression favored the assembly of Cul1/atrogin1/calcineurin complex and rendered the ubiquitination and degradation of calcineurin. Notably, CAND1 deficiency-induced hypertrophic phenotypes were partially rescued by knockdown of calcineurin, and application of exogenous CAND1 prevented TAC-induced cardiac hypertrophy. Taken together, our findings demonstrate that CAND1 exerts a protective effect against cardiac hypertrophy and heart failure partially by inducing the degradation of calcineurin.
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Affiliation(s)
- Xingda Li
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Yang Zhang
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Yue Zhao
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Yang Zhou
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Qilong Han
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Ying Yang
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Lingmin Zhang
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Ling Shi
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Xuexin Jin
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Ruixin Zhang
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Haiyu Gao
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Genlong Xue
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Desheng Li
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China
| | - Zhi-Ren Zhang
- Institute of Metabolic Disease, Heilongjiang Academy of Medical Science, Harbin, China; Departments of Cardiology and Clinical Pharmacy, Harbin Medical University Cancer Hospital, Heilongjiang Academy of Medical Science, Harbin, China; NHC Key Laboratory of Cell Transplantation, Harbin Medical University, Harbin, China
| | - Yanjie Lu
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China; Research Unit of Noninfectious Chronic Diseases in Frigid Zone, Chinese Academy of Medical Sciences, 2019RU070, China
| | - Baofeng Yang
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China; Research Unit of Noninfectious Chronic Diseases in Frigid Zone, Chinese Academy of Medical Sciences, 2019RU070, China.
| | - Zhenwei Pan
- Department of Pharmacology, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin 150086, China; Research Unit of Noninfectious Chronic Diseases in Frigid Zone, Chinese Academy of Medical Sciences, 2019RU070, China; NHC Key Laboratory of Cell Transplantation, Harbin Medical University, Harbin, China.
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Roles of Cullin-RING Ubiquitin Ligases in Cardiovascular Diseases. Biomolecules 2022; 12:biom12030416. [PMID: 35327608 PMCID: PMC8946067 DOI: 10.3390/biom12030416] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/18/2022] Open
Abstract
Maintenance of protein homeostasis is crucial for virtually every aspect of eukaryotic biology. The ubiquitin-proteasome system (UPS) represents a highly regulated quality control machinery that protects cells from a variety of stress conditions as well as toxic proteins. A large body of evidence has shown that UPS dysfunction contributes to the pathogenesis of cardiovascular diseases. This review highlights the latest findings regarding the physiological and pathological roles of cullin-RING ubiquitin ligases (CRLs), an essential player in the UPS, in the cardiovascular system. To inspire potential therapeutic invention, factors regulating CRL activities are also discussed.
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