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Hashemolhosseini S, Gessler L. Crosstalk among canonical Wnt and Hippo pathway members in skeletal muscle and at the neuromuscular junction. Neural Regen Res 2025; 20:2464-2479. [PMID: 39248171 PMCID: PMC11801303 DOI: 10.4103/nrr.nrr-d-24-00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/04/2024] [Accepted: 08/05/2024] [Indexed: 09/10/2024] Open
Abstract
Skeletal muscles are essential for locomotion, posture, and metabolic regulation. To understand physiological processes, exercise adaptation, and muscle-related disorders, it is critical to understand the molecular pathways that underlie skeletal muscle function. The process of muscle contraction, orchestrated by a complex interplay of molecular events, is at the core of skeletal muscle function. Muscle contraction is initiated by an action potential and neuromuscular transmission requiring a neuromuscular junction. Within muscle fibers, calcium ions play a critical role in mediating the interaction between actin and myosin filaments that generate force. Regulation of calcium release from the sarcoplasmic reticulum plays a key role in excitation-contraction coupling. The development and growth of skeletal muscle are regulated by a network of molecular pathways collectively known as myogenesis. Myogenic regulators coordinate the differentiation of myoblasts into mature muscle fibers. Signaling pathways regulate muscle protein synthesis and hypertrophy in response to mechanical stimuli and nutrient availability. Several muscle-related diseases, including congenital myasthenic disorders, sarcopenia, muscular dystrophies, and metabolic myopathies, are underpinned by dysregulated molecular pathways in skeletal muscle. Therapeutic interventions aimed at preserving muscle mass and function, enhancing regeneration, and improving metabolic health hold promise by targeting specific molecular pathways. Other molecular signaling pathways in skeletal muscle include the canonical Wnt signaling pathway, a critical regulator of myogenesis, muscle regeneration, and metabolic function, and the Hippo signaling pathway. In recent years, more details have been uncovered about the role of these two pathways during myogenesis and in developing and adult skeletal muscle fibers, and at the neuromuscular junction. In fact, research in the last few years now suggests that these two signaling pathways are interconnected and that they jointly control physiological and pathophysiological processes in muscle fibers. In this review, we will summarize and discuss the data on these two pathways, focusing on their concerted action next to their contribution to skeletal muscle biology. However, an in-depth discussion of the non-canonical Wnt pathway, the fibro/adipogenic precursors, or the mechanosensory aspects of these pathways is not the focus of this review.
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Affiliation(s)
- Said Hashemolhosseini
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Lea Gessler
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
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Sun Z, Cheng X, Wang Z, Qiao C, Qian H, Yuan T, Lv Z, Sun W, Zhang H, Liu Y, Lu Z, Lin J, Lai C, Wang Y, Yang X, Wang X, Meng J, Bao N. Single-nucleus transcriptomics reveals subsets of degenerative myonuclei after rotator cuff tear-induced muscle atrophy. Cell Prolif 2025; 58:e13763. [PMID: 39435630 PMCID: PMC11882757 DOI: 10.1111/cpr.13763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 09/06/2024] [Accepted: 09/23/2024] [Indexed: 10/23/2024] Open
Abstract
Rotator cuff tear (RCT) is the primary cause of shoulder pain and disability and frequently trigger muscle degeneration characterised by muscle atrophy, fatty infiltration and fibrosis. Single-nucleus RNA sequencing (snRNA-seq) was used to reveal the transcriptional changes in the supraspinatus muscle after RCT. Supraspinatus muscles were obtained from patients with habitual shoulder dislocation (n = 3) and RCT (n = 3). In response to the RCT, trajectory analysis showed progression from normal myonuclei to ANKRD1+ myonuclei, which captured atrophy-and fatty infiltration-related regulons (KLF5, KLF10, FOSL1 and BHLHE40). Transcriptomic alterations in fibro/adipogenic progenitors (FAPs) and muscle satellite cells (MuSCs) have also been studied. By predicting cell-cell interactions, we observed communication alterations between myofibers and muscle-resident cells following RCT. Our findings reveal the plasticity of muscle cells in response to RCT and offer valuable insights into the molecular mechanisms and potential therapeutic targets of RCT.
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Affiliation(s)
- Ziying Sun
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Xi Cheng
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Zheng Wang
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Chenfeng Qiao
- Department of Orthopedics, Jinling Clinical Medical CollegeNanjing University of Chinese MedicineNanjingJiangsuPeople's Republic of China
| | - Hong Qian
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Tao Yuan
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Zhongyang Lv
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Wenshuang Sun
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Hanwen Zhang
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Yuan Liu
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Zhihao Lu
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Jintao Lin
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Chengteng Lai
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Yang Wang
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Xiaojiang Yang
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
| | - Xingyun Wang
- Hongqiao International Institute of Medicine, Tongren HospitalShanghai Jiao Tong University School of MedicineShanghaiPeople's Republic of China
| | - Jia Meng
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
- Department of Orthopedics, Jinling Clinical Medical CollegeNanjing University of Chinese MedicineNanjingJiangsuPeople's Republic of China
| | - Nirong Bao
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsuPeople's Republic of China
- Department of Orthopedics, Jinling Clinical Medical CollegeNanjing University of Chinese MedicineNanjingJiangsuPeople's Republic of China
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Gustafson AL, Durbin AD, Artinger KB, Ford HL. Myogenesis gone awry: the role of developmental pathways in rhabdomyosarcoma. Front Cell Dev Biol 2025; 12:1521523. [PMID: 39902277 PMCID: PMC11788348 DOI: 10.3389/fcell.2024.1521523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 12/23/2024] [Indexed: 02/05/2025] Open
Abstract
Rhabdomyosarcoma is a soft-tissue sarcoma that occurs most frequently in pediatric patients and has poor survival rates in patients with recurrent or metastatic disease. There are two major sub-types of RMS: fusion-positive (FP-RMS) and fusion-negative (FN-RMS); with FP-RMS typically containing chromosomal translocations between the PAX3/7-FOXO1 loci. Regardless of subtype, RMS resembles embryonic skeletal muscle as it expresses the myogenic regulatory factors (MRFs), MYOD1 and MYOG. During normal myogenesis, these developmental transcription factors (TFs) orchestrate the formation of terminally differentiated, striated, and multinucleated skeletal muscle. However, in RMS these TFs become dysregulated such that they enable the sustained properties of malignancy. In FP-RMS, the PAX3/7-FOXO1 chromosomal translocation results in restructured chromatin, altering the binding of many MRFs and driving an oncogenic state. In FN-RMS, re-expression of MRFs, as well as other myogenic TFs, blocks terminal differentiation and holds cells in a proliferative, stem-cell-like state. In this review, we delve into the myogenic transcriptional networks that are dysregulated in and contribute to RMS progression. Advances in understanding the mechanisms through which myogenesis becomes stalled in RMS will lead to new tumor-specific therapies that target these aberrantly expressed developmental transcriptional pathways.
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Affiliation(s)
- Annika L. Gustafson
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Adam D. Durbin
- Division of Molecular Oncology, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Kristin B. Artinger
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, United States
| | - Heide L. Ford
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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Chambers TL, Dimet‐Wiley A, Keeble AR, Haghani A, Lo W, Kang G, Brooke R, Horvath S, Fry CS, Watowich SJ, Wen Y, Murach KA. Methylome-proteome integration after late-life voluntary exercise training reveals regulation and target information for improved skeletal muscle health. J Physiol 2025; 603:211-237. [PMID: 39058663 PMCID: PMC11702923 DOI: 10.1113/jp286681] [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: 04/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Exercise is a potent stimulus for combatting skeletal muscle ageing. To study the effects of exercise on muscle in a preclinical setting, we developed a combined endurance-resistance training stimulus for mice called progressive weighted wheel running (PoWeR). PoWeR improves molecular, biochemical, cellular and functional characteristics of skeletal muscle and promotes aspects of partial epigenetic reprogramming when performed late in life (22-24 months of age). In this investigation, we leveraged pan-mammalian DNA methylome arrays and tandem mass-spectrometry proteomics in skeletal muscle to provide detailed information on late-life PoWeR adaptations in female mice relative to age-matched sedentary controls (n = 7-10 per group). Differential CpG methylation at conserved promoter sites was related to transcriptional regulation genes as well as Nr4a3, Hes1 and Hox genes after PoWeR. Using a holistic method of -omics integration called binding and expression target analysis (BETA), methylome changes were associated with upregulated proteins related to global and mitochondrial translation after PoWeR (P = 0.03). Specifically, BETA implicated methylation control of ribosomal, mitoribosomal, and mitochondrial complex I protein abundance after training. DNA methylation may also influence LACTB, MIB1 and UBR4 protein induction with exercise - all are mechanistically linked to muscle health. Computational cistrome analysis predicted several transcription factors including MYC as regulators of the exercise trained methylome-proteome landscape, corroborating prior late-life PoWeR transcriptome data. Correlating the proteome to muscle mass and fatigue resistance revealed positive relationships with VPS13A and NPL levels, respectively. Our findings expose differential epigenetic and proteomic adaptations associated with translational regulation after PoWeR that could influence skeletal muscle mass and function in aged mice. KEY POINTS: Late-life combined endurance-resistance exercise training from 22-24 months of age in mice is shown to improve molecular, biochemical, cellular and in vivo functional characteristics of skeletal muscle and promote aspects of partial epigenetic reprogramming and epigenetic age mitigation. Integration of DNA CpG 36k methylation arrays using conserved sites (which also contain methylation ageing clock sites) with exploratory proteomics in skeletal muscle extends our prior work and reveals coordinated and widespread regulation of ribosomal, translation initiation, mitochondrial ribosomal (mitoribosomal) and complex I proteins after combined voluntary exercise training in a sizeable cohort of female mice (n = 7-10 per group and analysis). Multi-omics integration predicted epigenetic regulation of serine β-lactamase-like protein (LACTB - linked to tumour resistance in muscle), mind bomb 1 (MIB1 - linked to satellite cell and type 2 fibre maintenance) and ubiquitin protein ligase E3 component N-recognin 4 (UBR4 - linked to muscle protein quality control) after training. Computational cistrome analysis identified MYC as a regulator of the late-life training proteome, in agreement with prior transcriptional analyses. Vacuolar protein sorting 13 homolog A (VPS13A) was positively correlated to muscle mass, and the glycoprotein/glycolipid associated sialylation enzyme N-acetylneuraminate pyruvate lyase (NPL) was associated to in vivo muscle fatigue resistance.
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Affiliation(s)
- Toby L. Chambers
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and RecreationUniversity of ArkansasFayettevilleARUSA
| | | | - Alexander R. Keeble
- University of Kentucky Center for Muscle BiologyLexingtonKYUSA
- Department of Athletic Training and Clinical NutritionUniversity of KentuckyLexingtonKYUSA
| | - Amin Haghani
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCAUSA
- Altos LabsSan DiegoCAUSA
| | - Wen‐Juo Lo
- Department of Educational Statistics and Research MethodsUniversity of ArkansasFayettevilleARUSA
| | - Gyumin Kang
- University of Kentucky Center for Muscle BiologyLexingtonKYUSA
- Department of PhysiologyUniversity of KentuckyLexingtonKYUSA
- Division of Biomedical Informatics, Department of Internal MedicineUniversity of KentuckyLexingtonKYUSA
| | - Robert Brooke
- Epigenetic Clock Development FoundationLos AngelesCAUSA
| | - Steve Horvath
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCAUSA
- Altos LabsSan DiegoCAUSA
- Epigenetic Clock Development FoundationLos AngelesCAUSA
| | - Christopher S. Fry
- University of Kentucky Center for Muscle BiologyLexingtonKYUSA
- Department of Athletic Training and Clinical NutritionUniversity of KentuckyLexingtonKYUSA
| | - Stanley J. Watowich
- Ridgeline TherapeuticsHoustonTXUSA
- Department of Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonTXUSA
| | - Yuan Wen
- University of Kentucky Center for Muscle BiologyLexingtonKYUSA
- Department of PhysiologyUniversity of KentuckyLexingtonKYUSA
- Division of Biomedical Informatics, Department of Internal MedicineUniversity of KentuckyLexingtonKYUSA
| | - Kevin A. Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and RecreationUniversity of ArkansasFayettevilleARUSA
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Valenzi E, Jia M, Gerges P, Fan J, Tabib T, Behara R, Zhou Y, Sembrat J, Das J, Benos PV, Singh H, Lafyatis R. Altered AP-1, RUNX and EGR chromatin dynamics drive fibrotic lung disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.23.619858. [PMID: 39554071 PMCID: PMC11565795 DOI: 10.1101/2024.10.23.619858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Pulmonary fibrosis, including systemic sclerosis-associated interstitial lung disease (SSc-ILD), involves myofibroblasts and SPP1hi macrophages as drivers of fibrosis. Single-cell RNA sequencing has delineated fibroblast and macrophages transcriptomes, but limited insight into transcriptional control of profibrotic gene programs. To address this challenge, we analyzed multiomic snATAC/snRNA-seq on explanted SSc-ILD and donor control lungs. The neural network tool ChromBPNet inferred increased TF binding at single base pair resolution to profibrotic genes, including CTHRC1 and ADAM12, in fibroblasts and SPP1 and CCL18 in macrophages. The novel algorithm HALO confirmed AP-1, RUNX, and EGR TF activity controlling profibrotic gene programs and established TF-regulatory element-gene networks. This TF action atlas provides comprehensive insights into the transcriptional regulation of fibroblasts and macrophages in healthy and fibrotic human lungs.
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Affiliation(s)
- Eleanor Valenzi
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh
| | - Minxue Jia
- Department of Computational and Systems Biology, University of Pittsburgh
| | - Peter Gerges
- Center for Systems Immunology and Department of Immunology, University of Pittsburgh
| | - Jingyu Fan
- Center for Systems Immunology and Department of Immunology, University of Pittsburgh
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh
- Center for Systems Immunology and Department of Immunology, University of Pittsburgh
| | - Rithika Behara
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh
| | - Yuechen Zhou
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh
| | - John Sembrat
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh
| | - Jishnu Das
- Center for Systems Immunology and Department of Immunology, University of Pittsburgh
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh
- Department of Epidemiology, University of Florida
| | - Harinder Singh
- Center for Systems Immunology and Department of Immunology, University of Pittsburgh
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh
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Hikasa H, Kawahara K, Inui M, Yasuki Y, Yamashita K, Otsubo K, Kitajima S, Nishio M, Arima K, Endo M, Taira M, Suzuki A. A highly sensitive reporter system to monitor endogenous YAP1/TAZ activity and its application in various human cells. Cancer Sci 2024; 115:3370-3383. [PMID: 39155534 PMCID: PMC11447953 DOI: 10.1111/cas.16316] [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: 03/25/2024] [Revised: 07/22/2024] [Accepted: 08/01/2024] [Indexed: 08/20/2024] Open
Abstract
The activation of yes-associated protein 1 (YAP1) and transcriptional co-activator with PDZ-binding motif (TAZ) has been implicated in both regeneration and tumorigenesis, thus representing a double-edged sword in tissue homeostasis. However, how the activity of YAP1/TAZ is regulated or what leads to its dysregulation in these processes remains unknown. To explore the upstream stimuli modulating the cellular activity of YAP1/TAZ, we developed a highly sensitive YAP1/TAZ/TEAD-responsive DNA element (YRE) and incorporated it into a lentivirus-based reporter cell system to allow for sensitive and specific monitoring of the endogenous activity of YAP1/TAZ in terms of luciferase activity in vitro and Venus fluorescence in vivo. Furthermore, by replacing YRE with TCF- and NF-κB-binding DNA elements, we demonstrated the applicability of this reporter system to other pathways such as Wnt/β-catenin/TCF- and IL-1β/NF-κB-mediated signaling, respectively. The practicality of this system was evaluated by performing cell-based reporter screening of a chemical compound library consisting of 364 known inhibitors, using reporter-introduced cells capable of quantifying YAP1/TAZ- and β-catenin-mediated transcription activities, which led to the identification of multiple inhibitors, including previously known as well as novel modulators of these signaling pathways. We further confirmed that novel YAP1/TAZ modulators, such as potassium ionophores, Janus kinase inhibitors, platelet-derived growth factor receptor inhibitors, and genotoxic stress inducers, alter the protein level or phosphorylation of endogenous YAP1/TAZ and the expression of their target genes. Thus, this reporter system provides a powerful tool to monitor endogenous signaling activities of interest (even in living cells) and search for modulators in various cellular contexts.
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Affiliation(s)
- Hiroki Hikasa
- Department of Biochemistry, School of Medicine, University of Occupational and Environmental Health, Fukuoka, Japan
- Division of Cancer Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kohichi Kawahara
- Division of Cancer Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Masako Inui
- Department of Biochemistry, School of Medicine, University of Occupational and Environmental Health, Fukuoka, Japan
| | - Yukichika Yasuki
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Keita Yamashita
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Kohei Otsubo
- Division of Cancer Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shojiro Kitajima
- Department of Biochemistry, School of Medicine, University of Occupational and Environmental Health, Fukuoka, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Miki Nishio
- Division of Cancer Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazunari Arima
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Motoyoshi Endo
- Department of Molecular Biology, University of Occupational and Environmental Health, Fukuoka, Japan
| | - Masanori Taira
- Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Akira Suzuki
- Division of Cancer Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Japan
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Wang X, Zhang J, Su J, Huang T, Lian L, Nie Q, Zhang X, Li J, Wang Y. Genome-wide mapping of the binding sites of myocyte enhancer factor 2A in chicken primary myoblasts. Poult Sci 2024; 103:104097. [PMID: 39094502 PMCID: PMC11345569 DOI: 10.1016/j.psj.2024.104097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024] Open
Abstract
Myocyte enhancer factor 2A (MEF2A) is a transcription factor that plays a critical role in cell proliferation, differentiation and apoptosis. In contrast to the wide characterization of its regulation mechanism in mammalian skeletal muscle, its role in chickens is limited. Especially, its wide target genes remain to be identified. Therefore, we utilized Cleavage Under Targets and Tagmentation (CUT&Tag) technology to reveal the genome-wide binding profile of MEF2A in chicken primary myoblasts thus gaining insights into its potential role in muscle development. Our results revealed that MEF2A binding sites were primarily distributed in intergenic and intronic regions. Within the promoter region, although only 8.87% of MEF2A binding sites were found, these binding sites were concentrated around the transcription start site (TSS). Following peak annotation, a total of 1903 genes were identified as potential targets of MEF2A. Gene Ontology (GO) enrichment analysis further revealed that MEF2A target genes may be involved in the regulation of embryonic development in multiple organ systems, including muscle development, gland development, and visual system development. Moreover, a comparison of the MEF2A target genes identified in chicken primary myoblasts with those in mouse C2C12 cells revealed 388 target genes are conserved across species, 1515 target genes are chicken specific. Among these conserved genes, ankyrin repeat and SOCS box containing 5 (ASB5), transmembrane protein 182 (TMEM182), myomesin 2 (MYOM2), leucyl and cystinyl aminopeptidase (LNPEP), actinin alpha 2 (ACTN2), sorbin and SH3 domain containing 1 (SORBS1), ankyrin 3 (ANK3), sarcoglycan delta (SGCD), and ORAI calcium release-activated calcium modulator 1 (ORAI1) exhibited consistent expression patterns with MEF2A during embryonic muscle development. Finally, TMEM182, as an important negative regulator of muscle development, has been validated to be regulated by MEF2A by dual-luciferase and quantitative real-time PCR (qPCR) assays. In summary, our study for the first time provides a wide landscape of MEF2A target genes in chicken primary myoblasts, which supports the active role of MEF2A in chicken muscle development.
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Affiliation(s)
- Xinglong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Jiannan Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Jiancheng Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Tianjiao Huang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Ling Lian
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, PR China
| | - Qinghua Nie
- Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou, PR China
| | - Xin Zhang
- Joint Nutrition Center for Animal Feeding of Sichuan University-Shengliyuan Group
| | - Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Joint Nutrition Center for Animal Feeding of Sichuan University-Shengliyuan Group
| | - Yajun Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Joint Nutrition Center for Animal Feeding of Sichuan University-Shengliyuan Group.
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8
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Kazimierczak U, Przybyla A, Smielowska M, Kolenda T, Mackiewicz A. Targeting the Hippo Pathway in Cutaneous Melanoma. Cells 2024; 13:1062. [PMID: 38920690 PMCID: PMC11201827 DOI: 10.3390/cells13121062] [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: 03/29/2024] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 06/27/2024] Open
Abstract
Melanoma is the most aggressive form of skin cancer. In the advanced stage of development, it is resistant to currently available therapeutic modalities. Increased invasiveness and metastatic potential depend on several proteins involved in various signal transduction pathways. Hippo signaling plays a vital role in malignant transformation. Dysfunctions of the Hippo pathway initiate the expression of tumor growth factors and are associated with tumor growth and metastasis formation. This review summarizes the recent achievements in studying the role of the Hippo pathway in melanoma pathogenesis and points to the potential specific targets for anti-melanoma therapy.
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Affiliation(s)
- Urszula Kazimierczak
- Department of Cancer Immunology, Poznan University of Medical Sciences, Rokietnicka Street 8, 61-806 Poznan, Poland
| | - Anna Przybyla
- Department of Cancer Immunology, Poznan University of Medical Sciences, Rokietnicka Street 8, 61-806 Poznan, Poland
| | - Marianna Smielowska
- Department of Genome Engineering, The Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, Rokietnicka Street 8, 61-806 Poznan, Poland
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Garbary Street 15, 61-866 Poznan, Poland
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9
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Kim HJ, Choi Y, Lee Y, Hwangbo M, Kim J. OTUD6A orchestrates complex modulation of TEAD4-mediated transcriptional programs. FEBS Lett 2024; 598:1045-1060. [PMID: 38594215 DOI: 10.1002/1873-3468.14861] [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: 01/04/2024] [Revised: 02/28/2024] [Accepted: 03/02/2024] [Indexed: 04/11/2024]
Abstract
TEAD transcription factors play a central role in the Hippo signaling pathway. In this study, we focused on transcriptional enhancer factor TEF-3 (TEAD4), exploring its regulation by the deubiquitinase OTU domain-containing protein 6A (OTUD6A). We identified OTUD6A as a TEAD4-interacting deubiquitinase, positively influencing TEAD-driven transcription without altering TEAD4 stability. Structural analyses revealed specific interaction domains: the N-terminal domain of OTUD6A and the YAP-binding domain of TEAD4. Functional assays demonstrated the positive impact of OTUD6A on the transcription of YAP-TEAD target genes. Despite no impact on TEAD4 nuclear localization, OTUD6A selectively modulated nuclear interactions, enhancing YAP-TEAD4 complex formation while suppressing VGLL4 (transcription cofactor vestigial-like protein 4)-TEAD4 interaction. Critically, OTUD6A facilitated YAP-TEAD4 complex binding to target gene promoters. Our study unveils the regulatory landscape of OTUD6A on TEAD4, providing insights into diseases regulated by YAP-TEAD complexes.
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Affiliation(s)
- Hyo Jin Kim
- Department of Life Sciences, Sogang University, Seoul, Korea
| | - Yunsik Choi
- Department of Life Sciences, Sogang University, Seoul, Korea
| | - Yuri Lee
- Department of Life Sciences, Sogang University, Seoul, Korea
| | - Mi Hwangbo
- Department of Life Sciences, Sogang University, Seoul, Korea
| | - Jongchan Kim
- Department of Life Sciences, Sogang University, Seoul, Korea
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10
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Miller MJ, Gries KJ, Marcotte GR, Ryan Z, Strub MD, Kunz HE, Arendt BK, Dasari S, Ebert SM, Adams CM, Lanza IR. Human myofiber-enriched aging-induced lncRNA FRAIL1 promotes loss of skeletal muscle function. Aging Cell 2024; 23:e14097. [PMID: 38297807 PMCID: PMC11019130 DOI: 10.1111/acel.14097] [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: 10/05/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 02/02/2024] Open
Abstract
The loss of skeletal muscle mass during aging is a significant health concern linked to adverse outcomes in older individuals. Understanding the molecular basis of age-related muscle loss is crucial for developing strategies to combat this debilitating condition. Long noncoding RNAs (lncRNAs) are a largely uncharacterized class of biomolecules that have been implicated in cellular homeostasis and dysfunction across a many tissues and cell types. To identify lncRNAs that might contribute to skeletal muscle aging, we screened for lncRNAs whose expression was altered in vastus lateralis muscle from older compared to young adults. We identified FRAIL1 as an aging-induced lncRNA with high abundance in human skeletal muscle. In healthy young and older adults, skeletal muscle FRAIL1 was increased with age in conjunction with lower muscle function. Forced expression of FRAIL1 in mouse tibialis anterior muscle elicits a dose-dependent reduction in skeletal muscle fiber size that is independent of changes in muscle fiber type. Furthermore, this reduction in muscle size is dependent on an intact region of FRAIL1 that is highly conserved across non-human primates. Unbiased transcriptional and proteomic profiling of the effects of FRAIL1 expression in mouse skeletal muscle revealed widespread changes in mRNA and protein abundance that recapitulate age-related changes in pathways and processes that are known to be altered in aging skeletal muscle. Taken together, these findings shed light on the intricate molecular mechanisms underlying skeletal muscle aging and implicate FRAIL1 in age-related skeletal muscle phenotypes.
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Affiliation(s)
- Matthew J. Miller
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- University of IowaIowa CityIowaUSA
| | | | - George R. Marcotte
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- University of IowaIowa CityIowaUSA
| | - Zachary Ryan
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | | | - Hawley E. Kunz
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | | | - Surendra Dasari
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Scott M. Ebert
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Emmyon, Inc.RochesterMinnesotaUSA
| | - Christopher M. Adams
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Emmyon, Inc.RochesterMinnesotaUSA
| | - Ian R. Lanza
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
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11
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Gessler L, Huraskin D, Jian Y, Eiber N, Hu Z, Prószyński T, Hashemolhosseini S. The YAP1/TAZ-TEAD transcriptional network regulates gene expression at neuromuscular junctions in skeletal muscle fibers. Nucleic Acids Res 2024; 52:600-624. [PMID: 38048326 PMCID: PMC10810223 DOI: 10.1093/nar/gkad1124] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
We examined YAP1/TAZ-TEAD signaling pathway activity at neuromuscular junctions (NMJs) of skeletal muscle fibers in adult mice. Our investigations revealed that muscle-specific knockouts of Yap1 or Taz, or both, demonstrate that these transcriptional coactivators regulate synaptic gene expression, the number and morphology of NMJs, and synaptic nuclei. Yap1 or Taz single knockout mice display reduced grip strength, fragmentation of NMJs, and accumulation of synaptic nuclei. Yap1/Taz muscle-specific double knockout mice do not survive beyond birth and possess almost no NMJs, the few detectable show severely impaired morphology and are organized in widened endplate bands; and with motor nerve endings being mostly absent. Myogenic gene expression is significantly impaired in the denervated muscles of knockout mice. We found that Tead1 and Tead4 transcription rates were increased upon incubation of control primary myotubes with AGRN-conditioned medium. Reduced AGRN-dependent acetylcholine receptor clustering and synaptic gene transcription were observed in differentiated primary Tead1 and Tead4 knockout myotubes. In silico analysis of previously reported genomic occupancy sites of TEAD1/4 revealed evolutionary conserved regions of potential TEAD binding motifs in key synaptic genes, the relevance of which was functionally confirmed by reporter assays. Collectively, our data suggest a role for YAP1/TAZ-TEAD1/TEAD4 signaling, particularly through TAZ-TEAD4, in regulating synaptic gene expression and acetylcholine receptor clustering at NMJs.
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Affiliation(s)
- Lea Gessler
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Danyil Huraskin
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Yongzhi Jian
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Nane Eiber
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Zhaoyong Hu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz J Prószyński
- Łukasiewicz Research Network-PORT Polish Center for Technology Development, Wrocław, Poland
| | - Said Hashemolhosseini
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
- Muscle Research Center, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
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12
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Liu K, Zheng J, Wang Y, Li Y, Xiong Y, Wang Y, Cheng J, Huang X, Zhang L, Lin Y. Effect of TEA domain transcription factor 1 ( TEAD1) on the differentiation of intramuscular preadipocytes in goats. Anim Biotechnol 2023; 34:3589-3598. [PMID: 36866843 DOI: 10.1080/10495398.2023.2178932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
TEA domain transcription factor 1 (TEAD1), also called TEF-1, acts as a transcriptional enhancer to regulate muscle-specific gene expression. However, the role of TEAD1 in regulating intramuscular preadipocyte differentiation in goats is unclear. The aim of this study was to obtain the sequence of TEAD1 gene and elucidate the effect of TEAD1 on goat intramuscular preadipocyte differentiation in vitro and its possible mechanism. The results showed that the goat TEAD1 gene CDS region sequence was 1311 bp. TEAD1 gene was widely expressed in goat tissues, with the highest expression in brachial triceps (p < 0.01). The expression of TEAD1 gene in goat intramuscular adipocytes at 72 h was extremely significantly higher than that at 0 h (p < 0.01). Overexpression of goat TEAD1 inhibited the accumulation of lipid droplets in goat intramuscular adipocyte. The relative expression of differentiation marker genes SREBP1, PPARγ, C/EBPβ were significantly down-regulated (all p < 0.01), but PREF-1 was significantly up-regulated (p < 0.01). Binding analysis showed that there were multiple binding sites between the DNA binding domain of goat TEAD1 and the promoter binding region of SREBP1, PPARγ, C/EBPβ and PREF-1. In conclusion, TEAD1 negatively regulates the differentiation of goat intramuscular preadipocytes.
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Affiliation(s)
- Kehan Liu
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Ministry of Education/Sichuan Province, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Jianying Zheng
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Ministry of Education/Sichuan Province, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Yong Wang
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Ministry of Education/Sichuan Province, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Yanyan Li
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Ministry of Education/Sichuan Province, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Yan Xiong
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Ministry of Education/Sichuan Province, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Youli Wang
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Ministry of Education/Sichuan Province, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
| | - Jie Cheng
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Xinzhu Huang
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Liyi Zhang
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Yaqiu Lin
- Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Ministry of Education/Sichuan Province, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
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13
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Maehara H, Kokaji T, Hatano A, Suzuki Y, Matsumoto M, Nakayama KI, Egami R, Tsuchiya T, Ozaki H, Morita K, Shirai M, Li D, Terakawa A, Uematsu S, Hironaka KI, Ohno S, Kubota H, Araki H, Miura F, Ito T, Kuroda S. DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle. Sci Rep 2023; 13:19118. [PMID: 37926704 PMCID: PMC10625943 DOI: 10.1038/s41598-023-46393-5] [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: 08/18/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023] Open
Abstract
Each tissue has a dominant set of functional proteins required to mediate tissue-specific functions. Epigenetic modifications, transcription, and translational efficiency control tissue-dominant protein production. However, the coordination of these regulatory mechanisms to achieve such tissue-specific protein production remains unclear. Here, we analyzed the DNA methylome, transcriptome, and proteome in mouse liver and skeletal muscle. We found that DNA hypomethylation at promoter regions is globally associated with liver-dominant or skeletal muscle-dominant functional protein production within each tissue, as well as with genes encoding proteins involved in ubiquitous functions in both tissues. Thus, genes encoding liver-dominant proteins, such as those involved in glycolysis or gluconeogenesis, the urea cycle, complement and coagulation systems, enzymes of tryptophan metabolism, and cytochrome P450-related metabolism, were hypomethylated in the liver, whereas those encoding-skeletal muscle-dominant proteins, such as those involved in sarcomere organization, were hypomethylated in the skeletal muscle. Thus, DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins.
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Affiliation(s)
- Hideki Maehara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Toshiya Kokaji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916‑5 Takayama, Ikoma, Nara, Japan
| | - Atsushi Hatano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-Dori, Chuo-Ku, Niigata City, Niigata, 951-8510, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-Dori, Chuo-Ku, Niigata City, Niigata, 951-8510, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Riku Egami
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Takaho Tsuchiya
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Ibaraki, 305‑8575, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, Ibaraki, 305‑8577, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Ibaraki, 305‑8575, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, Ibaraki, 305‑8577, Japan
| | - Keigo Morita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Masaki Shirai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Dongzi Li
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Akira Terakawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Saori Uematsu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Ken-Ichi Hironaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Satoshi Ohno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
- Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, 7‑3‑1 Hongo, Bunkyo‑ku, Tokyo, 113‑0033, Japan
- Department of AI Systems Medicine, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Hiromitsu Araki
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
- Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, 7‑3‑1 Hongo, Bunkyo‑ku, Tokyo, 113‑0033, Japan.
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14
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Dos Santos M, Shah AM, Zhang Y, Bezprozvannaya S, Chen K, Xu L, Lin W, McAnally JR, Bassel-Duby R, Liu N, Olson EN. Opposing gene regulatory programs governing myofiber development and maturation revealed at single nucleus resolution. Nat Commun 2023; 14:4333. [PMID: 37468485 DOI: 10.1038/s41467-023-40073-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Skeletal muscle fibers express distinct gene programs during development and maturation, but the underlying gene regulatory networks that confer stage-specific myofiber properties remain unknown. To decipher these distinctive gene programs and how they respond to neural activity, we generated a combined multi-omic single-nucleus RNA-seq and ATAC-seq atlas of mouse skeletal muscle development at multiple stages of embryonic, fetal, and postnatal life. We found that Myogenin, Klf5, and Tead4 form a transcriptional complex that synergistically activates the expression of muscle genes in developing myofibers. During myofiber maturation, the transcription factor Maf acts as a transcriptional switch to activate the mature fast muscle gene program. In skeletal muscles of mutant mice lacking voltage-gated L-type Ca2+ channels (Cav1.1), Maf expression and myofiber maturation are impaired. These findings provide a transcriptional atlas of muscle development and reveal genetic links between myofiber formation, maturation, and contraction.
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Affiliation(s)
- Matthieu Dos Santos
- Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Akansha M Shah
- Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Yichi Zhang
- Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, 5323 Harry Hines Boulevard, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, 5323 Harry Hines Boulevard, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Weichun Lin
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - John R McAnally
- Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Ning Liu
- Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.
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15
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Lutz M, Levanti M, Karns R, Gourdon G, Lindquist D, Timchenko NA, Timchenko L. Therapeutic Targeting of the GSK3β-CUGBP1 Pathway in Myotonic Dystrophy. Int J Mol Sci 2023; 24:10650. [PMID: 37445828 PMCID: PMC10342152 DOI: 10.3390/ijms241310650] [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: 06/01/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Myotonic Dystrophy type 1 (DM1) is a neuromuscular disease associated with toxic RNA containing expanded CUG repeats. The developing therapeutic approaches to DM1 target mutant RNA or correct early toxic events downstream of the mutant RNA. We have previously described the benefits of the correction of the GSK3β-CUGBP1 pathway in DM1 mice (HSALR model) expressing 250 CUG repeats using the GSK3 inhibitor tideglusib (TG). Here, we show that TG treatments corrected the expression of ~17% of genes misregulated in DM1 mice, including genes involved in cell transport, development and differentiation. The expression of chloride channel 1 (Clcn1), the key trigger of myotonia in DM1, was also corrected by TG. We found that correction of the GSK3β-CUGBP1 pathway in mice expressing long CUG repeats (DMSXL model) is beneficial not only at the prenatal and postnatal stages, but also during adulthood. Using a mouse model with dysregulated CUGBP1, which mimics alterations in DM1, we showed that the dysregulated CUGBP1 contributes to the toxicity of expanded CUG repeats by changing gene expression and causing CNS abnormalities. These data show the critical role of the GSK3β-CUGBP1 pathway in DM1 muscle and in CNS pathologies, suggesting the benefits of GSK3 inhibitors in patients with different forms of DM1.
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Affiliation(s)
- Maggie Lutz
- Division of Neurology, Cincinnati Children’s Hospital, Cincinnati, OH 45229, USA; (M.L.); (M.L.)
| | - Miranda Levanti
- Division of Neurology, Cincinnati Children’s Hospital, Cincinnati, OH 45229, USA; (M.L.); (M.L.)
| | - Rebekah Karns
- Departments of Gastroenterology, Hepatology & Nutrition, Cincinnati Children’s Hospital, Cincinnati, OH 45229, USA;
| | - Genevieve Gourdon
- Sorbonne Université, Inserm, institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France;
| | - Diana Lindquist
- Imagine Research Center, Cincinnati Children’s Hospital, Cincinnati, OH 45229, USA;
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA;
| | - Nikolai A. Timchenko
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA;
- Department of Surgery, Cincinnati Children’s Hospital, Cincinnati, OH 45229, USA
| | - Lubov Timchenko
- Division of Neurology, Cincinnati Children’s Hospital, Cincinnati, OH 45229, USA; (M.L.); (M.L.)
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA;
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16
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Vokshi BH, Davidson G, Tawanaie Pour Sedehi N, Helleux A, Rippinger M, Haller AR, Gantzer J, Thouvenin J, Baltzinger P, Bouarich R, Manriquez V, Zaidi S, Rao P, Msaouel P, Su X, Lang H, Tricard T, Lindner V, Surdez D, Kurtz JE, Bourdeaut F, Tannir NM, Davidson I, Malouf GG. SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. Nat Commun 2023; 14:3034. [PMID: 37236926 DOI: 10.1038/s41467-023-38472-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Renal medullary carcinoma (RMC) is an aggressive tumour driven by bi-allelic loss of SMARCB1 and tightly associated with sickle cell trait. However, the cell-of-origin and oncogenic mechanism remain poorly understood. Using single-cell sequencing of human RMC, we defined transformation of thick ascending limb (TAL) cells into an epithelial-mesenchymal gradient of RMC cells associated with loss of renal epithelial transcription factors TFCP2L1, HOXB9 and MITF and gain of MYC and NFE2L2-associated oncogenic and ferroptosis resistance programs. We describe the molecular basis for this transcriptional switch that is reversed by SMARCB1 re-expression repressing the oncogenic and ferroptosis resistance programs leading to ferroptotic cell death. Ferroptosis resistance links TAL cell survival with the high extracellular medullar iron concentrations associated with sickle cell trait, an environment propitious to the mutagenic events associated with RMC development. This unique environment may explain why RMC is the only SMARCB1-deficient tumour arising from epithelial cells, differentiating RMC from rhabdoid tumours arising from neural crest cells.
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Affiliation(s)
- Bujamin H Vokshi
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Guillaume Davidson
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Nassim Tawanaie Pour Sedehi
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Alexandra Helleux
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Marc Rippinger
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Alexandre R Haller
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Justine Gantzer
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Jonathan Thouvenin
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Philippe Baltzinger
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Rachida Bouarich
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Valeria Manriquez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Priya Rao
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hervé Lang
- Department of Urology, CHRU Strasbourg, Strasbourg University, 67000, Strasbourg, France
| | - Thibault Tricard
- Department of Urology, CHRU Strasbourg, Strasbourg University, 67000, Strasbourg, France
| | - Véronique Lindner
- Department of Pathology, CHRU Strasbourg, Strasbourg University, 67200, Strasbourg, France
| | - Didier Surdez
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
- INSERM, U830, Pediatric Translational Research, PSL Research University, SIREDO Oncology Center, Institut Curie, Paris, France
| | - Jean-Emmanuel Kurtz
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Franck Bourdeaut
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Irwin Davidson
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France.
- 'Équipe Labellisée' Ligue National contre le Cancer, Paris, France.
| | - Gabriel G Malouf
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France.
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France.
- 'Équipe Labellisée' Ligue National contre le Cancer, Paris, France.
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17
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Lei YQ, Ye ZJ, Wei YL, Zhu LP, Zhuang XD, Wang XR, Cao H. Nono deficiency impedes the proliferation and adhesion of H9c2 cardiomyocytes through Pi3k/Akt signaling pathway. Sci Rep 2023; 13:7134. [PMID: 37130848 PMCID: PMC10154399 DOI: 10.1038/s41598-023-32572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/29/2023] [Indexed: 05/04/2023] Open
Abstract
Congenital heart disease (CHD) is the most common type of birth defect and the main noninfectious cause of death during the neonatal stage. The non-POU domain containing, octamer-binding gene, NONO, performs a variety of roles involved in DNA repair, RNA synthesis, transcriptional and post-transcriptional regulation. Currently, hemizygous loss-of-function mutation of NONO have been described as the genetic origin of CHD. However, essential effects of NONO during cardiac development have not been fully elucidated. In this study, we aim to understand role of Nono in cardiomyocytes during development by utilizing the CRISPR/Cas9 gene editing system to deplete Nono in the rat cardiomyocytes H9c2. Functional comparison of H9c2 control and knockout cells showed that Nono deficiency suppressed cell proliferation and adhesion. Furthermore, Nono depletion significantly affected the mitochondrial oxidative phosphorylation (OXPHOS) and glycolysis, resulting in H9c2 overall metabolic deficits. Mechanistically we demonstrated that the Nono knockout impeded the cardiomyocyte function by attenuating phosphatidyl inositol 3 kinase-serine/threonine kinase (Pi3k/Akt) signaling via the assay for transposase-accessible chromatin using sequencing in combination with RNA sequencing. From these results we propose a novel molecular mechanism of Nono to influence cardiomyocytes differentiation and proliferation during the development of embryonic heart. We conclude that NONO may represent an emerging possible biomarkers and targets for the diagnosis and treatment of human cardiac development defects.
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Affiliation(s)
- Yu-Qing Lei
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350000, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, 350000, China
- Department of Cardiac Surgery, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350011, China
| | - Zhou-Jie Ye
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350000, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, 350000, China
| | - Ya-Lan Wei
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350000, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, 350000, China
| | - Li-Ping Zhu
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350000, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, 350000, China
| | - Xu-Dong Zhuang
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350000, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, 350000, China
| | - Xin-Rui Wang
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350000, China.
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, 350000, China.
| | - Hua Cao
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350000, China.
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, 350000, China.
- Department of Cardiac Surgery, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350011, China.
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18
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Shah AM, Guo L, Morales MG, Jaichander P, Chen K, Huang H, Cano Hernandez K, Xu L, Bassel-Duby R, Olson EN, Liu N. TWIST2-mediated chromatin remodeling promotes fusion-negative rhabdomyosarcoma. SCIENCE ADVANCES 2023; 9:eade8184. [PMID: 37115930 PMCID: PMC10146891 DOI: 10.1126/sciadv.ade8184] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Rhabdomyosarcoma (RMS) is a common soft tissue sarcoma in children that resembles developing skeletal muscle. Unlike normal muscle cells, RMS cells fail to differentiate despite expression of the myogenic determination protein MYOD. The TWIST2 transcription factor is frequently overexpressed in fusion-negative RMS (FN-RMS). TWIST2 blocks differentiation by inhibiting MYOD activity in myoblasts, but its role in FN-RMS pathogenesis is incompletely understood. Here, we show that knockdown of TWIST2 enables FN-RMS cells to exit the cell cycle and undergo terminal myogenesis. TWIST2 knockdown also substantially reduces tumor growth in a mouse xenograft model of FN-RMS. Mechanistically, TWIST2 controls H3K27 acetylation at distal enhancers by interacting with the chromatin remodelers SMARCA4 and CHD3 to activate growth-related target genes and repress myogenesis-related target genes. These findings provide insights into the role of TWIST2 in maintaining an undifferentiated and tumorigenic state of FN-RMS and highlight the potential of suppressing TWIST2-regulated pathways to treat FN-RMS.
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Affiliation(s)
- Akansha M. Shah
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maria Gabriela Morales
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Priscilla Jaichander
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huocong Huang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Karla Cano Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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19
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Li F, Negi V, Yang P, Lee J, Ma K, Moulik M, Yechoor V. TEAD1 regulates cell proliferation through a pocket-independent transcription repression mechanism. Nucleic Acids Res 2022; 50:12723-12738. [PMID: 36484096 PMCID: PMC9825168 DOI: 10.1093/nar/gkac1063] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/13/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
The Hippo-TEAD pathway regulates cellular proliferation and function. The existing paradigm is that TEAD co-activators, YAP and TAZ, and co-repressor, VGLL4, bind to the pocket region of TEAD1 to enable transcriptional activation or repressive function. Here we demonstrate a pocket-independent transcription repression mechanism whereby TEAD1 controls cell proliferation in both non-malignant mature differentiated cells and in malignant cell models. TEAD1 overexpression can repress tumor cell proliferation in distinct cancer cell lines. In pancreatic β cells, conditional knockout of TEAD1 led to a cell-autonomous increase in proliferation. Genome-wide analysis of TEAD1 functional targets via transcriptomic profiling and cistromic analysis revealed distinct modes of target genes, with one class of targets directly repressed by TEAD1. We further demonstrate that TEAD1 controls target gene transcription in a motif-dependent and orientation-independent manner. Mechanistically, we show that TEAD1 has a pocket region-independent, direct repressive function via interfering with RNA polymerase II (POLII) binding to target promoters. Our study reveals that TEAD1 target genes constitute a mutually restricted regulatory loop to control cell proliferation and uncovers a novel direct repression mechanism involved in its transcriptional control that could be leveraged in future studies to modulate cell proliferation in tumors and potentially enhance the proliferation of normal mature cells.
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Affiliation(s)
- Feng Li
- Correspondence may also be addressed to Feng Li.
| | - Vinny Negi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ping Yang
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeongkyung Lee
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ke Ma
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Mousumi Moulik
- Division of Pediatric Cardiology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vijay K Yechoor
- To whom correspondence should be addressed. Tel: +1 412 383 4251; Fax: +1 412 648 3290;
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20
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Hazra R, Brine L, Garcia L, Benz B, Chirathivat N, Shen MM, Wilkinson JE, Lyons SK, Spector DL. Platr4 is an early embryonic lncRNA that exerts its function downstream on cardiogenic mesodermal lineage commitment. Dev Cell 2022; 57:2450-2468.e7. [PMID: 36347239 PMCID: PMC9680017 DOI: 10.1016/j.devcel.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022]
Abstract
The mammalian genome encodes thousands of long non-coding RNAs (lncRNAs), many of which are developmentally regulated and differentially expressed across tissues, suggesting their potential roles in cellular differentiation. Despite this expression pattern, little is known about how lncRNAs influence lineage commitment at the molecular level. Here, we demonstrate that perturbation of an embryonic stem cell/early embryonic lncRNA, pluripotency-associated transcript 4 (Platr4), directly influences the specification of cardiac-mesoderm-lineage differentiation. We show that Platr4 acts as a molecular scaffold or chaperone interacting with the Hippo-signaling pathway molecules Yap and Tead4 to regulate the expression of a downstream target gene, Ctgf, which is crucial to the cardiac-lineage program. Importantly, Platr4 knockout mice exhibit myocardial atrophy and valve mucinous degeneration, which are both associated with reduced cardiac output and sudden heart failure. Together, our findings provide evidence that Platr4 is required in cardiac-lineage specification and adult heart function in mice.
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Affiliation(s)
- Rasmani Hazra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Lily Brine
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Libia Garcia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Brian Benz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Napon Chirathivat
- Departments of Medicine, Genetics and Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael M Shen
- Departments of Medicine, Genetics and Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Scott K Lyons
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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21
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Lysyl Oxidases: Orchestrators of Cellular Behavior and ECM Remodeling and Homeostasis. Int J Mol Sci 2022; 23:ijms231911378. [PMID: 36232685 PMCID: PMC9569843 DOI: 10.3390/ijms231911378] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
Lysyl oxidases have long been considered key secreted extracellular matrix modifying enzymes. As such, their activity has been associated with the crosslinking of collagens and elastin, and as a result, they have been linked to multiple developmental and pathological processes. However, numerous lines of evidence also demonstrated that members of this enzyme family are localized and are active within the cytoplasm or cell nuclei, where they regulate and participate in distinct cellular events. In this review, we focus on a few of these events and highlight the intracellular role these enzymes play. Close examination of these events, suggest that the intracellular activities of lysyl oxidases is mostly observed in processes where concomitant changes in the extracellular matrix takes place. Here, we suggest that the LOX family members act in the relay between changes in the cells’ environment and the intracellular processes that promote them or that follow.
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22
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Wu BK, Mei SC, Chen EH, Zheng Y, Pan D. YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis. Nat Genet 2022; 54:1202-1213. [PMID: 35835915 PMCID: PMC9357225 DOI: 10.1038/s41588-022-01119-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 06/02/2022] [Indexed: 02/03/2023]
Abstract
Epigenetic remodeling is essential for oncogene-induced cellular transformation and malignancy. In contrast to histone post-translational modifications, how DNA methylation is remodeled by oncogenic signaling remains poorly understood. The oncoprotein YAP, a coactivator of the TEAD transcription factors mediating Hippo signaling, is widely activated in human cancers. Here, we identify the 5-methylcytosine dioxygenase TET1 as a direct YAP target and a master regulator that coordinates the genome-wide epigenetic and transcriptional reprogramming of YAP target genes in the liver. YAP activation induces the expression of TET1, which physically interacts with TEAD to cause regional DNA demethylation, histone H3K27 acetylation and chromatin opening in YAP target genes to facilitate transcriptional activation. Loss of TET1 not only reverses YAP-induced epigenetic and transcriptional changes but also suppresses YAP-induced hepatomegaly and tumorigenesis. These findings exemplify how oncogenic signaling regulates the site specificity of DNA demethylation to promote tumorigenesis and implicate TET1 as a potential target for modulating YAP signaling in physiology and disease.
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Affiliation(s)
- Bo-Kuan Wu
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Szu-Chieh Mei
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth H Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yonggang Zheng
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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23
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Lee U, Stuelsatz P, Karaz S, McKellar DW, Russeil J, Deak M, De Vlaminck I, Lepper C, Deplancke B, Cosgrove BD, Feige JN. A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle. iScience 2022; 25:104589. [PMID: 35789856 PMCID: PMC9250016 DOI: 10.1016/j.isci.2022.104589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 03/10/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Apelin (Apln) is a myokine that regulates skeletal muscle plasticity and metabolism and declines during aging. Through a yeast one-hybrid transcription factor binding screen, we identified the TEA domain transcription factor 1 (Tead1) as a novel regulator of the Apln promoter. Single-cell analysis of regenerating muscle revealed that the apelin receptor (Aplnr) is enriched in endothelial cells, whereas Tead1 is enriched in myogenic cells. Knock-down of Tead1 stimulates Apln secretion from muscle cells in vitro and myofiber-specific overexpression of Tead1 suppresses Apln secretion in vivo. Apln secretion via Tead1 knock-down in muscle cells stimulates endothelial cell expansion via endothelial Aplnr. In vivo, Apln peptide supplementation enhances endothelial cell expansion while Tead1 muscle overexpression delays endothelial remodeling following muscle injury. Our work describes a novel paracrine crosstalk in which Apln secretion is controlled by Tead1 in myogenic cells and influences endothelial remodeling during muscle repair.
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Affiliation(s)
- Umji Lee
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pascal Stuelsatz
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Sonia Karaz
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - David W. McKellar
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Julie Russeil
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Maria Deak
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christoph Lepper
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Bart Deplancke
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Jerome N. Feige
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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24
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Ong YT, Andrade J, Armbruster M, Shi C, Castro M, Costa ASH, Sugino T, Eelen G, Zimmermann B, Wilhelm K, Lim J, Watanabe S, Guenther S, Schneider A, Zanconato F, Kaulich M, Pan D, Braun T, Gerhardt H, Efeyan A, Carmeliet P, Piccolo S, Grosso AR, Potente M. A YAP/TAZ-TEAD signalling module links endothelial nutrient acquisition to angiogenic growth. Nat Metab 2022; 4:672-682. [PMID: 35726026 PMCID: PMC9236904 DOI: 10.1038/s42255-022-00584-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/13/2022] [Indexed: 12/13/2022]
Abstract
Angiogenesis, the process by which endothelial cells (ECs) form new blood vessels from existing ones, is intimately linked to the tissue's metabolic milieu and often occurs at nutrient-deficient sites. However, ECs rely on sufficient metabolic resources to support growth and proliferation. How endothelial nutrient acquisition and usage are regulated is unknown. Here we show that these processes are instructed by Yes-associated protein 1 (YAP)/WW domain-containing transcription regulator 1 (WWTR1/TAZ)-transcriptional enhanced associate domain (TEAD): a transcriptional module whose function is highly responsive to changes in the tissue environment. ECs lacking YAP/TAZ or their transcriptional partners, TEAD1, 2 and 4 fail to divide, resulting in stunted vascular growth in mice. Conversely, activation of TAZ, the more abundant paralogue in ECs, boosts proliferation, leading to vascular hyperplasia. We find that YAP/TAZ promote angiogenesis by fuelling nutrient-dependent mTORC1 signalling. By orchestrating the transcription of a repertoire of cell-surface transporters, including the large neutral amino acid transporter SLC7A5, YAP/TAZ-TEAD stimulate the import of amino acids and other essential nutrients, thereby enabling mTORC1 activation. Dissociating mTORC1 from these nutrient inputs-elicited by the loss of Rag GTPases-inhibits mTORC1 activity and prevents YAP/TAZ-dependent vascular growth. Together, these findings define a pivotal role for YAP/TAZ-TEAD in controlling endothelial mTORC1 and illustrate the essentiality of coordinated nutrient fluxes in the vasculature.
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Affiliation(s)
- Yu Ting Ong
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jorge Andrade
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Max Armbruster
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Chenyue Shi
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Marco Castro
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ana S H Costa
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Toshiya Sugino
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, and Department of Oncology and Leuven Cancer Institute, VIB and KU Leuven, Leuven, Belgium
| | - Barbara Zimmermann
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Kerstin Wilhelm
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Joseph Lim
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Shuichi Watanabe
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Guenther
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Andre Schneider
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Francesca Zanconato
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University, Frankfurt (Main), Germany
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Holger Gerhardt
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Integrative Vascular Biology Laboratory, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Vascular Patterning Laboratory, Center for Cancer Biology, VIB and KU Leuven, Leuven, Belgium
| | - Alejo Efeyan
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre, Madrid, Spain
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, and Department of Oncology and Leuven Cancer Institute, VIB and KU Leuven, Leuven, Belgium
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus, Denmark
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Ana Rita Grosso
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Michael Potente
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany.
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25
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Zhang S, Zhang Y, Chen C, Hu Q, Fu Y, Xu L, Wang C, Liu Y. Identification of Robust and Key Differentially Expressed Genes during C2C12 Cell Myogenesis Based on Multiomics Data. Int J Mol Sci 2022; 23:ijms23116002. [PMID: 35682680 PMCID: PMC9180599 DOI: 10.3390/ijms23116002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023] Open
Abstract
Myogenesis is a central step in prenatal myofiber formation, postnatal myofiber hypertrophy, and muscle damage repair in adulthood. RNA-Seq technology has greatly helped reveal the molecular mechanism of myogenesis, but batch effects in different experiments inevitably lead to misinterpretation of differentially expressed genes (DEGs). We previously applied the robust rank aggregation (RRA) method to effectively circumvent batch effects across multiple RNA-Seq datasets from 3T3-L1 cells. Here, we also used the RRA method to integrate nine RNA-Seq datasets from C2C12 cells and obtained 3140 robust DEGs between myoblasts and myotubes, which were then validated with array expression profiles and H3K27ac signals. The upregulated robust DEGs were highly enriched in gene ontology (GO) terms related to muscle cell differentiation and development. Considering that the cooperative binding of transcription factors (TFs) to enhancers to regulate downstream gene expression is a classical epigenetic mechanism, differentially expressed TFs (DETFs) were screened, and potential novel myogenic factors (MAF, BCL6, and ESR1) with high connection degree in protein-protein interaction (PPI) network were presented. Moreover, KLF5 cooperatively binds with the three key myogenic factors (MYOD, MYOG, and MEF2D) in C2C12 cells. Motif analysis speculates that the binding of MYOD and MYOG is KLF5-independent, while MEF2D is KLF5-dependent. It was revealed that KLF5-binding sites could be exploited to filter redundant MYOD-, MYOG-, and MEF2D-binding sites to focus on key enhancers for myogenesis. Further functional annotation of KLF5-binding sites suggested that KLF5 may regulate myogenesis through the PI3K-AKt signaling pathway, Rap1 signaling pathway, and the Hippo signaling pathway. In general, our study provides a wealth of untapped candidate targets for myogenesis and contributes new insights into the core regulatory mechanisms of myogenesis relying on KLF5-binding signal.
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Affiliation(s)
- Song Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (S.Z.); (Y.Z.); (C.C.); (Q.H.); (Y.F.); (L.X.); (C.W.)
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuanyuan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (S.Z.); (Y.Z.); (C.C.); (Q.H.); (Y.F.); (L.X.); (C.W.)
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Choulin Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (S.Z.); (Y.Z.); (C.C.); (Q.H.); (Y.F.); (L.X.); (C.W.)
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Hu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (S.Z.); (Y.Z.); (C.C.); (Q.H.); (Y.F.); (L.X.); (C.W.)
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (S.Z.); (Y.Z.); (C.C.); (Q.H.); (Y.F.); (L.X.); (C.W.)
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Lingna Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (S.Z.); (Y.Z.); (C.C.); (Q.H.); (Y.F.); (L.X.); (C.W.)
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Chao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (S.Z.); (Y.Z.); (C.C.); (Q.H.); (Y.F.); (L.X.); (C.W.)
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (S.Z.); (Y.Z.); (C.C.); (Q.H.); (Y.F.); (L.X.); (C.W.)
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China
- Correspondence:
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26
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Li Q, Wang Y, Hu X, Zhang Y, Li H, Zhang Q, Cai W, Wang Z, Zhu B, Xu L, Gao X, Chen Y, Gao H, Li J, Zhang L. Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation. Cell Prolif 2022; 55:e13219. [PMID: 35362202 PMCID: PMC9136495 DOI: 10.1111/cpr.13219] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/17/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
Objectives Although major advances have been made in bovine epigenome study, the epigenetic basis for fetal skeletal muscle development still remains poorly understood. The aim is to recapitulated the time course of fetal skeletal muscle development in vitro, and explore the dynamic changes of chromatin accessibility and gene expression during bovine myoblasts proliferation and differentiation. Methods PDGFR‐ cells were isolated from bovine fetal skeletal muscle, then cultured and induced myogenic differentiation in vitro in a time‐course study (P, D0, D2,and D4). The assay for transposase‐accessible chromatin sequencing (ATAC‐seq) and RNA sequencing (RNA‐seq) were performed. Results Among the enriched transcriptional factors with high variability, we determined the effects of MAFF, ZNF384, and KLF6 in myogenesis using RNA interference (RNAi). In addition, we identified both stage‐specific genes and chromatin accessibility regions to reveal the sequential order of gene expression, transcriptional regulatory, and signal pathways involved in bovine skeletal muscle development. Further investigation integrating chromatin accessibility and transcriptome data was conducted to explore cis‐regulatory regions in line with gene expression. Moreover, we combined bovine GWAS results of growth traits with regulatory regions defined by chromatin accessibility, providing a suggestive means for a more precise annotation of genetic variants of bovine growth traits. Conclusion Overall, these findings provide valuable information for understanding the stepwise regulatory mechanisms in skeletal muscle development and conducting beef cattle genetic improvement programs.
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Affiliation(s)
- Qian Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yahui Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xin Hu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yapeng Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Hongwei Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Qi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Wentao Cai
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zezhao Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Bo Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Lingyang Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xue Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yan Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Huijiang Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Junya Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Lupei Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
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27
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Haroon M, Boers HE, Bakker AD, Bloks NGC, Hoogaars WMH, Giordani L, Musters RJP, Deldicque L, Koppo K, Le Grand F, Klein-Nulend J, Jaspers RT. Reduced growth rate of aged muscle stem cells is associated with impaired mechanosensitivity. Aging (Albany NY) 2022; 14:28-53. [PMID: 35023852 PMCID: PMC8791224 DOI: 10.18632/aging.203830] [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] [Received: 02/24/2021] [Accepted: 01/03/2022] [Indexed: 11/25/2022]
Abstract
Aging-associated muscle wasting and impaired regeneration are caused by deficiencies in muscle stem cell (MuSC) number and function. We postulated that aged MuSCs are intrinsically impaired in their responsiveness to omnipresent mechanical cues through alterations in MuSC morphology, mechanical properties, and number of integrins, culminating in impaired proliferative capacity. Here we show that aged MuSCs exhibited significantly lower growth rate and reduced integrin-α7 expression as well as lower number of phospho-paxillin clusters than young MuSCs. Moreover, aged MuSCs were less firmly attached to matrigel-coated glass substrates compared to young MuSCs, as 43% of the cells detached in response to pulsating fluid shear stress (1 Pa). YAP nuclear localization was 59% higher than in young MuSCs, yet YAP target genes Cyr61 and Ctgf were substantially downregulated. When subjected to pulsating fluid shear stress, aged MuSCs exhibited reduced upregulation of proliferation-related genes. Together these results indicate that aged MuSCs exhibit impaired mechanosensitivity and growth potential, accompanied by altered morphology and mechanical properties as well as reduced integrin-α7 expression. Aging-associated impaired muscle regenerative capacity and muscle wasting is likely due to aging-induced intrinsic MuSC alterations and dysfunctional mechanosensitivity.
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Affiliation(s)
- Mohammad Haroon
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam 1081 HZ, The Netherlands
| | - Heleen E Boers
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam 1081 HZ, The Netherlands
| | - Astrid D Bakker
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam 1081 LA, The Netherlands
| | - Niek G C Bloks
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam 1081 HZ, The Netherlands
| | - Willem M H Hoogaars
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam 1081 HZ, The Netherlands
| | - Lorenzo Giordani
- Sorbonne Université, INSERM UMRS974, Center for Research in Myology, Paris 75013, France
| | - René J P Musters
- Department of Physiology, Amsterdam University Medical Center VUmc, Amsterdam Cardiovascular Sciences, Amsterdam 1081 HZ, The Netherlands
| | - Louise Deldicque
- Institute of Neuroscience, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Katrien Koppo
- Exercise Physiology Research Group, Department of Movement Sciences, KU Leuven, Leuven 3001, Belgium
| | - Fabien Le Grand
- Faculty of Medicine and Pharmacy, NeuroMyoGène UCBL-CNRS UMR 5310, INSERM U1217, Lyon 69008, France
| | - Jenneke Klein-Nulend
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam 1081 LA, The Netherlands
| | - Richard T Jaspers
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam 1081 HZ, The Netherlands
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28
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Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells. BMC Genomics 2021; 22:901. [PMID: 34915843 PMCID: PMC8675486 DOI: 10.1186/s12864-021-08224-7] [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: 07/09/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Satellite cells are the myogenic precursor cells in adult skeletal muscle. The objective of this study was to identify enhancers and transcription factors that regulate gene expression during the differentiation of bovine satellite cells into myotubes. RESULTS Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) was performed to identify genomic regions where lysine 27 of H3 histone is acetylated (H3K27ac), i.e., active enhancers, from bovine satellite cells before and during differentiation into myotubes. A total of 19,027 and 47,669 H3K27ac-marked enhancers were consistently identified from two biological replicates of before- and during-differentiation bovine satellite cells, respectively. Of these enhancers, 5882 were specific to before-differentiation, 35,723 to during-differentiation, and 13,199 common to before- and during-differentiation bovine satellite cells. Whereas most of the before- or during-differentiation-specific H3K27ac-marked enhancers were located distally to the transcription start site, the enhancers common to before- and during-differentiation were located both distally and proximally to the transcription start site. The three sets of H3K27ac-marked enhancers were associated with functionally different genes and enriched with different transcription factor binding sites. Specifically, many of the H3K27ac-marked enhancers specific to during-differentiation bovine satellite cells were associated with genes involved in muscle structure and development, and were enriched with binding sites for the MyoD, AP-1, KLF, TEAD, and MEF2 families of transcription factors. A positive role was validated for Fos and FosB, two AP-1 family transcription factors, in the differentiation of bovine satellite cells into myotubes by siRNA-mediated knockdown. CONCLUSIONS Tens of thousands of H3K27ac-marked active enhancers have been identified from bovine satellite cells before or during differentiation. These enhancers contain binding sites not only for transcription factors whose role in satellite cell differentiation is well known but also for transcription factors whose role in satellite cell differentiation is unknown. These enhancers and transcription factors are valuable resources for understanding the complex mechanism that mediates gene expression during satellite cell differentiation. Because satellite cell differentiation is a key step in skeletal muscle growth, the enhancers, the transcription factors, and their target genes identified in this study are also valuable resources for identifying and interpreting skeletal muscle trait-associated DNA variants in cattle.
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29
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McKellar DW, Walter LD, Song LT, Mantri M, Wang MFZ, De Vlaminck I, Cosgrove BD. Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration. Commun Biol 2021; 4:1280. [PMID: 34773081 PMCID: PMC8589952 DOI: 10.1038/s42003-021-02810-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 01/01/2023] Open
Abstract
Skeletal muscle repair is driven by the coordinated self-renewal and fusion of myogenic stem and progenitor cells. Single-cell gene expression analyses of myogenesis have been hampered by the poor sampling of rare and transient cell states that are critical for muscle repair, and do not inform the spatial context that is important for myogenic differentiation. Here, we demonstrate how large-scale integration of single-cell and spatial transcriptomic data can overcome these limitations. We created a single-cell transcriptomic dataset of mouse skeletal muscle by integration, consensus annotation, and analysis of 23 newly collected scRNAseq datasets and 88 publicly available single-cell (scRNAseq) and single-nucleus (snRNAseq) RNA-sequencing datasets. The resulting dataset includes more than 365,000 cells and spans a wide range of ages, injury, and repair conditions. Together, these data enabled identification of the predominant cell types in skeletal muscle, and resolved cell subtypes, including endothelial subtypes distinguished by vessel-type of origin, fibro-adipogenic progenitors defined by functional roles, and many distinct immune populations. The representation of different experimental conditions and the depth of transcriptome coverage enabled robust profiling of sparsely expressed genes. We built a densely sampled transcriptomic model of myogenesis, from stem cell quiescence to myofiber maturation, and identified rare, transitional states of progenitor commitment and fusion that are poorly represented in individual datasets. We performed spatial RNA sequencing of mouse muscle at three time points after injury and used the integrated dataset as a reference to achieve a high-resolution, local deconvolution of cell subtypes. We also used the integrated dataset to explore ligand-receptor co-expression patterns and identify dynamic cell-cell interactions in muscle injury response. We provide a public web tool to enable interactive exploration and visualization of the data. Our work supports the utility of large-scale integration of single-cell transcriptomic data as a tool for biological discovery.
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Affiliation(s)
- David W McKellar
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Lauren D Walter
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Leo T Song
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Madhav Mantri
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael F Z Wang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
| | - Benjamin D Cosgrove
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
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30
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Frede J, Anand P, Sotudeh N, Pinto RA, Nair MS, Stuart H, Yee AJ, Vijaykumar T, Waldschmidt JM, Potdar S, Kloeber JA, Kokkalis A, Dimitrova V, Mann M, Laubach JP, Richardson PG, Anderson KC, Raje NS, Knoechel B, Lohr JG. Dynamic transcriptional reprogramming leads to immunotherapeutic vulnerabilities in myeloma. Nat Cell Biol 2021; 23:1199-1211. [PMID: 34675390 PMCID: PMC8764878 DOI: 10.1038/s41556-021-00766-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
While there is extensive evidence for genetic variation as a basis for treatment resistance, other sources of variation result from cellular plasticity. Using multiple myeloma as an example of an incurable lymphoid malignancy, we show how cancer cells modulate lineage restriction, adapt their enhancer usage and employ cell-intrinsic diversity for survival and treatment escape. By using single-cell transcriptome and chromatin accessibility profiling, we show that distinct transcriptional states co-exist in individual cancer cells and that differential transcriptional regulon usage and enhancer rewiring underlie these alternative transcriptional states. We demonstrate that exposure to standard treatment further promotes transcriptional reprogramming and differential enhancer recruitment while simultaneously reducing developmental potential. Importantly, treatment generates a distinct complement of actionable immunotherapy targets, such as CXCR4, which can be exploited to overcome treatment resistance. Our studies therefore delineate how to transform the cellular plasticity that underlies drug resistance into immuno-oncologic therapeutic opportunities.
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Affiliation(s)
- Julia Frede
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Praveen Anand
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noori Sotudeh
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ricardo A. Pinto
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Monica S. Nair
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA
| | - Hannah Stuart
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA
| | - Andrew J. Yee
- Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital, Boston, MA, USA
| | - Tushara Vijaykumar
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA
| | - Johannes M. Waldschmidt
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sayalee Potdar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jake A. Kloeber
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA
| | - Antonis Kokkalis
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Valeriya Dimitrova
- Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mason Mann
- Massachusetts General Hospital, Boston, MA, USA
| | - Jacob P. Laubach
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Paul G. Richardson
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Kenneth C. Anderson
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Noopur S. Raje
- Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital, Boston, MA, USA
| | - Birgit Knoechel
- Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,These authors jointly supervised this work.,Correspondence: ,
| | - Jens G. Lohr
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,These authors jointly supervised this work.,Correspondence: ,
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31
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Chuang LSH, Ito Y. The Multiple Interactions of RUNX with the Hippo-YAP Pathway. Cells 2021; 10:2925. [PMID: 34831147 PMCID: PMC8616315 DOI: 10.3390/cells10112925] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/04/2023] Open
Abstract
The Hippo-YAP signaling pathway serves roles in cell proliferation, stem cell renewal/maintenance, differentiation and apoptosis. Many of its functions are central to early development, adult tissue repair/regeneration and not surprisingly, tumorigenesis and metastasis. The Hippo pathway represses the activity of YAP and paralog TAZ by modulating cell proliferation and promoting differentiation to maintain tissue homeostasis and proper organ size. Similarly, master regulators of development RUNX transcription factors have been shown to play critical roles in proliferation, differentiation, apoptosis and cell fate determination. In this review, we discuss the multiple interactions of RUNX with the Hippo-YAP pathway, their shared collaborators in Wnt, TGFβ, MYC and RB pathways, and their overlapping functions in development and tumorigenesis.
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Affiliation(s)
| | - Yoshiaki Ito
- NUS Centre for Cancer Research, Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore
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32
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Yilmaz O, Kizilaslan M, Arzik Y, Behrem S, Ata N, Karaca O, Elmaci C, Cemal I. Genome-wide association studies of preweaning growth and in vivo carcass composition traits in Esme sheep. J Anim Breed Genet 2021; 139:26-39. [PMID: 34331347 DOI: 10.1111/jbg.12640] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/06/2021] [Accepted: 07/22/2021] [Indexed: 01/15/2023]
Abstract
Sheep are considered as a major contributor of global food security. Moreover, sheep preweaning growth traits as well as in vivo carcass composition traits such as ultrasonic measurements of Longissimus dorsi muscle depth (UMD) and back-fat thickness (UFD) are crucially important indicators of meat yield and hot carcass composition. Despite their relative importance for productivity and profitability of a sheep production system, detected QTL for these traits are quite scarce. Therefore, we implemented GWAS for these traits using animal mixed model-based association approach provided by GenABEL in Esme sheep. Three genome-wide and 14 individual chromosome-wide associated SNPs were discovered. As a result, ESRP1, LOC105613082, ZNF641, DUSP5, TEAD1, SMOX, PTPRT, RALYL, POM121C, PHIP, LOC101106051, ZIM3, PEG3, TRPC7, FBXL4, LOC105610397, LOC105616489 and DNAAF2 were suggested as candidates. Some of the discovered genes and involved pathways were already annotated to contribute growth and development in various species including human, mice and cattle. All in all, the results of this study are expected to strongly contribute to shed a light on the underlying molecular mechanisms behind growth and carcass composition traits, with potential implications on studies aiming faster genetic improvement, targeted low-resolution SNP panel designs and genome-editing studies.
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Affiliation(s)
- Onur Yilmaz
- Department of Animal Science, Faculty of Agriculture, Aydin Adnan Menderes University, Aydin, Turkey
| | - Mehmet Kizilaslan
- Department of Animal Breeding and Genetics, International Center for Livestock Research and Training, Ankara, Turkey
| | - Yunus Arzik
- Department of Animal Breeding and Genetics, International Center for Livestock Research and Training, Ankara, Turkey
| | - Sedat Behrem
- Department of Animal Breeding and Genetics, International Center for Livestock Research and Training, Ankara, Turkey
| | - Nezih Ata
- Department of Animal Science, Faculty of Agriculture, Aydin Adnan Menderes University, Aydin, Turkey
| | - Orhan Karaca
- Department of Animal Science, Faculty of Agriculture, Aydin Adnan Menderes University, Aydin, Turkey
| | - Cengiz Elmaci
- Animal Science Department, Agriculture Faculty, Bursa Uludag University, Bursa, Turkey
| | - Ibrahim Cemal
- Department of Animal Science, Faculty of Agriculture, Aydin Adnan Menderes University, Aydin, Turkey
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Coto-Llerena M, Tosti N, Taha-Mehlitz S, Kancherla V, Paradiso V, Gallon J, Bianco G, Garofoli A, Ghosh S, Tang F, Ercan C, Christofori GM, Matter MS, Droeser RA, Zavolan M, Soysal SD, von Flüe M, Kollmar O, Terracciano LM, Ng CKY, Piscuoglio S. Transcriptional Enhancer Factor Domain Family member 4 Exerts an Oncogenic Role in Hepatocellular Carcinoma by Hippo-Independent Regulation of Heat Shock Protein 70 Family Members. Hepatol Commun 2021; 5:661-674. [PMID: 33860124 PMCID: PMC8034568 DOI: 10.1002/hep4.1656] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/10/2020] [Accepted: 11/24/2020] [Indexed: 12/25/2022] Open
Abstract
Transcriptional enhancer factor domain family member 4 (TEAD4) is a downstream effector of the conserved Hippo signaling pathway, regulating the expression of genes involved in cell proliferation and differentiation. It is up-regulated in several cancer types and is associated with metastasis and poor prognosis. However, its role in hepatocellular carcinoma (HCC) remains largely unexplored. Using data from The Cancer Genome Atlas, we found that TEAD4 was overexpressed in HCC and was associated with aggressive HCC features and worse outcome. Overexpression of TEAD4 significantly increased proliferation and migration rates in HCC cells in vitro as well as tumor growth in vivo. Additionally, RNA sequencing analysis of TEAD4-overexpressing HCC cells demonstrated that TEAD4 overexpression was associated with the up-regulation of genes involved in epithelial-to-mesenchymal transition, proliferation, and protein-folding pathways. Among the most up-regulated genes following TEAD4 overexpression were the 70-kDa heat shock protein (HSP70) family members HSPA6 and HSPA1A. Chromatin immunoprecipitation-quantitative real-time polymerase chain reaction experiments demonstrated that TEAD4 regulates HSPA6 and HSPA1A expression by directly binding to their promoter and enhancer regions. The pharmacologic inhibition of HSP70 expression in TEAD4-overexpressing cells reduced the effect of TEAD4 on cell proliferation. Finally, by overexpressing TEAD4 in yes-associated protein (YAP)/transcriptional coactivator with PDZ binding motif (TAZ)-knockdown HCC cells, we showed that the effect of TEAD4 on cell proliferation and its regulation of HSP70 expression does not require YAP and TAZ, the main effectors of the Hippo signaling pathway. Conclusion: A novel Hippo-independent mechanism for TEAD4 promotes cell proliferation and tumor growth in HCC by directly regulating HSP70 family members.
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Affiliation(s)
- Mairene Coto-Llerena
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland.,Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland
| | - Nadia Tosti
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Stephanie Taha-Mehlitz
- Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland.,ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Venkatesh Kancherla
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Viola Paradiso
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - John Gallon
- Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland
| | - Gaia Bianco
- Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland
| | - Andrea Garofoli
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Souvik Ghosh
- Computational and Systems Biology, BiozentrumUniversity of BaselBaselSwitzerland
| | - Fengyuan Tang
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Caner Ercan
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | | | - Matthias S Matter
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Raoul A Droeser
- ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, BiozentrumUniversity of BaselBaselSwitzerland
| | - Savas D Soysal
- ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Markus von Flüe
- ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Otto Kollmar
- ClarunisDepartment of Visceral SurgeryUniversity Center for Gastrointestinal and Liver DiseasesSt. Clara Hospital and University Hospital BaselBaselSwitzerland
| | - Luigi M Terracciano
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Charlotte K Y Ng
- Department for BioMedical ResearchUniversity of BernBernSwitzerland
| | - Salvatore Piscuoglio
- Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland.,Visceral Surgery and Precision Medicine Research LaboratoryDepartment of BiomedicineUniversity of BaselBaselSwitzerland
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Coassolo S, Davidson G, Negroni L, Gambi G, Daujat S, Romier C, Davidson I. Citrullination of pyruvate kinase M2 by PADI1 and PADI3 regulates glycolysis and cancer cell proliferation. Nat Commun 2021; 12:1718. [PMID: 33741961 PMCID: PMC7979715 DOI: 10.1038/s41467-021-21960-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/23/2021] [Indexed: 12/11/2022] Open
Abstract
Chromodomain helicase DNA binding protein 4 (CHD4) is an ATPase subunit of the Nucleosome Remodelling and Deacetylation (NuRD) complex that regulates gene expression. CHD4 is essential for growth of multiple patient derived melanoma xenografts and for breast cancer. Here we show that CHD4 regulates expression of PADI1 (Protein Arginine Deiminase 1) and PADI3 in multiple cancer cell types modulating citrullination of arginine residues of the allosterically-regulated glycolytic enzyme pyruvate kinase M2 (PKM2). Citrullination of PKM2 R106 reprogrammes cross-talk between PKM2 ligands lowering its sensitivity to the inhibitors Tryptophan, Alanine and Phenylalanine and promoting activation by Serine. Citrullination thus bypasses normal physiological regulation by low Serine levels to promote excessive glycolysis and reduced cell proliferation. We further show that PADI1 and PADI3 expression is up-regulated by hypoxia where PKM2 citrullination contributes to increased glycolysis. We provide insight as to how conversion of arginines to citrulline impacts key interactions within PKM2 that act in concert to reprogramme its activity as an additional mechanism regulating this important enzyme.
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Affiliation(s)
- Sébastien Coassolo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
- Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
| | - Giovanni Gambi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brandt, Illkirch, France
| | - Christophe Romier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France.
- Centre National de la Recherche Scientifique, Paris, France.
- Institut National de la Santé et de la Recherche Médicale, Paris, France.
- Université de Strasbourg, Strasbourg, France.
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Hippo pathway effectors YAP and TAZ and their association with skeletal muscle ageing. J Physiol Biochem 2021; 77:63-73. [PMID: 33495890 DOI: 10.1007/s13105-021-00787-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022]
Abstract
Skeletal muscle atrophy commonly occurs during ageing, thus pathways that regulate muscle mass may represent a potential therapeutic avenue for interventions. In this review, we explored the Hippo signalling pathway which plays an essential role in human oncogenesis and the pathway's influence on myogenesis and satellite cell functions, on supporting cells such as fibroblasts, and autophagy. YAP/TAZ was found to regulate both myoblast proliferation and differentiation, albeit with unique roles. Additionally, YAP/TAZ has different functions depending on the expressing cell type, making simple inference of their effects difficult. Studies in cancers have shown that the Hippo pathway influenced the autophagy pathway, although with mixed results. Most of the present researches on YAP/TAZ are focused on its oncogenicity and further studies are needed to translate these findings to physiological ageing. Taken together, the modulation of YAP/TAZ or the Hippo pathway in general may offer potential new strategies for the prevention or treatment of ageing.
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Filandrová R, Vališ K, Černý J, Chmelík J, Slavata L, Fiala J, Rosůlek M, Kavan D, Man P, Chum T, Cebecauer M, Fabris D, Novák P. Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA. Structure 2020; 29:345-356.e8. [PMID: 33333006 DOI: 10.1016/j.str.2020.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/29/2022]
Abstract
TEAD transcription factors regulate gene expression through interactions with DNA and other proteins. They are crucial for the development of eukaryotic organisms and to control the expression of genes involved mostly in cell proliferation and differentiation; however, their deregulation can lead to tumorigenesis. To study the interactions of TEAD1 with M-CAT motifs and their inverted versions, the KD of each complex was determined, and H/D exchange, quantitative chemical cross-linking, molecular docking, and smFRET were utilized for structural characterization. ChIP-qPCR was employed to correlate the results with a cell line model. The results obtained showed that although the inverted motif has 10× higher KD, the same residues were affected by the presence of M-CAT in both orientations. Molecular docking and smFRET revealed that TEAD1 binds the inverted motif rotated 180°. In addition, the inverted motif was proven to be occupied by TEAD1 in Jurkat cells, suggesting that the low-affinity binding sites present in the human genome may possess biological relevance.
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Affiliation(s)
- Růžena Filandrová
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Karel Vališ
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Lukáš Slavata
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Jan Fiala
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Michal Rosůlek
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Tomáš Chum
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 00, Czech Republic
| | - Marek Cebecauer
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 00, Czech Republic
| | - Daniele Fabris
- University of Connecticut, Department of Chemistry, 55 N. Eagleville Road, Storrs, CT 06269, USA
| | - Petr Novák
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic.
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Suo J, Feng X, Li J, Wang J, Wang Z, Zhang L, Zou W. VGLL4 promotes osteoblast differentiation by antagonizing TEADs-inhibited Runx2 transcription. SCIENCE ADVANCES 2020; 6:6/43/eaba4147. [PMID: 33097532 PMCID: PMC7608831 DOI: 10.1126/sciadv.aba4147] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 09/08/2020] [Indexed: 05/31/2023]
Abstract
VGLL4 has been identified as a YAP inhibitor. However, the exact function of VGLL4 in bone development and bone homeostasis remains unclear. In this study, we demonstrated that VGLL4 breaks TEADs-mediated transcriptional inhibition of RUNX2 to promote osteoblast differentiation and bone development. We found that knockout of VGLL4 in mesenchymal stem cells and preosteoblasts showed osteoporosis and a cleidocranial dysplasia-like phenotype due to osteoblast differentiation disorders. Mechanistically, we showed that the TEAD transcriptional factors severely inhibited osteoblast differentiation in a YAP binding-independent manner. TEADs interacted with RUNX2 to repress RUNX2 transcriptional activity. Furthermore, VGLL4 relieved the transcriptional inhibition of TEADs by directly competing with RUNX2 to bind TEADs through its two TDU domains. Collectively, our studies demonstrate that VGLL4 plays an important role in regulating osteoblast differentiation and bone development, and that TEADs regulate the transcriptional activity of RUNX2, which may shed light on treatment of cleidocranial dysplasia and osteoporosis.
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Affiliation(s)
- Jinlong Suo
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xue Feng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiayi Li
- Department of Laboratory Medicine, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China
| | - Jinghui Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zuoyun Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Lei Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
- Bio-Research Innovation Center, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Suzhou 215121, China
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
- Bio-Research Innovation Center, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Suzhou 215121, China
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Khilji S, Hamed M, Chen J, Li Q. Dissecting myogenin-mediated retinoid X receptor signaling in myogenic differentiation. Commun Biol 2020; 3:315. [PMID: 32555436 PMCID: PMC7303199 DOI: 10.1038/s42003-020-1043-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/21/2020] [Indexed: 11/18/2022] Open
Abstract
Deciphering the molecular mechanisms underpinning myoblast differentiation is a critical step in developing the best strategy to promote muscle regeneration in patients suffering from muscle-related diseases. We have previously established that a rexinoid x receptor (RXR)-selective agonist, bexarotene, enhances the differentiation and fusion of myoblasts through a direct regulation of MyoD expression, coupled with an augmentation of myogenin protein. Here, we found that RXR signaling associates with the distribution of myogenin at poised enhancers and a distinct E-box motif. We also found an association of myogenin with rexinoid-responsive gene expression and identified an epigenetic signature related to histone acetyltransferase p300. Moreover, RXR signaling augments residue-specific histone acetylation at enhancers co-occupied by p300 and myogenin. Thus, genomic distribution of transcriptional regulators is an important designate for identifying novel targets as well as developing therapeutics that modulate epigenetic landscape in a selective manner to promote muscle regeneration.
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Affiliation(s)
- Saadia Khilji
- Department of Cellular and Molecular Medicine and Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Munerah Hamed
- Department of Cellular and Molecular Medicine and Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jihong Chen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Qiao Li
- Department of Cellular and Molecular Medicine and Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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Gabay Yehezkely R, Zaffryar-Eilot S, Kaganovsky A, Fainshtain Malka N, Aviram R, Livneh I, Hasson P. Intracellular Role for the Matrix-Modifying Enzyme Lox in Regulating Transcription Factor Subcellular Localization and Activity in Muscle Regeneration. Dev Cell 2020; 53:406-417.e5. [DOI: 10.1016/j.devcel.2020.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 02/23/2020] [Accepted: 04/03/2020] [Indexed: 12/31/2022]
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Liu Z, Zhang X, Lei H, Lam N, Carter S, Yockey O, Xu M, Mendoza A, Hernandez ER, Wei JS, Khan J, Yohe ME, Shern JF, Thiele CJ. CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG. Nat Commun 2020; 11:911. [PMID: 32060262 PMCID: PMC7021771 DOI: 10.1038/s41467-020-14684-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 01/14/2020] [Indexed: 11/09/2022] Open
Abstract
Embryonal rhabdomyosarcoma (ERMS) is a childhood cancer that expresses myogenic master regulatory factor MYOD but fails to differentiate. Here, we show that the zinc finger transcription factor CASZ1 up-regulates MYOD signature genes and induces skeletal muscle differentiation in normal myoblasts and ERMS. The oncogenic activation of the RAS-MEK pathway suppresses CASZ1 expression in ERMS. ChIP-seq, ATAC-seq and RNA-seq experiments reveal that CASZ1 directly up-regulates skeletal muscle genes and represses non-muscle genes through affecting regional epigenetic modifications, chromatin accessibility and super-enhancer establishment. Next generation sequencing of primary RMS tumors identified a single nucleotide variant in the CASZ1 coding region that potentially contributes to ERMS tumorigenesis. Taken together, loss of CASZ1 activity, due to RAS-MEK signaling or genetic alteration, impairs ERMS differentiation, contributing to RMS tumorigenesis.
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Affiliation(s)
- Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Xiyuan Zhang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Haiyan Lei
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Norris Lam
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Sakereh Carter
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Oliver Yockey
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Max Xu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Arnulfo Mendoza
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Edjay R Hernandez
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jun S Wei
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marielle E Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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Wu SP, Anderson ML, Wang T, Zhou L, Emery OM, Li X, DeMayo FJ. Dynamic transcriptome, accessible genome, and PGR cistrome profiles in the human myometrium. FASEB J 2019; 34:2252-2268. [PMID: 31908010 DOI: 10.1096/fj.201902654r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 02/04/2023]
Abstract
The myometrium undergoes structural and functional remodeling during pregnancy. We hypothesize that myometrial genomic elements alter correspondingly in preparation for parturition. Human myometrial tissues from nonpregnant (NP) and term pregnant (TP) human subjects were examined by RNAseq, ATACseq, and PGR ChIPseq assays to profile transcriptome, assessible genome, and PGR occupancy. NP and TP specimens exhibit 2890 differentially expressed genes, reflecting an increase of metabolic, inflammatory, and PDGF signaling, among others, in adaptation to pregnancy. At the epigenome level, patterns of accessible genome change between NP and TP myometrium, leading to the altered enrichment of binding motifs for hormone and muscle regulators such as the progesterone receptor (PGR), Krüppel-like factors, and MEF2A transcription factors. PGR genome occupancy exhibits a significant difference between the two stages of the myometrium, concomitant with distinct transcriptomic profiles including genes such as ENO1, LHDA, and PLCL1 in the glycolytic and calcium signaling pathways. Over-representation of SRF, MYOD, and STAT binding motifs in PGR occupying sites further suggests interactions between PGR and major muscle regulators for myometrial gene expression. In conclusion, changes in accessible genome and PGR occupancy are part of the myometrial remodeling process and may serve as mechanisms to formulate the state-specific transcriptome profiles.
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Affiliation(s)
- San-Pin Wu
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Matthew L Anderson
- Department of Obstetrics & Gynecology, University of South Florida Morsani College of Medicine and Moffitt Cancer Center, Tampa, FL
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Lecong Zhou
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Olivia M Emery
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Xilong Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Francesco J DeMayo
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC
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42
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Selvaraj S, Mondragon-Gonzalez R, Xu B, Magli A, Kim H, Lainé J, Kiley J, Mckee H, Rinaldi F, Aho J, Tabti N, Shen W, Perlingeiro RCR. Screening identifies small molecules that enhance the maturation of human pluripotent stem cell-derived myotubes. eLife 2019; 8:e47970. [PMID: 31710288 PMCID: PMC6845233 DOI: 10.7554/elife.47970] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 10/29/2019] [Indexed: 01/14/2023] Open
Abstract
Targeted differentiation of pluripotent stem (PS) cells into myotubes enables in vitro disease modeling of skeletal muscle diseases. Although various protocols achieve myogenic differentiation in vitro, resulting myotubes typically display an embryonic identity. This is a major hurdle for accurately recapitulating disease phenotypes in vitro, as disease commonly manifests at later stages of development. To address this problem, we identified four factors from a small molecule screen whose combinatorial treatment resulted in myotubes with enhanced maturation, as shown by the expression profile of myosin heavy chain isoforms, as well as the upregulation of genes related with muscle contractile function. These molecular changes were confirmed by global chromatin accessibility and transcriptome studies. Importantly, we also observed this maturation in three-dimensional muscle constructs, which displayed improved in vitro contractile force generation in response to electrical stimulus. Thus, we established a model for in vitro muscle maturation from PS cells.
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Affiliation(s)
- Sridhar Selvaraj
- Lillehei Heart Institute, Department of MedicineUniversity of MinnesotaMinneapolisUnited States
| | - Ricardo Mondragon-Gonzalez
- Lillehei Heart Institute, Department of MedicineUniversity of MinnesotaMinneapolisUnited States
- Departamento de Genética y Biología MolecularCentro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN)Ciudad de MéxicoMexico
| | - Bin Xu
- Department of Biomedical EngineeringUniversity of MinnesotaMinneapolisUnited States
| | - Alessandro Magli
- Lillehei Heart Institute, Department of MedicineUniversity of MinnesotaMinneapolisUnited States
- Stem Cell InstituteUniversity of MinnesotaMinneapolisUnited States
| | - Hyunkee Kim
- Lillehei Heart Institute, Department of MedicineUniversity of MinnesotaMinneapolisUnited States
| | - Jeanne Lainé
- Département de PhysiologieSorbonne Universités, Faculté de Médecine site Pitié-SalpêtrièreParisFrance
| | - James Kiley
- Lillehei Heart Institute, Department of MedicineUniversity of MinnesotaMinneapolisUnited States
| | - Holly Mckee
- Lillehei Heart Institute, Department of MedicineUniversity of MinnesotaMinneapolisUnited States
| | | | - Joy Aho
- Stem Cell DepartmentBio-TechneMinneapolisUnited States
| | - Nacira Tabti
- Département de PhysiologieSorbonne Universités, Faculté de Médecine site Pitié-SalpêtrièreParisFrance
| | - Wei Shen
- Lillehei Heart Institute, Department of MedicineUniversity of MinnesotaMinneapolisUnited States
- Department of Biomedical EngineeringUniversity of MinnesotaMinneapolisUnited States
- Stem Cell InstituteUniversity of MinnesotaMinneapolisUnited States
| | - Rita CR Perlingeiro
- Lillehei Heart Institute, Department of MedicineUniversity of MinnesotaMinneapolisUnited States
- Stem Cell InstituteUniversity of MinnesotaMinneapolisUnited States
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43
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Feng X, Wang Z, Wang F, Lu T, Xu J, Ma X, Li J, He L, Zhang W, Li S, Yang W, Zhang S, Ge G, Zhao Y, Hu P, Zhang L. Dual function of VGLL4 in muscle regeneration. EMBO J 2019; 38:e101051. [PMID: 31328806 DOI: 10.15252/embj.2018101051] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 06/17/2019] [Accepted: 06/28/2019] [Indexed: 01/07/2023] Open
Abstract
VGLL4 has previously been identified as a negative regulator of YAP. Here we show that VGLL4 regulates muscle regeneration in both YAP-dependent and YAP-independent manners at different stages. Knockout of VGLL4 in mice leads to smaller myofiber size and defective muscle contraction force. Furthermore, our studies reveal that knockout of VGLL4 results in increased muscle satellite cells proliferation and impaired myoblast differentiation, which ultimately leads to delayed muscle regeneration. Mechanistically, the results show that VGLL4 works as a conventional repressor of YAP at the proliferation stage of muscle regeneration. At the differentiation stage, VGLL4 acts as a co-activator of TEAD4 to promote MyoG transactivation and facilitate the initiation of differentiation in a YAP-independent manner. Moreover, VGLL4 stabilizes the protein-protein interactions between MyoD and TEAD4 to achieve efficient MyoG transactivation. Our findings define the dual roles of VGLL4 in regulating muscle regeneration at different stages and may open novel therapeutic perspectives for muscle regeneration.
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Affiliation(s)
- Xue Feng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zuoyun Wang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Fei Wang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Tiantian Lu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinjin Xu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xueyan Ma
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinhui Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Lingli He
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenxiang Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Sheng Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenjun Yang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Shu Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Gaoxiang Ge
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yun Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ping Hu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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44
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Laurette P, Coassolo S, Davidson G, Michel I, Gambi G, Yao W, Sohier P, Li M, Mengus G, Larue L, Davidson I. Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma. Cell Death Differ 2019; 27:29-43. [PMID: 31065107 DOI: 10.1038/s41418-019-0333-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 03/04/2019] [Accepted: 03/28/2019] [Indexed: 11/09/2022] Open
Abstract
Somatic oncogenic mutation of BRAF coupled with inactivation of PTEN constitute a frequent combination of genomic alterations driving the development of human melanoma. Mice genetically engineered to conditionally express oncogenic BrafV600E and inactivate Pten in melanocytes following tamoxifen treatment rapidly develop melanoma. While early-stage melanomas comprised melanin-pigmented Mitf and Dct-expressing cells, expression of these and other melanocyte identity genes was lost in later stage tumours that showed histological and molecular characteristics of de-differentiated neural crest type cells. Melanocyte identity genes displayed loss of active chromatin marks and RNA polymerase II and gain of heterochromatin marks, indicating epigenetic reprogramming during tumour progression. Nevertheless, late-stage tumour cells grown in culture re-expressed Mitf, and melanocyte markers and Mitf together with Sox10 coregulated a large number of genes essential for their growth. In this melanoma model, somatic inactivation that the catalytic Brg1 (Smarca4) subunit of the SWI/SNF complex and the scaffolding Bptf subunit of the NuRF complex delayed tumour formation and deregulated large and overlapping gene expression programs essential for normal tumour cell growth. Moreover, we show that Brg1 and Bptf coregulated many genes together with Mitf and Sox10. Together these transcription factors and chromatin remodelling complexes orchestrate essential gene expression programs in mouse melanoma cells.
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Affiliation(s)
- Patrick Laurette
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Sébastien Coassolo
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Guillaume Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Isabelle Michel
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Giovanni Gambi
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Wenjin Yao
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Pierre Sohier
- INSERM U1021, Normal and Pathological Development of Melanocytes, Institut Curie, PSL Research University, Orsay, France.,Univ. Paris-Sud, Univ. Paris-Saclay, CNRS UMR3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Mei Li
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Lionel Larue
- INSERM U1021, Normal and Pathological Development of Melanocytes, Institut Curie, PSL Research University, Orsay, France.,Univ. Paris-Sud, Univ. Paris-Saclay, CNRS UMR3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France. .,Equipes Labellisées Ligue Contre le Cancer, Paris, France.
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45
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Liu R, Jagannathan R, Li F, Lee J, Balasubramanyam N, Kim BS, Yang P, Yechoor VK, Moulik M. Tead1 is required for perinatal cardiomyocyte proliferation. PLoS One 2019; 14:e0212017. [PMID: 30811446 PMCID: PMC6392249 DOI: 10.1371/journal.pone.0212017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/25/2019] [Indexed: 01/05/2023] Open
Abstract
Adult heart size is determined predominantly by the cardiomyocyte number and size. The cardiomyocyte number is determined primarily in the embryonic and perinatal period, as adult cardiomyocyte proliferation is restricted in comparison to that seen during the perinatal period. Recent evidence has implicated the mammalian Hippo kinase pathway as being critical in cardiomyocyte proliferation. Though the transcription factor, Tead1, is the canonical downstream transcriptional factor of the hippo kinase pathway in cardiomyocytes, the specific role of Tead1 in cardiomyocyte proliferation in the perinatal period has not been determined. Here, we report the generation of a cardiomyocyte specific perinatal deletion of Tead1, using Myh6-Cre deletor mice (Tead1-cKO). Perinatal Tead1 deletion was lethal by postnatal day 9 in Tead1-cKO mice due to dilated cardiomyopathy. Tead1-deficient cardiomyocytes have significantly decreased proliferation during the immediate postnatal period, when proliferation rate is normally high. Deletion of Tead1 in HL-1 cardiac cell line confirmed that cell-autonomous Tead1 function is required for normal cardiomyocyte proliferation. This was secondary to significant decrease in levels of many proteins, in vivo, that normally promote cell cycle in cardiomyocytes. Taken together this demonstrates the non-redundant critical requirement for Tead1 in regulating cell cycle proteins and proliferation in cardiomyocytes in the perinatal heart.
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Affiliation(s)
- Ruya Liu
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rajaganapathi Jagannathan
- Division of Cardiology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Feng Li
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeongkyung Lee
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nikhil Balasubramanyam
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Byung S. Kim
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ping Yang
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Vijay K. Yechoor
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mousumi Moulik
- Division of Cardiology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Cardiology, Department of Pediatrics, UTHealth McGovern Medical School, Houston, Texas, United States of America
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46
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Magli A, Baik J, Mills LJ, Kwak IY, Dillon BS, Mondragon Gonzalez R, Stafford DA, Swanson SA, Stewart R, Thomson JA, Garry DJ, Dynlacht BD, Perlingeiro RCR. Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm. PLoS Biol 2019; 17:e3000153. [PMID: 30807574 PMCID: PMC6390996 DOI: 10.1371/journal.pbio.3000153] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 02/01/2019] [Indexed: 12/26/2022] Open
Abstract
The transcriptional mechanisms driving lineage specification during development are still largely unknown, as the interplay of multiple transcription factors makes it difficult to dissect these molecular events. Using a cell-based differentiation platform to probe transcription function, we investigated the role of the key paraxial mesoderm and skeletal myogenic commitment factors-mesogenin 1 (Msgn1), T-box 6 (Tbx6), forkhead box C1 (Foxc1), paired box 3 (Pax3), Paraxis, mesenchyme homeobox 1 (Meox1), sine oculis-related homeobox 1 (Six1), and myogenic factor 5 (Myf5)-in paraxial mesoderm and skeletal myogenesis. From this study, we define a genetic hierarchy, with Pax3 emerging as the gatekeeper between the presomitic mesoderm and the myogenic lineage. By assaying chromatin accessibility, genomic binding and transcription profiling in mesodermal cells from mouse and human Pax3-induced embryonic stem cells and Pax3-null embryonic day (E)9.5 mouse embryos, we identified conserved Pax3 functions in the activation of the skeletal myogenic lineage through modulation of Hedgehog, Notch, and bone morphogenetic protein (BMP) signaling pathways. In addition, we demonstrate that Pax3 molecular function involves chromatin remodeling of its bound elements through an increase in chromatin accessibility and cooperation with sine oculis-related homeobox 4 (Six4) and TEA domain family member 2 (Tead2) factors. To our knowledge, these data provide the first integrated analysis of Pax3 function, demonstrating its ability to remodel chromatin in mesodermal cells from developing embryos and proving a mechanistic footing for the transcriptional hierarchy driving myogenesis.
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Affiliation(s)
- Alessandro Magli
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - June Baik
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lauren J. Mills
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Il-Youp Kwak
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Bridget S. Dillon
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ricardo Mondragon Gonzalez
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - David A. Stafford
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Scott A. Swanson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - James A. Thomson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Daniel J. Garry
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian D. Dynlacht
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, New York, United States of America
| | - Rita C. R. Perlingeiro
- Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
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47
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Smith SA, Sessions RB, Shoemark DK, Williams C, Ebrahimighaei R, McNeill MC, Crump MP, McKay TR, Harris G, Newby AC, Bond M. Antiproliferative and Antimigratory Effects of a Novel YAP-TEAD Interaction Inhibitor Identified Using in Silico Molecular Docking. J Med Chem 2019; 62:1291-1305. [PMID: 30640473 PMCID: PMC6701825 DOI: 10.1021/acs.jmedchem.8b01402] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
The Hippo pathway is an important
regulator of cell growth, proliferation,
and migration. TEAD transcription factors, which lie at the core of
the Hippo pathway, are essential for regulation of organ growth and
wound repair. Dysregulation of TEAD and its regulatory cofactor Yes-associated
protein (YAP) have been implicated in numerous human cancers and hyperproliferative
pathological processes. Hence, the YAP–TEAD complex is a promising
therapeutic target. Here, we use in silico molecular docking using
Bristol University Docking Engine to screen a library of more than
8 million druglike molecules for novel disrupters of the YAP–TEAD
interaction. We report the identification of a novel compound (CPD3.1)
with the ability to disrupt YAP–TEAD protein–protein
interaction and inhibit TEAD activity, cell proliferation, and cell
migration. The YAP–TEAD complex is a viable drug target, and
CPD3.1 is a lead compound for the development of more potent TEAD
inhibitors for treating cancer and other hyperproliferative pathologies.
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Affiliation(s)
- Sarah A Smith
- School of Translational Health Sciences, Faculty of Health Sciences , University of Bristol , Research Floor Level 7, Bristol Royal Infirmary , Bristol BS2 8HW , U.K
| | - Richard B Sessions
- School of Biochemistry, Faculty of Biomedical Sciences , University of Bristol , Biomedical Sciences Building, University Walk , Bristol BS8 1TD , U.K
| | - Deborah K Shoemark
- School of Biochemistry, Faculty of Biomedical Sciences , University of Bristol , Biomedical Sciences Building, University Walk , Bristol BS8 1TD , U.K
| | - Christopher Williams
- School of Chemistry, Faculty of Science , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Reza Ebrahimighaei
- School of Translational Health Sciences, Faculty of Health Sciences , University of Bristol , Research Floor Level 7, Bristol Royal Infirmary , Bristol BS2 8HW , U.K
| | - Madeleine C McNeill
- School of Translational Health Sciences, Faculty of Health Sciences , University of Bristol , Research Floor Level 7, Bristol Royal Infirmary , Bristol BS2 8HW , U.K
| | - Matthew P Crump
- School of Chemistry, Faculty of Science , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Tristan R McKay
- Centre for Bioscience , Manchester Metropolitan University , John Dalton Building , Manchester M1 5GD , U.K
| | - Gemma Harris
- Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot, Oxfordshire OX11 0FA , U.K
| | - Andrew C Newby
- School of Translational Health Sciences, Faculty of Health Sciences , University of Bristol , Research Floor Level 7, Bristol Royal Infirmary , Bristol BS2 8HW , U.K
| | - Mark Bond
- School of Translational Health Sciences, Faculty of Health Sciences , University of Bristol , Research Floor Level 7, Bristol Royal Infirmary , Bristol BS2 8HW , U.K
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48
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Thymine DNA glycosylase as a novel target for melanoma. Oncogene 2019; 38:3710-3728. [PMID: 30674989 PMCID: PMC6563616 DOI: 10.1038/s41388-018-0640-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 11/08/2018] [Accepted: 12/04/2018] [Indexed: 12/27/2022]
Abstract
Melanoma is an aggressive neoplasm with increasing incidence that is classified by the NCI as a recalcitrant cancer, i.e., a cancer with poor prognosis, lacking progress in diagnosis and treatment. In addition to conventional therapy, melanoma treatment is currently based on targeting the BRAF/MEK/ERK signaling pathway and immune checkpoints. As drug resistance remains a major obstacle to treatment success, advanced therapeutic approaches based on novel targets are still urgently needed. We reasoned that the base excision repair enzyme thymine DNA glycosylase (TDG) could be such a target for its dual role in safeguarding the genome and the epigenome, by performing the last of the multiple steps in DNA demethylation. Here we show that TDG knockdown in melanoma cell lines causes cell cycle arrest, senescence, and death by mitotic alterations; alters the transcriptome and methylome; and impairs xenograft tumor formation. Importantly, untransformed melanocytes are minimally affected by TDG knockdown, and adult mice with conditional knockout of Tdg are viable. Candidate TDG inhibitors, identified through a high-throughput fluorescence-based screen, reduced viability and clonogenic capacity of melanoma cell lines and increased cellular levels of 5-carboxylcytosine, the last intermediate in DNA demethylation, indicating successful on-target activity. These findings suggest that TDG may provide critical functions specific to cancer cells that make it a highly suitable anti-melanoma drug target. By potentially disrupting both DNA repair and the epigenetic state, targeting TDG may represent a completely new approach to melanoma therapy.
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49
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Rausch V, Bostrom JR, Park J, Bravo IR, Feng Y, Hay DC, Link BA, Hansen CG. The Hippo Pathway Regulates Caveolae Expression and Mediates Flow Response via Caveolae. Curr Biol 2018; 29:242-255.e6. [PMID: 30595521 PMCID: PMC6345631 DOI: 10.1016/j.cub.2018.11.066] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 09/27/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022]
Abstract
The Hippo pathway plays major roles in development, regeneration, and cancer. Its activity is tightly regulated by both diffusible chemical ligands and mechanical stimuli. The pathway consists of a series of kinases that can control the sub-cellular localization and stability of YAP or TAZ, homologous transcriptional co-factors. Caveolae, small (60–100 nm) bulb-like invaginations of the plasma membrane, are comprised predominantly of caveolin and cavin proteins and can respond to mechanical stimuli. Here, we show that YAP/TAZ, the major transcriptional mediators of the Hippo pathway, are critical for expression of caveolae components and therefore caveolae formation in both mammalian cells and zebrafish. In essence, without YAP/TAZ, the cell loses an entire organelle. CAVEOLIN1 and CAVIN1, the two essential caveolar genes, are direct target genes of YAP/TAZ, regulated via TEA domain (TEAD) transcription factors. Notably, YAP/TAZ become nuclear enriched and facilitate target gene transcription in cells with diminished levels of caveolae. Furthermore, caveolar-mediated shear stress response activates YAP/TAZ. These data link caveolae to Hippo signaling in the context of cellular responses to mechanical stimuli and suggest activity-based feedback regulation between components of caveolae and the outputs of the Hippo pathway. YAP/TAZ are critical for CAVIN1 and CAVEOLIN1 expression and caveolae formation The essential caveolar genes CAVIN1 and CAVEOLIN1 are direct YAP/TAZ-TEAD target genes YAP/TAZ are hyperactivated in caveolae-deficient cells Caveolae facilitate YAP/TAZ-mediated shear stress response
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Affiliation(s)
- Valentina Rausch
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh bioQuarter, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Jonathan R Bostrom
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jiwon Park
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh bioQuarter, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Isabel R Bravo
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh bioQuarter, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Yi Feng
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh bioQuarter, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - David C Hay
- MRC Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Carsten G Hansen
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh bioQuarter, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
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50
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Watt KI, Goodman CA, Hornberger TA, Gregorevic P. The Hippo Signaling Pathway in the Regulation of Skeletal Muscle Mass and Function. Exerc Sport Sci Rev 2018; 46:92-96. [PMID: 29346163 PMCID: PMC6319272 DOI: 10.1249/jes.0000000000000142] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Hippo signaling pathway regulates the activity of the proteins Yes-associated protein (Yap) and transcriptional co-activator with PDZ-binding motif (Taz) to control tissue growth in many different cell types. Previously, we demonstrated that Yap is a critical regulator of skeletal muscle mass. We hypothesize that alterations in Yap and Taz activity modulate the anabolic adaptations of skeletal muscle to resistance exercise.
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Affiliation(s)
- Kevin I. Watt
- Baker Heart and Diabetes Institute, Victoria, 3004, Australia
- Department of Diabetes, Monash University, Victoria, 3004, Australia
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Washington, USA
| | - Craig A. Goodman
- College of Health & Biomedicine, Victoria University, Melbourne, Victoria 8001, Australia
- Institute for Sport, Exercise and Active Living (ISEAL), Victoria University, Melbourne, Victoria, 8001, Australia
- Australian Institute of Musculoskeletal Science (AIMSS),Victoria University, St Albans, Victoria 3021, Australia
| | - Troy A. Hornberger
- Dept of Comparative Bioscience, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Paul Gregorevic
- Dept of Physiology, The University of Melbourne, Victoria, Australia, 3010
- Dept of Biochemistry and Molecular Biology, Monash University, Victoria, Australia, 3800
- Dept of Neurology, The University of Washington School of Medicine, Seattle, Washington, USA 98195
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