1
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Gomez‐Cardona E, Dehkordi MH, Van Baar K, Vitkauskaite A, Julien O, Fearnhead HO. An atlas of caspase cleavage events in differentiating muscle cells. Protein Sci 2024; 33:e5156. [PMID: 39180494 PMCID: PMC11344277 DOI: 10.1002/pro.5156] [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: 05/28/2024] [Revised: 08/02/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024]
Abstract
Executioner caspases, such as caspase-3, are known to induce apoptosis, but in other contexts, they can control very different fates, including cell differentiation and neuronal plasticity. While hundreds of caspase substrates are known to be specifically targeted during cell death, we know very little about how caspase activity brings about non-apoptotic fates. Here, we report the first proteome identification of cleavage events in C2C12 cells undergoing myogenic differentiation and its comparison to undifferentiated or dying C2C12 cells. These data have identified new caspase substrates, including caspase substrates specifically associated with differentiation, and show that caspases are regulating proteins involved in myogenesis in myotubes, several days after caspase-3 initiated differentiation. Cytoskeletal proteins emerged as a major group of non-apoptotic caspase substrates. We also identified proteins with well-established roles in muscle differentiation as substrates cleaved in differentiating cells.
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Affiliation(s)
- Erik Gomez‐Cardona
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaAlbertaCanada
| | - Mahshid H. Dehkordi
- Pharmacology and Therapeutics, School of MedicineUniversity of GalwayGalwayIreland
| | - Kolden Van Baar
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaAlbertaCanada
| | - Aiste Vitkauskaite
- Pharmacology and Therapeutics, School of MedicineUniversity of GalwayGalwayIreland
| | - Olivier Julien
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaAlbertaCanada
| | - Howard O. Fearnhead
- Pharmacology and Therapeutics, School of MedicineUniversity of GalwayGalwayIreland
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2
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Lei H, Xu H, Wu Y. Role of UCHL3 in health and disease. Biochem Biophys Res Commun 2024; 734:150626. [PMID: 39226739 DOI: 10.1016/j.bbrc.2024.150626] [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: 05/31/2024] [Revised: 08/16/2024] [Accepted: 08/28/2024] [Indexed: 09/05/2024]
Abstract
Ubiquitin C-terminal hydrolase 3 (UCHL3) is a cysteine protease that plays a crucial role in cell cycle regulation, DNA repair, and apoptosis by carrying out deubiquitination and deneddylation activities. It has emerged as a promising therapeutic target for certain cancers due to its ability to stabilize oncoproteins. The dysregulation of UCHL3 also has been associated with neurodegenerative diseases, underscoring its significance in maintaining protein homeostasis within cells. Research on UCHL3, including studies on Uchl3 knockout mice, has revealed its involvement in learning deficits, cellular stress responses, and retinal degeneration. This review delves into the cellular processes controlled by UCHL3 and its role in health and disease progression, as well as the development of UCHL3 inhibitors. Further investigation into the molecular mechanisms and physiological functions of UCHL3 is crucial for a comprehensive understanding of its impact on health and disease.
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Affiliation(s)
- Hu Lei
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Hanzhang Xu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yingli Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Pathophysiology, Research Unit of Stress and Cancer, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Shanghai Jiao Tong University, Research Units of Stress and Tumor (2019RU043), Chinese Academy of Medical Sciences, Sch Med, Shanghai 200025, China.
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3
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Fleischer S, Nash TR, Tamargo MA, Lock RI, Venturini G, Morsink M, Graney PL, Li V, Lamberti MJ, Liberman M, Kim Y, Tavakol DN, Zhuang RZ, Whitehead J, Friedman RA, Soni RK, Seidman JG, Seidman CE, Geraldino-Pardilla L, Winchester R, Vunjak-Novakovic G. An engineered human cardiac tissue model reveals contributions of systemic lupus erythematosus autoantibodies to myocardial injury. NATURE CARDIOVASCULAR RESEARCH 2024:10.1038/s44161-024-00525-w. [PMID: 39195859 DOI: 10.1038/s44161-024-00525-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 07/18/2024] [Indexed: 08/29/2024]
Abstract
Systemic lupus erythematosus (SLE) is a heterogenous autoimmune disease that affects multiple organs, including the heart. The mechanisms of myocardial injury in SLE remain poorly understood. In this study, we engineered human cardiac tissues and cultured them with IgG from patients with SLE, with and without myocardial involvement. IgG from patients with elevated myocardial inflammation exhibited increased binding to apoptotic cells within cardiac tissues subjected to stress, whereas IgG from patients with systolic dysfunction exhibited enhanced binding to the surface of live cardiomyocytes. Functional assays and RNA sequencing revealed that, in the absence of immune cells, IgG from patients with systolic dysfunction altered cellular composition, respiration and calcium handling. Phage immunoprecipitation sequencing (PhIP-seq) confirmed distinctive IgG profiles between patient subgroups. Coupling IgG profiling with cell surfaceome analysis identified four potential pathogenic autoantibodies that may directly affect the myocardium. Overall, these insights may improve patient risk stratification and inform the development of new therapeutic strategies.
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Affiliation(s)
- Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Manuel A Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Roberta I Lock
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Margaretha Morsink
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Vanessa Li
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Morgan J Lamberti
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Daniel N Tavakol
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jaron Whitehead
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Robert Winchester
- Department of Medicine, Columbia University, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
- College of Dental Medicine, Columbia University, New York, NY, USA.
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4
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Dai S, Peng Y, Wang G, Chen C, Chen Q, Yin L, Yan H, Zhang K, Tu M, Lu Z, Wei J, Li Q, Wu J, Jiang K, Zhu Y, Miao Y. LIM domain only 7: a novel driver of immune evasion through regulatory T cell differentiation and chemotaxis in pancreatic ductal adenocarcinoma. Cell Death Differ 2024:10.1038/s41418-024-01358-7. [PMID: 39143228 DOI: 10.1038/s41418-024-01358-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 08/03/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
With advancements in genomics and immunology, immunotherapy has emerged as a revolutionary strategy for tumor treatment. However, pancreatic ductal adenocarcinoma (PDAC), an immunologically "cold" tumor, exhibits limited responsiveness to immunotherapy. This study aimed to address the urgent need to uncover PDAC's immune microenvironment heterogeneity and identify the molecular mechanisms driving immune evasion. Using single-cell RNA sequencing datasets and spatial proteomics, we discovered LIM domain only 7 (LMO7) in PDAC cells as a previously unrecognized driver of immune evasion through Treg cell enrichment. LMO7 was positively correlated with infiltrating regulatory T cells (Tregs) and dysfunctional CD8+ T cells. A series of in vitro and in vivo experiments demonstrated LMO7's significant role in promoting Treg cell differentiation and chemotaxis while inhibiting CD8+ T cells and natural killer cell cytotoxicity. Mechanistically, LMO7, through its LIM domain, directly bound and promoted the ubiquitination and degradation of Foxp1. Foxp1 negatively regulated transforming growth factor-beta (TGF-β) and C-C motif chemokine ligand 5 (CCL5) expression by binding to sites 2 and I/III, respectively. Elevated TGF-β and CCL5 levels contribute to Treg cell enrichment, inducing immune evasion in PDAC. Combined treatment with TGF-β/CCL5 antibodies, along with LMO7 inhibition, effectively reversed immune evasion in PDAC, activated the immune response, and prolonged mouse survival. Therefore, this study identified LMO7 as a novel facilitator in driving immune evasion by promoting Treg cell enrichment and inhibiting cytotoxic effector functions. Targeting the LMO7-Foxp1-TGF-β/CCL5 axis holds promise as a therapeutic strategy for PDAC. Graphical abstract revealing LMO7 as a novel facilitator in driving immune evasion by promoting Tregs differentiation and chemotaxis, inducing CD8+ T/natural killer cells inhibition.
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Affiliation(s)
- Shangnan Dai
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Yunpeng Peng
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Guangfu Wang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Chongfa Chen
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Qiuyang Chen
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Lingdi Yin
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Han Yan
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Kai Zhang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Min Tu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Zipeng Lu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Jishu Wei
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Qiang Li
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Junli Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Kuirong Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China
| | - Yi Zhu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China.
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China.
| | - Yi Miao
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, PR China.
- Pancreas Institute, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, PR China.
- Pancreas Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China.
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5
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Israelsson P, Oda H, Öfverman C, Stefansson K, Lindquist D. Immunoreactivity of LMO7 and other molecular markers as potential prognostic factors in oropharyngeal squamous cell carcinoma. BMC Oral Health 2024; 24:729. [PMID: 38918827 PMCID: PMC11197244 DOI: 10.1186/s12903-024-04510-4] [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: 12/19/2023] [Accepted: 06/20/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Despite the better prognosis associated with human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (OPSCC), some patients experience relapse and succumb to the disease; thus, there is a need for biomarkers identifying these patients for intensified treatment. Leucine-rich repeats and immunoglobulin-like domain (LRIG) protein 1 is a negative regulator of receptor tyrosine kinase signaling and a positive prognostic factor in OPSCC. Studies indicate that LRIG1 interacts with the LIM domain 7 protein (LMO7), a stabilizer of adherence junctions. Its role in OPSCC has not been studied before. METHODS A total of 145 patients diagnosed with OPSCC were enrolled. Immunohistochemical LMO7 expression and staining intensity were evaluated in the tumors and correlated with known clinical and pathological prognostic factors, such as HPV status and LRIG1, CD44, Ki67, and p53 expression. RESULTS Our results show that high LMO7 expression is associated with significantly longer overall survival (OS) (p = 0.044). LMO7 was a positive prognostic factor for OS in univariate analysis (HR 0.515, 95% CI: 0.267-0.994, p = 0.048) but not in multivariate analysis. The LMO7 expression correlated with LRIG1 expression (p = 0.048), consistent with previous findings. Interestingly, strong LRIG1 staining intensity was an independent negative prognostic factor in the HPV-driven group of tumors (HR 2.847, 95% Cl: 1.036-7.825, p = 0.043). CONCLUSIONS We show for the first time that high LMO7 expression is a positive prognostic factor in OPSCC, and we propose that LMO7 should be further explored as a biomarker. In contrast to previous reports, LRIG1 expression was shown to be an independent negative prognostic factor in HPV-driven OPSCC.
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Affiliation(s)
- Pernilla Israelsson
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, 90185, Sweden.
| | - Husam Oda
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, 90185, Sweden
| | - Charlotte Öfverman
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, 90185, Sweden
| | - Kristina Stefansson
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, Umeå, 90185, Sweden
| | - David Lindquist
- Department of Clinical Sciences, Professional Development, Umeå University, Umeå, 90185, Sweden
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6
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Fleischer S, Nash TR, Tamargo MA, Lock RI, Venturini G, Morsink M, Li V, Lamberti MJ, Graney PL, Liberman M, Kim Y, Zhuang RZ, Whitehead J, Friedman RA, Soni RK, Seidman JG, Seidman CE, Geraldino-Pardilla L, Winchester R, Vunjak-Novakovic G. An engineered human cardiac tissue model reveals contributions of systemic lupus erythematosus autoantibodies to myocardial injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583787. [PMID: 38559188 PMCID: PMC10979865 DOI: 10.1101/2024.03.07.583787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Systemic lupus erythematosus (SLE) is a highly heterogenous autoimmune disease that affects multiple organs, including the heart. The mechanisms by which myocardial injury develops in SLE, however, remain poorly understood. Here we engineered human cardiac tissues and cultured them with IgG fractions containing autoantibodies from SLE patients with and without myocardial involvement. We observed unique binding patterns of IgG from two patient subgroups: (i) patients with severe myocardial inflammation exhibited enhanced binding to apoptotic cells within cardiac tissues subjected to stress, and (ii) patients with systolic dysfunction exhibited enhanced binding to the surfaces of viable cardiomyocytes. Functional assays and RNA sequencing (RNA-seq) revealed that IgGs from patients with systolic dysfunction exerted direct effects on engineered tissues in the absence of immune cells, altering tissue cellular composition, respiration and calcium handling. Autoantibody target characterization by phage immunoprecipitation sequencing (PhIP-seq) confirmed distinctive IgG profiles between patient subgroups. By coupling IgG profiling with cell surface protein analyses, we identified four pathogenic autoantibody candidates that may directly alter the function of cells within the myocardium. Taken together, these observations provide insights into the cellular processes of myocardial injury in SLE that have the potential to improve patient risk stratification and inform the development of novel therapeutic strategies.
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Affiliation(s)
- Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Manuel A Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Roberta I Lock
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Margaretha Morsink
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Vanessa Li
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Morgan J Lamberti
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jaron Whitehead
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Robert Winchester
- Department of Medicine, Columbia University, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
- College of Dental Medicine, Columbia University, New York, NY, USA
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7
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Wu T, Chen X, Xu K, Dai C, Li X, Zhang YWQ, Li J, Gao M, Liu Y, Liu F, Zhang X, Wang B, Xia P, Li Z, Ma W, Yuan Y. LIM domain only 7 negatively controls nonalcoholic steatohepatitis in the setting of hyperlipidemia. Hepatology 2024; 79:149-166. [PMID: 37676481 PMCID: PMC10718224 DOI: 10.1097/hep.0000000000000585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND AND AIMS Hyperlipidemia has been extensively recognized as a high-risk factor for NASH; however, clinical susceptibility to NASH is highly heterogeneous. The key controller(s) of NASH susceptibility in patients with hyperlipidemia has not yet been elucidated. Here, we aimed to reveal the key regulators of NASH in patients with hyperlipidemia and to explore its role and underlying mechanisms. APPROACH AND RESULTS To identify the predominant suppressors of NASH in the setting of hyperlipidemia, we collected liver biopsy samples from patients with hyperlipidemia, with or without NASH, and performed RNA-sequencing analysis. Notably, decreased Lineage specific Interacting Motif domain only 7 (LMO7) expression robustly correlated with the occurrence and severity of NASH. Although overexpression of LMO7 effectively blocked hepatic lipid accumulation and inflammation, LMO7 deficiency in hepatocytes greatly exacerbated diet-induced NASH progression. Mechanistically, lysine 48 (K48)-linked ubiquitin-mediated proteasomal degradation of tripartite motif-containing 47 (TRIM47) and subsequent inactivation of the c-Jun N-terminal kinase (JNK)/p38 mitogen-activated protein kinase (MAPK) cascade are required for the protective function of LMO7 in NASH. CONCLUSIONS These findings provide proof-of-concept evidence supporting LMO7 as a robust suppressor of NASH in the context of hyperlipidemia, indicating that targeting the LMO7-TRIM47 axis is a promising therapeutic strategy for NASH.
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Affiliation(s)
- Tiangen Wu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Xi Chen
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Kequan Xu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Caixia Dai
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Xiaomian Li
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Yang-Wen-Qing Zhang
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Jinghua Li
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Meng Gao
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Yingyi Liu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Fusheng Liu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Xutao Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Bicheng Wang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Peng Xia
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Zhen Li
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Weijie Ma
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Yufeng Yuan
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, PR China
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8
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Duan S, Lou X, Chen S, Jiang H, Chen D, Yin R, Li M, Gou Y, Zhao W, Sun L, Qian F. Macrophage LMO7 deficiency facilitates inflammatory injury via metabolic-epigenetic reprogramming. Acta Pharm Sin B 2023; 13:4785-4800. [PMID: 38045056 PMCID: PMC10692378 DOI: 10.1016/j.apsb.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/21/2023] [Accepted: 09/11/2023] [Indexed: 12/05/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a formidable disease due to its complex pathogenesis. Macrophages, as a major immune cell population in IBD, are crucial for gut homeostasis. However, it is still unveiled how macrophages modulate IBD. Here, we found that LIM domain only 7 (LMO7) was downregulated in pro-inflammatory macrophages, and that LMO7 directly degraded 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) through K48-mediated ubiquitination in macrophages. As an enzyme that regulates glycolysis, PFKFB3 degradation led to the glycolytic process inhibition in macrophages, which in turn inhibited macrophage activation and ultimately attenuated murine colitis. Moreover, we demonstrated that PFKFB3 was required for histone demethylase Jumonji domain-containing protein 3 (JMJD3) expression, thereby inhibiting the protein level of trimethylation of histone H3 on lysine 27 (H3K27me3). Overall, our results indicated the LMO7/PFKFB3/JMJD3 axis is essential for modulating macrophage function and IBD pathogenesis. Targeting LMO7 or macrophage metabolism could potentially be an effective strategy for treating inflammatory diseases.
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Affiliation(s)
- Shixin Duan
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinyi Lou
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiyi Chen
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongchao Jiang
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongxin Chen
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rui Yin
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengkai Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuseng Gou
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenjuan Zhao
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Sun
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Qian
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Zhou X, Tan F, Zhang S, Zhang T. Combining single-cell RNA sequencing data and transcriptomic data to unravel potential mechanisms and signature genes of the progression of idiopathic pulmonary fibrosis to lung adenocarcinoma and predict therapeutic agents. Funct Integr Genomics 2023; 23:346. [PMID: 37996625 DOI: 10.1007/s10142-023-01274-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/29/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Patients with idiopathic pulmonary fibrosis (IPF) have a significantly higher prevalence of lung adenocarcinoma (LUAD) than normal subjects, although the underlying association is unclear. The raw data involved were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis were used to screen for differentially expressed genes (DEGs) and modular signature genes (MSGs). Genes intersecting DEGs and MSGs were considered hub genes for IPF and LUAD. Machine learning algorithms were applied to capture epithelial cell-derived signature genes (EDSGs) shared. External cohort data were exploited to validate the robustness of EDSGs. Immunohistochemical staining and K-M plots were used to denote the prognostic value of EDSGs in LUAD. Based on EDSGs, we constructed a TF-gene-miRNA regulatory network. Molecular docking can validate the strength of action between candidate drugs and EDSGs. Epithelial cells, 650 DEGs, and 1773 MSGs were shared by IPF and LUAD. As for 379 hub genes, we performed pathway and functional enrichment analysis. By analyzing sc-RNA seq data, we identified 1234 marker genes of IPF epithelial cell-derived and 1481 of LUAD. And these genes shared 8 items with 379 hub genes. Through the machine learning algorithms, we further fished TRIM2, S100A14, CYP4B1, LMO7, and SFN. The ROC curves emphasized the significance of EDSGs in predicting the onset of LUAD and IPF. The TF-gene-miRNA network revealed regulatory relationships behind EDSGs. Finally, we predicted appropriate therapeutic agents. Our study preliminarily identified potential mechanisms between IPF and LUAD, which will inform subsequent studies.
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Affiliation(s)
- Xianqiang Zhou
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China
- Department of Pulmonary Diseases, Jing'an District Hospital of Traditional Chinese Medicine, Shanghai, 200072, China
| | - Fang Tan
- Department of Neurology, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, 230031, Anhui Province, China
| | - Suxian Zhang
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China
| | - Tiansong Zhang
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China.
- Department of Pulmonary Diseases, Jing'an District Hospital of Traditional Chinese Medicine, Shanghai, 200072, China.
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10
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Elzamzami FD, Samal A, Arun AS, Dharmaraj T, Prasad NR, Rendon-Jonguitud A, DeVine L, Walston JD, Cole RN, Wilson KL. Native lamin A/C proteomes and novel partners from heart and skeletal muscle in a mouse chronic inflammation model of human frailty. Front Cell Dev Biol 2023; 11:1240285. [PMID: 37936983 PMCID: PMC10626543 DOI: 10.3389/fcell.2023.1240285] [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: 06/14/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
Clinical frailty affects ∼10% of people over age 65 and is studied in a chronically inflamed (Interleukin-10 knockout; "IL10-KO") mouse model. Frailty phenotypes overlap the spectrum of diseases ("laminopathies") caused by mutations in LMNA. LMNA encodes nuclear intermediate filament proteins lamin A and lamin C ("lamin A/C"), important for tissue-specific signaling, metabolism and chromatin regulation. We hypothesized that wildtype lamin A/C associations with tissue-specific partners are perturbed by chronic inflammation, potentially contributing to dysfunction in frailty. To test this idea we immunoprecipitated native lamin A/C and associated proteins from skeletal muscle, hearts and brains of old (21-22 months) IL10-KO versus control C57Bl/6 female mice, and labeled with Tandem Mass Tags for identification and quantitation by mass spectrometry. We identified 502 candidate lamin-binding proteins from skeletal muscle, and 340 from heart, including 62 proteins identified in both tissues. Candidates included frailty phenotype-relevant proteins Perm1 and Fam210a, and nuclear membrane protein Tmem38a, required for muscle-specific genome organization. These and most other candidates were unaffected by IL10-KO, but still important as potential lamin A/C-binding proteins in native heart or muscle. A subset of candidates (21 in skeletal muscle, 30 in heart) showed significantly different lamin A/C-association in an IL10-KO tissue (p < 0.05), including AldoA and Gins3 affected in heart, and Lmcd1 and Fabp4 affected in skeletal muscle. To screen for binding, eleven candidates plus prelamin A and emerin controls were arrayed as synthetic 20-mer peptides (7-residue stagger) and incubated with recombinant purified lamin A "tail" residues 385-646 under relatively stringent conditions. We detected strong lamin A binding to peptides solvent exposed in Lmcd1, AldoA, Perm1, and Tmem38a, and plausible binding to Csrp3 (muscle LIM protein). These results validated both proteomes as sources for native lamin A/C-binding proteins in heart and muscle, identified four candidate genes for Emery-Dreifuss muscular dystrophy (CSRP3, LMCD1, ALDOA, and PERM1), support a lamin A-interactive molecular role for Tmem38A, and supported the hypothesis that lamin A/C interactions with at least two partners (AldoA in heart, transcription factor Lmcd1 in muscle) are altered in the IL10-KO model of frailty.
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Affiliation(s)
- Fatima D. Elzamzami
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Arushi Samal
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Adith S. Arun
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tejas Dharmaraj
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Neeti R. Prasad
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alex Rendon-Jonguitud
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lauren DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeremy D. Walston
- Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert N. Cole
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Katherine L. Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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11
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Bun T, Sato Y, Futami H, Tagawa Y, Murakami Y, Takahashi M. Cytoskeletal fractionation identifies LMO7 as a positive regulator of fibroblast polarization and directed migration. Biochem Biophys Res Commun 2023; 638:58-65. [PMID: 36442233 DOI: 10.1016/j.bbrc.2022.11.048] [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: 11/02/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
Abstract
Cell migration is a cytoskeleton-driven cellular process involved in physiological and pathological events such as embryonic development and cancer metastasis. Fibroblasts have often been used to elucidate the mechanism of cell migration due to their high morphological polarity and migratory activity. We recently reported that human lung fibroblasts migrate straight for a long duration without external stimuli, which phenomenon we named intrinsic and directed migration (IDM) of fibroblasts. In this study, we explored proteins involved in IDM in order to elucidate the molecular mechanism. First, we focused on the differences in morphology and migratory behaviors between normal and immortalized fibroblasts-the former exhibit obvious polarity and IDM; the latter exhibit poorly polarized morphology and random migration. We compared the abundance of proteins functioning as the cytoskeletal components between them through proteomic analysis and found that LIM domain only protein 7 (LMO7) is overwhelmingly incorporated into the cytoskeletons of normal fibroblasts. Depletion of LMO7 inhibited the directed migration of normal fibroblast on the fibronectin (FN)-rich surface, suggesting that LMO7 is important for IDM. Moreover, on the FN-free surface, LMO7-depleted fibroblasts often failed to establish morphological polarity and hardly migrated. Thus, the present study identified LMO7 as a positive regulator of fibroblast polarization and IDM, especially in an environment where integrin-mediated substrate attachment is insufficient.
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Affiliation(s)
- Taichi Bun
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Yuta Sato
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Hajime Futami
- Department of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuki Tagawa
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Yota Murakami
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Department of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Masayuki Takahashi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Department of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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12
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Schirmer EC, Latonen L, Tollis S. Nuclear size rectification: A potential new therapeutic approach to reduce metastasis in cancer. Front Cell Dev Biol 2022; 10:1022723. [PMID: 36299481 PMCID: PMC9589484 DOI: 10.3389/fcell.2022.1022723] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 03/07/2024] Open
Abstract
Research on metastasis has recently regained considerable interest with the hope that single cell technologies might reveal the most critical changes that support tumor spread. However, it is possible that part of the answer has been visible through the microscope for close to 200 years. Changes in nuclear size characteristically occur in many cancer types when the cells metastasize. This was initially discarded as contributing to the metastatic spread because, depending on tumor types, both increases and decreases in nuclear size could correlate with increased metastasis. However, recent work on nuclear mechanics and the connectivity between chromatin, the nucleoskeleton, and the cytoskeleton indicate that changes in this connectivity can have profound impacts on cell mobility and invasiveness. Critically, a recent study found that reversing tumor type-dependent nuclear size changes correlated with reduced cell migration and invasion. Accordingly, it seems appropriate to now revisit possible contributory roles of nuclear size changes to metastasis.
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Affiliation(s)
- Eric C. Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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13
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Zhang C, Cui J, Cao L, Tian X, Miao Y, Wang Y, Qiu S, Guo W, Ma L, Xia J, Zhang X. ISGylation of EMD promotes its interaction with PDHA to inhibit aerobic oxidation in lung adenocarcinoma. J Cell Mol Med 2022; 26:5078-5094. [PMID: 36071546 PMCID: PMC9549505 DOI: 10.1111/jcmm.17536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/16/2022] [Accepted: 08/26/2022] [Indexed: 11/27/2022] Open
Abstract
Abnormal nuclear structure caused by dysregulation of skeletal proteins is a common phenomenon in tumour cells. However, how skeletal proteins promote tumorigenesis remains uncovered. Here, we revealed the mechanism by which skeletal protein Emerin (EMD) promoted glucose metabolism to induce lung adenocarcinoma (LUAD). Firstly, we identified that EMD was highly expressed and promoted the malignant phenotypes in LUAD. The high expression of EMD might be due to its low level of ubiquitination. Additionally, the ISGylation at lysine 37 of EMD inhibited lysine 36 ubiquitination and upregulated EMD stability. We further explored that EMD could inhibit aerobic oxidation and stimulate glycolysis. Mechanistically, via its β‐catenin interaction domain, EMD bound with PDHA, stimulated serine 293 and 300 phosphorylation and inhibited PDHA expression, facilitated glycolysis of glucose that should enter the aerobic oxidation pathway, and EMD ISGylation was essential for EMD‐PDHA interaction. In clinical LUAD specimens, EMD was negatively associated with PDHA, while positively associated with EMD ISGylation, tumour stage and diameter. In LUAD with higher glucose level, EMD expression and ISGylation were higher. Collectively, EMD was a stimulator for LUAD by inhibiting aerobic oxidation via interacting with PDHA. Restricting cancer‐promoting role of EMD might be helpful for LUAD treatment.
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Affiliation(s)
- Congcong Zhang
- Anhui University of Science and Technology School of Medicine, Huainan, Anhui, China
| | - Jiangtao Cui
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leiqun Cao
- Anhui University of Science and Technology School of Medicine, Huainan, Anhui, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yikun Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyu Qiu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wanxin Guo
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinjing Xia
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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14
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Rampoldi A, Forghani P, Li D, Hwang H, Armand LC, Fite J, Boland G, Maxwell J, Maher K, Xu C. Space microgravity improves proliferation of human iPSC-derived cardiomyocytes. Stem Cell Reports 2022; 17:2272-2285. [PMID: 36084640 PMCID: PMC9561632 DOI: 10.1016/j.stemcr.2022.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022] Open
Abstract
In microgravity, cells undergo profound changes in their properties. However, how human cardiac progenitors respond to space microgravity is unknown. In this study, we evaluated the effect of space microgravity on differentiation of human induced pluripotent stem cell (hiPSC)-derived cardiac progenitors compared with 1G cultures on the International Space Station (ISS). Cryopreserved 3D cardiac progenitors were cultured for 3 weeks on the ISS. Compared with 1G cultures, the microgravity cultures had 3-fold larger sphere sizes, 20-fold higher counts of nuclei, and increased expression of proliferation markers. Highly enriched cardiomyocytes generated in space microgravity showed improved Ca2+ handling and increased expression of contraction-associated genes. Short-term exposure (3 days) of cardiac progenitors to space microgravity upregulated genes involved in cell proliferation, survival, cardiac differentiation, and contraction, consistent with improved microgravity cultures at the late stage. These results indicate that space microgravity increased proliferation of hiPSC-cardiomyocytes, which had appropriate structure and function. Cryopreserved 3D hiPSC-cardiac progenitors differentiated efficiently in space Microgravity cultures had increased sphere sizes and cellular proliferation Beating cardiomyocytes in microgravity cultures had improved Ca2+ handling Microgravity cultures had upregulated genes in cardiac contraction
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Affiliation(s)
- Antonio Rampoldi
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Parvin Forghani
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Dong Li
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Hyun Hwang
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Lawrence Christian Armand
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | | | - Joshua Maxwell
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Kevin Maher
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Chunhui Xu
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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15
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Liu G, Wang L, Wess J, Dean A. Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors. Nucleic Acids Res 2022; 50:9195-9211. [PMID: 36018801 PMCID: PMC9458430 DOI: 10.1093/nar/gkac707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022] Open
Abstract
Enhancers establish proximity with distant target genes to regulate temporospatial gene expression and specify cell identity. Lim domain binding protein 1 (LDB1) is a conserved and widely expressed protein that functions as an enhancer looping factor. Previous studies in erythroid cells and neuronal cells showed that LDB1 forms protein complexes with different transcription factors to regulate cell-specific gene expression. Here, we show that LDB1 regulates expression of liver genes by occupying enhancer elements and cooperating with hepatic transcription factors HNF4A, FOXA1, TCF7 and GATA4. Using the glucose transporter SLC2A2 gene, encoding GLUT2, as an example, we find that LDB1 regulates gene expression by mediating enhancer-promoter interactions. In vivo, we find that LDB1 deficiency in primary mouse hepatocytes dysregulates metabolic gene expression and changes the enhancer landscape. Conditional deletion of LDB1 in adult mouse liver induces glucose intolerance. However, Ldb1 knockout hepatocytes show improved liver pathology under high-fat diet conditions associated with increased expression of genes related to liver fatty acid metabolic processes. Thus, LDB1 is linked to liver metabolic functions under normal and obesogenic conditions.
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Affiliation(s)
- Guoyou Liu
- Correspondence may also be addressed to Guoyou Liu. Tel: +1 301 435 9396;
| | - Lei Wang
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jürgen Wess
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Dean
- To whom correspondence should be addressed. Tel: +1 301 496 6068;
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16
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Han L, Shi J, Zhao L, Deng J, Li Y, Zhao H, Wang H, Yan Y, Zou F. BCAP31 is involved in modulating colorectal cancer cell proliferation via the Emerin/β-catenin axis. Exp Cell Res 2022; 418:113265. [PMID: 35716785 DOI: 10.1016/j.yexcr.2022.113265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/12/2022] [Accepted: 06/13/2022] [Indexed: 11/15/2022]
Abstract
Understanding the mechanisms of colorectal cancer (CRC) progression is critical for developing innovative treatment strategies. As an endoplasmic reticulum-located protein, B cell receptor-associated protein 31 (BCAP31) has been identified to be highly expressed in multiple cancers. However, its function and molecular mechanism in CRC remain not fully understood. In the present study, BCAP31 expression and its correlation with the clinical stage were analyzed based on TCGA database. We demonstrated that loss of BCAP31 suppressed CRC cell proliferation in vitro and tumor growth in vivo. Mechanistically, we demonstrated that Emerin was an interaction partner and downstream molecule of BCAP31. Knockdown of BCAP31 promoted the nuclear envelope localization of Emerin, leading to a reduction of β-catenin accumulation in the nucleus, which resulted in downregulation of Wnt/β-catenin downstream target genes, including c-Myc, cyclin D1, Survivin, and Mcl-1. Moreover, downregulation of Emerin partially restored the BCAP31 depletion-mediated β-catenin protein level and tumor suppressive effects in CRC cells.Our data highlights the pivotal role of BCAP31 depletion in inhibiting cell proliferation in CRC cells, and mechanistically via Emerin/β-catenin signaling, which may serve as a promising target for CRC treatment.
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Affiliation(s)
- Liping Han
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Junyang Shi
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lili Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jiaqiang Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Hong Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huani Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yan Yan
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Fangdong Zou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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17
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Matsuda M, Chu CW, Sokol SY. Lmo7 recruits myosin II heavy chain to regulate actomyosin contractility and apical domain size in Xenopus ectoderm. Development 2022; 149:275389. [PMID: 35451459 PMCID: PMC9188752 DOI: 10.1242/dev.200236] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/30/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Apical constriction, or a reduction in size of the apical domain, underlies many morphogenetic events during development. Actomyosin complexes play an essential role in apical constriction; however, the detailed analysis of molecular mechanisms is still pending. Here, we show that Lim domain only protein 7 (Lmo7), a multidomain adaptor at apical junctions, promotes apical constriction in the Xenopus superficial ectoderm, whereas apical domain size increases in Lmo7-depleted cells. Lmo7 is primarily localized at apical junctions and promotes the formation of the dense circumferential actomyosin belt. Strikingly, Lmo7 binds non-muscle myosin II (NMII) and recruits it to apical junctions and the apical cortex. This NMII recruitment is essential for Lmo7-mediated apical constriction. Lmo7 knockdown decreases NMIIA localization at apical junctions and delays neural tube closure in Xenopus embryos. Our findings suggest that Lmo7 serves as a scaffold that regulates actomyosin contractility and apical domain size.
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Affiliation(s)
- Miho Matsuda
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chih-Wen Chu
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergei Y. Sokol
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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18
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Gomes G, do Amaral MJ, Bagri KM, Vasconcellos LM, Almeida MDS, Alvares LE, Mermelstein C. New Findings on LMO7 Transcripts, Proteins and Regulatory Regions in Human and Vertebrate Model Organisms and the Intracellular Distribution in Skeletal Muscle Cells. Int J Mol Sci 2021; 22:ijms222312885. [PMID: 34884689 PMCID: PMC8657913 DOI: 10.3390/ijms222312885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
LMO7 is a multifunctional PDZ–LIM protein that can interact with different molecular partners and is found in several intracellular locations. The aim of this work was to shed light on LMO7 evolution, alternative transcripts, protein structure and gene regulation through multiple in silico analyses. We also explored the intracellular distribution of the LMO7 protein in chicken and zebrafish embryonic skeletal muscle cells by means of confocal fluorescence microscopy. Our results revealed a single LMO7 gene in mammals, sauropsids, Xenopus and in the holostean fish spotted gar while two lmo7 genes (lmo7a and lmo7b) were identified in teleost fishes. In addition, several different transcripts were predicted for LMO7 in human and in major vertebrate model organisms (mouse, chicken, Xenopus and zebrafish). Bioinformatics tools revealed several structural features of the LMO7 protein including intrinsically disordered regions. We found the LMO7 protein in multiple intracellular compartments in chicken and zebrafish skeletal muscle cells, such as membrane adhesion sites and the perinuclear region. Curiously, the LMO7 protein was detected within the nuclei of muscle cells in chicken but not in zebrafish. Our data showed that a conserved regulatory element may be related to muscle-specific LMO7 expression. Our findings uncover new and important information about LMO7 and open new challenges to understanding how the diverse regulation, structure and distribution of this protein are integrated into highly complex vertebrate cellular milieux, such as skeletal muscle cells.
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Affiliation(s)
- Geyse Gomes
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (G.G.); (K.M.B.); (L.M.V.)
| | | | - Kayo Moreira Bagri
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (G.G.); (K.M.B.); (L.M.V.)
| | - Larissa Melo Vasconcellos
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (G.G.); (K.M.B.); (L.M.V.)
| | - Marcius da Silva Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Lúcia Elvira Alvares
- Departamento de Bioquímica e Biologia Tecidual, Universidade de Campinas (UNICAMP), Campinas, São Paulo 13083-872, Brazil;
| | - Claudia Mermelstein
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (G.G.); (K.M.B.); (L.M.V.)
- Correspondence:
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19
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Shen X, Wei Y, Liu W, You G, Tang S, Su Z, Du M, He J, Zhao J, Tian Y, Zhang Y, Ma M, Zhu Q, Yin H. A Novel Circular RNA circITSN2 Targets the miR-218-5p/LMO7 Axis to Promote Chicken Embryonic Myoblast Proliferation and Differentiation. Front Cell Dev Biol 2021; 9:748844. [PMID: 34692701 PMCID: PMC8526564 DOI: 10.3389/fcell.2021.748844] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/13/2021] [Indexed: 12/22/2022] Open
Abstract
Circular RNA (circRNA) is a class of endogenous non-coding RNAs without 5′ and 3′ ends; an increasing number of studies show that circRNA is involved in skeletal muscle development. From our previous sequencing data, the circRNAome in breast muscle of two chicken lines with a distinct rate of muscle development, which included a fast muscle growing broiler (FMGB) and a slow muscle growing layer (SMGL), we found a novel differentially expressed circRNA generated by intersectin 2 (ITSN2) gene (named circITSN2). We verified that circITSN2 is a skeletal muscle-enriched circRNA that promotes chicken primary myoblast (CPM) proliferation and differentiation. Further molecular mechanism analysis of circITSN2 in chicken myogenesis was performed, and we found circITSN2 directly targeting miR-218-5p. Besides, miR-218-5p inhibits CPM proliferation and differentiation, which is contrary to circITSN2. Commonly, circRNAs act as a miRNA sponge to alleviate the inhibition of miRNAs on mRNAs. Thus, we also identified that a downstream gene LIM domain 7 (LMO7) was inhibited by miR-218-5p, while circITSN2 could block the inhibitory effect of miR-218-5p by targeting it. Functional analysis revealed that LMO7 also accelerates CPM proliferation and differentiation, which was similar to circITSN2 but contrary to miR-218-5p. Taken together, these results suggested that circITSN2 promotes chicken embryonic skeletal muscle development via relieving the inhibition of miR-218-5p on LMO7. Our findings revealed a novel circITSN2/miR-218-5p/LMO7 axis in chicken embryonic skeletal muscle development, which expands our understanding of the complex muscle development regulatory network.
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Affiliation(s)
- Xiaoxu Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yuanhang Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guishuang You
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shuyue Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhenyu Su
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingxin Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jian He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongtong Tian
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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20
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The Role of Emerin in Cancer Progression and Metastasis. Int J Mol Sci 2021; 22:ijms222011289. [PMID: 34681951 PMCID: PMC8537873 DOI: 10.3390/ijms222011289] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly recognized in the field that cancer cells exhibit changes in the size and shape of their nuclei. These features often serve as important biomarkers in the diagnosis and prognosis of cancer patients. Nuclear size can significantly impact cell migration due to its incredibly large size. Nuclear structural changes are predicted to regulate cancer cell migration. Nuclear abnormalities are common across a vast spectrum of cancer types, regardless of tissue source, mutational spectrum, and signaling dependencies. The pervasiveness of nuclear alterations suggests that changes in nuclear structure may be crucially linked to the transformation process. The factors driving these nuclear abnormalities, and the functional consequences, are not completely understood. Nuclear envelope proteins play an important role in regulating nuclear size and structure in cancer. Altered expression of nuclear lamina proteins, including emerin, is found in many cancers and this expression is correlated with better clinical outcomes. A model is emerging whereby emerin, as well as other nuclear lamina proteins, binding to the nucleoskeleton regulates the nuclear structure to impact metastasis. In this model, emerin and lamins play a central role in metastatic transformation, since decreased emerin expression during transformation causes the nuclear structural defects required for increased cell migration, intravasation, and extravasation. Herein, we discuss the cellular functions of nuclear lamina proteins, with a particular focus on emerin, and how these functions impact cancer progression and metastasis.
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21
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do Amaral MJ, de Andrade Rosa I, Andrade SA, Fang X, Andrade LR, Costa ML, Mermelstein C. The perinuclear region concentrates disordered proteins with predicted phase separation distributed in a 3D network of cytoskeletal filaments and organelles. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119161. [PMID: 34655689 DOI: 10.1016/j.bbamcr.2021.119161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022]
Abstract
Membraneless organelles have emerged during the evolution of eukaryotic cells as intracellular domains in which multiple proteins organize into complex structures to perform specialized functions without the need of a lipid bilayer compartment. Here we describe the perinuclear space of eukaryotic cells as a highly organized network of cytoskeletal filaments that facilitates assembly of biomolecular condensates. Using bioinformatic analyses, we show that the perinuclear proteome is enriched in intrinsic disorder with several proteins predicted to undergo liquid-liquid phase separation. We also analyze immunofluorescence and transmission electron microscopy images showing the association between the nucleus and other organelles, such as mitochondria and lysosomes, or the labeling of specific proteins within the perinuclear region of cells. Altogether our data support the existence of a perinuclear dense sub-micron region formed by a well-organized three-dimensional network of structural and signaling proteins, including several proteins containing intrinsically disordered regions with phase behavior. This network of filamentous cytoskeletal proteins extends a few micrometers from the nucleus, contributes to local crowding, and organizes the movement of molecular complexes within the perinuclear space. Our findings take a key step towards understanding how membraneless regions within eukaryotic cells can serve as hubs for biomolecular condensates assembly, in particular the perinuclear space. Finally, evaluation of the disease context of the perinuclear proteins revealed that alterations in their expression can lead to several pathological conditions, and neurological disorders and cancer are among the most frequent.
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Affiliation(s)
| | - Ivone de Andrade Rosa
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Sarah Azevedo Andrade
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Xi Fang
- Department of Medicine, University of California, La Jolla, CA, USA
| | - Leonardo Rodrigues Andrade
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, RJ, Brazil; Salk Institute for Biological Studies, Waitt Advanced Biophotonics Core, La Jolla, CA, USA
| | - Manoel Luis Costa
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Claudia Mermelstein
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, RJ, Brazil.
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22
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Liu L, Chen Y, Diao J, Luo L, Gao Z. Identification and Characterization of Novel circRNAs Involved in Muscle Growth of Blunt Snout Bream ( Megalobrama amblycephala). Int J Mol Sci 2021; 22:ijms221810056. [PMID: 34576220 PMCID: PMC8467684 DOI: 10.3390/ijms221810056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Circular RNAs (circRNAs), a novel class of endogenous RNAs, have been recognized to play important roles in the growth of animals. However, the regulatory mechanism of circRNAs on fish muscle growth is still unclear. In this study, we performed whole transcriptome analysis of skeletal muscles from two populations with different growth rates (fast-growing and slow-growing) of blunt snout bream (Megalobrama amblycephala), an important fish species for aquaculture. The selected circRNAs were validated by qPCR and Sanger sequencing. Pairs of circRNA–miRNA–mRNA networks were constructed with the predicted differentially expressed (DE) pairs, which revealed regulatory roles in muscle myogenesis and hypertrophy. As a result, a total of 445 circRNAs were identified, including 42 DE circRNAs between fast-growing (FG) and slow-growing (SG) groups. Many of these DE circRNAs were related with aminoglycan biosynthetic and metabolic processes, cytokinetic processes, and the adherens junction pathway. The functional prediction results showed that novel_circ_0001608 and novel_circ_0002886, competing to bind with dre-miR-153b-5p and dre-miR-124-6-5p, might act as competing endogenous RNAs (ceRNAs) to control MamblycephalaGene14755 (pik3r1) and MamblycephalaGene10444 (apip) level, respectively, thus playing an important regulatory role in muscle growth. Overall, these results will not only help us to further understand the novel RNA transcripts in M. amblycephala, but also provide new clues to investigate the potential mechanism of circRNAs regulating fish growth and muscle development.
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Affiliation(s)
- Lifang Liu
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Yulong Chen
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jinghan Diao
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Lifei Luo
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
- Correspondence: (L.L.); or (Z.G.); Tel.: +86-2787282113 (Z.G.); Fax: +86-2787282114 (Z.G.)
| | - Zexia Gao
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
- Correspondence: (L.L.); or (Z.G.); Tel.: +86-2787282113 (Z.G.); Fax: +86-2787282114 (Z.G.)
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23
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Pawar S, Kutay U. The Diverse Cellular Functions of Inner Nuclear Membrane Proteins. Cold Spring Harb Perspect Biol 2021; 13:a040477. [PMID: 33753404 PMCID: PMC8411953 DOI: 10.1101/cshperspect.a040477] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nuclear compartment is delimited by a specialized expanded sheet of the endoplasmic reticulum (ER) known as the nuclear envelope (NE). Compared to the outer nuclear membrane and the contiguous peripheral ER, the inner nuclear membrane (INM) houses a unique set of transmembrane proteins that serve a staggering range of functions. Many of these functions reflect the exceptional position of INM proteins at the membrane-chromatin interface. Recent research revealed that numerous INM proteins perform crucial roles in chromatin organization, regulation of gene expression, genome stability, and mediation of signaling pathways into the nucleus. Other INM proteins establish mechanical links between chromatin and the cytoskeleton, help NE remodeling, or contribute to the surveillance of NE integrity and homeostasis. As INM proteins continue to gain prominence, we review these advancements and give an overview on the functional versatility of the INM proteome.
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Affiliation(s)
- Sumit Pawar
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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24
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Liddane AG, McNamara CA, Campbell MC, Mercier I, Holaska JM. Defects in Emerin-Nucleoskeleton Binding Disrupt Nuclear Structure and Promote Breast Cancer Cell Motility and Metastasis. Mol Cancer Res 2021; 19:1196-1207. [PMID: 33771882 PMCID: PMC8254762 DOI: 10.1158/1541-7786.mcr-20-0413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/27/2020] [Accepted: 03/19/2021] [Indexed: 01/17/2023]
Abstract
Nuclear envelope proteins play an important role in regulating nuclear size and structure in cancer. Altered expression of nuclear lamins are found in many cancers and its expression is correlated with better clinical outcomes. The nucleus is the largest organelle in the cell with a diameter between 10 and 20 μm. Nuclear size significantly impacts cell migration. Nuclear structural changes are predicted to impact cancer metastasis by regulating cancer cell migration. Here we show emerin regulates nuclear structure in invasive breast cancer cells to impact cancer metastasis. Invasive breast cancer cells had 40% to 50% less emerin than control cells, which resulted in decreased nuclear size. Overexpression of GFP-emerin in invasive breast cancer cells rescued nuclear size and inhibited migration through 3.0 and 8.0 μm pores. Mutational analysis showed emerin binding to nucleoskeletal proteins was important for its regulation of nuclear structure, migration, and invasion. Importantly, emerin expression inhibited lung metastasis by 91% in orthotopic mouse models of breast cancer. Emerin nucleoskeleton-binding mutants failed to inhibit metastasis. These results support a model whereby emerin binding to the nucleoskeleton regulates nuclear structure to impact metastasis. In this model, emerin plays a central role in metastatic transformation, because decreased emerin expression during transformation causes the nuclear structural defects required for increased cell migration, intravasation, and extravasation. IMPLICATIONS: Modulating emerin expression and function represents new targets for therapeutic interventions of metastasis, because increased emerin expression rescued cancer metastasis.
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Affiliation(s)
- Alexandra G Liddane
- Department of Pharmaceutical Sciences, University of the Sciences, Philadelphia, Pennsylvania
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey
| | - Chelsea A McNamara
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey
| | - Mallory C Campbell
- Department of Pharmaceutical Sciences, University of the Sciences, Philadelphia, Pennsylvania
| | - Isabelle Mercier
- Department of Pharmaceutical Sciences, University of the Sciences, Philadelphia, Pennsylvania
| | - James M Holaska
- Department of Pharmaceutical Sciences, University of the Sciences, Philadelphia, Pennsylvania.
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey
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25
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Costa ML, Jurberg AD, Mermelstein C. The Role of Embryonic Chick Muscle Cell Culture in the Study of Skeletal Myogenesis. Front Physiol 2021; 12:668600. [PMID: 34093232 PMCID: PMC8173222 DOI: 10.3389/fphys.2021.668600] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
The mechanisms involved in the development of skeletal muscle fibers have been studied in the last 70 years and yet many aspects of this process are still not completely understood. A myriad of in vivo and in vitro invertebrate and vertebrate animal models has been used for dissecting the molecular and cellular events involved in muscle formation. Among the most used animal models for the study of myogenesis are the rodents rat and mouse, the fruit fly Drosophila, and the birds chicken and quail. Here, we describe the robustness and advantages of the chick primary muscle culture model for the study of skeletal myogenesis. In the myoblast culture obtained from embryonic chick pectoralis muscle it is possible to analyze all the steps involved in skeletal myogenesis, such as myoblast proliferation, withdrawal from cell cycle, cell elongation and migration, myoblast alignment and fusion, the assembly of striated myofibrils, and the formation of multinucleated myotubes. The fact that in vitro chick myotubes can harbor hundreds of nuclei, whereas myotubes from cell lines have only a dozen nuclei demonstrates the high level of differentiation of the autonomous chick myogenic program. This striking differentiation is independent of serum withdrawal, which points to the power of the model. We also review the major pro-myogenic and anti-myogenic molecules and signaling pathways involved in chick myogenesis, in addition to providing a detailed protocol for the preparation of embryonic chick myogenic cultures. Moreover, we performed a bibliometric analysis of the articles that used this model to evaluate which were the main explored topics of interest and their contributors. We expect that by describing the major findings, and their advantages, of the studies using the embryonic chick myogenic model we will foster new studies on the molecular and cellular process involved in muscle proliferation and differentiation that are more similar to the actual in vivo condition than the muscle cell lines.
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Affiliation(s)
- Manoel L Costa
- Laboratório de Diferenciação Muscular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Arnon D Jurberg
- Laboratório de Diferenciação Muscular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Faculdade de Medicina-Presidente Vargas, Universidade Estácio de Sá, Rio de Janeiro, Brazil
| | - Claudia Mermelstein
- Laboratório de Diferenciação Muscular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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26
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Liu X, Yuan H, Zhou J, Wang Q, Qi X, Bernal C, Avella D, Kaifi JT, Kimchi ET, Timothy P, Cheng K, Miao Y, Jiang K, Li G. LMO7 as an Unrecognized Factor Promoting Pancreatic Cancer Progression and Metastasis. Front Cell Dev Biol 2021; 9:647387. [PMID: 33763427 PMCID: PMC7982467 DOI: 10.3389/fcell.2021.647387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Pancreatic cancer (PC) is one of the most lethal human malignancies without effective treatment. In an effort to discover key genes and molecular pathways underlying PC growth, we have identified LIM domain only 7 (LMO7) as an under-investigated molecule, which highly expresses in primary and metastatic human and mouse PC with the potential of impacting PC tumorigenesis and metastasis. Using genetic methods with siRNA, shRNA, and CRISPR-Cas9, we have successfully generated stable mouse PC cells with LMO7 knockdown or knockout. Using these cells with loss of LMO7 function, we have demonstrated that intrinsic LMO7 defect significantly suppresses PC cell proliferation, anchorage-free colony formation, and mobility in vitro and slows orthotopic PC tumor growth and metastasis in vivo. Mechanistic studies demonstrated that loss of LMO7 function causes PC cell-cycle arrest and apoptosis. These data indicate that LMO7 functions as an independent and unrecognized druggable factor significantly impacting PC growth and metastasis, which could be harnessed for developing a new targeted therapy for PC.
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Affiliation(s)
- Xinjian Liu
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States.,Department of Pathogen Biology, Key Laboratory of Antibody Technique of National Health Commission of China, Nanjing Medical University, Nanjing, China
| | - Hao Yuan
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States.,Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Zhou
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States
| | - Qiongling Wang
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States
| | - Xiaoqiang Qi
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States
| | - Catharine Bernal
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States
| | - Diego Avella
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States.,Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO, United States
| | - Jussuf T Kaifi
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States.,Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO, United States
| | - Eric T Kimchi
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States.,Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO, United States
| | - Parrett Timothy
- Department of Pathology and Anatomical Sciences, University of Missouri-Columbia, Columbia, MO, United States
| | - Kun Cheng
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Yi Miao
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kuirong Jiang
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States.,Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guangfu Li
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, United States.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
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27
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Alvelos MI, Brüggemann M, Sutandy FXR, Juan-Mateu J, Colli ML, Busch A, Lopes M, Castela Â, Aartsma-Rus A, König J, Zarnack K, Eizirik DL. The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Sci Alliance 2021; 4:e202000825. [PMID: 33376132 PMCID: PMC7772782 DOI: 10.26508/lsa.202000825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
In pancreatic β-cells, the expression of the splicing factor SRSF6 is regulated by GLIS3, a transcription factor encoded by a diabetes susceptibility gene. SRSF6 down-regulation promotes β-cell demise through splicing dysregulation of central genes for β-cells function and survival, but how RNAs are targeted by SRSF6 remains poorly understood. Here, we define the SRSF6 binding landscape in the human pancreatic β-cell line EndoC-βH1 by integrating individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) under basal conditions with RNA sequencing after SRSF6 knockdown. We detect thousands of SRSF6 bindings sites in coding sequences. Motif analyses suggest that SRSF6 specifically recognizes a purine-rich consensus motif consisting of GAA triplets and that the number of contiguous GAA triplets correlates with increasing binding site strength. The SRSF6 positioning determines the splicing fate. In line with its role in β-cell function, we identify SRSF6 binding sites on regulated exons in several diabetes susceptibility genes. In a proof-of-principle, the splicing of the susceptibility gene LMO7 is modulated by antisense oligonucleotides. Our present study unveils the splicing regulatory landscape of SRSF6 in immortalized human pancreatic β-cells.
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Affiliation(s)
- Maria Inês Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mirko Brüggemann
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Jonàs Juan-Mateu
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maikel Luis Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Anke Busch
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Miguel Lopes
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ângela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Julian König
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Kathi Zarnack
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Décio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
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De Queiroz Andrade E, Gomes GMC, Collison A, Grehan J, Murphy VE, Gibson P, Mattes J, Karmaus W. Variation of DNA Methylation in Newborns Associated with Exhaled Carbon Monoxide during Pregnancy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:1597. [PMID: 33567599 PMCID: PMC7915220 DOI: 10.3390/ijerph18041597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 11/23/2022]
Abstract
Fetal exposure to tobacco smoke is an adverse risk factor for newborns. A plausible mechanism of how this exposure may negatively impact long term health is differential methylation of deoxyribonucleic acid (DNAm) and its relation to birth weight. We examined whether self-reported gestational smoking status and maternal exhaled carbon monoxide (eCO) during early pregnancy were associated with methylation of cytosine by guanines (CpG) sites that themselves predicted birth weight. We focused first on CpGs associated with maternal smoking, and secondly, among these, on CpGs related to birth weight found in another cohort. Then in 94 newborns from the Breathing for Life Trial (BLT) DNAm levels in cord blood were determined using Infinium Methylation EPIC BeadChip measuring >850K CpGs. We regressed CpGs on eCO and tested via mediation analysis whether CpGs link eCO to birth weight. Nine smoking related CpG sites were significantly associated with birth weight. Among these nine CpGs the methylation of cg02264407 on the LMO7 gene was statistically significant and linked with eCO measurements. eCO greater than six ppm showed a 2.3% decrease in infant DNAm (p = 0.035) on the LMO7 gene. A 1% decrease in methylation at this site resulted in decreased birth weight by 44.8 g (p = 0.003). None of the nine CpGs tested was associated with self-reported smoking. This is the first study to report potential mediation of DNA methylation, linking eCO measurements during early pregnancy with birth weight.
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Affiliation(s)
- Ediane De Queiroz Andrade
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2308, Australia; (E.D.Q.A.); (G.M.C.G.); (J.G.); (V.E.M.); (J.M.)
- Priority Research Centre GrowUpWell, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Gabriela Martins Costa Gomes
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2308, Australia; (E.D.Q.A.); (G.M.C.G.); (J.G.); (V.E.M.); (J.M.)
- Priority Research Centre GrowUpWell, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Adam Collison
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2308, Australia; (E.D.Q.A.); (G.M.C.G.); (J.G.); (V.E.M.); (J.M.)
- Priority Research Centre GrowUpWell, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Jane Grehan
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2308, Australia; (E.D.Q.A.); (G.M.C.G.); (J.G.); (V.E.M.); (J.M.)
- Priority Research Centre GrowUpWell, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Vanessa E. Murphy
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2308, Australia; (E.D.Q.A.); (G.M.C.G.); (J.G.); (V.E.M.); (J.M.)
- Priority Research Centre GrowUpWell, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Peter Gibson
- Priority Research Centre Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2308, Australia;
- Respiratory & Sleep Medicine Department, John Hunter Hospital, Newcastle, NSW 2305, Australia
| | - Joerg Mattes
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2308, Australia; (E.D.Q.A.); (G.M.C.G.); (J.G.); (V.E.M.); (J.M.)
- Priority Research Centre GrowUpWell, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2308, Australia
- Paediatric Respiratory & Sleep Medicine Department, John Hunter Children’s Hospital, Newcastle, NSW 2305, Australia
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, The University of Memphis, Memphis, TN 38152, USA
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Goodman CA, Davey JR, Hagg A, Parker BL, Gregorevic P. Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β. Mol Cell Proteomics 2021; 20:100050. [PMID: 33516941 PMCID: PMC8042406 DOI: 10.1016/j.mcpro.2021.100050] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
Ubiquitination is a posttranslational protein modification that has been shown to have a range of effects, including regulation of protein function, interaction, localization, and degradation. We have previously shown that the muscle-specific ubiquitin E3 ligase, ASB2β, is downregulated in models of muscle growth and that overexpression ASB2β is sufficient to induce muscle atrophy. To gain insight into the effects of increased ASB2β expression on skeletal muscle mass and function, we used liquid chromatography coupled to tandem mass spectrometry to investigate ASB2β-mediated changes to the skeletal muscle proteome and ubiquitinome, via a parallel analysis of remnant diGly-modified peptides. The results show that viral vector-mediated ASB2β overexpression in murine muscles causes progressive muscle atrophy and impairment of force-producing capacity, while ASB2β knockdown induces mild muscle hypertrophy. ASB2β-induced muscle atrophy and dysfunction were associated with the early downregulation of mitochondrial and contractile protein abundance and the upregulation of proteins involved in proteasome-mediated protein degradation (including other E3 ligases), protein synthesis, and the cytoskeleton/sarcomere. The overexpression ASB2β also resulted in marked changes in protein ubiquitination; however, there was no simple relationship between changes in ubiquitination status and protein abundance. To investigate proteins that interact with ASB2β and, therefore, potential ASB2β targets, Flag-tagged wild-type ASB2β, and a mutant ASB2β lacking the C-terminal SOCS box domain (dSOCS) were immunoprecipitated from C2C12 myotubes and subjected to label-free proteomic analysis to determine the ASB2β interactome. ASB2β was found to interact with a range of cytoskeletal and nuclear proteins. When combined with the in vivo ubiquitinomic data, our studies have identified novel putative ASB2β target substrates that warrant further investigation. These findings provide novel insight into the complexity of proteome and ubiquitinome changes that occur during E3 ligase-mediated skeletal muscle atrophy and dysfunction.
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Affiliation(s)
- Craig A Goodman
- Department of Physiology, Centre for Muscle Research (CMR), The University of Melbourne, Victoria, Australia; Australian Institute for Musculoskeletal Science (AIMSS), Sunshine Hospital, The University of Melbourne, St Albans, Victoria, Australia
| | - Jonathan R Davey
- Department of Physiology, Centre for Muscle Research (CMR), The University of Melbourne, Victoria, Australia; Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Adam Hagg
- Department of Physiology, Centre for Muscle Research (CMR), The University of Melbourne, Victoria, Australia; Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Benjamin L Parker
- Department of Physiology, Centre for Muscle Research (CMR), The University of Melbourne, Victoria, Australia; Charles Perkins Centre, School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia.
| | - Paul Gregorevic
- Department of Physiology, Centre for Muscle Research (CMR), The University of Melbourne, Victoria, Australia; Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Department of Neurology, The University of Washington School of Medicine, Seattle, Washington, USA.
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LRIG1 is a conserved EGFR regulator involved in melanoma development, survival and treatment resistance. Oncogene 2021; 40:3707-3718. [PMID: 33947959 PMCID: PMC8154585 DOI: 10.1038/s41388-021-01808-3] [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: 08/24/2020] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 02/03/2023]
Abstract
Leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) is a pan-negative regulator of receptor tyrosine kinase (RTK) signaling and a tumor suppressor in several cancers, but its involvement in melanoma is largely unexplored. Here, we aim to determine the role of LRIG1 in melanoma tumorigenesis, RTK signaling, and BRAF inhibitor resistance. We find that LRIG1 is downregulated during early tumorigenesis and that LRIG1 affects activation of the epidermal growth factor receptor (EGFR) in melanoma cells. LRIG1-dependent regulation of EGFR signaling is evolutionary conserved to the roundworm C. elegans, where negative regulation of the EGFR-Ras-Raf pathway by sma-10/LRIG completely depends on presence of the receptor let-23/EGFR. In a cohort of metastatic melanoma patients, we observe an association between LRIG1 and survival in the triple wild-type subtype and in tumors with high EGFR expression. During in vitro development of BRAF inhibitor resistance, LRIG1 expression decreases; and mimics LRIG1 knockout cells for increased EGFR expression. Treating resistant cells with recombinant LRIG1 suppresses AKT activation and proliferation. Together, our results show that sma-10/LRIG is a conserved regulator of RTK signaling, add to our understanding of LRIG1 in melanoma and identifies recombinant LRIG1 as a potential therapeutic against BRAF inhibitor-resistant melanoma.
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Brhane Y, Yang P, Christiani DC, Liu G, McLaughlin JR, Brennan P, Shete S, Field JK, Tardón A, Kohno T, Shiraishi K, Matsuo K, Bossé Y, Amos CI, Hung RJ. Genetic Determinants of Lung Cancer Prognosis in Never Smokers: A Pooled Analysis in the International Lung Cancer Consortium. Cancer Epidemiol Biomarkers Prev 2020; 29:1983-1992. [PMID: 32699080 PMCID: PMC7541720 DOI: 10.1158/1055-9965.epi-20-0248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/12/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lung cancer remains the leading cause of cancer death worldwide, with 15% to 20% occurring in never smokers. To assess genetic determinants for prognosis among never smokers, we conducted a genome-wide investigation in the International Lung Cancer Consortium (ILCCO). METHODS Genomic and clinical data from 1,569 never-smoking patients with lung cancer of European ancestry from 10 ILCCO studies were included. HRs and 95% confidence intervals of overall survival were estimated. We assessed whether the associations were mediated through mRNA expression-based 1,553 normal lung tissues from the lung expression quantitative trait loci (eQTL) dataset and Genotype-Tissue Expression (GTEx). For cross-ethnicity generalization, we assessed the associations in a Japanese study (N = 887). RESULTS One locus at 13q22.2 was associated with lung adenocarcinoma survival at genome-wide level, with carriers of rs12875562-T allele exhibiting poor prognosis [HR = 1.71 (1.41-2.07), P = 3.60 × 10-8], and altered mRNA expression of LMO7DN in lung tissue (GTEx, P = 9.40 × 10-7; Lung eQTL dataset, P = 0.003). Furthermore, 2 of 11 independent loci that reached the suggestive significance level (P < 10-6) were significant eQTL affecting mRNA expression of nearby genes in lung tissues, including CAPZB at 1p36.13 and UBAC1 at 9q34.3. One locus encoding NWD2/KIAA1239 at 4p14 showed associations in both European [HR = 0.50 (0.38-0.66), P = 6.92 × 10-7] and Japanese populations [HR = 0.79 (0.67-0.94), P = 0.007]. CONCLUSIONS Based on the largest genomic investigation on the lung cancer prognosis of never smokers to date, we observed that lung cancer prognosis is affected by inherited genetic variants. IMPACT We identified one locus near LMO7DN at genome-wide level and several potential prognostic genes with cis-effect on mRNA expression. Further functional genomics work is required to understand their role in tumor progression.
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Affiliation(s)
- Yonathan Brhane
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | | | | | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - John R McLaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Sanjay Shete
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Institute of Translational Medicine, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Adonina Tardón
- University of Oviedo, ISPA and CIBERESP, Faculty of Medicine, Campus del Cristo, Oviedo, Spain
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Department of Preventive Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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The Molecular Basis and Biologic Significance of the β-Dystroglycan-Emerin Interaction. Int J Mol Sci 2020; 21:ijms21175944. [PMID: 32824881 PMCID: PMC7504044 DOI: 10.3390/ijms21175944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 01/04/2023] Open
Abstract
β-dystroglycan (β-DG) assembles with lamins A/C and B1 and emerin at the nuclear envelope (NE) to maintain proper nuclear architecture and function. To provide insight into the nuclear function of β-DG, we characterized the interaction between β-DG and emerin at the molecular level. Emerin is a major NE protein that regulates multiple nuclear processes and whose deficiency results in Emery–Dreifuss muscular dystrophy (EDMD). Using truncated variants of β-DG and emerin, via a series of in vitro and in vivo binding experiments and a tailored computational analysis, we determined that the β-DG–emerin interaction is mediated at least in part by their respective transmembrane domains (TM). Using surface plasmon resonance assays we showed that emerin binds to β-DG with high affinity (KD in the nanomolar range). Remarkably, the analysis of cells in which DG was knocked out demonstrated that loss of β-DG resulted in a decreased emerin stability and impairment of emerin-mediated processes. β-DG and emerin are reciprocally required for their optimal targeting within the NE, as shown by immunofluorescence, western blotting and immunoprecipitation assays using emerin variants with mutations in the TM domain and B-lymphocytes of a patient with EDMD. In summary, we demonstrated that β-DG plays a role as an emerin interacting partner modulating its stability and function.
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Liu J, Huang ZP, Nie M, Wang G, Silva WJ, Yang Q, Freire PP, Hu X, Chen H, Deng Z, Pu WT, Wang DZ. Regulation of myonuclear positioning and muscle function by the skeletal muscle-specific CIP protein. Proc Natl Acad Sci U S A 2020; 117:19254-19265. [PMID: 32719146 PMCID: PMC7430979 DOI: 10.1073/pnas.1922911117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The appropriate arrangement of myonuclei within skeletal muscle myofibers is of critical importance for normal muscle function, and improper myonuclear localization has been linked to a variety of skeletal muscle diseases, such as centronuclear myopathy and muscular dystrophies. However, the molecules that govern myonuclear positioning remain elusive. Here, we report that skeletal muscle-specific CIP (sk-CIP) is a regulator of nuclear positioning. Genetic deletion of sk-CIP in mice results in misalignment of myonuclei along the myofibers and at specialized structures such as neuromuscular junctions (NMJs) and myotendinous junctions (MTJs) in vivo, impairing myonuclear positioning after muscle regeneration, leading to severe muscle dystrophy in mdx mice, a mouse model of Duchenne muscular dystrophy. sk-CIP is localized to the centrosome in myoblasts and relocates to the outer nuclear envelope in myotubes upon differentiation. Mechanistically, we found that sk-CIP interacts with the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex and the centriole Microtubule Organizing Center (MTOC) proteins to coordinately modulate myonuclear positioning and alignment. These findings indicate that sk-CIP may function as a muscle-specific anchoring protein to regulate nuclear position in multinucleated muscle cells.
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MESH Headings
- Animals
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Co-Repressor Proteins
- Humans
- Mice
- Mice, Inbred mdx
- Mice, Knockout
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/physiopathology
- Myoblasts/metabolism
- Myopathies, Structural, Congenital/genetics
- Myopathies, Structural, Congenital/metabolism
- Myopathies, Structural, Congenital/physiopathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Organ Specificity
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Affiliation(s)
- Jianming Liu
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
| | - Zhan-Peng Huang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
- Center for Translational Medicine, National Health Commission (NHC) Key Laboratory of Assisted Circulation, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mao Nie
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
- Department of Orthopaedic Surgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Gang Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
| | - William J Silva
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
- Laboratório de Biologia Celular e Molecular do Músculo Estriado, University of São Paulo, CEP 05508-000 Cidade Universitária, São Paulo, Brazil
| | - Qiumei Yang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
- Department of Animal Sciences, Sichuan Agriculture University, Chengdu, 611130, China
| | - Paula P Freire
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
- Department of Morphology, Institute of Biosciences, São Paulo State University, CEP 18618-000, Botucatu, São Paulo, Brazil
| | - Xiaoyun Hu
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
| | - Huaqun Chen
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
- Department of Biology, Nanjing Normal University, Nanjing, 225300, China
| | - Zhongliang Deng
- Department of Orthopaedic Surgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115;
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
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EDMD-Causing Emerin Mutant Myogenic Progenitors Exhibit Impaired Differentiation Using Similar Mechanisms. Cells 2020; 9:cells9061463. [PMID: 32549231 PMCID: PMC7349064 DOI: 10.3390/cells9061463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 11/17/2022] Open
Abstract
Mutations in the gene encoding emerin (EMD) cause Emery–Dreifuss muscular dystrophy (EDMD1), an inherited disorder characterized by progressive skeletal muscle wasting, irregular heart rhythms and contractures of major tendons. The skeletal muscle defects seen in EDMD are caused by failure of muscle stem cells to differentiate and regenerate the damaged muscle. However, the underlying mechanisms remain poorly understood. Most EDMD1 patients harbor nonsense mutations and have no detectable emerin protein. There are three EDMD-causing emerin mutants (S54F, Q133H, and Δ95–99) that localize correctly to the nuclear envelope and are expressed at wildtype levels. We hypothesized these emerin mutants would share in the disruption of key molecular pathways involved in myogenic differentiation. We generated myogenic progenitors expressing wildtype emerin and each EDMD1-causing emerin mutation (S54F, Q133H, Δ95–99) in an emerin-null (EMD−/y) background. S54F, Q133H, and Δ95–99 failed to rescue EMD−/y myogenic differentiation, while wildtype emerin efficiently rescued differentiation. RNA sequencing was done to identify pathways and networks important for emerin regulation of myogenic differentiation. This analysis significantly reduced the number of pathways implicated in EDMD1 muscle pathogenesis.
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Muscle cell differentiation and development pathway defects in Emery-Dreifuss muscular dystrophy. Neuromuscul Disord 2020; 30:443-456. [DOI: 10.1016/j.nmd.2020.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/20/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022]
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Xie Y, Ostriker AC, Jin Y, Hu H, Sizer AJ, Peng G, Morris AH, Ryu C, Herzog EL, Kyriakides T, Zhao H, Dardik A, Yu J, Hwa J, Martin KA. LMO7 Is a Negative Feedback Regulator of Transforming Growth Factor β Signaling and Fibrosis. Circulation 2019; 139:679-693. [PMID: 30586711 PMCID: PMC6371979 DOI: 10.1161/circulationaha.118.034615] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Vascular smooth muscle cells (SMCs) synthesize extracellular matrix (ECM) that contributes to tissue remodeling after revascularization interventions. The cytokine transforming growth factor β (TGF-β) is induced on tissue injury and regulates tissue remodeling and wound healing, but dysregulated signaling results in excess ECM deposition and fibrosis. The LIM (Lin11, Isl-1 & Mec-3) domain protein LIM domain only 7 (LMO7) is a TGF-β1 target gene in hepatoma cells, but its role in vascular physiology and fibrosis is unknown. METHODS We use carotid ligation and femoral artery denudation models in mice with global or inducible smooth muscle-specific deletion of LMO7, and knockout, knockdown, overexpression, and mutagenesis approaches in mouse and human SMC, and human arteriovenous fistula and cardiac allograft vasculopathy samples to assess the role of LMO7 in neointima and fibrosis. RESULTS We demonstrate that LMO7 is induced postinjury and by TGF-β in SMC in vitro. Global or SMC-specific LMO7 deletion enhanced neointimal formation, TGF-β signaling, ECM deposition, and proliferation in vascular injury models. LMO7 loss of function in human and mouse SMC enhanced ECM protein expression at baseline and after TGF-β treatment. TGF-β neutralization or receptor antagonism prevented the exacerbated neointimal formation and ECM synthesis conferred by loss of LMO7. Notably, loss of LMO7 coordinately amplified TGF-β signaling by inducing expression of Tgfb1 mRNA, TGF-β protein, αv and β3 integrins that promote activation of latent TGF-β, and downstream effectors SMAD3 phosphorylation and connective tissue growth factor. Mechanistically, the LMO7 LIM domain interacts with activator protein 1 transcription factor subunits c-FOS and c-JUN and promotes their ubiquitination and degradation, disrupting activator protein 1-dependent TGF-β autoinduction. Importantly, preliminary studies suggest that LMO7 is upregulated in human intimal hyperplastic arteriovenous fistula and cardiac allograft vasculopathy samples, and inversely correlates with SMAD3 phosphorylation in cardiac allograft vasculopathy. CONCLUSIONS LMO7 is induced by TGF-β and serves to limit vascular fibrotic responses through negative feedback regulation of the TGF-β pathway. This mechanism has important implications for intimal hyperplasia, wound healing, and fibrotic diseases.
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Affiliation(s)
- Yi Xie
- Departments of Medicine (Cardiovascular Medicine) (Y.X., A.C.O., Y.J., K.A.M., J.H.), Yale University, New Haven, CT.,Pharmacology (Y.X., A.C.O., Y.J., K.A.M.), Yale University, New Haven, CT
| | - Allison C Ostriker
- Departments of Medicine (Cardiovascular Medicine) (Y.X., A.C.O., Y.J., K.A.M., J.H.), Yale University, New Haven, CT.,Pharmacology (Y.X., A.C.O., Y.J., K.A.M.), Yale University, New Haven, CT
| | - Yu Jin
- Departments of Medicine (Cardiovascular Medicine) (Y.X., A.C.O., Y.J., K.A.M., J.H.), Yale University, New Haven, CT.,Pharmacology (Y.X., A.C.O., Y.J., K.A.M.), Yale University, New Haven, CT
| | - Haidi Hu
- Surgery (Vascular) (H.H., A.D.), Yale University, New Haven, CT
| | | | - Gang Peng
- Biostatistics (G.P., H.Z.), Yale University, New Haven, CT
| | - Aaron H Morris
- Pathology (A.H.M., T.K.), Yale University, New Haven, CT.,Department of Biomedical Engineering (A.H.M., T.K.), Yale University, New Haven, CT
| | - Changwan Ryu
- Medicine (Pulmonary) (C.R., E.L.H.), Yale University School of Medicine, Yale University, New Haven, CT
| | - Erica L Herzog
- Medicine (Pulmonary) (C.R., E.L.H.), Yale University School of Medicine, Yale University, New Haven, CT
| | - Themis Kyriakides
- Pathology (A.H.M., T.K.), Yale University, New Haven, CT.,Department of Biomedical Engineering (A.H.M., T.K.), Yale University, New Haven, CT
| | - Hongyu Zhao
- Biostatistics (G.P., H.Z.), Yale University, New Haven, CT
| | - Alan Dardik
- Surgery (Vascular) (H.H., A.D.), Yale University, New Haven, CT
| | - Jun Yu
- Department of Physiology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA (J.Y.)
| | - John Hwa
- Departments of Medicine (Cardiovascular Medicine) (Y.X., A.C.O., Y.J., K.A.M., J.H.), Yale University, New Haven, CT
| | - Kathleen A Martin
- Departments of Medicine (Cardiovascular Medicine) (Y.X., A.C.O., Y.J., K.A.M., J.H.), Yale University, New Haven, CT.,Pharmacology (Y.X., A.C.O., Y.J., K.A.M.), Yale University, New Haven, CT
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Gabián M, Morán P, Fernández AI, Villanueva B, Chtioui A, Kent MP, Covelo-Soto L, Fernández A, Saura M. Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data. BMC Genomics 2019; 20:764. [PMID: 31640542 PMCID: PMC6805462 DOI: 10.1186/s12864-019-6104-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs to the family Salmonidae of fishes and represents a species of great commercial value. Although the species is assumed to be male heterogametic with XY sex determination, the precise genetic basis of sexual development remains unclear. The complexity is likely associated to the relatively recent salmonid specific whole genome duplication that may be responsible for certain genome instability. This instability together with the capacity of the sex-determining gene to move across the genome as reported by previous studies, may explain that sexual development genes are not circumscribed to the same chromosomes in all members of the species. In this study, we have used a 220 K SNP panel developed for Atlantic salmon to identify the chromosomes explaining the highest proportion of the genetic variance for sex as well as candidate regions and genes associated to sexual development in this species. Results Results from regional heritability analysis showed that the chromosomes explaining the highest proportion of variance in these populations were Ssa02 (heritability = 0.42, SE = 0.12) and Ssa21 (heritability = 0.26, SE = 0.11). After pruning by linkage disequilibrium, genome-wide association analyses revealed 114 SNPs that were significantly associated with sex, being Ssa02 the chromosome containing a greatest number of regions. Close examination of the candidate regions evidenced important genes related to sex in other species of Class Actinopterygii, including SDY, genes from family SOX, RSPO1, ESR1, U2AF2A, LMO7, GNRH-R, DND and FIGLA. Conclusions The combined results from regional heritability analysis and genome-wide association have provided new advances in the knowledge of the genetic regulation of sex determination in Atlantic salmon, supporting that Ssa02 is the candidate chromosome for sex in this species and suggesting an alternative population lineage in Spanish wild populations according to the results from Ssa21.
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Affiliation(s)
- María Gabián
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, 36310, Spain
| | - Paloma Morán
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, 36310, Spain
| | - Ana I Fernández
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - Amel Chtioui
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - Matthew P Kent
- Center for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Bioscience, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway
| | - Lara Covelo-Soto
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, 36310, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain.
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Iglesias-Bartolome R, Uchiyama A, Molinolo AA, Abusleme L, Brooks SR, Callejas-Valera JL, Edwards D, Doci C, Asselin-Labat ML, Onaitis MW, Moutsopoulos NM, Gutkind JS, Morasso MI. Transcriptional signature primes human oral mucosa for rapid wound healing. Sci Transl Med 2019; 10:10/451/eaap8798. [PMID: 30045979 DOI: 10.1126/scitranslmed.aap8798] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 02/13/2018] [Accepted: 06/20/2018] [Indexed: 12/15/2022]
Abstract
Oral mucosal wound healing has long been regarded as an ideal system of wound resolution. However, the intrinsic characteristics that mediate optimal healing at mucosal surfaces are poorly understood, particularly in humans. We present a unique comparative analysis between human oral and cutaneous wound healing using paired and sequential biopsies during the repair process. Using molecular profiling, we determined that wound-activated transcriptional networks are present at basal state in the oral mucosa, priming the epithelium for wound repair. We show that oral mucosal wound-related networks control epithelial cell differentiation and regulate inflammatory responses, highlighting fundamental global mechanisms of repair and inflammatory responses in humans. The paired comparative analysis allowed for the identification of differentially expressed SOX2 (sex-determining region Y-box 2) and PITX1 (paired-like homeodomain 1) transcriptional regulators in oral versus skin keratinocytes, conferring a unique identity to oral keratinocytes. We show that SOX2 and PITX1 transcriptional function has the potential to reprogram skin keratinocytes to increase cell migration and improve wound resolution in vivo. Our data provide insights into therapeutic targeting of chronic and nonhealing wounds based on greater understanding of the biology of healing in human mucosal and cutaneous environments.
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Affiliation(s)
- Ramiro Iglesias-Bartolome
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA.,Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA
| | - Akihiko Uchiyama
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA
| | - Alfredo A Molinolo
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA.,Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Loreto Abusleme
- Oral Immunity and Inflammation Unit, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA
| | - Juan Luis Callejas-Valera
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA.,Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dean Edwards
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA
| | - Colleen Doci
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA
| | | | - Mark W Onaitis
- Moores Cancer Center, University California, San Diego, La Jolla, CA 92093, USA
| | - Niki M Moutsopoulos
- Oral Immunity and Inflammation Unit, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA
| | - J S Gutkind
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA. .,Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maria I Morasso
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA.
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Capitanchik C, Dixon CR, Swanson SK, Florens L, Kerr ARW, Schirmer EC. Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins. Nucleus 2019; 9:410-430. [PMID: 29912636 PMCID: PMC7000147 DOI: 10.1080/19491034.2018.1469351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Laminopathies yield tissue-specific pathologies, yet arise from mutation of ubiquitously-expressed genes. A little investigated hypothesis to explain this is that the mutated proteins or their partners have tissue-specific splice variants. To test this, we analyzed RNA-Seq datasets, finding novel isoforms or isoform tissue-specificity for: Lap2, linked to cardiomyopathy; Nesprin 2, linked to Emery-Dreifuss muscular dystrophy and Lmo7, that regulates the Emery-Dreifuss muscular dystrophy linked emerin gene. Interestingly, the muscle-specific Lmo7 exon is rich in serine phosphorylation motifs, suggesting regulatory function. Muscle-specific splice variants in non-nuclear envelope proteins linked to other muscular dystrophies were also found. Nucleoporins tissue-specific variants were found for Nup54, Nup133, Nup153 and Nup358/RanBP2. RT-PCR confirmed novel Lmo7 and RanBP2 variants and specific knockdown of the Lmo7 variantreduced myogenic index. Nuclear envelope proteins were enriched for tissue-specific splice variants compared to the rest of the genome, suggesting that splice variants contribute to its tissue-specific functions.
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Affiliation(s)
- Charlotte Capitanchik
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Charles R Dixon
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Selene K Swanson
- b Stowers Institute for Medical Research , Kansas City , MO , USA
| | - Laurence Florens
- b Stowers Institute for Medical Research , Kansas City , MO , USA
| | - Alastair R W Kerr
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Eric C Schirmer
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
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Mishra S, Peña JS, Redenti S, Vazquez M. A novel electro-chemotactic approach to impact the directional migration of transplantable retinal progenitor cells. Exp Eye Res 2019; 185:107688. [PMID: 31185219 PMCID: PMC6698415 DOI: 10.1016/j.exer.2019.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 12/23/2022]
Abstract
Photoreceptor degeneration is a significant cause of visual impairment in the United States and globally. Cell replacement therapy shows great promise in restoring vision by transplanting stem-like cells into the sub-retinal space as substitutes for damaged photoreceptors. However, vision repair via transplantation has been limited, in large part, by low numbers of replacement cells able to migrate into damaged retinal tissue and integrate with native photoreceptors. Projects have used external chemical fields and applied electric fields to induce the chemotaxis and electrotaxis of replacement cells, respectively, with limited success. However, the application of combined electro-chemotactic fields in directing cells within biomaterials and host tissue has been surprisingly understudied. The current work examined the ability of combined electro-chemotactic fields to direct the migration of transplantable retinal progenitor cells (RPCs) in controlled microenvironments. Experiments used our established galvano-microfluidic system (Gal-MμS) to generate tunable chemotactic concentration fields with and without superimposed electric fields. Result illustrate that combination fields increased the distance migrated by RPCs by over three times that seen in either field, individually, and with greater directionality towards increasing gradients. Interestingly, immunofluorescence assays showed no significant differences in the distribution of the total and/or activated cognate receptor of interest, indicating that changes in ligand binding alone were not responsible for the measured increases in migration. Bioinformatics analysis was then performed to identity potential, synergistic mechanistic pathways involved in the electro-chemotaxis measured. Results indicate that increased RPC migration in electro-chemotactic fields may arise from down-regulation of cell adhesion proteins in tandem with up-regulation of cytoskeletal regulation proteins. These comprehensive results point towards a novel migration-targeted treatment that may dramatically improve transplantation outcomes as well as elucidate unreported synergy across biological mechanisms in response to electro-chemotactic fields.
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Affiliation(s)
| | - Juan S Peña
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | | | - Maribel Vazquez
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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Kuciauskas D, Dreize N, Ger M, Kaupinis A, Zemaitis K, Stankevicius V, Suziedelis K, Cicenas J, Graves LM, Valius M. Proteomic Analysis of Breast Cancer Resistance to the Anticancer Drug RH1 Reveals the Importance of Cancer Stem Cells. Cancers (Basel) 2019; 11:E972. [PMID: 31336714 PMCID: PMC6678540 DOI: 10.3390/cancers11070972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
Antitumor drug resistance remains a major challenge in cancer chemotherapy. Here we investigated the mechanism of acquired resistance to a novel anticancer agent RH1 designed to be activated in cancer cells by the NQO1 enzyme. Data show that in some cancer cells RH1 may act in an NQO1-independent way. Differential proteomic analysis of breast cancer cells with acquired resistance to RH1 revealed changes in cell energy, amino acid metabolism and G2/M cell cycle transition regulation. Analysis of phosphoproteomics and protein kinase activity by multiplexed kinase inhibitor beads showed an increase in the activity of protein kinases involved in the cell cycle and stemness regulation and downregulation of proapoptotic kinases such as JNK in RH1-resistant cells. Suppression of JNK leads to the increase of cancer cell resistance to RH1. Moreover, resistant cells have enhanced expression of stem cell factor (SCF) and stem cell markers. Inhibition of SCF receptor c-KIT resulted in the attenuation of cancer stem cell enrichment and decreased amounts of tumor-initiating cells. RH1-resistant cells also acquire resistance to conventional therapeutics while remaining susceptible to c-KIT-targeted therapy. Data show that RH1 can be useful to treat cancers in the NQO1-independent way, and targeting of the cancer stem cells might be an effective approach for combating resistance to RH1 therapy.
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Affiliation(s)
- Dalius Kuciauskas
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Nadezda Dreize
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Marija Ger
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Algirdas Kaupinis
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Kristijonas Zemaitis
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
| | - Vaidotas Stankevicius
- Laboratory of Molecular Oncology, National Cancer Institute, 08660 Vilnius, Lithuania
| | - Kestutis Suziedelis
- Laboratory of Molecular Oncology, National Cancer Institute, 08660 Vilnius, Lithuania
| | - Jonas Cicenas
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania
- MAP Kinase Resource, 3027 Bern, Switzerland
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mindaugas Valius
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, Vilnius University, 10223 Vilnius, Lithuania.
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An Interaction Network of the Human SEPT9 Established by Quantitative Mass Spectrometry. G3-GENES GENOMES GENETICS 2019; 9:1869-1880. [PMID: 30975701 PMCID: PMC6553528 DOI: 10.1534/g3.119.400197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Septins regulate the organization of the actin cytoskeleton, vesicle transport and fusion, chromosome alignment and segregation, and cytokinesis in mammalian cells. SEPT9 is part of the core septin hetero-octamer in human cells which is composed of SEPT2, SEPT6, SEPT7, and SEPT9. SEPT9 has been linked to a variety of intracellular functions as well as to diseases and diverse types of cancer. A targeted high-throughput approach to systematically identify the interaction partners of SEPT9 has not yet been performed. We applied a quantitative proteomics approach to establish an interactome of SEPT9 in human fibroblast cells. Among the newly identified interaction partners were members of the myosin family and LIM domain containing proteins. Fluorescence microscopy of SEPT9 and its interaction partners provides additional evidence that SEPT9 might participate in vesicle transport from and to the plasma membrane as well as in the attachment of actin stress fibers to cellular adhesions.
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Ignatieva EV, Yurchenko AA, Voevoda MI, Yudin NS. Exome-wide search and functional annotation of genes associated in patients with severe tick-borne encephalitis in a Russian population. BMC Med Genomics 2019; 12:61. [PMID: 31122248 PMCID: PMC6533173 DOI: 10.1186/s12920-019-0503-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Tick-borne encephalitis (TBE) is a viral infectious disease caused by tick-borne encephalitis virus (TBEV). TBEV infection is responsible for a variety of clinical manifestations ranging from mild fever to severe neurological illness. Genetic factors involved in the host response to TBEV that may potentially play a role in the severity of the disease are still poorly understood. In this study, using whole-exome sequencing, we aimed to identify genetic variants and genes associated with severe forms of TBE as well as biological pathways through which the identified variants may influence the severity of the disease. Results Whole-exome sequencing data analysis was performed on 22 Russian patients with severe forms of TBE and 17 Russian individuals from the control group. We identified 2407 candidate genes harboring rare, potentially pathogenic variants in exomes of patients with TBE and not containing any rare, potentially pathogenic variants in exomes of individuals from the control group. According to DAVID tool, this set of 2407 genes was enriched with genes involved in extracellular matrix proteoglycans pathway and genes encoding proteins located at the cell periphery. A total of 154 genes/proteins from these functional groups have been shown to be involved in protein-protein interactions (PPIs) with the known candidate genes/proteins extracted from TBEVHostDB database. By ranking these genes according to the number of rare harmful minor alleles, we identified two genes (MSR1 and LMO7), harboring five minor alleles, and three genes (FLNA, PALLD, PKD1) harboring four minor alleles. When considering genes harboring genetic variants associated with severe forms of TBE at the suggestive P-value < 0.01, 46 genes containing harmful variants were identified. Out of these 46 genes, eight (MAP4, WDFY4, ACTRT2, KLHL25, MAP2K3, MBD1, OR10J1, and OR2T34) were additionally found among genes containing rare pathogenic variants identified in patients with TBE; and five genes (WDFY4,ALK, MAP4, BNIPL, EPPK1) were found to encode proteins that are involved in PPIs with proteins encoded by genes from TBEVHostDB. Three genes out of five (MAP4, EPPK1, ALK) were found to encode proteins located at cell periphery. Conclusions Whole-exome sequencing followed by systems biology approach enabled to identify eight candidate genes (MAP4, WDFY4, ACTRT2, KLHL25, MAP2K3, MBD1, OR10J1, and OR2T34) that can potentially determine predisposition to severe forms of TBE. Analyses of the genetic risk factors for severe forms of TBE revealed a significant enrichment with genes controlling extracellular matrix proteoglycans pathway as well as genes encoding components of cell periphery. Electronic supplementary material The online version of this article (10.1186/s12920-019-0503-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena V Ignatieva
- Laboratory of Evolutionary Bioinformatics and Theoretical Genetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Andrey A Yurchenko
- Laboratory of Infectious Disease Genomics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Mikhail I Voevoda
- Novosibirsk State University, Novosibirsk, 630090, Russia.,Research Institute of Internal and Preventive Medicine-Branch of Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630004, Russia
| | - Nikolay S Yudin
- Laboratory of Infectious Disease Genomics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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Ranade D, Pradhan R, Jayakrishnan M, Hegde S, Sengupta K. Lamin A/C and Emerin depletion impacts chromatin organization and dynamics in the interphase nucleus. BMC Mol Cell Biol 2019; 20:11. [PMID: 31117946 PMCID: PMC6532135 DOI: 10.1186/s12860-019-0192-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/16/2019] [Indexed: 12/26/2022] Open
Abstract
Background Nuclear lamins are type V intermediate filament proteins that maintain nuclear structure and function. Furthermore, Emerin - an interactor of Lamin A/C, facilitates crosstalk between the cytoskeleton and the nucleus as it also interacts with actin and Nuclear Myosin 1 (NM1). Results Here we show that the depletion of Lamin A/C or Emerin, alters the localization of the nuclear motor protein - Nuclear Myosin 1 (NM1) that manifests as an increase in NM1 foci in the nucleus and are rescued to basal levels upon the combined knockdown of Lamin A/C and Emerin. Furthermore, Lamin A/C-Emerin co-depletion destabilizes cytoskeletal organization as it increases actin stress fibers. This further impinges on nuclear organization, as it enhances chromatin mobility more toward the nuclear interior in Lamin A/C-Emerin co-depleted cells. This enhanced chromatin mobility was restored to basal levels either upon inhibition of Nuclear Myosin 1 (NM1) activity or actin depolymerization. In addition, the combined loss of Lamin A/C and Emerin alters the otherwise highly conserved spatial positions of chromosome territories. Furthermore, knockdown of Lamin A/C or Lamin A/C-Emerin combined, deregulates expression levels of a candidate subset of genes. Amongst these genes, both KLK10 (Chr.19, Lamina Associated Domain (LAD+)) and MADH2 (Chr.18, LAD-) were significantly repressed, while BCL2L12 (Chr.19, LAD-) is de-repressed. These genes differentially reposition with respect to the nuclear envelope. Conclusions Taken together, these studies underscore a remarkable interplay between Lamin A/C and Emerin in modulating cytoskeletal organization of actin and NM1 that impinges on chromatin dynamics and function in the interphase nucleus. Electronic supplementary material The online version of this article (10.1186/s12860-019-0192-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devika Ranade
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Roopali Pradhan
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Muhunden Jayakrishnan
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Sushmitha Hegde
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Kundan Sengupta
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India.
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Dharmaraj T, Guan Y, Liu J, Badens C, Gaborit B, Wilson KL. Rare BANF1 Alleles and Relatively Frequent EMD Alleles Including 'Healthy Lipid' Emerin p.D149H in the ExAC Cohort. Front Cell Dev Biol 2019; 7:48. [PMID: 31024910 PMCID: PMC6459885 DOI: 10.3389/fcell.2019.00048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/19/2019] [Indexed: 01/05/2023] Open
Abstract
Emerin (EMD) and barrier to autointegration factor 1 (BANF1) each bind A-type lamins (LMNA) as fundamental components of nuclear lamina structure. Mutations in LMNA, EMD and BANF1 are genetically linked to many tissue-specific disorders including Emery-Dreifuss muscular dystrophy and cardiomyopathy (LMNA, EMD), lipodystrophy, insulin resistance and type 2 diabetes (LMNA) and progeria (LMNA, BANF1). To explore human genetic variation in these genes, we analyzed EMD and BANF1 alleles in the Exome Aggregation Consortium (ExAC) cohort of 60,706 unrelated individuals. We identified 13 rare heterozygous BANF1 missense variants (p.T2S, p.H7Y, p.D9N, p.S22R, p.G25E, p.D55N, p.D57Y, p.L63P, p.N70T, p.K72R, p.R75W, p.R75Q, p.G79R), and one homozygous variant (p.D9H). Several variants are known (p.G25E) or predicted (e.g., p.D9H, p.D9N, p.L63P) to perturb BANF1 and warrant further study. Analysis of EMD revealed two previously identified variants associated with adult-onset cardiomyopathy (p.K37del, p.E35K) and one deemed 'benign' in an Emery-Dreifuss patient (p.D149H). Interestingly p.D149H was the most frequent emerin variant in ExAC, identified in 58 individuals (overall allele frequency 0.06645%), of whom 55 were East Asian (allele frequency 0.8297%). Furthermore, p.D149H associated with four 'healthy' traits: reduced triglycerides (-0.336; p = 0.0368), reduced waist circumference (-0.321; p = 0.0486), reduced cholesterol (-0.572; p = 0.000346) and reduced LDL cholesterol (-0.599; p = 0.000272). These traits are distinct from LMNA-associated metabolic disorders and provide the first insight that emerin influences metabolism. We also identified one novel in-frame deletion (p.F39del) and 62 novel emerin missense variants, many of which were relatively frequent and potentially disruptive including p.N91S and p.S143F (∼0.041% and ∼0.034% of non-Finnish Europeans, respectively), p.G156S (∼0.39% of Africans), p.R204G (∼0.18% of Latinx), p.R207P (∼0.08% of South Asians) and p.R221L (∼0.15% of Latinx). Many novel BANF1 variants are predicted to disrupt dimerization or binding to DNA, histones, emerin or A-type lamins. Many novel emerin variants are predicted to disrupt emerin filament dynamics or binding to BANF1, HDAC3, A-type lamins or other partners. These new human variants provide a foundational resource for future studies to test the molecular mechanisms of BANF1 and emerin function, and to understand the link between emerin variant p.D149H and a 'healthy' lipid profile.
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Affiliation(s)
- Tejas Dharmaraj
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Youchen Guan
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Julie Liu
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | | | - Katherine L Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Dubińska-Magiera M, Kozioł K, Machowska M, Piekarowicz K, Filipczak D, Rzepecki R. Emerin Is Required for Proper Nucleus Reassembly after Mitosis: Implications for New Pathogenetic Mechanisms for Laminopathies Detected in EDMD1 Patients. Cells 2019; 8:E240. [PMID: 30871242 PMCID: PMC6468536 DOI: 10.3390/cells8030240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 12/29/2022] Open
Abstract
Emerin is an essential LEM (LAP2, Emerin, MAN1) domain protein in metazoans and an integral membrane protein associated with inner and outer nuclear membranes. Mutations in the human EMD gene coding for emerin result in the rare genetic disorder: Emery⁻Dreifuss muscular dystrophy type 1 (EDMD1). This disease belongs to a broader group called laminopathies-a heterogeneous group of rare genetic disorders affecting tissues of mesodermal origin. EDMD1 phenotype is characterized by progressive muscle wasting, contractures of the elbow and Achilles tendons, and cardiac conduction defects. Emerin is involved in many cellular and intranuclear processes through interactions with several partners: lamins; barrier-to-autointegration factor (BAF), β-catenin, actin, and tubulin. Our study demonstrates the presence of the emerin fraction which associates with mitotic spindle microtubules and centrosomes during mitosis and colocalizes during early mitosis with lamin A/C, BAF, and membranes at the mitotic spindle. Transfection studies with cells expressing EGFP-emerin protein demonstrate that the emerin fusion protein fraction also localizes to centrosomes and mitotic spindle microtubules during mitosis. Transient expression of emerin deletion mutants revealed that the resulting phenotypes vary and are mutant dependent. The most frequent phenotypes include aberrant nuclear shape, tubulin network mislocalization, aberrant mitosis, and mislocalization of centrosomes. Emerin deletion mutants demonstrated different chromatin binding capacities in an in vitro nuclear assembly assay and chromatin-binding properties correlated with the strength of phenotypic alteration in transfected cells. Aberrant tubulin staining and microtubule network phenotype appearance depended on the presence of the tubulin binding region in the expressed deletion mutants. We believe that the association with tubulin might help to "deliver" emerin and associated membranes to decondensing chromatin. Preliminary analyses of cells from Polish patients with EDMD1 revealed that for several mutations thought to be null for emerin protein, a truncated emerin protein was present. We infer that the EDMD1 phenotype may be strengthened by the toxicity of truncated emerin expressed in patients with certain nonsense mutations in EMD.
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Affiliation(s)
- Magda Dubińska-Magiera
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335 Wroclaw, Poland.
| | - Katarzyna Kozioł
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Magdalena Machowska
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Katarzyna Piekarowicz
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Daria Filipczak
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Ryszard Rzepecki
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
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Du TT, Dewey JB, Wagner EL, Cui R, Heo J, Park JJ, Francis SP, Perez-Reyes E, Guillot SJ, Sherman NE, Xu W, Oghalai JS, Kachar B, Shin JB. LMO7 deficiency reveals the significance of the cuticular plate for hearing function. Nat Commun 2019; 10:1117. [PMID: 30850599 PMCID: PMC6408450 DOI: 10.1038/s41467-019-09074-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/15/2019] [Indexed: 12/25/2022] Open
Abstract
Sensory hair cells, the mechanoreceptors of the auditory and vestibular systems, harbor two specialized elaborations of the apical surface, the hair bundle and the cuticular plate. In contrast to the extensively studied mechanosensory hair bundle, the cuticular plate is not as well understood. It is believed to provide a rigid foundation for stereocilia motion, but specifics about its function, especially the significance of its integrity for long-term maintenance of hair cell mechanotransduction, are not known. We discovered that a hair cell protein called LIM only protein 7 (LMO7) is specifically localized in the cuticular plate and the cell junction. Lmo7 KO mice suffer multiple cuticular plate deficiencies, including reduced filamentous actin density and abnormal stereociliar rootlets. In addition to the cuticular plate defects, older Lmo7 KO mice develop abnormalities in inner hair cell stereocilia. Together, these defects affect cochlear tuning and sensitivity and give rise to late-onset progressive hearing loss.
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MESH Headings
- Actins/metabolism
- Animals
- Cochlea/physiology
- Disease Models, Animal
- Hair Cells, Auditory/physiology
- Hair Cells, Auditory/ultrastructure
- Hair Cells, Auditory, Inner/physiology
- Hair Cells, Auditory, Inner/ultrastructure
- Hearing/genetics
- Hearing/physiology
- Hearing Loss/etiology
- Hearing Loss/genetics
- Hearing Loss/physiopathology
- LIM Domain Proteins/deficiency
- LIM Domain Proteins/genetics
- LIM Domain Proteins/physiology
- Mice
- Mice, Inbred C57BL
- Mice, Inbred CBA
- Mice, Knockout
- Microscopy, Electron, Scanning
- Stereocilia/genetics
- Stereocilia/physiology
- Stereocilia/ultrastructure
- Transcription Factors/deficiency
- Transcription Factors/genetics
- Transcription Factors/physiology
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Affiliation(s)
- Ting-Ting Du
- Department of Neuroscience, University of Virginia, Charlottesville, VA, 22908, USA
| | - James B Dewey
- Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, 90033, USA
| | - Elizabeth L Wagner
- Department of Neuroscience, University of Virginia, Charlottesville, VA, 22908, USA
| | - Runjia Cui
- National Institute for Deafness and Communications Disorders, National Institute of Health, Bethesda, MD, 20892, USA
| | - Jinho Heo
- Center for Cell Signaling and Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jeong-Jin Park
- Biomolecular Analysis Facility, University of Virginia, Charlottesville, VA, 22908, USA
| | - Shimon P Francis
- Department of Neuroscience, University of Virginia, Charlottesville, VA, 22908, USA
| | - Edward Perez-Reyes
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Stacey J Guillot
- Advanced Microscopy core, University of Virginia, Charlottesville, VA, 22908, USA
| | - Nicholas E Sherman
- Biomolecular Analysis Facility, University of Virginia, Charlottesville, VA, 22908, USA
| | - Wenhao Xu
- Genetically Engineered Murine Model (GEMM) core, University of Virginia, Charlottesville, VA, 22908, USA
| | - John S Oghalai
- Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, 90033, USA
| | - Bechara Kachar
- National Institute for Deafness and Communications Disorders, National Institute of Health, Bethesda, MD, 20892, USA
| | - Jung-Bum Shin
- Department of Neuroscience, University of Virginia, Charlottesville, VA, 22908, USA.
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Hashimoto Y, Kinoshita N, Greco TM, Federspiel JD, Jean Beltran PM, Ueno N, Cristea IM. Mechanical Force Induces Phosphorylation-Mediated Signaling that Underlies Tissue Response and Robustness in Xenopus Embryos. Cell Syst 2019; 8:226-241.e7. [PMID: 30852251 DOI: 10.1016/j.cels.2019.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/17/2018] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
Mechanical forces are essential drivers of numerous biological processes, notably during development. Although it is well recognized that cells sense and adapt to mechanical forces, the signal transduction pathways that underlie mechanosensing have remained elusive. Here, we investigate the impact of mechanical centrifugation force on phosphorylation-mediated signaling in Xenopus embryos. By monitoring temporal phosphoproteome and proteome alterations in response to force, we discover and validate elevated phosphorylation on focal adhesion and tight junction components, leading to several mechanistic insights into mechanosensing and tissue restoration. First, we determine changes in kinase activity profiles during mechanoresponse, identifying the activation of basophilic kinases. Pathway interrogation using kinase inhibitor treatment uncovers a crosstalk between the focal adhesion kinase (FAK) and protein kinase C (PKC) in mechanoresponse. Second, we find LIM domain 7 protein (Lmo7) as upregulated upon centrifugation, contributing to mechanoresponse. Third, we discover that mechanical compression force induces a mesenchymal-to-epithelial transition (MET)-like phenotype.
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Affiliation(s)
- Yutaka Hashimoto
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA; Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Noriyuki Kinoshita
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Joel D Federspiel
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Pierre M Jean Beltran
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Naoto Ueno
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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Tanaka R, Miyata S, Yamaguchi M, Yoshida H. Role of the smallish gene during Drosophila eye development. Gene 2019; 684:10-19. [DOI: 10.1016/j.gene.2018.10.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/15/2018] [Accepted: 10/19/2018] [Indexed: 02/06/2023]
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50
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Ma Z, Shi H, Shen Y, Li H, Yang Y, Yang J, Zhao H, Wang G, Wang J. Emerin anchors Msx1 and its protein partners at the nuclear periphery to inhibit myogenesis. Cell Biosci 2019; 9:34. [PMID: 31044068 PMCID: PMC6460851 DOI: 10.1186/s13578-019-0296-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Previous studies have shown that in myogenic precursors, the homeoprotein Msx1 and its protein partners, histone methyltransferases and repressive histone marks, tend to be enriched on target myogenic regulatory genes at the nuclear periphery. The nuclear periphery localization of Msx1 and its protein partners is required for Msx1's function of preventing myogenic precursors from pre-maturation through repressing target myogenic regulatory genes. However, the mechanisms underlying the maintenance of Msx1 and its protein partners' nuclear periphery localization are unknown. RESULTS We show that an inner nuclear membrane protein, Emerin, performs as an anchor settled at the inner nuclear membrane to keep Msx1 and its protein partners Ezh2, H3K27me3 enriching at the nuclear periphery, and participates in inhibition of myogenesis mediated by Msx1. Msx1 interacts with Emerin both in C2C12 myoblasts and mouse developing limbs, which is the prerequisite for Emerin mediating the precise location of Msx1, Ezh2, and H3K27me3. The deficiency of Emerin in C2C12 myoblasts disturbs the nuclear periphery localization of Msx1, Ezh2, and H3K27me3, directly indicating Emerin functioning as an anchor. Furthermore, Emerin cooperates with Msx1 to repress target myogenic regulatory genes, and assists Msx1 with inhibition of myogenesis. CONCLUSIONS Emerin cooperates with Msx1 to inhibit myogenesis through maintaining the nuclear periphery localization of Msx1 and Msx1's protein partners.
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Affiliation(s)
- Zhangjing Ma
- 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 People's Republic of China
| | - Huiyuan Shi
- 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 People's Republic of China
| | - Yi Shen
- 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 People's Republic of China
| | - Huixia Li
- 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 People's Republic of China
| | - Yu Yang
- 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 People's Republic of China
| | - Jiange Yang
- 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 People's Republic of China
| | - Hui Zhao
- Zhengzhou Revogene Inc, Zhengzhou, 450000 People's Republic of China
| | - Gang Wang
- 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 People's Republic of China.,3State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 People's Republic of China
| | - Jingqiang Wang
- 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 People's Republic of China
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