1
|
Srisawat K, Stead CA, Hesketh K, Pogson M, Strauss JA, Cocks M, Siekmann I, Phillips SM, Lisboa PJ, Shepherd S, Burniston JG. People with obesity exhibit losses in muscle proteostasis that are partly improved by exercise training. Proteomics 2024; 24:e2300395. [PMID: 37963832 DOI: 10.1002/pmic.202300395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023]
Abstract
This pilot experiment examines if a loss in muscle proteostasis occurs in people with obesity and whether endurance exercise positively influences either the abundance profile or turnover rate of proteins in this population. Men with (n = 3) or without (n = 4) obesity were recruited and underwent a 14-d measurement protocol of daily deuterium oxide (D2O) consumption and serial biopsies of vastus lateralis muscle. Men with obesity then completed 10-weeks of high-intensity interval training (HIIT), encompassing 3 sessions per week of cycle ergometer exercise with 1 min intervals at 100% maximum aerobic power interspersed by 1 min recovery periods. The number of intervals per session progressed from 4 to 8, and during weeks 8-10 the 14-d measurement protocol was repeated. Proteomic analysis detected 352 differences (p < 0.05, false discovery rate < 5%) in protein abundance and 19 (p < 0.05) differences in protein turnover, including components of the ubiquitin-proteasome system. HIIT altered the abundance of 53 proteins and increased the turnover rate of 22 proteins (p < 0.05) and tended to benefit proteostasis by increasing muscle protein turnover rates. Obesity and insulin resistance are associated with compromised muscle proteostasis, which may be partially restored by endurance exercise.
Collapse
Affiliation(s)
| | - Connor A Stead
- Research Institute for Sport, & Exercise Sciences, Liverpool, UK
| | - Katie Hesketh
- Research Institute for Sport, & Exercise Sciences, Liverpool, UK
| | - Mark Pogson
- Research Institute for Sport, & Exercise Sciences, Liverpool, UK
| | | | - Matt Cocks
- Research Institute for Sport, & Exercise Sciences, Liverpool, UK
| | - Ivo Siekmann
- Department of Applied Mathematics, Liverpool John Moores University, Liverpool, UK
| | - Stuart M Phillips
- Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Paulo J Lisboa
- Department of Applied Mathematics, Liverpool John Moores University, Liverpool, UK
| | - Sam Shepherd
- Research Institute for Sport, & Exercise Sciences, Liverpool, UK
| | | |
Collapse
|
2
|
Zhang Y, Wei Y, Wu M, Liu M, Liang S, Zhu X, Liu X, Lin F. Cand2 inhibits CRL-mediated ubiquitination and suppresses autophagy to facilitate pathogenicity of phytopathogenic fungi. PLANT COMMUNICATIONS 2024; 5:100720. [PMID: 37718510 PMCID: PMC10873881 DOI: 10.1016/j.xplc.2023.100720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
The ubiquitin-proteasome system and the autophagy system are the two primary mechanisms used by eukaryotes to maintain protein homeostasis, and both are closely related to the pathogenicity of the rice blast fungus. In this research, we identified MoCand2 as an inhibitor of ubiquitination in Magnaporthe oryzae. Through this role, MoCand2 participates in the regulation of autophagy and pathogenicity. Specifically, we found that deletion of MoCand2 increased the ubiquitination level in M. oryzae, whereas overexpression of MoCand2 inhibited the accumulation of ubiquitinated proteins. Interaction analyses showed that MoCand2 is a subunit of Cullin-RING ligases (CRLs). It suppresses ubiquitination by blocking the assembly of CRLs and downregulating the expression of key CRL subunits. Further research indicated that MoCand2 regulates autophagy through ubiquitination. MoCand2 knockout led to over-ubiquitination and over-degradation of MoTor, and we confirmed that MoTor content was negatively correlated with autophagy level. In addition, MoCand2 knockout accelerated the K63 ubiquitination of MoAtg6 and strengthened the assembly and activity of the phosphatidylinositol-3-kinase class 3 complex, thus enhancing autophagy. Abnormal ubiquitination and autophagy in ΔMocand2 resulted in defects in growth, conidiation, stress resistance, and pathogenicity. Finally, sequence alignment and functional analyses in other phytopathogenic fungi confirmed the high conservation of fungal Cand2s. Our research thus reveals a novel mechanism by which ubiquitination regulates autophagy and pathogenicity in phytopathogenic fungi.
Collapse
Affiliation(s)
- Yunran Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Yunyun Wei
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China
| | - Minghua Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengyu Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaohong Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| |
Collapse
|
3
|
Long J, Mariossi A, Cao C, Mo Z, Thompson JW, Levine MS, Lemaire LA. Cereblon influences the timing of muscle differentiation in Ciona tadpoles. Proc Natl Acad Sci U S A 2023; 120:e2309989120. [PMID: 37856545 PMCID: PMC10614628 DOI: 10.1073/pnas.2309989120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/09/2023] [Indexed: 10/21/2023] Open
Abstract
Thalidomide has a dark history as a teratogen, but in recent years, its derivates have been shown to function as potent chemotherapeutic agents. These drugs bind cereblon (CRBN), the substrate receptor of an E3 ubiquitin ligase complex, and modify its degradation targets. Despite these insights, remarkably little is known about the normal function of cereblon in development. Here, we employ Ciona, a simple invertebrate chordate, to identify endogenous Crbn targets. In Ciona, Crbn is specifically expressed in developing muscles during tail elongation before they acquire contractile activity. Crbn expression is activated by Mrf, the ortholog of MYOD1, a transcription factor important for muscle differentiation. CRISPR/Cas9-mediated mutations of Crbn lead to precocious onset of muscle contractions. By contrast, overexpression of Crbn delays contractions and is associated with decreased expression of contractile protein genes such as troponin. This reduction is possibly due to reduced Mrf protein levels without altering Mrf mRNA levels. Our findings suggest that Mrf and Crbn form a negative feedback loop to control the precision of muscle differentiation during tail elongation.
Collapse
Affiliation(s)
- Juanjuan Long
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Chen Cao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | | | | | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
| | - Laurence A. Lemaire
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Biology, Saint Louis University, St. Louis, MO63103
| |
Collapse
|
4
|
Zhang H, Xia P, Yang Z, Liu J, Zhu Y, Huang Z, Zhang Z, Yuan Y. Cullin-associated and neddylation-dissociated 1 regulate reprogramming of lipid metabolism through SKP1-Cullin-1-F-box FBXO11 -mediated heterogeneous nuclear ribonucleoprotein A2/B1 ubiquitination and promote hepatocellular carcinoma. Clin Transl Med 2023; 13:e1443. [PMID: 37837399 PMCID: PMC10576442 DOI: 10.1002/ctm2.1443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/20/2023] [Accepted: 10/01/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Enhanced de novo lipogenesis is essential for hepatocellular carcinoma (HCC). Abnormally high cullin-associated and neddylation-dissociated 1 (CAND1) expression is associated with poor clinical prognosis in HCC. The SKP1-Cullin-1-F-box (SCF) complex consists of the SKP1, Cullin-1 and F-box proteins (FBPs) and performs multiple functions including adipogenesis. SCF complex was modulated by CAND1, but Whether and how the CAND1 promotes HCC by regulating SCF complex and lipogenesis are unknown. METHODS HCC samples were used to analyze the correlations between CAND1 expression and clinicopathological characteristics such as survival and prognosis. The in vitro functions of CAND1, FBXO11 and heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1) were measured by cell proliferation, colony formation and migration assays. The in vivo functions were tested in multiple mouse liver cancer models including patient-derived xenograft (PDX), cell line-derived xenograft and AKT/NRASV12-induced primary liver cancer models. Injections of adeno-associated virus targeting CAND1 (AAV-shCAND1) were performed to evaluate the therapeutic efficacy of targeting CAND1. RNA-Seq and lipidomic assays followed by serial biochemical experiments including mass spectrometry, immunoprecipitation and GST pull-down were performed to dissect the underlying mechanisms. RESULTS CAND1 promoted the expression of lipid synthesis genes by disrupting SCF complex assembly and lipid accumulation. Furthermore, we identified hnRNPA2B1 as a novel F-box protein 11 (FBXO11)-binding partner. FBXO11 directly bound to hnRNPA2B1 and promoted hnRNPA2B1 ubiquitination and subsequent degradation. Our evaluations of the therapeutic efficacy of AAV-shCAND1 injections confirmed that targeting the CAND1-SCFFBXO11 -hnRNPA2B1A signalling axis was therapeutically effective. CAND1 downregulation significantly reduced the tumour burden in a primary mouse liver cancer model and a PDX model. CONCLUSIONS Our results highlight that CAND1 is associated with poor prognosis in HCC and regulates lipid metabolic reprogramming by dissociating the SCF complex. Targeting the CAND1-SCFFBXO11 -hnRNPA2B1 axis may be a novel strategy for HCC treatment.
Collapse
Affiliation(s)
- Hao Zhang
- Department of Hepatobiliary and Pancreatic SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei ProvinceWuhanChina
- Department of Organ TransplantationQilu Hospital of Shandong UniversityJinanChina
| | - Peng Xia
- Department of Hepatobiliary and Pancreatic SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei ProvinceWuhanChina
| | - Zhangshuo Yang
- Department of Hepatobiliary and Pancreatic SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei ProvinceWuhanChina
- Department of Breast SurgeryAffiliated Hospital of Hebei UniversityBaodingChina
| | - Jie Liu
- Department of Hepatobiliary and Pancreatic SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei ProvinceWuhanChina
- TaiKang Center for Life and Medical SciencesWuhan UniversityWuhanChina
| | - Yimin Zhu
- Department of Hepatobiliary and Pancreatic SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei ProvinceWuhanChina
| | - Zan Huang
- College of Life SciencesWuhan UniversityWuhanChina
| | - Zhonglin Zhang
- Department of Hepatobiliary and Pancreatic SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei ProvinceWuhanChina
| | - Yufeng Yuan
- Department of Hepatobiliary and Pancreatic SurgeryZhongnan Hospital of Wuhan UniversityWuhanChina
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei ProvinceWuhanChina
- TaiKang Center for Life and Medical SciencesWuhan UniversityWuhanChina
| |
Collapse
|
5
|
Roles of Cullin-RING Ubiquitin Ligases in Cardiovascular Diseases. Biomolecules 2022; 12:biom12030416. [PMID: 35327608 PMCID: PMC8946067 DOI: 10.3390/biom12030416] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/18/2022] Open
Abstract
Maintenance of protein homeostasis is crucial for virtually every aspect of eukaryotic biology. The ubiquitin-proteasome system (UPS) represents a highly regulated quality control machinery that protects cells from a variety of stress conditions as well as toxic proteins. A large body of evidence has shown that UPS dysfunction contributes to the pathogenesis of cardiovascular diseases. This review highlights the latest findings regarding the physiological and pathological roles of cullin-RING ubiquitin ligases (CRLs), an essential player in the UPS, in the cardiovascular system. To inspire potential therapeutic invention, factors regulating CRL activities are also discussed.
Collapse
|
6
|
Olguín HC. The Gentle Side of the UPS: Ubiquitin-Proteasome System and the Regulation of the Myogenic Program. Front Cell Dev Biol 2022; 9:821839. [PMID: 35127730 PMCID: PMC8811165 DOI: 10.3389/fcell.2021.821839] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022] Open
Abstract
In recent years, the ubiquitin-proteasome system (UPS) has emerged as an important regulator of stem cell function. Here we review recent findings indicating that UPS also plays critical roles in the biology of satellite cells, the muscle stem cell responsible for its maintenance and regeneration. While we focus our attention on the control of key transcriptional regulators of satellite cell function, we briefly discuss early studies suggesting the UPS participates more broadly in the regulation of satellite cell stemness and regenerative capacity.
Collapse
|
7
|
Górska AA, Sandmann C, Riechert E, Hofmann C, Malovrh E, Varma E, Kmietczyk V, Ölschläger J, Jürgensen L, Kamuf-Schenk V, Stroh C, Furkel J, Konstandin MH, Sticht C, Boileau E, Dieterich C, Frey N, Katus HA, Doroudgar S, Völkers M. Muscle-specific Cand2 is translationally upregulated by mTORC1 and promotes adverse cardiac remodeling. EMBO Rep 2021; 22:e52170. [PMID: 34605609 PMCID: PMC8647021 DOI: 10.15252/embr.202052170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) promotes pathological remodeling in the heart by activating ribosomal biogenesis and mRNA translation. Inhibition of mTOR in cardiomyocytes is protective; however, a detailed role of mTOR in translational regulation of specific mRNA networks in the diseased heart is unknown. We performed cardiomyocyte genome-wide sequencing to define mTOR-dependent gene expression control at the level of mRNA translation. We identify the muscle-specific protein Cullin-associated NEDD8-dissociated protein 2 (Cand2) as a translationally upregulated gene, dependent on the activity of mTOR. Deletion of Cand2 protects the myocardium against pathological remodeling. Mechanistically, we show that Cand2 links mTOR signaling to pathological cell growth by increasing Grk5 protein expression. Our data suggest that cell-type-specific targeting of mTOR might have therapeutic value against pathological cardiac remodeling.
Collapse
Affiliation(s)
- Agnieszka A Górska
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Clara Sandmann
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Eva Riechert
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Christoph Hofmann
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Ellen Malovrh
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Eshita Varma
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Vivien Kmietczyk
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Julie Ölschläger
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Lonny Jürgensen
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Verena Kamuf-Schenk
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Claudia Stroh
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Jennifer Furkel
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Mathias H Konstandin
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Carsten Sticht
- Medical Research Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Etienne Boileau
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany.,Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Christoph Dieterich
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany.,Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Norbert Frey
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Hugo A Katus
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Shirin Doroudgar
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| | - Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, Heidelberg/Mannheim, Germany
| |
Collapse
|
8
|
Takeshita LY, Davidsen PK, Herbert JM, Antczak P, Hesselink MKC, Schrauwen P, Weisnagel SJ, Robbins JM, Gerszten RE, Ghosh S, Sarzynski MA, Bouchard C, Falciani F. Genomics and transcriptomics landscapes associated to changes in insulin sensitivity in response to endurance exercise training. Sci Rep 2021; 11:23314. [PMID: 34857871 PMCID: PMC8639975 DOI: 10.1038/s41598-021-98792-1] [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: 01/14/2021] [Accepted: 08/25/2021] [Indexed: 01/14/2023] Open
Abstract
Despite good adherence to supervised endurance exercise training (EET), some individuals experience no or little improvement in peripheral insulin sensitivity. The genetic and molecular mechanisms underlying this phenomenon are currently not understood. By investigating genome-wide variants associated with baseline and exercise-induced changes (∆) in insulin sensitivity index (Si) in healthy volunteers, we have identified novel candidate genes whose mouse knockouts phenotypes were consistent with a causative effect on Si. An integrative analysis of functional genomic and transcriptomic profiles suggests genetic variants have an aggregate effect on baseline Si and ∆Si, focused around cholinergic signalling, including downstream calcium and chemokine signalling. The identification of calcium regulated MEF2A transcription factor as the most statistically significant candidate driving the transcriptional signature associated to ∆Si further strengthens the relevance of calcium signalling in EET mediated Si response.
Collapse
Affiliation(s)
- Louise Y. Takeshita
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Peter K. Davidsen
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - John M. Herbert
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Philipp Antczak
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK ,grid.411097.a0000 0000 8852 305XCenter for Molecular Medicine Cologne, University Hospital Cologne, 50931 Cologne, Germany
| | - Matthijs K. C. Hesselink
- grid.5012.60000 0001 0481 6099Department of Nutrition and Movement Sciences, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Centre, Maastricht, The Netherlands
| | - Patrick Schrauwen
- grid.5012.60000 0001 0481 6099Department of Nutrition and Movement Sciences, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Centre, Maastricht, The Netherlands
| | - S. John Weisnagel
- grid.23856.3a0000 0004 1936 8390Diabetes Research Unit, Endocrinology and Nephrology Axis, CRCHU de Québec, Université Laval, Québec City, Canada
| | - Jeremy M. Robbins
- grid.239395.70000 0000 9011 8547Division of Cardiovascular Medicine, and Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
| | - Robert E. Gerszten
- grid.239395.70000 0000 9011 8547Division of Cardiovascular Medicine, and Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
| | - Sujoy Ghosh
- grid.428397.30000 0004 0385 0924Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Mark A. Sarzynski
- grid.254567.70000 0000 9075 106XDepartment of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia, SC USA
| | - Claude Bouchard
- grid.250514.70000 0001 2159 6024Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA USA
| | - Francesco Falciani
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| |
Collapse
|
9
|
Moksnes MR, Røsjø H, Richmond A, Lyngbakken MN, Graham SE, Hansen AF, Wolford BN, Gagliano Taliun SA, LeFaive J, Rasheed H, Thomas LF, Zhou W, Aung N, Surakka I, Douville NJ, Campbell A, Porteous DJ, Petersen SE, Munroe PB, Welsh P, Sattar N, Smith GD, Fritsche LG, Nielsen JB, Åsvold BO, Hveem K, Hayward C, Willer CJ, Brumpton BM, Omland T. Genome-wide association study of cardiac troponin I in the general population. Hum Mol Genet 2021; 30:2027-2039. [PMID: 33961016 PMCID: PMC8522636 DOI: 10.1093/hmg/ddab124] [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: 01/05/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
Circulating cardiac troponin proteins are associated with structural heart disease and predict incident cardiovascular disease in the general population. However, the genetic contribution to cardiac troponin I (cTnI) concentrations and its causal effect on cardiovascular phenotypes are unclear. We combine data from two large population-based studies, the Trøndelag Health Study and the Generation Scotland Scottish Family Health Study, and perform a genome-wide association study of high-sensitivity cTnI concentrations with 48 115 individuals. We further use two-sample Mendelian randomization to investigate the causal effects of circulating cTnI on acute myocardial infarction (AMI) and heart failure (HF). We identified 12 genetic loci (8 novel) associated with cTnI concentrations. Associated protein-altering variants highlighted putative functional genes: CAND2, HABP2, ANO5, APOH, FHOD3, TNFAIP2, KLKB1 and LMAN1. Phenome-wide association tests in 1688 phecodes and 83 continuous traits in UK Biobank showed associations between a genetic risk score for cTnI and cardiac arrhythmias, metabolic and anthropometric measures. Using two-sample Mendelian randomization, we confirmed the non-causal role of cTnI in AMI (5948 cases, 355 246 controls). We found indications for a causal role of cTnI in HF (47 309 cases and 930 014 controls), but this was not supported by secondary analyses using left ventricular mass as outcome (18 257 individuals). Our findings clarify the biology underlying the heritable contribution to circulating cTnI and support cTnI as a non-causal biomarker for AMI in the general population. Using genetically informed methods for causal inference helps inform the role and value of measuring cTnI in the general population.
Collapse
Affiliation(s)
- Marta R Moksnes
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Helge Røsjø
- Division of Research and Innovation, Akershus University Hospital, 1478 Lørenskog, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Magnus N Lyngbakken
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
- Division of Medicine, Department of Cardiology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Sarah E Graham
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ailin Falkmo Hansen
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Brooke N Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah A Gagliano Taliun
- Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Montréal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Jonathon LeFaive
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Humaira Rasheed
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Laurent F Thomas
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- BioCore - Bioinformatics Core Facility, NTNU - Norwegian University of Science and Technology, 7491 Trondheim. Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7491 Trondheim, Norway
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nay Aung
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- National Institute for Health Research Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London E1 4NS, UK
- Barts Heart Centre, St. Bartholomew’s Hospital, Barts Health NHS Trust, London EC1A 7BE, UK
| | - Ida Surakka
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicholas J Douville
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Archie Campbell
- Medical Genetics Section, CGEM, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - David J Porteous
- Medical Genetics Section, CGEM, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Steffen E Petersen
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- National Institute for Health Research Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London E1 4NS, UK
- Barts Heart Centre, St. Bartholomew’s Hospital, Barts Health NHS Trust, London EC1A 7BE, UK
| | - Patricia B Munroe
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- National Institute for Health Research Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London E1 4NS, UK
| | - Paul Welsh
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Lars G Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Jonas B Nielsen
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology Research, Statens Serum Institute, 2300 Copenhagen, Denmark
- Department of Cardiology, Copenhagen University Hospital, 2100 Copenhagen, Denmark
| | - Bjørn Olav Åsvold
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Public Health and Nursing, HUNT Research Centre, NTNU - Norwegian University of Science and Technology, 7600 Levanger, Norway
- Department of Endocrinology, St. Olavs Hospital, Trondheim University Hospital, 7006 Trondheim, Norway
| | - Kristian Hveem
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Public Health and Nursing, HUNT Research Centre, NTNU - Norwegian University of Science and Technology, 7600 Levanger, Norway
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Cristen J Willer
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ben M Brumpton
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
- Clinic of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, 7006 Trondheim, Norway
| | - Torbjørn Omland
- Division of Research and Innovation, Akershus University Hospital, 1478 Lørenskog, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
- Division of Medicine, Department of Cardiology, Akershus University Hospital, 1478 Lørenskog, Norway
| |
Collapse
|
10
|
Zhou H, Su H, Chen W. Neddylation Regulates Class IIa and III Histone Deacetylases to Mediate Myoblast Differentiation. Int J Mol Sci 2021; 22:ijms22179509. [PMID: 34502418 PMCID: PMC8431717 DOI: 10.3390/ijms22179509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 11/16/2022] Open
Abstract
As the largest tissue in the body, skeletal muscle has multiple functions in movement and energy metabolism. Skeletal myogenesis is controlled by a transcriptional cascade including a set of muscle regulatory factors (MRFs) that includes Myogenic Differentiation 1 (MYOD1), Myocyte Enhancer Factor 2 (MEF2), and Myogenin (MYOG), which direct the fusion of myogenic myoblasts into multinucleated myotubes. Neddylation is a posttranslational modification that covalently conjugates ubiquitin-like NEDD8 (neural precursor cell expressed, developmentally downregulated 8) to protein targets. Inhibition of neddylation impairs muscle differentiation; however, the underlying molecular mechanisms remain less explored. Here, we report that neddylation is temporally regulated during myoblast differentiation. Inhibition of neddylation through pharmacological blockade using MLN4924 (Pevonedistat) or genetic deletion of NEDD8 Activating Enzyme E1 Subunit 1 (NAE1), a subunit of the E1 neddylation-activating enzyme, blocks terminal myoblast differentiation partially through repressing MYOG expression. Mechanistically, we found that neddylation deficiency enhances the mRNA and protein expressions of class IIa histone deacetylases 4 and 5 (HDAC4 and 5) and prevents the downregulation and nuclear export of class III HDAC (NAD-Dependent Protein Deacetylase Sirtuin-1, SIRT1), all of which have been shown to repress MYOD1-mediated MYOG transcriptional activation. Together, our findings for the first time identify the crucial role of neddylation in mediating class IIa and III HDAC co-repressors to control myogenic program and provide new insights into the mechanisms of muscle disease and regeneration.
Collapse
Affiliation(s)
- Hongyi Zhou
- Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA;
- Correspondence: ; Tel.: +1-706-721-8779
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA;
| | - Weiqin Chen
- Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA;
| |
Collapse
|
11
|
An Insight into the microRNAs Associated with Arteriovenous and Cavernous Malformations of the Brain. Cells 2021; 10:cells10061373. [PMID: 34199498 PMCID: PMC8227573 DOI: 10.3390/cells10061373] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 12/17/2022] Open
Abstract
Background: Brain arteriovenous malformations (BAVMs) and cerebral cavernous malformations (CCMs) are rare developmental anomalies of the intracranial vasculature, with an irregular tendency to rupture, and as of yet incompletely deciphered pathophysiology. Because of their variety in location, morphology, and size, as well as unpredictable natural history, they represent a management challenge. MicroRNAs (miRNAs) are strands of non-coding RNA of around 20 nucleotides that are able to modulate the expression of target genes by binding completely or partially to their respective complementary sequences. Recent breakthroughs have been made on elucidating their contribution to BAVM and CCM occurrence, growth, and evolution; however, there are still countless gaps in our understanding of the mechanisms involved. Methods: We have searched the Medline (PubMed; PubMed Central) database for pertinent articles on miRNAs and their putative implications in BAVMs and CCMs. To this purpose, we employed various permutations of the terms and idioms: ‘arteriovenous malformation’, ‘AVM’, and ‘BAVM’, or ‘cavernous malformation’, ‘cavernoma’, and ‘cavernous angioma’ on the one hand; and ‘microRNA’, ‘miRNA’, and ‘miR’ on the other. Using cross-reference search; we then investigated additional articles concerning the individual miRNAs identified in other cerebral diseases. Results: Seven miRNAs were discovered to play a role in BAVMs, three of which were downregulated (miR-18a, miR-137, and miR-195*) and four upregulated (miR-7-5p, miR-199a-5p, miR-200b-3p, and let-7b-3p). Similarly, eight miRNAs were identified in CCM in humans and experimental animal models, two being upregulated (miR-27a and mmu-miR-3472a), and six downregulated (miR-125a, miR-361-5p, miR-370-3p, miR-181a-2-3p, miR-95-3p, and let-7b-3p). Conclusions: The following literature review endeavored to address the recent discoveries related to the various implications of miRNAs in the formation and growth of BAVMs and CCMs. Additionally, by presenting other cerebral pathologies correlated with these miRNAs, it aimed to emphasize the potential directions of upcoming research and biological therapies.
Collapse
|
12
|
Kapoor S, Subba P, Shenoy P S, Bose B. Sca1 + Progenitor Cells (Ex vivo) Exhibits Differential Proteomic Signatures From the Culture Adapted Sca1 + Cells (In vitro), Both Isolated From Murine Skeletal Muscle Tissue. Stem Cell Rev Rep 2021; 17:1754-1767. [PMID: 33742350 DOI: 10.1007/s12015-021-10134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 10/21/2022]
Abstract
Stem cell antigen-1 (Sca-1) is a glycosyl-phosphatidylinositol-anchored membrane protein that is expressed in a sub-population of muscle stem and progenitor cell types. Reportedly, Sca-1 regulates the myogenic property of myoblasts and Sca-1-/- mice exhibited defective muscle regeneration. Although the role of Sca-1 in muscle development and maintenance is well-acknowledged, molecular composition of muscle derived Sca-1+ cells is not characterized. Here, we applied a high-resolution mass spectrometry-based workflow to characterize the proteomic landscape of mouse hindlimb skeletal muscle derived Sca-1+ cells. Furthermore, we characterized the impact of the cellular microenvironments on the proteomes of Sca-1+ cells. The proteome component of freshly isolated Sca-1+ cells (ex vivo) was compared with that of Sca-1+ cells expanded in cell culture (in vitro). The analysis revealed significant differences in the protein abundances in the two conditions reflective of their functional variations. The identified proteins were enriched in various biological pathways. Notably, we identified proteins related to myotube differentiation, myotube cell development and myoblast fusion. We also identified a panel of cell surface marker proteins that can be leveraged in future to enrich Sca-1+ cells using combinatorial strategies. Comparative analysis implicated the activation of various pathways leading to increased protein synthesis under in vitro condition. We report here the most comprehensive proteome map of Sca-1+ cells that provides insights into the molecular networks operative in Sca-1+ cells. Importantly, through our work we generated the proteomic blueprint of protein abundances significantly altered in Sca-1+ cells under ex vivo and in vitro conditions. The curated data can also be visualized at https://yenepoya.res.in/database/Sca-1-Proteomics .
Collapse
Affiliation(s)
- Saketh Kapoor
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka, 575018, India
| | - Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, Karnataka, 575018, India
| | - Sudheer Shenoy P
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka, 575018, India.
| | - Bipasha Bose
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka, 575018, India.
| |
Collapse
|
13
|
Blondelle J, Biju A, Lange S. The Role of Cullin-RING Ligases in Striated Muscle Development, Function, and Disease. Int J Mol Sci 2020; 21:E7936. [PMID: 33114658 PMCID: PMC7672578 DOI: 10.3390/ijms21217936] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
The well-orchestrated turnover of proteins in cross-striated muscles is one of the fundamental processes required for muscle cell function and survival. Dysfunction of the intricate protein degradation machinery is often associated with development of cardiac and skeletal muscle myopathies. Most muscle proteins are degraded by the ubiquitin-proteasome system (UPS). The UPS involves a number of enzymes, including E3-ligases, which tightly control which protein substrates are marked for degradation by the proteasome. Recent data reveal that E3-ligases of the cullin family play more diverse and crucial roles in cross striated muscles than previously anticipated. This review highlights some of the findings on the multifaceted functions of cullin-RING E3-ligases, their substrate adapters, muscle protein substrates, and regulatory proteins, such as the Cop9 signalosome, for the development of cross striated muscles, and their roles in the etiology of myopathies.
Collapse
Affiliation(s)
- Jordan Blondelle
- Department of Medicine, University of California, La Jolla, CA 92093, USA
| | - Andrea Biju
- Department of Medicine, University of California, La Jolla, CA 92093, USA
| | - Stephan Lange
- Department of Medicine, University of California, La Jolla, CA 92093, USA
- Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden
| |
Collapse
|
14
|
Weng LC, Hall AW, Choi SH, Jurgens SJ, Haessler J, Bihlmeyer NA, Grarup N, Lin H, Teumer A, Li-Gao R, Yao J, Guo X, Brody JA, Müller-Nurasyid M, Schramm K, Verweij N, van den Berg ME, van Setten J, Isaacs A, Ramírez J, Warren HR, Padmanabhan S, Kors JA, de Boer RA, van der Meer P, Sinner MF, Waldenberger M, Psaty BM, Taylor KD, Völker U, Kanters JK, Li M, Alonso A, Perez MV, Vaartjes I, Bots ML, Huang PL, Heckbert SR, Lin HJ, Kornej J, Munroe PB, van Duijn CM, Asselbergs FW, Stricker BH, van der Harst P, Kääb S, Peters A, Sotoodehnia N, Rotter JI, Mook-Kanamori DO, Dörr M, Felix SB, Linneberg A, Hansen T, Arking DE, Kooperberg C, Benjamin EJ, Lunetta KL, Ellinor PT, Lubitz SA. Genetic Determinants of Electrocardiographic P-Wave Duration and Relation to Atrial Fibrillation. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2020; 13:387-395. [PMID: 32822252 PMCID: PMC7578098 DOI: 10.1161/circgen.119.002874] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND The P-wave duration (PWD) is an electrocardiographic measurement that represents cardiac conduction in the atria. Shortened or prolonged PWD is associated with atrial fibrillation (AF). We used exome-chip data to examine the associations between common and rare variants with PWD. METHODS Fifteen studies comprising 64 440 individuals (56 943 European, 5681 African, 1186 Hispanic, 630 Asian) and ≈230 000 variants were used to examine associations with maximum PWD across the 12-lead ECG. Meta-analyses summarized association results for common variants; gene-based burden and sequence kernel association tests examined low-frequency variant-PWD associations. Additionally, we examined the associations between PWD loci and AF using previous AF genome-wide association studies. RESULTS We identified 21 common and low-frequency genetic loci (14 novel) associated with maximum PWD, including several AF loci (TTN, CAND2, SCN10A, PITX2, CAV1, SYNPO2L, SOX5, TBX5, MYH6, RPL3L). The top variants at known sarcomere genes (TTN, MYH6) were associated with longer PWD and increased AF risk. However, top variants at other loci (eg, PITX2 and SCN10A) were associated with longer PWD but lower AF risk. CONCLUSIONS Our results highlight multiple novel genetic loci associated with PWD, and underscore the shared mechanisms of atrial conduction and AF. Prolonged PWD may be an endophenotype for several different genetic mechanisms of AF.
Collapse
Affiliation(s)
- Lu-Chen Weng
- Cardiovascular Rsrch Ctr, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
| | - Amelia Weber Hall
- Cardiovascular Rsrch Ctr, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
| | - Sean J. Jurgens
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
| | - Jeffrey Haessler
- Fred Hutchinson Cancer Rsrch Ctr, Division of Public Health Sciences, Seattle WA
| | - Nathan A. Bihlmeyer
- McKusick-Nathans Dept of Genetic Medicine, Johns Hopkins Univ School of Med, Baltimore, MD
| | - Niels Grarup
- Novo Nordisk Foundation Ctr for Basic Metabolic Rsrch, Faculty of Health & Med Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Honghuang Lin
- Boston Univ & NHLBI’s Framingham Heart Study, Framingham
- Section of Computational Biomedicine, Dept of Med, Boston Univ School of Med, Boston, MA
| | - Alexander Teumer
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Greifswald
- Inst for Community Med, Univ Medicine Greifswald, Greifswald, Germany
| | - Ruifang Li-Gao
- Dept of Clinical Epidemiology, Leiden Univ Medical Ctr, the Netherlands
| | - Jie Yao
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
| | - Xiuqing Guo
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
- Dept of Pediatrics, David Geffen School of Med at UCLA, Los Angeles, CA
| | - Jennifer A. Brody
- Cardiovascular Health Rsrch Unit, Dept of Med, Dept of Epidemiology, Univ of Washington
| | - Martina Müller-Nurasyid
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich
- Dept of Internal Med I (Cardiology), Hospital of the Ludwig-Maximilians-Univ (LMU) Munich, Munich
- Inst of Genetic Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
| | - Katharina Schramm
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich
- Dept of Internal Med I (Cardiology), Hospital of the Ludwig-Maximilians-Univ (LMU) Munich, Munich
- Inst of Genetic Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
| | - Niek Verweij
- Genomics plc, Oxford, UK
- Dept of Cardiology, Univ of Groningen & Univ Medical Ctr, Groningen
| | - Marten E. van den Berg
- Dept of Epidemiology, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
| | - Jessica van Setten
- Dept of Cardiology, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
| | - Aaron Isaacs
- CARIM School for Cardiovascular Diseases, Maastricht Univ, Maastricht, the Netherlands
- Dept of Physiology, Maastricht Univ, Maastricht, the Netherlands
| | - Julia Ramírez
- Nat Inst for Health Rsrch, Barts Cardiovascular Biomedical Rsrch Ctr, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
- William Harvey Rsrch Inst, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
| | - Helen R. Warren
- Nat Inst for Health Rsrch, Barts Cardiovascular Biomedical Rsrch Ctr, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
- William Harvey Rsrch Inst, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
| | - Sandosh Padmanabhan
- Inst of Cardiovascular & Medical Sciences, College of Medical, Veterinary & Life Sciences, Univ of Glasgow, Glasgow, UK
| | - Jan A. Kors
- Dept of Med Informatics, Erasmus Univ Medical Ctr, Rotterdam, the Netherlands
| | | | | | - Moritz F. Sinner
- Dept of Internal Med I (Cardiology), Hospital of the Ludwig-Maximilians-Univ (LMU) Munich, Munich
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Munich Heart Alliance, Munich
| | - Melanie Waldenberger
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Munich Heart Alliance, Munich
- Inst of Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
- Rsrch unit of Molecular Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
| | - Bruce M. Psaty
- Cardiovascular Health Rsrch Unit, Depts of Med, Epidemiology & Health Services, Dept of Epidemiology, Univ of Washington
- Kaiser Permanente Washington Health Rsrch Inst, Seattle, WA
| | - Kent D. Taylor
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
- Dept of Pediatrics, David Geffen School of Med at UCLA, Los Angeles, CA
| | - Uwe Völker
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Greifswald
- Interfaculty Inst for Genetics & Functional Genomics, Univ Medicine Greifswald, Greifswald, Germany
| | - Jørgen K. Kanters
- Lab of Experimental Cardiology, Faculty of Health & Med Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Man Li
- Division of Nephrology & Hypertensions, Dept of Internal Med, Univ of Utah School of Med, Salt Lake City, UT
| | - Alvaro Alonso
- Dept of Epidemiology, Rollins School of Public Health, Emory Univ, Atlanta, GA
| | | | - Ilonca Vaartjes
- Julius Ctr for Health Sciences & Primary Care, Univ Medical Ctr Utrecht, Utrecht Univ, the Netherlands
| | - Michiel L. Bots
- Julius Ctr for Health Sciences & Primary Care, Univ Medical Ctr Utrecht, Utrecht Univ, the Netherlands
| | | | - Susan R. Heckbert
- Cardiovascular Health Rsrch Unit, Dept of Epidemiology, Univ of Washington
| | - Henry J. Lin
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
- Dept of Pediatrics, David Geffen School of Med at UCLA, Los Angeles, CA
| | - Jelena Kornej
- Boston Univ & NHLBI’s Framingham Heart Study, Framingham
| | - Patricia B. Munroe
- Nat Inst for Health Rsrch, Barts Cardiovascular Biomedical Rsrch Ctr, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
- William Harvey Rsrch Inst, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
| | - Cornelia M. van Duijn
- Dept of Epidemiology, Erasmus Univ Medical Ctr, Rotterdam, the Netherlands
- Nuffield Dept of Population Health, Medical Sciences Division, St. Cross College, Oxford Univ, Oxford
| | - Folkert W. Asselbergs
- Dept of Cardiology, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
- Health Data Rsrch UK & Inst of Health Informatics, Faculty of Population Health Sciences, Univ College London, London, UK
- Inst of Cardiovascular Science, Faculty of Population Health Sciences, Univ College London, London, UK
| | - Bruno H. Stricker
- Dept of Internal Medicine, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
- Dept of Med Informatics, Erasmus MC, Medical Ctr Rotterdam, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
- Inspectorate of Health Care
| | - Pim van der Harst
- Dept of Cardiology, Univ of Groningen & Univ Medical Ctr, Groningen
- Durrer Ctr for Cardiogenetic Rsrch, ICIN-Netherlands Heart Inst, Utrecht, the Netherlands
- Dept of Genetics, Univ of Groningen & Univ Medical Ctr, Groningen
| | - Stefan Kääb
- Dept of Internal Med I (Cardiology), Hospital of the Ludwig-Maximilians-Univ (LMU) Munich, Munich
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Munich Heart Alliance, Munich
| | - Annette Peters
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Munich Heart Alliance, Munich
- Inst of Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
- German Ctr for Diabetes Rsrch, Neuherberg, Germany
| | - Nona Sotoodehnia
- Cardiovascular Health Rsrch Unit, Dept of Med, Dept of Epidemiology, Univ of Washington
| | - Jerome I. Rotter
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
- Depts of Pediatrics & Human Genetics, David Geffen School of Med at UCLA, Los Angeles, CA
| | - Dennis O. Mook-Kanamori
- Dept of Clinical Epidemiology, Leiden Univ Medical Ctr, the Netherlands
- Dept of Public Health & Primary Care, Leiden Univ Medical Ctr, the Netherlands
| | - Marcus Dörr
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Greifswald
- Dept of Internal Med B, Univ Medicine Greifswald, Greifswald, Germany
| | - Stephan B. Felix
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Greifswald
- Dept of Internal Med B, Univ Medicine Greifswald, Greifswald, Germany
| | - Allan Linneberg
- Ctr for Clinical Rsrch & Prevention, Bispebjerg & Frederiksberg Hospital, Copenhagen, Denamrk
- Dept of Clinical Med, Faculty of Health & Med Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Ctr for Basic Metabolic Rsrch, Faculty of Health & Med Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Dan E. Arking
- McKusick-Nathans Dept of Genetic Medicine, Johns Hopkins Univ School of Med, Baltimore, MD
| | - Charles Kooperberg
- Fred Hutchinson Cancer Rsrch Ctr, Division of Public Health Sciences, Seattle WA
| | - Emelia J. Benjamin
- Boston Univ & NHLBI’s Framingham Heart Study, Framingham
- Dept of Epidemiology, Boston Univ School of Public Health, Boston, MA
- Dept of Med, Boston Univ School of Med, Boston, MA
| | - Kathryn L. Lunetta
- Boston Univ & NHLBI’s Framingham Heart Study, Framingham
- Dept of Biostatistics, Boston Univ School of Public Health, Boston, MA
| | - Patrick T. Ellinor
- Cardiovascular Rsrch Ctr, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
- Cardiac Arrhythmia Service, MGH, Boston
| | - Steven A. Lubitz
- Cardiovascular Rsrch Ctr, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
- Cardiac Arrhythmia Service, MGH, Boston
| |
Collapse
|
15
|
Cheng W, Yin S, Tu Y, Mei H, Wang Y, Yang Y. SlCAND1, encoding cullin-associated Nedd8-dissociated protein 1, regulates plant height, flowering time, seed germination, and root architecture in tomato. PLANT MOLECULAR BIOLOGY 2020; 102:537-551. [PMID: 31916084 DOI: 10.1007/s11103-020-00963-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
Silencing of SlCAND1 expression resulted in dwarfish, loss of apical dominance, early flowering, suppression of seed germination, and abnormal root architecture in tomato Cullin-RING E3 ligases (CRLs)-dependent ubiquitin proteasome system mediates degradation of numerous proteins that controls a wide range of developmental and physiological processes in eukaryotes. Cullin-associated Nedd8-dissociated protein 1 (CAND1) acts as an exchange factor allowing substrate recognition part exchange and plays a vital role in reactivating CRLs. The present study reports on the identification of SlCAND1, the only one CAND gene in tomato. SlCAND1 expression is ubiquitous and positively regulated by multiple plant hormones. Silencing of SlCAND1 expression using RNAi strategy resulted in a pleiotropic and gibberellin/auxin-associated phenotypes, including dwarf plant with reduced internode length, loss of apical dominance, early flowering, low seed germination percentage, delayed seed germination speed, short primary root, and increased lateral root proliferation and elongation. Moreover, application of exogenous GA3 or IAA could partly rescue some SlCAND1-silenced phenotypes, and the expression levels of gibberellin/auxin-related genes were altered in SlCAND1-RNAi lines. These facts revealed that SlCAND1 is required for gibberellin/auxin-associated regulatory network in tomato. Although SlCAND1 is crucial for multiple developmental processes during vegetative growth stage, SlCAND1-RNAi lines didn't exhibit visible effect on fruit development and ripening. Meanwhile, we discussed that multiple physiological functions of SlCAND1 in tomato are different to previous report of its ortholog in Arabidopsis. Our study adds a new perspective on the functional roles of CAND1 in plants, and strongly supports the hypothesis that CAND1 and its regulated ubiquitin proteasome system are pivotal for plant vegetative growth but possibly have different roles in diverse plant species.
Collapse
Affiliation(s)
- Wenjing Cheng
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Shuangqin Yin
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Yun Tu
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Hu Mei
- Bioengineering College, Chongqing University, Chongqing, 400044, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Yongzhong Wang
- Bioengineering College, Chongqing University, Chongqing, 400044, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Yingwu Yang
- Bioengineering College, Chongqing University, Chongqing, 400044, China.
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China.
| |
Collapse
|
16
|
Horibata Y, Mitsuhashi S, Shimizu H, Maejima S, Sakamoto H, Aoyama C, Ando H, Sugimoto H. The phosphatidylcholine transfer protein StarD7 is important for myogenic differentiation in mouse myoblast C2C12 cells and human primary skeletal myoblasts. Sci Rep 2020; 10:2845. [PMID: 32071354 PMCID: PMC7029042 DOI: 10.1038/s41598-020-59444-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/27/2020] [Indexed: 01/05/2023] Open
Abstract
StarD7 is a phosphatidylcholine (PC)-specific lipid transfer protein essential for the maintenance of mitochondrial PC composition, morphogenesis, and respiration. Here, we studied the role of StarD7 in skeletal myoblast differentiation using mouse myoblast C2C12 cells and human primary myoblasts. Immunofluorescence and immuno-electron microscopy revealed that StarD7 was distributed in the cytosol, inner mitochondria space, and outer leaflet of the outer mitochondrial membrane in C2C12 cells. Unlike human kidney embryonic cell line HEK293 cells, the mitochondrial proteinase PARL was not involved in the processing and maturation of StarD7 in C2C12 cells. StarD7 was constantly expressed during myogenic differentiation of C2C12 cells. The siRNA-mediated knockdown of StarD7 in C2C12 cells and human primary myoblasts significantly impaired myogenic differentiation and reduced the expression of myomaker, myomerger and PGC-1α. The reduction in mitochondrial PC levels and oxygen consumption rates, decreased expression of myomaker, myomerger and PGC-1α, as well as impaired myogenic differentiation, were completely restored when the protein was reintroduced into StarD7-knockout C2C12 cells. These results suggest that StarD7 is important for skeletal myogenesis in mammals.
Collapse
Affiliation(s)
- Yasuhiro Horibata
- Department of Biochemistry, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, 321-0293, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Hiroaki Shimizu
- Department of Biochemistry, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, 321-0293, Japan
| | - Sho Maejima
- Ushimado Marine Institute (UMI), Graduate School of Natural Science and Technology, Okayama University, Ushimado, Setouchi, Okayama, 701-4303, Japan
| | - Hirotaka Sakamoto
- Ushimado Marine Institute (UMI), Graduate School of Natural Science and Technology, Okayama University, Ushimado, Setouchi, Okayama, 701-4303, Japan
| | - Chieko Aoyama
- Department of Biochemistry, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, 321-0293, Japan
| | - Hiromi Ando
- Department of Biochemistry, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, 321-0293, Japan
| | - Hiroyuki Sugimoto
- Department of Biochemistry, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, 321-0293, Japan.
| |
Collapse
|
17
|
CAND1 regulates lunapark for the proper tubular network of the endoplasmic reticulum. Sci Rep 2019; 9:13152. [PMID: 31511573 PMCID: PMC6739345 DOI: 10.1038/s41598-019-49542-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/27/2019] [Indexed: 12/31/2022] Open
Abstract
Endoplasmic reticulum (ER) tubules connect each other by three-way junctions, resulting in a tubular ER network. Oligomerization of three-way junction protein lunapark (Lnp) is important for its localization and the three-way junction stability. On the other hand, Lnp has an N-terminal ubiquitin ligase activity domain, which is also important for the three-way junction localization. To understand the mode of action of Lnp, we isolated Cullin-associated and neddylation-dissociated 1 (CAND1), a regulator of Skp1-Cul1-F-box (SCF) ubiquitin ligase, as a Lnp-binding protein by affinity chromatography. CAND1 and Lnp form a higher-molecular-weight complex in vitro, while they do not co-localize at the three-way junctions. CAND1 reduces the auto-ubiquitination activity of Lnp. CAND1 knockdown enhances proteasomal degradation of Lnp and reduces the tubular ER network in mammalian cells. These results suggest that CAND1 has the potency to promote the formation of the higher-molecular-weight complex with Lnp and reduce the auto-ubiquitination activity of Lnp, thereby regulating the three-way junction stability of the tubular ER network.
Collapse
|
18
|
Dong SS, Yao S, Chen YX, Guo Y, Zhang YJ, Niu HM, Hao RH, Shen H, Tian Q, Deng HW, Yang TL. Detecting epistasis within chromatin regulatory circuitry reveals CAND2 as a novel susceptibility gene for obesity. Int J Obes (Lond) 2018; 43:450-456. [PMID: 29717274 DOI: 10.1038/s41366-018-0069-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/14/2018] [Accepted: 02/13/2018] [Indexed: 01/03/2023]
Abstract
BACKGROUND Genome-wide association studies have identified many susceptibility loci for obesity. However, missing heritability problem is still challenging and ignorance of genetic interactions is believed to be an important cause. Current methods for detecting interactions usually do not consider regulatory elements in non-coding regions. Interaction analyses within chromatin regulatory circuitry may identify new susceptibility loci. METHODS We developed a pipeline named interaction analyses within chromatin regulatory circuitry (IACRC), to identify genetic interactions impacting body mass index (BMI). Potential interacting SNP pairs were obtained based on Hi-C datasets, PreSTIGE (Predicting Specific Tissue Interactions of Genes and Enhancers) algorithm, and super enhancer regions. SNP × SNP analyses were next performed in three GWAS datasets, including 2286 unrelated Caucasians from Kansas City, 3062 healthy Caucasians from the Gene Environment Association Studies initiative, and 3164 Hispanic subjects from the Women's Health Initiative. RESULTS A total of 16,643,227 SNP × SNP analyses were performed. Meta-analyses showed that two SNP pairs, rs6808450-rs9813534 (combined P = 2.39 × 10-9) and rs6808450-rs3773306 (combined P = 2.89 × 10-9) were associated with BMI after multiple testing corrections. Single-SNP analyses did not detect significant association signals for these three SNPs. In obesity relevant cells, rs6808450 is located in intergenic enhancers, while rs9813534 and rs3773306 are located in the region of strong transcription regions of CAND2 and RPL32, respectively. The expression of CAND2 was significantly downregulated after the differentiation of human Simpson-Golabi-Behmel syndrome (SGBS) preadipocyte cells (P = 0.0241). Functional validation in the International Mouse Phenotyping Consortium database showed that CAND2 was associated with increased lean body mass and decreased total body fat amount. CONCLUSIONS Detecting epistasis within chromatin regulatory circuitry identified CAND2 as a novel obesity susceptibility gene. We hope IACRC could facilitate the interaction analyses for complex diseases and offer new insights into solving the missing heritability problem.
Collapse
Affiliation(s)
- Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Hui-Min Niu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Ruo-Han Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Hui Shen
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Qing Tian
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
| |
Collapse
|
19
|
The functional versatility of the nuclear pore complex proteins. Semin Cell Dev Biol 2017; 68:2-9. [DOI: 10.1016/j.semcdb.2017.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/11/2017] [Indexed: 12/28/2022]
|
20
|
Small molecule perturbation of the CAND1-Cullin1-ubiquitin cycle stabilizes p53 and triggers Epstein-Barr virus reactivation. PLoS Pathog 2017; 13:e1006517. [PMID: 28715492 PMCID: PMC5531659 DOI: 10.1371/journal.ppat.1006517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 07/27/2017] [Accepted: 07/06/2017] [Indexed: 12/13/2022] Open
Abstract
The chemical probe C60 efficiently triggers Epstein-Barr Virus (EBV) reactivation from latency through an unknown mechanism. Here, we identify the Cullin exchange factor CAND1 as a biochemical target of C60. We also identified CAND1 in an shRNA library screen for EBV lytic reactivation. Gene expression profiling revealed that C60 activates the p53 pathway and protein analysis revealed a strong stabilization and S15 phosphorylation of p53. C60 reduced Cullin1 association with CAND1 and led to a global accumulation of ubiquitylated substrates. C60 also stabilized the EBV immediate early protein ZTA through a Cullin-CAND1-interaction motif in the ZTA transcription activation domain. We propose that C60 perturbs the normal interaction and function of CAND1 with Cullins to promote the stabilization of substrates like ZTA and p53, leading to EBV reactivation from latency. Understanding the mechanism of action of C60 may provide new approaches for treatment of EBV associated tumors, as well as new tools to stabilize p53.
Collapse
|
21
|
Mukherjee R, Das A, Chakrabarti S, Chakrabarti O. Calcium dependent regulation of protein ubiquitination - Interplay between E3 ligases and calcium binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1227-1235. [PMID: 28285986 DOI: 10.1016/j.bbamcr.2017.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 11/18/2022]
Abstract
The ubiquitination status of proteins and intracellular calcium levels are two factors which keep changing inside any living cell. These two events appear to be independent of each other but recent experimental evidences show that ubiquitination of cellular proteins are influenced by calcium, Calmodulin, Calmodulin-dependent kinase II and other proteins of calcium dependent pathways. E3 ligases like Nedd4, SCF complex, APC, GP78 and ITCH are important regulators of calcium mediated processes. A bioinformatics analysis to inspect sequences and interacting partners of 242 candidate E3 ligases show the presence of calcium and/or Calmodulin binding motifs/domains within their sequences. Building a protein-protein interaction (PPI) network of human E3 ligase proteins identifies Ca2+ related proteins as direct interacting partners of E3 ligases. Review of literature, analysis of E3 ligase sequences and their interactome suggests an interconnectivity between calcium signaling and the overall UPS system, especially emphasizing that a subset of E3 ligases have importance in physiological pathways modulated by calcium.
Collapse
Affiliation(s)
- Rukmini Mukherjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Aneesha Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S C Mullick Road, Jadavpur, Kolkata 700032, India.
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.
| |
Collapse
|
22
|
Nakazato A, Maeda R, Ishikawa K, Suzuki H, Tamura TA. TBP-like protein (TLP) represses myogenesis via inhibition of the myogenin promoter. Biochem Biophys Res Commun 2016; 479:814-819. [PMID: 27680312 DOI: 10.1016/j.bbrc.2016.09.127] [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: 09/06/2016] [Accepted: 09/24/2016] [Indexed: 11/30/2022]
Abstract
TBP-like protein (TLP) is one of the metazoan-restricted transcription factors participating in development and differentiation, though the molecular mechanism by which TLP regulates these processes remains unclear. In this study, we investigated the relationship between TLP and myogenesis of mouse C2C12 myoblasts. We found that TLP gene expression decreases during myogenic differentiation. Overexpression and knockdown of TLP revealed that the levels of muscle-specific myosin heavy chain and the myogenic transcription factor myogenin are downregulated by TLP. TLP inhibits the progression of morphological change from myoblasts to myotubes, thereby suppressing myogenesis. We further show that TLP represses the promoter activity of myogenin. The proximal AT-rich sequence of the myogenin promoter is responsible for TLP-mediated transcriptional repression. The results of this study suggest that TLP inhibits myogenesis through downregulation of the myogenin gene.
Collapse
Affiliation(s)
- Aki Nakazato
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Ryo Maeda
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Kohei Ishikawa
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Hidefumi Suzuki
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Taka-Aki Tamura
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan.
| |
Collapse
|
23
|
Huang SC, Zhou A, Nguyen DT, Zhang HS, Benz EJ. Protein 4.1R Influences Myogenin Protein Stability and Skeletal Muscle Differentiation. J Biol Chem 2016; 291:25591-25607. [PMID: 27780863 DOI: 10.1074/jbc.m116.761296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Indexed: 01/28/2023] Open
Abstract
Protein 4.1R (4.1R) isoforms are expressed in both cardiac and skeletal muscle. 4.1R is a component of the contractile apparatus. It is also associated with dystrophin at the sarcolemma in skeletal myofibers. However, the expression and function of 4.1R during myogenesis have not been characterized. We now report that 4.1R expression increases during C2C12 myoblast differentiation into myotubes. Depletion of 4.1R impairs skeletal muscle differentiation and is accompanied by a decrease in the levels of myosin heavy and light chains and caveolin-3. Furthermore, the expression of myogenin at the protein, but not mRNA, level is drastically decreased in 4.1R knockdown myocytes. Similar results were obtained using MyoD-induced differentiation of 4.1R-/- mouse embryonic fibroblast cells. von Hippel-Lindau (VHL) protein is known to destabilize myogenin via the ubiquitin-proteasome pathway. We show that 4.1R associates with VHL and, when overexpressed, reverses myogenin ubiquitination and stability. This suggests that 4.1R may influence myogenesis by preventing VHL-mediated myogenin degradation. Together, our results define a novel biological function for 4.1R in muscle differentiation and provide a molecular mechanism by which 4.1R promotes myogenic differentiation.
Collapse
Affiliation(s)
- Shu-Ching Huang
- From the Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, .,the Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115.,the Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, and
| | - Anyu Zhou
- From the Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115
| | - Dan T Nguyen
- From the Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115
| | - Henry S Zhang
- From the Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115
| | - Edward J Benz
- From the Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115.,the Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115.,the Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, and.,the Dana-Farber/Harvard Cancer Center, Boston, Massachusetts 02115
| |
Collapse
|
24
|
Isogai M, Suzuki H, Maeda R, Tamura TA. Ubiquitin-proteasome-dependent degradation of TBP-like protein is prevented by direct binding of TFIIA. Genes Cells 2016; 21:1223-1232. [PMID: 27696626 DOI: 10.1111/gtc.12441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/28/2016] [Indexed: 11/27/2022]
Abstract
Although the majority of gene expression is driven by TATA-binding protein (TBP)-based transcription machinery, it has been reported that TBP-related factors (TRFs) are also involved in the regulation of gene expression. TBP-like protein (TLP), which is one of the TRFs and exhibits the highest affinity to TFIIA among known proteins, has recently been showed to have significant roles in gene regulation. However, how the level of TLP is maintained in vivo has remained unknown. In this study, we explored the mechanism by which TLP protein is turned over in vivo and the factor that maintains the amount of TLP. We showed that TLP is rapidly degraded by the ubiquitin-proteasome system and that tight interaction with TFIIA results in protection of TLP from ubiquitin-proteasome-dependent degradation. The half-life of TLP was shown to be less than a few hours, and the proteasome inhibitor MG132 specifically suppressed TLP degradation. Moreover, knockdown and over-expression experiments showed that TFIIA is engaged in stabilization of TLPin vivo. Thus, we showed a novel characteristic of TLP, that is, interaction with TFIIA is essential to suppress proteasome-dependent turnover of TLP, providing a further insight into TLP-governed gene regulation.
Collapse
Affiliation(s)
- Momoko Isogai
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - Hidefumi Suzuki
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - Ryo Maeda
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - Taka-Aki Tamura
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| |
Collapse
|
25
|
Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex. Genes (Basel) 2015; 7:genes7010001. [PMID: 26729172 PMCID: PMC4728381 DOI: 10.3390/genes7010001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/07/2015] [Accepted: 12/22/2015] [Indexed: 01/06/2023] Open
Abstract
The aim of our study was to analyze the presence of 5-methyl-cytosine (5-mC) and 5-hydroxymethyl-cytosine (5-hmC) in the genome of crustacean Daphnia pulex. First, the presence of 5-mC and 5-hmC in genomic DNA was demonstrated by using antibodies specific to either 5-mC or 5-hmC. Then, analysis of 5-mC and 5-hmC using pairs of restriction enzymes with different sensitivity to methylation and hydroxymethylation confirmed the presence of both modifications in selected regions of three genes (Cox4, Cand2 and Ephx1). To get a detailed picture of 5-hmC distribution over the D. pulex genome, we performed 5-hmC enrichment and sequenced the enriched fraction using next generation sequencing and non-enriched library (input) as a control. Comparison of input and enriched libraries showed that 5-hmC in exons is twice as frequent as in introns. Functional analysis indicated that 5-hmC abundance is associated with genes that are involved in the adenylate cyclase-activating G-protein-coupled receptor signaling pathway, molting cycles, morphogenesis and cell fate determination. Genes that lack 5-hmC tend to be involved in the regulation of the transforming growth factor beta receptor signaling pathway and in many mRNA-related processes. Our results suggest that epigenetic modifications are present in the genome of D. pulex and most likely are involved in the regulation of gene expression of this crustacean.
Collapse
|
26
|
Dmitriev AA, Rosenberg EE, Krasnov GS, Gerashchenko GV, Gordiyuk VV, Pavlova TV, Kudryavtseva AV, Beniaminov AD, Belova AA, Bondarenko YN, Danilets RO, Glukhov AI, Kondratov AG, Alexeyenko A, Alekseev BY, Klein G, Senchenko VN, Kashuba VI. Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis. DISEASE MARKERS 2015; 2015:241301. [PMID: 26491211 PMCID: PMC4602334 DOI: 10.1155/2015/241301] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/11/2015] [Accepted: 07/14/2015] [Indexed: 12/30/2022]
Abstract
A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarkers for characterization of different types of prostate tumors. NotI-microarrays with 180 clones associated with chromosome 3 genes/loci were applied to determine genetic and epigenetic alterations in 33 prostate tumors. For 88 clones, aberrations were detected in more than 10% of tumors. The major types of alterations were DNA methylation and/or deletions. Frequent methylation of the discovered loci was confirmed by bisulfite sequencing on selective sampling of genes: FGF12, GATA2, and LMCD1. Three genes (BHLHE40, BCL6, and ITGA9) were tested for expression level alterations using qPCR, and downregulation associated with hypermethylation was shown in the majority of tumors. Based on these data, we proposed the set of potential biomarkers for detection of prostate cancer and discrimination between prostate tumors with different malignancy and aggressiveness: BHLHE40, FOXP1, LOC285205, ITGA9, CTDSPL, FGF12, LOC440944/SETD5, VHL, CLCN2, OSBPL10/ZNF860, LMCD1, FAM19A4, CAND2, MAP4, KY, and LRRC58. Moreover, we probabilistically estimated putative functional relations between the genes within each set using the network enrichment analysis.
Collapse
Affiliation(s)
- Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia
| | - Eugenia E. Rosenberg
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ganna V. Gerashchenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Vasily V. Gordiyuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Tatiana V. Pavlova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Artemy D. Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anastasia A. Belova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Yuriy N. Bondarenko
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kiev 04053, Ukraine
| | - Rostislav O. Danilets
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kiev 04053, Ukraine
| | - Alexander I. Glukhov
- Department of Molecular Biology, Kurchatov NBIC Centre NRC “Kurchatov Institute”, Moscow 123182, Russia
| | - Aleksandr G. Kondratov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Andrey Alexeyenko
- Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institute, 17177 Stockholm, Sweden
| | - Boris Y. Alekseev
- P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia
| | - George Klein
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Vera N. Senchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| |
Collapse
|
27
|
Cep68 can be regulated by Nek2 and SCF complex. Eur J Cell Biol 2015; 94:162-72. [PMID: 25704143 DOI: 10.1016/j.ejcb.2015.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/28/2015] [Accepted: 01/28/2015] [Indexed: 01/01/2023] Open
Abstract
Centrosome cohesion maintains centrosomes in close proximity until mitosis, when cell cycle-dependent regulatory signaling events dissolve cohesion and promote centrosome separation in preparation for bipolar spindle assembly at mitosis. Cohesion is regulated by the antagonistic activities of the mitotic NIMA-related kinase 2 (Nek2), protein phosphatase 1, the cohesion fiber components rootletin, centrosomal Nek2-associated protein 1 (C-Nap1) and Cep68. The centrosomal protein Cep68 is essential for centrosome cohesion and dissociates from centrosomes at the onset of mitosis. Here, our cell line studies show the C-terminal 300-400 amino acids of Cep68 are necessary to localize Cep68 to interphase centrosomes while C-terminal 400-500 amino acids might regulate Cep68 dissociation from centrosomes at mitotic onset. In addition, Nek2 was demonstrated to phosphorylate Cep68 in vivo and this phosphorylation appears to promote Cep68 degradation in mitosis. We further show that the SCF complex destroys Cep68 at mitosis through recognition by the beta-Trcp F box component of SCF. Together, the findings provide a new insight into the control of centrosome separation by Cep68 during mitosis.
Collapse
|
28
|
Maeda R, Suzuki H, Tanaka Y, Tamura TA. Interaction between transactivation domain of p53 and middle part of TBP-like protein (TLP) is involved in TLP-stimulated and p53-activated transcription from the p21 upstream promoter. PLoS One 2014; 9:e90190. [PMID: 24594805 PMCID: PMC3940844 DOI: 10.1371/journal.pone.0090190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/30/2014] [Indexed: 11/18/2022] Open
Abstract
TBP-like protein (TLP) is involved in transcriptional activation of an upstream promoter of the human p21 gene. TLP binds to p53 and facilitates p53-activated transcription from the upstream promoter. In this study, we clarified that in vitro affinity between TLP and p53 is about one-third of that between TBP and p53. Extensive mutation analyses revealed that the TLP-stimulated function resides in transcription activating domain 1 (TAD1) in the N-terminus of p53. Among the mutants, #22.23, which has two amino acid substitutions in TAD1, exhibited a typical mutant phenotype. Moreover, #22.23 exhibited the strongest mutant phenotype for TLP-binding ability. It is thus thought that TLP-stimulated and p53-dependent transcriptional activation is involved in TAD1 binding of TLP. #22.23 had a decreased transcriptional activation function, especially for the upstream promoter of the endogenous p21 gene, compared with wild-type p53. This mutant did not facilitate p53-dependent growth repression and etoposide-mediated cell-death as wild-type p53 does. Moreover, mutation analysis revealed that middle part of TLP, which is requited for p53 binding, is involved in TLP-stimulated and p53-dependent promoter activation and cell growth repression. These results suggest that activation of the p21 upstream promoter is mediated by interaction between specific regions of TLP and p53.
Collapse
Affiliation(s)
- Ryo Maeda
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Hidefumi Suzuki
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yuta Tanaka
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Taka-aki Tamura
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
- * E-mail:
| |
Collapse
|
29
|
Buanne P, Renzone G, Monteleone F, Vitale M, Monti SM, Sandomenico A, Garbi C, Montanaro D, Accardo M, Troncone G, Zatovicova M, Csaderova L, Supuran CT, Pastorekova S, Scaloni A, De Simone G, Zambrano N. Characterization of Carbonic Anhydrase IX Interactome Reveals Proteins Assisting Its Nuclear Localization in Hypoxic Cells. J Proteome Res 2012. [DOI: 10.1021/pr300565w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | - Giovanni Renzone
- Proteomics and Mass Spectrometry
Laboratory, ISPAAM, CNR, Naples, Italy
| | | | - Monica Vitale
- CEINGE Biotecnologie Avanzate SCaRL, Naples, Italy
- Dipartimento di Medicina Molecolare
e Biotecnologie Mediche, Università di Napoli Federico II, Italy
| | | | | | - Corrado Garbi
- Dipartimento di Biologia e Patologia
Cellulare e Molecolare, Università di Napoli Federico II, Italy
| | | | - Marina Accardo
- Department
of Public Health, Section
of Pathology, Seconda Università di Napoli, Italy
| | - Giancarlo Troncone
- CEINGE Biotecnologie Avanzate SCaRL, Naples, Italy
- Dipartimento di
Scienze Biomorfologiche
e Funzionali, Università di Napoli Federico II, Italy
| | - Miriam Zatovicova
- Department of
Molecular Medicine,
Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Lucia Csaderova
- Department of
Molecular Medicine,
Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | | | - Silvia Pastorekova
- Department of
Molecular Medicine,
Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry
Laboratory, ISPAAM, CNR, Naples, Italy
| | | | - Nicola Zambrano
- CEINGE Biotecnologie Avanzate SCaRL, Naples, Italy
- Dipartimento di Medicina Molecolare
e Biotecnologie Mediche, Università di Napoli Federico II, Italy
| |
Collapse
|
30
|
Interplay between two myogenesis-related proteins: TBP-interacting protein 120B and MyoD. Gene 2012; 504:213-9. [PMID: 22613845 DOI: 10.1016/j.gene.2012.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 05/09/2012] [Accepted: 05/11/2012] [Indexed: 11/23/2022]
Abstract
Gene expression in myogenesis is governed by multiple myogenic factors including MyoD. Previously, we demonstrated that TBP-interacting protein 120B (TIP120B) promotes in vitro myogenesis through its anti-ubiquitination ability. In this study, we investigated interplay between MyoD and TIP120B. Mouse C2C12 cells subjected to myotube differentiation contained increased amounts of TIP120B and MyoD. Dexamethasone, which inhibits myogenic signaling, decreased the amounts of those proteins. Mouse and human TIP120B promoters, which carry multiple E-box motifs, were potentiated by MyoD. In the human TIP120B, a proximal E-box binds to MyoD in vitro and exhibits MyoD-dependent transcription activation function. Expression of the endogenous TIP120B gene was correlated with the level of MyoD in different types of muscle-related cells. Furthermore, MyoD binds specifically to a proximal E-box-carrying promoter region in chromatin. Proteasome-sensitive MyoD was increased and decreased by overexpression and knockdown of TIP120B, respectively. Moreover, stability of MyoD was increased by TIP120B. The results suggest that MyoD and TIP120B potentiate each other at gene expression and post-translation levels, respectively, which may promote myogenesis cooperatively.
Collapse
|
31
|
Suzuki H, Ito R, Ikeda K, Tamura TA. TATA-binding protein (TBP)-like protein is required for p53-dependent transcriptional activation of upstream promoter of p21Waf1/Cip1 gene. J Biol Chem 2012; 287:19792-803. [PMID: 22511763 DOI: 10.1074/jbc.m112.369629] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
TATA-binding protein-like protein (TLP) is involved in development, checkpoint, and apoptosis through potentiation of gene expression. TLP-overexpressing human cells, especially p53-containing cells, exhibited a decreased growth rate and increased proportion of G(1) phase cells. TLP stimulated expression of several growth-related genes including p21 (p21(Waf1/Cip1)). TLP-mediated activation of the p21 upstream promoter in cells was shown by a promoter-luciferase reporter assay. The p53-binding sequence located in the p21 upstream promoter and p53 itself are required for TLP-mediated transcriptional activation. TLP and p53 bound to each other and synergistically enhanced activity of the upstream promoter. TLP specifically activated transcription from the endogenous upstream promoter, and p53 was required for this activation. Etoposide treatment also resulted in activation of the upstream promoter as well as nuclear accumulation of TLP and p53. Moreover, the upstream promoter was associated with endogenous p53 and TLP, and the p53 recruitment was enhanced by TLP. The results of the present study suggest that TLP mediates p53-governed transcriptional activation of the p21 upstream promoter.
Collapse
Affiliation(s)
- Hidefumi Suzuki
- Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba 263-8522, Japan
| | | | | | | |
Collapse
|
32
|
D'Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer MW. A change in nuclear pore complex composition regulates cell differentiation. Dev Cell 2012; 22:446-58. [PMID: 22264802 DOI: 10.1016/j.devcel.2011.11.021] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 10/06/2011] [Accepted: 11/14/2011] [Indexed: 12/11/2022]
Abstract
Nuclear pore complexes (NPCs) are built from ∼30 different proteins called nucleoporins or Nups. Previous studies have shown that several Nups exhibit cell-type-specific expression and that mutations in NPC components result in tissue-specific diseases. Here we show that a specific change in NPC composition is required for both myogenic and neuronal differentiation. The transmembrane nucleoporin Nup210 is absent in proliferating myoblasts and embryonic stem cells (ESCs) but becomes expressed and incorporated into NPCs during cell differentiation. Preventing Nup210 production by RNAi blocks myogenesis and the differentiation of ESCs into neuroprogenitors. We found that the addition of Nup210 to NPCs does not affect nuclear transport but is required for the induction of genes that are essential for cell differentiation. Our results identify a single change in NPC composition as an essential step in cell differentiation and establish a role for Nup210 in gene expression regulation and cell fate determination.
Collapse
Affiliation(s)
- Maximiliano A D'Angelo
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
| | | | | | | | | |
Collapse
|
33
|
Kitamura T, Suzuki H, Tamura TA. Mouse Wee1 gene is repressed by Krüppel-like factor 3 (KLF3) via interaction with multiple upstream elements. Gene 2011; 492:361-7. [PMID: 22115574 DOI: 10.1016/j.gene.2011.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/25/2011] [Accepted: 11/02/2011] [Indexed: 11/18/2022]
Abstract
Wee1 protein kinase represses CDK1 required for G(2)/M transition. The mouse wee1 promoter contains multiple CACCC-boxes between -306 and +1 that can bind to Krüppel-like factor 3 (KLF3) transcriptional repressor. We found that increasing amounts of intracellular KLF3 decreased the amount of wee1 mRNA. A promoter reporter assay demonstrated that wee1 promoter activity was repressed by KLF3 overexpression. Elimination of the first and fourth CACCC-boxes suppressed KLF3-governed transcriptional repression. A gel-shift assay demonstrated that KLF3 binds to the first, third, and fourth CACCC-boxes with various strengths. Moreover, KLF3 was suggested to interact with the wee1 regulatory region in a physiological condition. Therefore, we concluded that KLF3 is a transcriptional repressor for wee1 gene. In a previous study, we demonstrated that TBP-like protein (TLP) inhibits wee1 promoter function. In this study, we found that the chromosomal wee1 gene is also down-regulated by KLF3. Since KLF3-repressed wee1 promoter function was further inhibited by TLP overexpression regardless of the inhibition degree of KLF3, we propose that TLP and KLF3 repress wee1 promoter independently.
Collapse
Affiliation(s)
- Takuya Kitamura
- Graduate School of Science, Chiba University, 1–33 Yayoicho, Chiba 263–8522, Japan
| | | | | |
Collapse
|
34
|
Bosu DR, Feng H, Min K, Kim Y, Wallenfang MR, Kipreos ET. C. elegans CAND-1 regulates cullin neddylation, cell proliferation and morphogenesis in specific tissues. Dev Biol 2010; 346:113-26. [PMID: 20659444 DOI: 10.1016/j.ydbio.2010.07.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 07/14/2010] [Accepted: 07/18/2010] [Indexed: 11/26/2022]
Abstract
Cullin-RING ubiquitin ligases (CRLs) are critical regulators of multiple developmental and cellular processes in eukaryotes. CAND1 is a biochemical inhibitor of CRLs, yet has been shown to promote CRL activity in plant and mammalian cells. Here we analyze CAND1 function in the context of a developing metazoan organism. Caenorhabditis elegans CAND-1 is capable of binding to all of the cullins, and we show that it physically interacts with CUL-2 and CUL-4 in vivo. The covalent attachment of the ubiquitin-like protein Nedd8 is required for cullin activity in animals and plants. In cand-1 mutants, the levels of the neddylated isoforms of CUL-2 and CUL-4 are increased, indicating that CAND-1 is a negative regulator of cullin neddylation. cand-1 mutants are hypersensitive to the partial loss of cullin activity, suggesting that CAND-1 facilitates CRL functions. cand-1 mutants exhibit impenetrant phenotypes, including developmental arrest, morphological defects of the vulva and tail, and reduced fecundity. cand-1 mutants share with cul-1 and lin-23 mutants the phenotypes of supernumerary seam cell divisions, defective alae formation, and the accumulation of the SCF(LIN-23) target the glutamate receptor GLR-1. The observation that cand-1 mutants have phenotypes associated with the loss of the SCF(LIN-23) complex, but lack phenotypes associated with other specific CRL complexes, suggests that CAND-1 is differentially required for the activity of distinct CRL complexes.
Collapse
Affiliation(s)
- Dimple R Bosu
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | | | | | | | | | | |
Collapse
|
35
|
Costa MDC, Bajanca F, Rodrigues AJ, Tomé RJ, Corthals G, Macedo-Ribeiro S, Paulson HL, Logarinho E, Maciel P. Ataxin-3 plays a role in mouse myogenic differentiation through regulation of integrin subunit levels. PLoS One 2010; 5:e11728. [PMID: 20668528 PMCID: PMC2909204 DOI: 10.1371/journal.pone.0011728] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 06/28/2010] [Indexed: 12/29/2022] Open
Abstract
Background During myogenesis several transcription factors and regulators of protein synthesis and assembly are rapidly degraded by the ubiquitin-proteasome system (UPS). Given the potential role of the deubiquitinating enzyme (DUB) ataxin-3 in the UPS, and the high expression of the murine ataxin-3 homolog in muscle during embryogenesis, we sought to define its role in muscle differentiation. Methodology/Principal Findings Using immunofluorescence analysis, we found murine ataxin-3 (mATX3) to be highly expressed in the differentiated myotome of E9.5 mouse embryos. C2C12 myoblasts depleted of mATX3 by RNA interference exhibited a round morphology, cell misalignment, and a delay in differentiation following myogenesis induction. Interestingly, these cells showed a down-regulation of α5 and α7 integrin subunit levels both by immunoblotting and immunofluorescence. Mouse ATX3 was found to interact with α5 integrin subunit and to stabilize this protein by repressing its degradation through the UPS. Proteomic analysis of mATX3-depleted C2C12 cells revealed alteration of the levels of several proteins related to integrin signaling. Conclusions Ataxin-3 is important for myogenesis through regulation of integrin subunit levels.
Collapse
Affiliation(s)
- Maria do Carmo Costa
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Fernanda Bajanca
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
| | - Ana-João Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
| | - Ricardo J. Tomé
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | | | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Henry L. Paulson
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Elsa Logarinho
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- * E-mail:
| |
Collapse
|
36
|
Regulation of myoblast differentiation by the nuclear envelope protein NET39. Mol Cell Biol 2009; 29:5800-12. [PMID: 19704009 DOI: 10.1128/mcb.00684-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, several transmembrane proteins of the nuclear envelope have been implicated in regulation of signaling and gene expression. Here we demonstrate that the nuclear lamina-associated nuclear envelope transmembrane protein NET39 (Ppapdc3) functions as a negative regulator of myoblast differentiation, in part through effects on mTOR signaling. We found that NET39 is highly expressed in cardiac and skeletal muscle tissues and becomes strongly upregulated during cultured myoblast differentiation. Knockdown of NET39 by RNA interference in myoblasts strongly promoted differentiation, whereas overexpression of NET39 repressed myogenesis. Proteomic analysis of NET39 complexes immunoprecipitated from myotubes, in combination with other methods, identified mTOR as an interaction partner of NET39. We found that ectopic expression of NET39 in myoblasts negatively regulated myogenesis by diminishing mTOR activity, which in turn decreased insulin-like growth factor II production and autocrine signaling. Our results indicate that NET39 is part of the regulatory machinery for myogenesis and raise the possibility that it may be important for muscle homeostasis.
Collapse
|
37
|
Jogo M, Shiraishi S, Tamura TA. Identification of MAFbx as a myogenin-engaged F-box protein in SCF ubiquitin ligase. FEBS Lett 2009; 583:2715-9. [PMID: 19631210 DOI: 10.1016/j.febslet.2009.07.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 07/01/2009] [Accepted: 07/14/2009] [Indexed: 01/29/2023]
Abstract
Myogenesis is conducted by transcription factors including MyoD and myogenin. Myogenin is known to be polyubiquitinated by SCF (Skp1/Cullin 1/F-box protein) followed by proteasomal degradation, though the participating F-box protein is remaining unidentified. In this study, we found that myogenin in differentiated myoblasts is destabilized by muscle atrophy-inducing dexamethasone and that MAFbx (muscle atrophy F-box protein) is increased in atrophying myotubes. MAFbx overexpression resulted in MG132-sensitive reduction of myogenin. Myogenin had a MAFbx-recognition motif and interacted with MAFbx. MAFbx activated polyubiquitination of myogenin. The results of this study suggest that MAFbx functions as an F-box protein for ubiquitination of myogenin.
Collapse
Affiliation(s)
- Misako Jogo
- Department of Biology, Graduate School of Science, Chiba University, Inage-ku, Chiba, Japan
| | | | | |
Collapse
|
38
|
Shiraishi S, Tamamura N, Jogo M, Tanaka Y, Tamura TA. Rapid proteasomal degradation of transcription factor IIB in accordance with F9 cell differentiation. Gene 2009; 436:115-20. [PMID: 19393171 DOI: 10.1016/j.gene.2009.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 12/15/2008] [Accepted: 01/25/2009] [Indexed: 11/28/2022]
Abstract
We found that the levels of all general transcription factors (GTFs) for RNA polymerase II decreased in F9 cells when the cells were subjected to a differentiation procedure. Different from other GTFs, decrease of TFIIB during the differentiation was suppressed by addition of a proteasome inhibitor, MG132. The half-life of TFIIB in the differentiated cells was remarkably reduced compared with that in the undifferentiated cells. Moreover, it was demonstrated that TFIIB is a poly-ubiquitinated protein. Results of this study suggest that components of the transcription machinery decreased in accordance with cell differentiation and that TFIIB is specifically and rapidly degraded by the ubiquitin-proteasome pathway.
Collapse
Affiliation(s)
- Seiji Shiraishi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | | | | | | | | |
Collapse
|