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Bei Y, Zhu Y, Zhou J, Ai S, Yao J, Yin M, Hu M, Qi W, Spanos M, Li L, Wei M, Huang Z, Gao J, Liu C, van der Kraak PH, Li G, Lei Z, Sluijter JPG, Xiao J. Inhibition of Hmbox1 Promotes Cardiomyocyte Survival and Glucose Metabolism Through Gck Activation in Ischemia/Reperfusion Injury. Circulation 2024; 150:848-866. [PMID: 38708602 DOI: 10.1161/circulationaha.123.067592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 04/11/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Exercise-induced physiological cardiac growth regulators may protect the heart from ischemia/reperfusion (I/R) injury. Homeobox-containing 1 (Hmbox1), a homeobox family member, has been identified as a putative transcriptional repressor and is downregulated in the exercised heart. However, its roles in exercise-induced physiological cardiac growth and its potential protective effects against cardiac I/R injury remain largely unexplored. METHODS We studied the function of Hmbox1 in exercise-induced physiological cardiac growth in mice after 4 weeks of swimming exercise. Hmbox1 expression was then evaluated in human heart samples from deceased patients with myocardial infarction and in the animal cardiac I/R injury model. Its role in cardiac I/R injury was examined in mice with adeno-associated virus 9 (AAV9) vector-mediated Hmbox1 knockdown and in those with cardiac myocyte-specific Hmbox1 ablation. We performed RNA sequencing, promoter prediction, and binding assays and identified glucokinase (Gck) as a downstream effector of Hmbox1. The effects of Hmbox1 together with Gck were examined in cardiomyocytes to evaluate their cell size, proliferation, apoptosis, mitochondrial respiration, and glycolysis. The function of upstream regulator of Hmbox1, ETS1, was investigated through ETS1 overexpression in cardiac I/R mice in vivo. RESULTS We demonstrated that Hmbox1 downregulation was required for exercise-induced physiological cardiac growth. Inhibition of Hmbox1 increased cardiomyocyte size in isolated neonatal rat cardiomyocytes and human embryonic stem cell-derived cardiomyocytes but did not affect cardiomyocyte proliferation. Under pathological conditions, Hmbox1 was upregulated in both human and animal postinfarct cardiac tissues. Furthermore, both cardiac myocyte-specific Hmbox1 knockout and AAV9-mediated Hmbox1 knockdown protected against cardiac I/R injury and heart failure. Therapeutic effects were observed when sh-Hmbox1 AAV9 was administered after I/R injury. Inhibition of Hmbox1 activated the Akt/mTOR/P70S6K pathway and transcriptionally upregulated Gck, leading to reduced apoptosis and improved mitochondrial respiration and glycolysis in cardiomyocytes. ETS1 functioned as an upstream negative regulator of Hmbox1 transcription, and its overexpression was protective against cardiac I/R injury. CONCLUSIONS Our studies unravel a new role for the transcriptional repressor Hmbox1 in exercise-induced physiological cardiac growth. They also highlight the therapeutic potential of targeting Hmbox1 to improve myocardial survival and glucose metabolism after I/R injury.
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Affiliation(s)
- Yihua Bei
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Yujiao Zhu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Jingwen Zhou
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Songwei Ai
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Jianhua Yao
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, China (J.Y.)
| | - Mingming Yin
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Meiyu Hu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Weitong Qi
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Michail Spanos
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston (M.S., G.L.)
| | - Lin Li
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Meng Wei
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Zhenzhen Huang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Juan Gao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Chang Liu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
| | - Petra H van der Kraak
- Department of Pathology (P.H.v.d.K.), University Medical Center Utrecht, University Utrecht, The Netherlands
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston (M.S., G.L.)
| | - Zhiyong Lei
- Department of Cardiology, Laboratory of Experimental Cardiology (Z.L., J.P.G.S.), University Medical Center Utrecht, University Utrecht, The Netherlands
- Division Laboratory, Central Diagnosis Laboratory Research (Z.L.), University Medical Center Utrecht, University Utrecht, The Netherlands
| | - Joost P G Sluijter
- Department of Cardiology, Laboratory of Experimental Cardiology (Z.L., J.P.G.S.), University Medical Center Utrecht, University Utrecht, The Netherlands
- Utrecht Regenerative Medicine Center (J.P.G.S.), University Medical Center Utrecht, University Utrecht, The Netherlands
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital (Sixth People's Hospital of Nantong) and School of Life Science of Shanghai University, China (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.)
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education) (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
- Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Medicine (Y.B., Y.Z., J.Z., S.A., M.Y., M.H., W.Q., L.L., M.W., Z.H., J.G., C.L., J.X.), Shanghai University, China
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2
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Maestas MM, Ishahak M, Augsornworawat P, Veronese-Paniagua DA, Maxwell KG, Velazco-Cruz L, Marquez E, Sun J, Shunkarova M, Gale SE, Urano F, Millman JR. Identification of unique cell type responses in pancreatic islets to stress. Nat Commun 2024; 15:5567. [PMID: 38956087 PMCID: PMC11220140 DOI: 10.1038/s41467-024-49724-w] [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: 07/25/2023] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
Diabetes involves the death or dysfunction of pancreatic β-cells. Analysis of bulk sequencing from human samples and studies using in vitro and in vivo models suggest that endoplasmic reticulum and inflammatory signaling play an important role in diabetes progression. To better characterize cell type-specific stress response, we perform multiplexed single-cell RNA sequencing to define the transcriptional signature of primary human islet cells exposed to endoplasmic reticulum and inflammatory stress. Through comprehensive pair-wise analysis of stress responses across pancreatic endocrine and exocrine cell types, we define changes in gene expression for each cell type under different diabetes-associated stressors. We find that β-, α-, and ductal cells have the greatest transcriptional response. We utilize stem cell-derived islets to study islet health through the candidate gene CIB1, which was upregulated under stress in primary human islets. Our findings provide insights into cell type-specific responses to diabetes-associated stress and establish a resource to identify targets for diabetes therapeutics.
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Affiliation(s)
- Marlie M Maestas
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Matthew Ishahak
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Punn Augsornworawat
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Daniel A Veronese-Paniagua
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Kristina G Maxwell
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Leonardo Velazco-Cruz
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Erica Marquez
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Jiameng Sun
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Mira Shunkarova
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Sarah E Gale
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Fumihiko Urano
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, USA
| | - Jeffrey R Millman
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA.
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA.
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3
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Kind L, Molnes J, Tjora E, Raasakka A, Myllykoski M, Colclough K, Saint-Martin C, Adelfalk C, Dusatkova P, Pruhova S, Valtonen-André C, Bellanné-Chantelot C, Arnesen T, Kursula P, Njølstad PR. Molecular mechanism of HNF-1A-mediated HNF4A gene regulation and promoter-driven HNF4A-MODY diabetes. JCI Insight 2024; 9:e175278. [PMID: 38855865 PMCID: PMC11382887 DOI: 10.1172/jci.insight.175278] [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: 09/28/2023] [Accepted: 04/25/2024] [Indexed: 06/11/2024] Open
Abstract
Monogenic diabetes is a gateway to precision medicine through molecular mechanistic insight. Hepatocyte nuclear factor 1A (HNF-1A) and HNF-4A are transcription factors that engage in crossregulatory gene transcription networks to maintain glucose-stimulated insulin secretion in pancreatic β cells. Variants in the HNF1A and HNF4A genes are associated with maturity-onset diabetes of the young (MODY). Here, we explored 4 variants in the P2-HNF4A promoter region: 3 in the HNF-1A binding site and 1 close to the site, which were identified in 63 individuals from 21 families of different MODY disease registries across Europe. Our goal was to study the disease causality for these variants and to investigate diabetes mechanisms on the molecular level. We solved a crystal structure of HNF-1A bound to the P2-HNF4A promoter and established a set of techniques to probe HNF-1A binding and transcriptional activity toward different promoter variants. We used isothermal titration calorimetry, biolayer interferometry, x-ray crystallography, and transactivation assays, which revealed changes in HNF-1A binding or transcriptional activities for all 4 P2-HNF4A variants. Our results suggest distinct disease mechanisms of the promoter variants, which can be correlated with clinical phenotype, such as age of diagnosis of diabetes, and be important tools for clinical utility in precision medicine.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine and
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics and
| | - Erling Tjora
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics and Adolescent Medicine, Haukeland University Hospital, Bergen, Norway
| | | | | | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Cécile Saint-Martin
- Department of Medical Genetics, Sorbonne Université, AP-HP, Pitié-Salpêtrière Hospital, DMU BioGeM, Paris, France
- Monogenic Diabetes Study Group of the Société Francophone du Diabète, Paris, France
| | - Caroline Adelfalk
- Clinical Genetics, Pathology and Molecular Diagnostics, University Hospital Skåne, Lund, Sweden
| | - Petra Dusatkova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Stepanka Pruhova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | - Christine Bellanné-Chantelot
- Department of Medical Genetics, Sorbonne Université, AP-HP, Pitié-Salpêtrière Hospital, DMU BioGeM, Paris, France
- Monogenic Diabetes Study Group of the Société Francophone du Diabète, Paris, France
| | - Thomas Arnesen
- Department of Biomedicine and
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine and
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
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4
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Braun H, Xu Z, Chang F, Viceconte N, Rane G, Levin M, Lototska L, Roth F, Hillairet A, Fradera-Sola A, Khanchandani V, Sin ZW, Yong WK, Dreesen O, Yang Y, Shi Y, Li F, Butter F, Kappei D. ZNF524 directly interacts with telomeric DNA and supports telomere integrity. Nat Commun 2023; 14:8252. [PMID: 38086788 PMCID: PMC10716145 DOI: 10.1038/s41467-023-43397-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
Telomeres are nucleoprotein structures at the ends of linear chromosomes. In humans, they consist of TTAGGG repeats, which are bound by dedicated proteins such as the shelterin complex. This complex blocks unwanted DNA damage repair at telomeres, e.g. by suppressing nonhomologous end joining (NHEJ) through its subunit TRF2. Here, we describe ZNF524, a zinc finger protein that directly binds telomeric repeats with nanomolar affinity, and reveal base-specific sequence recognition by cocrystallization with telomeric DNA. ZNF524 localizes to telomeres and specifically maintains the presence of the TRF2/RAP1 subcomplex at telomeres without affecting other shelterin members. Loss of ZNF524 concomitantly results in an increase in DNA damage signaling and recombination events. Overall, ZNF524 is a direct telomere-binding protein involved in the maintenance of telomere integrity.
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Affiliation(s)
- Hanna Braun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Ziyan Xu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fiona Chang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | | | - Grishma Rane
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Michal Levin
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | | | - Franziska Roth
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Alexia Hillairet
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | | | - Vartika Khanchandani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zi Wayne Sin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wai Khang Yong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Oliver Dreesen
- Cell Aging Laboratory, A*STAR Skin Research Labs, Singapore, 138648, Singapore
| | - Yang Yang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yunyu Shi
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fudong Li
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany.
- Institute of Molecular Virology and Cell Biology (IMVZ), Friedrich Loeffler Institute, Greifswald, 17493, Germany.
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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5
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Chua BH, Zaal Anuar N, Ferry L, Domrane C, Wittek A, Mukundan VT, Jha S, Butter F, Tenen DG, Defossez PA, Kappei D. E4F1 and ZNF148 are transcriptional activators of the -57A > C and wild-type TERT promoter. Genome Res 2023; 33:1893-1905. [PMID: 37918959 PMCID: PMC10760450 DOI: 10.1101/gr.277724.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Point mutations within the TERT promoter are the most recurrent somatic noncoding mutations identified across different cancer types, including glioblastoma, melanoma, hepatocellular carcinoma, and bladder cancer. They are most abundant at -146C > T and -124C > T, and rarer at -57A > C, with the latter originally described as a familial case, but subsequently shown also to occur somatically. All three mutations create de novo E26-specific (ETS) binding sites and result in activation of the TERT gene, allowing cancer cells to achieve replicative immortality. Here, we used a systematic proteomics screen to identify transcription factors preferentially binding to the -146C > T, -124C > T, and -57A > C mutations. Although we confirmed binding of multiple ETS factors to the mutant -146C > T and -124C > T sequences, we identified E4F1 as a -57A > C-specific binder and ZNF148 as a TERT wild-type (WT) promoter binder that showed reduced interaction with the -124C > T allele. Both proteins are activating transcription factors that bind specifically to the -57A > C and WT (at position 124) TERT promoter sequence in corresponding cell lines, and up-regulate TERT transcription and telomerase activity. Our work describes new regulators of TERT gene expression with possible roles in cancer.
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Affiliation(s)
- Boon Haow Chua
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596 Singapore
| | - Nurkaiyisah Zaal Anuar
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Laure Ferry
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Cecilia Domrane
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Anna Wittek
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Vineeth T Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596 Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
- Institute of Molecular Virology and Cell Biology (IMVZ), Friedrich Loeffler Institute, 17493 Greifswald, Germany
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore;
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596 Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
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6
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Tsatsakis A, Oikonomopoulou T, Nikolouzakis TK, Vakonaki E, Tzatzarakis M, Flamourakis M, Renieri E, Fragkiadaki P, Iliaki E, Bachlitzanaki M, Karzi V, Katsikantami I, Kakridonis F, Hatzidaki E, Tolia M, Svistunov AA, Spandidos DA, Nikitovic D, Tsiaoussis J, Berdiaki A. Role of telomere length in human carcinogenesis (Review). Int J Oncol 2023; 63:78. [PMID: 37232367 PMCID: PMC10552730 DOI: 10.3892/ijo.2023.5526] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Cancer is considered the most important clinical, social and economic issue regarding cause‑specific disability‑adjusted life years among all human pathologies. Exogenous, endogenous and individual factors, including genetic predisposition, participate in cancer triggering. Telomeres are specific DNA structures positioned at the end of chromosomes and consist of repetitive nucleotide sequences, which, together with shelterin proteins, facilitate the maintenance of chromosome stability, while protecting them from genomic erosion. Even though the connection between telomere status and carcinogenesis has been identified, the absence of a universal or even a cancer‑specific trend renders consent even more complex. It is indicative that both short and long telomere lengths have been associated with a high risk of cancer incidence. When evaluating risk associations between cancer and telomere length, a disparity appears to emerge. Even though shorter telomeres have been adopted as a marker of poorer health status and an older biological age, longer telomeres due to increased cell growth potential are associated with the acquirement of cancer‑initiating somatic mutations. Therefore, the present review aimed to comprehensively present the multifaceted pattern of telomere length and cancer incidence association.
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Affiliation(s)
- Aristidis Tsatsakis
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion
| | - Tatiana Oikonomopoulou
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion
- Department of Anatomy, School of Medicine, University of Crete, 71003 Heraklion
| | - Taxiarchis Konstantinos Nikolouzakis
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion
- Department of Anatomy, School of Medicine, University of Crete, 71003 Heraklion
| | - Elena Vakonaki
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion
| | - Manolis Tzatzarakis
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion
| | | | - Elisavet Renieri
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion
| | | | - Evaggelia Iliaki
- Laboratory of Microbiology, University Hospital of Heraklion, 71500 Heraklion
| | - Maria Bachlitzanaki
- Department of Medical Oncology, Venizeleion General Hospital of Heraklion, 71409 Heraklion
| | - Vasiliki Karzi
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion
| | - Ioanna Katsikantami
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion
| | - Fotios Kakridonis
- Department of Spine Surgery and Scoliosis, KAT General Hospital, 14561 Athens
| | - Eleftheria Hatzidaki
- Department of Neonatology and Neonatal Intensive Care Unit (NICU), University Hospital of Heraklion, 71500 Heraklion
| | - Maria Tolia
- Department of Radiation Oncology, University Hospital of Crete, 71110 Heraklion, Greece
| | - Andrey A. Svistunov
- Department of Pharmacology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russia
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Dragana Nikitovic
- Laboratory of Histology-Embryology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - John Tsiaoussis
- Department of Anatomy, School of Medicine, University of Crete, 71003 Heraklion
| | - Aikaterini Berdiaki
- Laboratory of Histology-Embryology, School of Medicine, University of Crete, 71003 Heraklion, Greece
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7
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Vulsteke JB, Smith V, Bonroy C, Derua R, Blockmans D, De Haes P, Vanderschueren S, Lenaerts JL, Claeys KG, Wuyts WA, Verschueren P, Vanhandsaeme G, Piette Y, De Langhe E, Bossuyt X. Identification of new telomere- and telomerase-associated autoantigens in systemic sclerosis. J Autoimmun 2023; 135:102988. [PMID: 36634459 DOI: 10.1016/j.jaut.2022.102988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
PURPOSE In up to 20% of patients with systemic sclerosis (SSc) no known autoantibody specificity can be identified. Recently discovered autoantigens, such as telomeric repeat binding factor 1 (TERF1), as well as established autoantigens, like RuvBL1/2, are associated with telomere and telomerase biology. We aimed to identify new telomere- and telomerase-associated autoantigens in patients with SSc without known autoantibody specificity. METHODS Unlabelled protein immunoprecipitation combined with gel-free liquid chromatography-tandem mass spectrometry (IP-MS) was performed with sera of 106 patients with SSc from two tertiary referral centres that had a nuclear pattern on HEp-2 indirect immunofluorescence without previously identified autoantibody. Telomere- or telomerase-associated proteins or protein complexes precipitated by individual sera were identified. Candidate autoantigens were confirmed through immunoprecipitation-western blot (IP-WB). A custom Luminex xMAP assay for 5 proteins was evaluated with sera from persons with SSc (n = 467), other systemic autoimmune rheumatic diseases (n = 923), non-rheumatic disease controls (n = 187) and healthy controls (n = 199). RESULTS Eight telomere- and telomerase-associated autoantigens were identified in a total of 11 index patients, including the THO complex (n = 3, all with interstitial lung disease and two with cardiac involvement), telomeric repeat-binding factor 2 (TERF2, n = 1), homeobox-containing protein 1 (HMBOX1, n = 2), regulator of chromosome condensation 1 (RCC1, n = 1), nucleolar and coiled-body phosphoprotein 1 (NOLC1, n = 1), dyskerin (DKC1, n = 1), probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase (NOP2, n = 1) and nuclear valosin-containing protein-like (NVL, n = 2). A Luminex xMAP assay for THO complex subunit 1 (THOC1), TERF2, NOLC1, NOP2 and NVL revealed high reactivity in all index patients, but also in other patients with SSc and disease controls. However, the reactivity by xMAP assay in these other patients was not confirmed by IP-WB. CONCLUSION IP-MS revealed key telomere- and telomerase-associated proteins and protein complexes as autoantigens in patients with SSc.
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Affiliation(s)
- Jean-Baptiste Vulsteke
- KU Leuven, Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, Leuven, Belgium; Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Vanessa Smith
- Ghent University, Department of Internal Medicine, Ghent, Belgium; Unit for Molecular Immunology and Inflammation, VIB Inflammation Research Center (IRC), Ghent, Belgium; Rheumatology, Ghent University Hospital, Ghent, Belgium; European Reference Network on Rare and Complex Connective Tissue and Musculoskeletal Diseases (ERN ReCONNET), Belgium
| | - Carolien Bonroy
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium; Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Rita Derua
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, Leuven, Belgium; KU Leuven, SyBioMa, Leuven, Belgium
| | - Daniel Blockmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, Leuven, Belgium; General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Petra De Haes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Leuven, Belgium; Dermatology, University Hospitals Leuven, Leuven, Belgium
| | - Steven Vanderschueren
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, Leuven, Belgium; General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; European Reference Network on Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases (ERN RITA), Belgium
| | - Jan L Lenaerts
- Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Kristl G Claeys
- KU Leuven, Department of Neurosciences, Laboratory for Muscle Diseases and Neuropathies, Neurology, University Hospitals Leuven, Leuven, Belgium; European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Belgium
| | - Wim A Wuyts
- KU Leuven, Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery, Unit for Interstitial Lung Diseases, Respiratory Medicine, University Hospitals Leuven, Leuven, Belgium; European Reference Network on Rare Respiratory Diseases (ERN LUNG), Belgium
| | - Patrick Verschueren
- KU Leuven, Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, Leuven, Belgium; Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | | | - Yves Piette
- Ghent University, Department of Internal Medicine, Ghent, Belgium; Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Ellen De Langhe
- KU Leuven, Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, Leuven, Belgium; Rheumatology, University Hospitals Leuven, Leuven, Belgium; European Reference Network on Rare and Complex Connective Tissue and Musculoskeletal Diseases (ERN ReCONNET), Belgium; European Reference Network on Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases (ERN RITA), Belgium
| | - Xavier Bossuyt
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Clinical and Diagnostic Immunology, Leuven, Belgium; Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium.
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8
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Hong J, Xu K, Lee JH. Biological roles of the RNA m 6A modification and its implications in cancer. Exp Mol Med 2022; 54:1822-1832. [PMID: 36446846 PMCID: PMC9722703 DOI: 10.1038/s12276-022-00897-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/30/2022] Open
Abstract
The N6-Methyladenosine (m6A) modification of RNA transcripts is the most prevalent and abundant internal modification in eukaryotic messenger RNAs (mRNAs) and plays diverse and important roles in normal biological processes. Extensive studies have indicated that dysregulated m6A modification and m6A-associated proteins play critical roles in tumorigenesis and cancer progression. However, m6A-mediated physiological consequences often lead to opposite outcomes in a biological context-dependent manner. Therefore, context-related complexity must be meaningfully considered to obtain a comprehensive understanding of RNA methylation. Recently, it has been reported that m6A-modified RNAs are closely related to the regulation of the DNA damage response and genomic integrity maintenance. Here, we present an overview of the current knowledge on the m6A modification and its function in human cancer, particularly in relation to the DNA damage response and genomic instability.
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Affiliation(s)
- Juyeong Hong
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Kexin Xu
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Ji Hoon Lee
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
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9
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Zhu X, Fu H, Sun J, Di Q, Xu Q. N6-methyladenosine modification on Hmbox1 is related to telomere dysfunction in DEHP-induced male reproductive injury. Life Sci 2022; 309:121005. [PMID: 36174712 DOI: 10.1016/j.lfs.2022.121005] [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: 07/14/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/19/2022]
Abstract
AIMS Di (2-ethylhexyl) phthalate (DEHP), as an environmental endocrine-disrupting chemical (EDC), can induce male reproductive injury. N6-methyladenosine (m6A) plays a vital role in environmental exposure-induced diseases by regulating gene expression. Therefore, we aim to investigate the role of m6A in DEHP-induced reproductive injury. MAIN METHODS We established an in vivo model of mice exposed to DEHP to explore the effect of DEHP on reproductive injury and m6A. To further explore the molecular mechanism of DEHP toxicity, we built a model of GC-2 cells exposed to mono-(2-ethylhexyl) phthalate (MEHP) in vitro and further silenced Mettl3 in GC-2cells. Besides, we also conducted MeRIP-qPCR and RIP assays to identify the target genes for m6A modification. KEY FINDINGS DEHP induced testicular injury and senescence. And telomeres shortening, reduced levels of telomere repeat-binding factor 1 (TRF1), TRF2, protection of telomeres 1 (POT1), and telomerase reverse transcriptase (TERT) can be observed in DEHP-treated testes. MEHP also induced GC-2 cellular senescence and telomere dysfunction. Besides, increased m6A mediated by METTL3 stabilized homeobox containing 1 (Hmbox1) in an m6A-dependent manner in MEHP-exposed GC-2 cells. Mettl3 knockdown led to lower m6A modification and reduced Hmbox1 stability, resulting in further shortening of telomere length. SIGNIFICANCE our work uncovered that DEHP led to male reproductive injury by telomere dysfunction and m6A modified Hmbox1 contributed to maintaining telomere homeostasis in this process, suggesting that accurate regulation of m6A modification level by drugs has potential value in the treatment of DEHP-induced male reproductive injury.
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Affiliation(s)
- Xiaofang Zhu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Haowei Fu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Jiahui Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qiannan Di
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qian Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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10
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Marnik EA, Almeida MV, Cipriani PG, Chung G, Caspani E, Karaulanov E, Gan HH, Zinno J, Isolehto IJ, Kielisch F, Butter F, Sharp CS, Flanagan RM, Bonnet FX, Piano F, Ketting RF, Gunsalus KC, Updike DL. The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline. PLoS Genet 2022; 18:e1010245. [PMID: 35657999 PMCID: PMC9200344 DOI: 10.1371/journal.pgen.1010245] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 06/15/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
LOTUS and Tudor domain containing proteins have critical roles in the germline. Proteins that contain these domains, such as Tejas/Tapas in Drosophila, help localize the Vasa helicase to the germ granules and facilitate piRNA-mediated transposon silencing. The homologous proteins in mammals, TDRD5 and TDRD7, are required during spermiogenesis. Until now, proteins containing both LOTUS and Tudor domains in Caenorhabditis elegans have remained elusive. Here we describe LOTR-1 (D1081.7), which derives its name from its LOTUS and Tudor domains. Interestingly, LOTR-1 docks next to P granules to colocalize with the broadly conserved Z-granule helicase, ZNFX-1. The Tudor domain of LOTR-1 is required for its Z-granule retention. Like znfx-1 mutants, lotr-1 mutants lose small RNAs from the 3' ends of WAGO and mutator targets, reminiscent of the loss of piRNAs from the 3' ends of piRNA precursor transcripts in mouse Tdrd5 mutants. Our work shows that LOTR-1 acts with ZNFX-1 to bring small RNA amplifying mechanisms towards the 3' ends of its RNA templates.
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Affiliation(s)
- Elisabeth A. Marnik
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
- Husson University, Bangor, Maine, United States of America
| | - Miguel V. Almeida
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | - P. Giselle Cipriani
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - George Chung
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Edoardo Caspani
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | | | - Hin Hark Gan
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - John Zinno
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Ida J. Isolehto
- Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | | | - Falk Butter
- Institute of Molecular Biology, Mainz, Germany
| | - Catherine S. Sharp
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Roisin M. Flanagan
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Frederic X. Bonnet
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Fabio Piano
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Kristin C. Gunsalus
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Dustin L. Updike
- The MDI Biological Laboratory, Bar Harbor, Maine, United States of America
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11
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Kind L, Raasakka A, Molnes J, Aukrust I, Bjørkhaug L, Njølstad PR, Kursula P, Arnesen T. Structural and biophysical characterization of transcription factor HNF-1A as a tool to study MODY3 diabetes variants. J Biol Chem 2022; 298:101803. [PMID: 35257744 PMCID: PMC8988010 DOI: 10.1016/j.jbc.2022.101803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 11/05/2022] Open
Abstract
Hepatocyte nuclear factor 1A (HNF-1A) is a transcription factor expressed in several embryonic and adult tissues, modulating the expression of numerous target genes. Pathogenic variants in the HNF1A gene are known to cause maturity-onset diabetes of the young 3 (MODY3 or HNF1A MODY), a disease characterized by dominant inheritance, age of onset before 25 to 35 years of age, and pancreatic β-cell dysfunction. A precise diagnosis can alter management of this disease, as insulin can be exchanged with sulfonylurea tablets and genetic counseling differs from polygenic forms of diabetes. Therefore, more knowledge on the mechanisms of HNF-1A function and the level of pathogenicity of the numerous HNF1A variants is required for precise diagnostics. Here, we structurally and biophysically characterized an HNF-1A protein containing both the DNA-binding domain and the dimerization domain, and determined the folding and DNA-binding capacity of two established MODY3 HNF-1A variant proteins (P112L, R263C) and one variant of unknown significance (N266S). All three variants showed reduced functionality compared to the WT protein. Furthermore, while the R263C and N266S variants displayed reduced binding to an HNF-1A target promoter, we found the P112L variant was unstable in vitro and in cells. Our results support and mechanistically explain disease causality for these investigated variants and present a novel approach for the dissection of structurally unstable and DNA-binding defective variants. This study indicates that structural and biochemical investigation of HNF-1A is a valuable tool in reliable variant classification needed for precision diabetes diagnostics and management.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Janne Molnes
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Lise Bjørkhaug
- Department of Safety, Chemistry, and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Pål Rasmus Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway; Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Biological Sciences, University of Bergen, Bergen, Norway; Department of Surgery, Haukeland University Hospital, Bergen, Norway.
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12
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Membrane-associated cytoplasmic granules carrying the Argonaute protein WAGO-3 enable paternal epigenetic inheritance in Caenorhabditis elegans. Nat Cell Biol 2022; 24:217-229. [PMID: 35132225 PMCID: PMC9973253 DOI: 10.1038/s41556-021-00827-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/03/2021] [Indexed: 01/04/2023]
Abstract
Epigenetic inheritance describes the transmission of gene regulatory information across generations without altering DNA sequences, enabling offspring to adapt to environmental conditions. Small RNAs have been implicated in this, through both the oocyte and the sperm. However, as much of the cellular content is extruded during spermatogenesis, it is unclear whether cytoplasmic small RNAs can contribute to epigenetic inheritance through sperm. Here we identify a sperm-specific germ granule, termed the paternal epigenetic inheritance (PEI) granule, that mediates paternal epigenetic inheritance by retaining the cytoplasmic Argonaute protein WAGO-3 during spermatogenesis in Caenorhabditis elegans. We identify the PEI granule proteins PEI-1 and PEI-2, which have distinct functions in this process: granule formation, Argonaute selectivity and subcellular localization. We show that PEI granule segregation is coupled to the transport of sperm-specific secretory vesicles through PEI-2 in an S-palmitoylation-dependent manner. PEI-like proteins are found in humans, suggesting that the identified mechanism may be conserved.
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13
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Dermawan JK, Azzato EM, Goldblum JR, Rubin BP, Billings SD, Ko JS. Superficial ALK-rearranged myxoid spindle cell neoplasm: a cutaneous soft tissue tumor with distinctive morphology and immunophenotypic profile. Mod Pathol 2021; 34:1710-1718. [PMID: 34088997 DOI: 10.1038/s41379-021-00830-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/12/2022]
Abstract
Gene rearrangements involving the anaplastic lymphoma kinase (ALK) receptor tyrosine kinase gene have been identified in various neoplasms, including inflammatory myofibroblastic tumor and epithelioid fibrous histiocytoma. We present an ALK-rearranged cutaneous soft tissue tumor with unique morphologic and immunophenotypic features that are not shared by other entities with ALK rearrangements. The six cases involved two females and four males, aged 18-84 (mean 51) years old. Three tumors were on the back and three on the lower extremities (thigh, knee, shin); ranging from 0.5 to 5.6 (mean 2.1) cm. Four were confined to the dermis; two involved the subcutis. All six cases were characterized by the presence of spindled to ovoid cells arranged in concentric whorls and cords against a myxoid to myxohyaline stroma and relatively cellular aggregates of plump ovoid to epithelioid cells. Four cases showed distinct hyalinized blood vessels. Both cases that involved the subcutis showed peripheral lipofibromatosis-like areas. Tumor-infiltrating lymphocytes were absent to moderate. Severe cytologic atypia or conspicuous mitotic activity was not identified. Immunohistochemically, all tumors diffusely expressed ALK (D5F3) and CD34. All but one tumor was diffusely positive for S100 protein. All tumors were negative for EMA, AE1/AE3, SMA, and SOX10. Next-generation sequencing revealed ALK fusions with FLNA (3 cases), MYH10 (2 cases), and HMBOX1 (1 case) as the partner genes. In all six cases, the breakpoints involved exon 20 of ALK, which preserves the receptor tyrosine kinase domains of ALK in the fusion product. Of the four cases with limited follow-up information (2-18 months), none recurred. In conclusion, we report an ALK-rearranged cutaneous soft tissue tumor characterized by the presence of myxoid spindle cell whorls and cords, and co-expression of ALK, CD34, and frequently S100 protein, we term "superficial ALK-rearranged myxoid spindle cell neoplasm".
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Affiliation(s)
- Josephine K Dermawan
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Elizabeth M Azzato
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - John R Goldblum
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Steven D Billings
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer S Ko
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
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14
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Lee JH, Hong J, Zhang Z, de la Peña Avalos B, Proietti CJ, Deamicis AR, Guzmán G P, Lam HM, Garcia J, Roudier MP, Sisk AE, De La Rosa R, Vu K, Yang M, Liao Y, Scheirer J, Pechacek D, Yadav P, Rao MK, Zheng S, Johnson-Pais TL, Leach RJ, Elizalde PV, Dray E, Xu K. Regulation of telomere homeostasis and genomic stability in cancer by N 6-adenosine methylation (m 6A). SCIENCE ADVANCES 2021; 7:7/31/eabg7073. [PMID: 34321211 PMCID: PMC8318370 DOI: 10.1126/sciadv.abg7073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/11/2021] [Indexed: 05/04/2023]
Abstract
The role of RNA methylation on N 6-adenosine (m6A) in cancer has been acknowledged, but the underlying mechanisms remain obscure. Here, we identified homeobox containing 1 (HMBOX1) as an authentic target mRNA of m6A machinery, which is highly methylated in malignant cells compared to the normal counterparts and subject to expedited degradation upon the modification. m6A-mediated down-regulation of HMBOX1 causes telomere dysfunction and inactivation of p53 signaling, which leads to chromosome abnormalities and aggressive phenotypes. CRISPR-based, m6A-editing tools further prove that the methyl groups on HMBOX1 per se contribute to the generation of altered cancer genome. In multiple types of human cancers, expression of the RNA methyltransferase METTL3 is negatively correlated with the telomere length but favorably with fractions of altered cancer genome, whereas HMBOX1 mRNA levels show the opposite patterns. Our work suggests that the cancer-driving genomic alterations may potentially be fixed by rectifying particular epitranscriptomic program.
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Affiliation(s)
- Ji Hoon Lee
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Juyeong Hong
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Bárbara de la Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
| | - Cecilia J Proietti
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Agustina Roldán Deamicis
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Pablo Guzmán G
- Departamento de Anatomía Patológica (BIOREN), Universidad de La Frontera, Temuco Casilla 54-D, Chile
| | - Hung-Ming Lam
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Jose Garcia
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Martine P Roudier
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Anthony E Sisk
- Department of Pathology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Richard De La Rosa
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Kevin Vu
- Department of Medical Education, Joe R. and Teresa Lozano Long School of Medicine, San Antonio, TX 78229, USA
| | - Mei Yang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yiji Liao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jessica Scheirer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Douglas Pechacek
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Pooja Yadav
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Manjeet K Rao
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Teresa L Johnson-Pais
- Department of Urology, University of Texas Health Sciences Center at San Antonio, San Antonio, TX 78229, USA
| | - Robin J Leach
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Patricia V Elizalde
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires C1428ADN, Argentina
| | - Eloïse Dray
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX 78229, USA
| | - Kexin Xu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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15
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Bartlett T. Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development. BMC Bioinformatics 2021; 22:301. [PMID: 34088262 PMCID: PMC8176738 DOI: 10.1186/s12859-021-04201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Network models are well-established as very useful computational-statistical tools in cell biology. However, a genomic network model based only on gene expression data can, by definition, only infer gene co-expression networks. Hence, in order to infer gene regulatory patterns, it is necessary to also include data related to binding of regulatory factors to DNA. RESULTS We propose a new dynamic genomic network model, for inferring patterns of genomic regulatory influence in dynamic processes such as development. Our model fuses experiment-specific gene expression data with publicly available DNA-binding data. The method we propose is computationally efficient, and can be applied to genome-wide data with tens of thousands of transcripts. Thus, our method is well suited for use as an exploratory tool for genome-wide data. We apply our method to data from human fetal cortical development, and our findings confirm genomic regulatory patterns which are recognised as being fundamental to neuronal development. CONCLUSIONS Our method provides a mathematical/computational toolbox which, when coupled with targeted experiments, will reveal and confirm important new functional genomic regulatory processes in mammalian development.
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Affiliation(s)
- Thomas Bartlett
- University College London, Gower Street, London, WC1E 6BT, UK.
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16
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The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1. Nat Commun 2021; 12:2668. [PMID: 33976151 PMCID: PMC8113555 DOI: 10.1038/s41467-021-22861-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
Telomeres are bound by dedicated proteins, which protect them from DNA damage and regulate telomere length homeostasis. In the nematode Caenorhabditis elegans, a comprehensive understanding of the proteins interacting with the telomere sequence is lacking. Here, we harnessed a quantitative proteomics approach to identify TEBP-1 and TEBP-2, two paralogs expressed in the germline and embryogenesis that associate to telomeres in vitro and in vivo. tebp-1 and tebp-2 mutants display strikingly distinct phenotypes: tebp-1 mutants have longer telomeres than wild-type animals, while tebp-2 mutants display shorter telomeres and a Mortal Germline. Notably, tebp-1;tebp-2 double mutant animals have synthetic sterility, with germlines showing signs of severe mitotic and meiotic arrest. Furthermore, we show that POT-1 forms a telomeric complex with TEBP-1 and TEBP-2, which bridges TEBP-1/-2 with POT-2/MRT-1. These results provide insights into the composition and organization of a telomeric protein complex in C. elegans.
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17
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Song Y, An O, Ren X, Chan THM, Tay DJT, Tang SJ, Han J, Hong H, Ng VHE, Ke X, Shen H, Pitcheshwar P, Lin JS, Leong KW, Molias FB, Yang H, Kappei D, Chen L. RNA editing mediates the functional switch of COPA in a novel mechanism of hepatocarcinogenesis. J Hepatol 2021; 74:135-147. [PMID: 32693003 DOI: 10.1016/j.jhep.2020.07.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS RNA editing introduces nucleotide changes in RNA sequences. Recent studies have reported that aberrant adenosine-to-inosine RNA editing is implicated in cancers. Until now, very few functionally important protein-recoding editing targets have been discovered. Here, we investigated the role of a recently discovered protein-recoding editing target COPA (coatomer subunit α) in hepatocellular carcinoma (HCC). METHODS Clinical implication of COPA editing was studied in a cohort of 125 HCC patients. CRISPR/Cas9-mediated knockout of the editing site complementary sequence (ECS) was used to delete edited COPA transcripts endogenously. COPA editing-mediated change in its transcript or protein stability was investigated upon actinomycin D or cycloheximide treatment, respectively. Functional difference in tumourigenesis between wild-type and edited COPA (COPAWTvs. COPAI164V) and the exact mechanisms were also studied in cell models and mice. RESULTS ADAR2 binds to double-stranded RNA formed between edited exon 6 and the ECS at intron 6 of COPA pre-mRNA, causing an isoleucine-to-valine substitution at residue 164. Reduced editing of COPA is implicated in the pathogenesis of HCC, and more importantly, it may be involved in many cancer types. Upon editing, COPAWT switches from a tumour-promoting gene to a tumour suppressor that has a dominant-negative effect. Moreover, COPAI164V may undergo protein conformational change and therefore become less stable than COPAWT. Mechanistically, COPAI164V may deactivate the PI3K/AKT/mTOR pathway through downregulation of caveolin-1 (CAV1). CONCLUSIONS We uncover an RNA editing-associated mechanism of hepatocarcinogenesis by which downregulation of ADAR2 caused the loss of tumour suppressive COPAI164V and concurrent accumulation of tumour-promoting COPAWT in tumours; a rapid degradation of COPAI164V protein and hyper-activation of the PI3K/AKT/mTOR pathway further promote tumourigenesis. LAY SUMMARY RNA editing is a process in which RNA is changed after it is made from DNA, resulting in an altered gene product. In this study, we found that RNA editing of a gene known as coatomer subunit α (COPA) is lower in tumour samples and discovered that this editing process changes COPA protein from a tumour-promoting form to a tumour-suppressive form. Loss of the edited COPA promotes the development of liver cancer.
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Affiliation(s)
- Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore 119074, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - HuiQi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117549, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Xinyu Ke
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Priyankaa Pitcheshwar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Jaymie Siqi Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Ka Wai Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Fernando Bellido Molias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore.
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18
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Greither T, Schumacher J, Dejung M, Behre HM, Zischler H, Butter F, Herlyn H. Fertility Relevance Probability Analysis Shortlists Genetic Markers for Male Fertility Impairment. Cytogenet Genome Res 2020; 160:506-522. [PMID: 33238277 DOI: 10.1159/000511117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022] Open
Abstract
Impairment of male fertility is one of the major public health issues worldwide. Nevertheless, genetic causes of male sub- and infertility can often only be suspected due to the lack of reliable and easy-to-use routine tests. Yet, the development of a marker panel is complicated by the large quantity of potentially predictive markers. Actually, hundreds or even thousands of genes could have fertility relevance. Thus, a systematic method enabling a selection of the most predictive markers out of the many candidates is required. As a criterion for marker selection, we derived a gene-specific score, which we refer to as fertility relevance probability (FRP). For this purpose, we first categorized 2,753 testis-expressed genes as either candidate markers or non-candidates, according to phenotypes in male knockout mice. In a parallel approach, 2,502 genes were classified as candidate markers or non-candidates based on phenotypes in men. Subsequently, we conducted logistic regression analyses with evolutionary rates of genes (dN/dS), transcription levels in testis relative to other organs, and connectivity of the encoded proteins in a protein-protein interaction network as covariates. In confirmation of the procedure, FRP values showed the expected pattern, thus being overall higher in genes with known relevance for fertility than in their counterparts without corresponding evidence. In addition, higher FRP values corresponded with an increased dysregulation of protein abundance in spermatozoa of 37 men with normal and 38 men with impaired fertility. Present analyses resulted in a ranking of genes according to their probable predictive power as candidate markers for male fertility impairment. Thus, AKAP4, TNP1, DAZL, BRDT, DMRT1, SPO11, ZPBP, HORMAD1, and SMC1B are prime candidates toward a marker panel for male fertility impairment. Additional candidate markers are DDX4, SHCBP1L, CCDC155, ODF1, DMRTB1, ASZ1, BOLL, FKBP6, SLC25A31, PRSS21, and RNF17. FRP inference additionally provides clues for potential new markers, thereunder TEX37 and POU4F2. The results of our logistic regression analyses are freely available at the PreFer Genes website (https://prefer-genes.uni-mainz.de/).
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Affiliation(s)
- Thomas Greither
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Julia Schumacher
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Mario Dejung
- Quantitative Proteomics, Institute of Molecular Biology (IMB) Mainz, Mainz, Germany
| | - Hermann M Behre
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Hans Zischler
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB) Mainz, Mainz, Germany
| | - Holger Herlyn
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany,
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19
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Ma H, Su L, He X, Miao J. Loss of HMBOX1 promotes LPS-induced apoptosis and inhibits LPS-induced autophagy of vascular endothelial cells in mouse. Apoptosis 2020; 24:946-957. [PMID: 31583496 DOI: 10.1007/s10495-019-01572-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Our previous study revealed that Homeobox containing 1 (HMBOX1), essential for the survival of vascular endothelial cells (VECs), was involved in the progression of atherosclerosis. Knockdown of HMBOX1 promoted apoptosis and inhibited autophagy through regulating intracellular free zinc level in cultured VECs. In current study, in order to investigate the roles of HMBOX1 in vivo and in endothelium, we generated a knockout (KO) mouse for HMBOX1 by using transcription activator-like effector nucleases (TALENs) technology. Herein, we reported that the protein level of HMBOX1 was gradually increased during mouse development. The HMBOX1 KO mouse was viable and fertile. There existed no differences in apoptosis and autophagy of aortic endothelial cells between wild type and KO mouse. Whereas, loss of HMBOX1 promoted apoptosis and inhibited autophagy of aortic endothelial cells under lipopolysaccharide (LPS) stimulation in mouse. We also demonstrated that HMBOX1 deletion had no influence on the secretion of inflammatory cytokines TNF-α and IL-6. Moreover, overexpression or knockdown of HMBOX1 failed to regulate multiple pro-apoptotic genes expression in vitro. In conclusion, HMBOX1 participated in the functional maintenance of mouse aortic endothelial cells, the aortic endothelial cells of HMBOX1 KO mouse showed increased apoptosis and decreased autophagy with LPS treatment.
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Affiliation(s)
- HanLin Ma
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, 266237, People's Republic of China.,Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, 250012, People's Republic of China
| | - Le Su
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, 266237, People's Republic of China
| | - XiaoYing He
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, 266237, People's Republic of China
| | - JunYing Miao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, 266237, People's Republic of China. .,The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, Shandong University Qilu Hospital, Jinan, 250012, People's Republic of China.
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20
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Huang Y, Xiang Y, Xie Z, Cai Y, Yang Q, Huang H, Chen Z, Xiao Z, He Q. Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer. Clin Exp Metastasis 2020; 37:477-487. [PMID: 32613480 DOI: 10.1007/s10585-020-10045-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/07/2020] [Indexed: 12/20/2022]
Abstract
MACC1 (metastasis associated in colon cancer 1) is a key driver that induces metastasis in colon cancer. However, the mechanisms by which MACC1 expression is transcriptionally regulated and the factors enriched at the MACC1 promoter remain largely unknown. The binding of proteins to specific DNA sites in the genome is a major determinant of genomic maintenance and the regulation of specific genes. The study herein utilized two methods to study the binding proteins of the MACC1 promoter region in colon cancer. Specifically, we adopted CRISPR-based chromatin affinity purification with mass spectrometry (CRISPR-ChAP-MS) and a biotin-streptavidin pulldown assay coupled with MS to identify the specific proteome bound to the MACC1 promoter in two colon cell lines with different metastatic potential. A total of 24 proteins were identified by CRISPR-ChAP-MS as binding to the MACC1 promoter, among which c-JUN was validated by ChIP-PCR. A total of 739 binding protein candidates were identified by biotin-streptavidin pulldown assays coupled with MS, of which HNF4G and PAX6 were validated and compared for their binding to the same promoter sites in the two cell lines. Our studies suggest distinctive proteomic factors associated with the MACC1 promoter in colon cells with different metastatic potential. The dynamic regulatory factors accumulated at the promoter of MACC1 may provide novel insights into the regulatory mechanisms of MACC1 transcription.
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Affiliation(s)
- Yahui Huang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.,Department of Pathology, Xuchang Central Hospital, Henan University of Science and Technology, Xuchang, Henan, People's Republic of China
| | - Yi Xiang
- School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhongpeng Xie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.,Department of Pathology, Hainan General Hospital, Haikou, Hainan, People's Republic of China
| | - Yuxiang Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Qiongzhi Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Huichao Huang
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhuchu Chen
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhefeng Xiao
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.
| | - Qiongqiong He
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China. .,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.
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21
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Purification and enrichment of specific chromatin loci. Nat Methods 2020; 17:380-389. [PMID: 32152500 DOI: 10.1038/s41592-020-0765-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then describe the published strategies and discuss their advantages and limitations. We conclude by discussing why significant technology developments are required to unambiguously describe the composition of small single loci.
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22
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Wieczór M, Czub J. Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models. Free Radic Biol Med 2020; 148:162-169. [PMID: 31926882 DOI: 10.1016/j.freeradbiomed.2020.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/02/2020] [Accepted: 01/05/2020] [Indexed: 12/15/2022]
Abstract
Oxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres - structures that cap chromosome ends - due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5'-GGG-3' motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments consistently show that telomeric oxidative lesions are more abundant and persistent than elsewhere in the genome. This led to a hypothesis that telomeres act as sensors of prolonged oxidative stress and prevent carcinogenesis, as disruption of telomeric integrity triggers senescence or apoptosis. Here, we use atomistic alchemical Molecular Dynamics simulations to perform a combinatorial assessment of changes in DNA binding affinity of telomeric proteins induced by oxidative guanine lesions. We rank lesions by their effect on telomere integrity, as well as telomeric proteins by their sensitivity to DNA oxidation. While the binding of most proteins is abolished by DNA oxidation, HOT1 emerges as a notable exception, suggesting its potential role in sensing of oxidative damage. Through statistical analysis and free energy decomposition, we also identify common trends in structural responses of protein-DNA complexes that contribute to decreased binding affinity.
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Affiliation(s)
- Miłosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology, Gdańsk, Poland.
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, Gdańsk, Poland.
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23
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Udroiu I, Sgura A. Alternative Lengthening of Telomeres and Chromatin Status. Genes (Basel) 2019; 11:genes11010045. [PMID: 31905921 PMCID: PMC7016797 DOI: 10.3390/genes11010045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 12/16/2022] Open
Abstract
Telomere length is maintained by either telomerase, a reverse transcriptase, or alternative lengthening of telomeres (ALT), a mechanism that utilizes homologous recombination (HR) proteins. Since access to DNA for HR enzymes is regulated by the chromatin status, it is expected that telomere elongation is linked to epigenetic modifications. The aim of this review is to elucidate the epigenetic features of ALT-positive cells. In order to do this, it is first necessary to understand the telomeric chromatin peculiarities. So far, the epigenetic nature of telomeres is still controversial: some authors describe them as heterochromatic, while for others, they are euchromatic. Similarly, ALT activity should be characterized by the loss (according to most researchers) or formation (as claimed by a minority) of heterochromatin in telomeres. Besides reviewing the main works in this field and the most recent findings, some hypotheses involving the role of telomere non-canonical sequences and the possible spatial heterogeneity of telomeres are given.
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24
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Liew PS, Chen Q, Ng AWR, Chew YC, Ravin NV, Sim EUH, Lee CW, Narayanan K. Phage N15 protelomerase resolves its tos recognition site into hairpin telomeres within mammalian cells. Anal Biochem 2019; 583:113361. [DOI: 10.1016/j.ab.2019.113361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
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25
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Reis H, Schwebs M, Dietz S, Janzen CJ, Butter F. TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomes. Nucleic Acids Res 2019; 46:2820-2833. [PMID: 29385523 PMCID: PMC5888660 DOI: 10.1093/nar/gky028] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/25/2018] [Indexed: 11/14/2022] Open
Abstract
During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host, immune evasion of T. brucei bloodstream form (BSF) cells relies on antigenic variation, which includes monoallelic expression and periodic switching of variant surface glycoprotein (VSG) genes. The active VSG is transcribed from only 1 of the 15 subtelomeric expression sites (ESs). During differentiation from BSF to the insect-resident procyclic form (PCF), the active ES is transcriptionally silenced. We used mass spectrometry-based interactomics to determine the composition of telomere protein complexes in T. brucei BSF and PCF stages to learn more about the structure and functions of telomeres in trypanosomes. Our data suggest a different telomere complex composition in the two forms of the parasite. One of the novel telomere-associated proteins, TelAP1, forms a complex with telomeric proteins TbTRF, TbRAP1 and TbTIF2 and influences ES silencing kinetics during developmental differentiation.
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Affiliation(s)
- Helena Reis
- Department of Cell & Developmental Biology, Biocenter University of Würzburg, Würzburg 97074, Germany
| | - Marie Schwebs
- Department of Cell & Developmental Biology, Biocenter University of Würzburg, Würzburg 97074, Germany
| | - Sabrina Dietz
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter University of Würzburg, Würzburg 97074, Germany
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz 55128, Germany
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26
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Telomeres in Plants and Humans: Not So Different, Not So Similar. Cells 2019; 8:cells8010058. [PMID: 30654521 PMCID: PMC6356271 DOI: 10.3390/cells8010058] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/01/2023] Open
Abstract
Parallel research on multiple model organisms shows that while some principles of telomere biology are conserved among all eukaryotic kingdoms, we also find some deviations that reflect different evolutionary paths and life strategies, which may have diversified after the establishment of telomerase as a primary mechanism for telomere maintenance. Much more than animals, plants have to cope with environmental stressors, including genotoxic factors, due to their sessile lifestyle. This is, in principle, made possible by an increased capacity and efficiency of the molecular systems ensuring maintenance of genome stability, as well as a higher tolerance to genome instability. Furthermore, plant ontogenesis differs from that of animals in which tissue differentiation and telomerase silencing occur during early embryonic development, and the “telomere clock” in somatic cells may act as a preventive measure against carcinogenesis. This does not happen in plants, where growth and ontogenesis occur through the serial division of apical meristems consisting of a small group of stem cells that generate a linear series of cells, which differentiate into an array of cell types that make a shoot and root. Flowers, as generative plant organs, initiate from the shoot apical meristem in mature plants which is incompatible with the human-like developmental telomere shortening. In this review, we discuss differences between human and plant telomere biology and the implications for aging, genome stability, and cell and organism survival. In particular, we provide a comprehensive comparative overview of telomere proteins acting in humans and in Arabidopsis thaliana model plant, and discuss distinct epigenetic features of telomeric chromatin in these species.
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27
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Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F, Ketting RF. GTSF-1 is required for formation of a functional RNA-dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J 2018; 37:embj.201899325. [PMID: 29769402 DOI: 10.15252/embj.201899325] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 11/09/2022] Open
Abstract
Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf-1 and characterized it in the context of the sRNA pathways of C. elegans We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying rrf-3 mutants. We show, both in vivo and in vitro, that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activities.
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Affiliation(s)
| | - Sabrina Dietz
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - Stefan Redl
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Emil Karaulanov
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Andrea Hildebrandt
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Christian Renz
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Helle D Ulrich
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Julian König
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
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Gupta R, Somyajit K, Narita T, Maskey E, Stanlie A, Kremer M, Typas D, Lammers M, Mailand N, Nussenzweig A, Lukas J, Choudhary C. DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. Cell 2018; 173:972-988.e23. [PMID: 29656893 PMCID: PMC8108093 DOI: 10.1016/j.cell.2018.03.050] [Citation(s) in RCA: 288] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/27/2018] [Accepted: 03/21/2018] [Indexed: 01/13/2023]
Abstract
Repair of damaged DNA is essential for maintaining genome integrity and for preventing genome-instability-associated diseases, such as cancer. By combining proximity labeling with quantitative mass spectrometry, we generated high-resolution interaction neighborhood maps of the endogenously expressed DNA repair factors 53BP1, BRCA1, and MDC1. Our spatially resolved interaction maps reveal rich network intricacies, identify shared and bait-specific interaction modules, and implicate previously concealed regulators in this process. We identified a novel vertebrate-specific protein complex, shieldin, comprising REV7 plus three previously uncharacterized proteins, RINN1 (CTC-534A2.2), RINN2 (FAM35A), and RINN3 (C20ORF196). Recruitment of shieldin to DSBs, via the ATM-RNF8-RNF168-53BP1-RIF1 axis, promotes NHEJ-dependent repair of intrachromosomal breaks, immunoglobulin class-switch recombination (CSR), and fusion of unprotected telomeres. Shieldin functions as a downstream effector of 53BP1-RIF1 in restraining DNA end resection and in sensitizing BRCA1-deficient cells to PARP inhibitors. These findings have implications for understanding cancer-associated PARPi resistance and the evolution of antibody CSR in higher vertebrates.
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Affiliation(s)
- Rajat Gupta
- Proteomics Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Kumar Somyajit
- Protein Signaling Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Takeo Narita
- Proteomics Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Elina Maskey
- Proteomics Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Andre Stanlie
- Laboratory of Genome Integrity, NIH, Bethesda, MD 20892, USA
| | - Magdalena Kremer
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Joseph-Stelzmann-Str. 26, University of Cologne, 50931 Cologne, Germany
| | - Dimitris Typas
- Protein Signaling Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Michael Lammers
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Joseph-Stelzmann-Str. 26, University of Cologne, 50931 Cologne, Germany; Institute for Biochemistry, Synthetic and Structural Biochemistry, Felix-Hausdorff-Str. 4, University of Greifswald, 17487 Greifswald, Germany
| | - Niels Mailand
- Protein Signaling Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | | | - Jiri Lukas
- Protein Signaling Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark; Center for Chromosome Stability (CCS), Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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29
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Trajano LADSN, Trajano ETL, Silva MADS, Stumbo AC, Mencalha AL, Fonseca ADSD. Genomic stability and telomere regulation in skeletal muscle tissue. Biomed Pharmacother 2018; 98:907-915. [DOI: 10.1016/j.biopha.2018.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 02/07/2023] Open
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30
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Alqadah A, Hsieh YW, Xiong R, Chuang CF. Stochastic left-right neuronal asymmetry in Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0407. [PMID: 27821536 DOI: 10.1098/rstb.2015.0407] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 12/28/2022] Open
Abstract
Left-right asymmetry in the nervous system is observed across species. Defects in left-right cerebral asymmetry are linked to several neurological diseases, but the molecular mechanisms underlying brain asymmetry in vertebrates are still not very well understood. The Caenorhabditis elegans left and right amphid wing 'C' (AWC) olfactory neurons communicate through intercellular calcium signalling in a transient embryonic gap junction neural network to specify two asymmetric subtypes, AWCOFF (default) and AWCON (induced), in a stochastic manner. Here, we highlight the molecular mechanisms that establish and maintain stochastic AWC asymmetry. As the components of the AWC asymmetry pathway are highly conserved, insights from the model organism C. elegans may provide a window onto how brain asymmetry develops in humans.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.
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Affiliation(s)
- Amel Alqadah
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
| | - Yi-Wen Hsieh
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
| | - Rui Xiong
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
| | - Chiou-Fen Chuang
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
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31
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Zhao Y, Zhang G, He C, Mei Y, Shi Y, Li F. The 11th C2H2 zinc finger and an adjacent C-terminal arm are responsible for TZAP recognition of telomeric DNA. Cell Res 2017; 28:130-134. [PMID: 29134956 DOI: 10.1038/cr.2017.141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Yaqing Zhao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Guang Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chao He
- Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Yide Mei
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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32
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Rajagopalan D, Pandey AK, Xiuzhen MC, Lee KK, Hora S, Zhang Y, Chua BH, Kwok HS, Bhatia SS, Deng LW, Tenen DG, Kappei D, Jha S. TIP60 represses telomerase expression by inhibiting Sp1 binding to the TERT promoter. PLoS Pathog 2017; 13:e1006681. [PMID: 29045464 PMCID: PMC5662243 DOI: 10.1371/journal.ppat.1006681] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/30/2017] [Accepted: 10/04/2017] [Indexed: 12/13/2022] Open
Abstract
HIV1-TAT interactive protein (TIP60) is a haploinsufficient tumor suppressor. However, the potential mechanisms endowing its tumor suppressor ability remain incompletely understood. It plays a vital role in virus-induced cancers where TIP60 down-regulates the expression of human papillomavirus (HPV) oncoprotein E6 which in turn destabilizes TIP60. This intrigued us to identify the role of TIP60, in the context of a viral infection, where it is targeted by oncoproteins. Through an array of molecular biology techniques such as Chromatin immunoprecipitation, expression analysis and mass spectrometry, we establish the hitherto unknown role of TIP60 in repressing the expression of the catalytic subunit of the human telomerase complex, TERT, a key driver for immortalization. TIP60 acetylates Sp1 at K639, thus inhibiting Sp1 binding to the TERT promoter. We identified that TIP60-mediated growth suppression of HPV-induced cervical cancer is mediated in part due to TERT repression through Sp1 acetylation. In summary, our study has identified a novel substrate for TIP60 catalytic activity and a unique repressive mechanism acting at the TERT promoter in virus-induced malignancies.
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Affiliation(s)
- Deepa Rajagopalan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Amit Kumar Pandey
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Magdalene Claire Xiuzhen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kwok Kin Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Shainan Hora
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yanzhou Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Boon Haow Chua
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Hui Si Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Lih Wen Deng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Daniel G. Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, United States of America
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Abstract
Bacteria and viruses possess circular DNA, whereas eukaryotes with typically very large DNA molecules have had to evolve into linear chromosomes to circumvent the problem of supercoiling circular DNA of that size. Consequently, such organisms possess telomeres to cap chromosome ends. Telomeres are essentially tandem repeats of any DNA sequence that are present at the ends of chromosomes. Their biology has been an enigmatic one, involving various molecules interacting dynamically in an evolutionarily well-trimmed fashion. Telomeres range from canonical hexameric repeats in most eukaryotes to unimaginably random retrotransposons, which attach to chromosome ends and reverse-transcribe to DNA in some plants and insects. Telomeres invariably associate with specialised protein complexes that envelop it, also regulating access of the ends to legitimate enzymes involved in telomere metabolism. They also transcribe into repetitive RNA which also seems to be playing significant roles in telomere maintenance. Telomeres thus form the intersection of DNA, protein, and RNA molecules acting in concert to maintain chromosome integrity. Telomere biology is emerging to appear ever more complex than previously envisaged, with the continual discovery of more molecules and interplays at the telomeres. This review also includes a section dedicated to the history of telomere biology, and intends to target the scientific audience new to the field by rendering an understanding of the phenomenon of chromosome end protection at large, with more emphasis on the biology of human telomeres. The review provides an update on the field and mentions the questions that need to be addressed.
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Affiliation(s)
- Shriram Venkatesan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Singapore.
| | - Aik Kia Khaw
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Singapore.
- Clinical Research Unit, Khoo Teck Puat Hospital, 768828 Singapore, Singapore.
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Singapore.
- Tembusu College, National University of Singapore, 138598 Singapore, Singapore.
- VIT University, Vellore 632014, India.
- Mangalore University, Mangalore 574199, India.
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Zhou S, Xiao Y, Zhuang Y, Liu Y, Zhao H, Yang H, Xie C, Zhou F, Zhou Y. Knockdown of homeobox containing 1 increases the radiosensitivity of cervical cancer cells through telomere shortening. Oncol Rep 2017. [PMID: 28628186 DOI: 10.3892/or.2017.5707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homeobox containing 1 (HMBOX1) modulates telomere length in various types of tumor cells by binding to double‑stranded telomeric DNA. There is a negative correlation between telomere length and radiosensitivity in tumor cells. In the present study, we aimed to investigate the relationship among HMBOX1, telomere and radiosensitivity in cervical cancer cells. Lentivirus-based shRNAs were used to establish stable transfected cell lines in which protein and mRNA levels of HMBOX1 were notably decreased. Knockdown of HMBOX1 increased the radiosensitivity of HeLa and C33A cells. TERT protein was also decreased while HMBOX1 was downregulated. Knockdown of HMBOX1 shortened telomere length in the HeLa cells, while TERT overexpression rescued telomere shortening in the HeLa-HMBOX1 cells. Knockdown of HMBOX1 increased the apoptosis rate, decreased radiation-induced DNA damage foci, and inhibited the expression of ATM, ATR, p-ATM, p-ATR and BRCA1 in the homologous recombination repair pathway. Our data suggest a possible role of HMBOX1 in regulating radiosensitivity in cervical cancer cells. Moreover, HMBOX1 may be a potential factor in the radiotherapy of cervical cancer.
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Affiliation(s)
- Shuliang Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Youde Xiao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yafei Zhuang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yinyin Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Hong Zhao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Hui Yang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Fuxiang Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yunfeng Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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35
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Jahn A, Rane G, Paszkowski-Rogacz M, Sayols S, Bluhm A, Han CT, Draškovič I, Londoño-Vallejo JA, Kumar AP, Buchholz F, Butter F, Kappei D. ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator. EMBO Rep 2017; 18:929-946. [PMID: 28500257 PMCID: PMC5452029 DOI: 10.15252/embr.201744095] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/31/2017] [Accepted: 04/18/2017] [Indexed: 11/09/2022] Open
Abstract
Telomeres constitute the ends of linear chromosomes and together with the shelterin complex form a structure essential for genome maintenance and stability. In addition to the constitutive binding of the shelterin complex, other direct, yet more transient interactions are mediated by the CST complex and HOT1/HMBOX1, while subtelomeric variant repeats are recognized by NR2C/F transcription factors. Recently, the Kruppel-like zinc finger protein ZBTB48/HKR3/TZAP has been described as a novel telomere-associated factor in the vertebrate lineage. Here, we show that ZBTB48 binds directly both to telomeric and to subtelomeric variant repeat sequences. ZBTB48 is found at telomeres of human cancer cells regardless of the mode of telomere maintenance and it acts as a negative regulator of telomere length. In addition to its telomeric function, we demonstrate through a combination of RNAseq, ChIPseq and expression proteomics experiments that ZBTB48 acts as a transcriptional activator on a small set of target genes, including mitochondrial fission process 1 (MTFP1). This discovery places ZBTB48 at the interface of telomere length regulation, transcriptional control and mitochondrial metabolism.
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Affiliation(s)
- Arne Jahn
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany.,Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Grishma Rane
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Sergi Sayols
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Alina Bluhm
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Chung-Ting Han
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Irena Draškovič
- Telomeres & Cancer Laboratory, UMR3244, Institut Curie-CNRS-UPMC, Paris Cedex 05, France
| | | | - Alan Prem Kumar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine National University of Singapore, Singapore City, Singapore.,Curtin Medical School, Faculty of Health Sciences Curtin University, Perth, Australia
| | - Frank Buchholz
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany .,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK) Partner Site Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore
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Kappei D, Scheibe M, Paszkowski-Rogacz M, Bluhm A, Gossmann TI, Dietz S, Dejung M, Herlyn H, Buchholz F, Mann M, Butter F. Phylointeractomics reconstructs functional evolution of protein binding. Nat Commun 2017; 8:14334. [PMID: 28176777 PMCID: PMC5309834 DOI: 10.1038/ncomms14334] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022] Open
Abstract
Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics. We develop this concept by investigating the molecular evolution of the shelterin complex, which protects telomeres, across 16 vertebrate species from zebrafish to humans covering 450 million years of evolution. Our phylointeractomics screen discovers previously unknown telomere-associated proteins and reveals how homologous proteins undergo functional evolution. For instance, we show that TERF1 evolved as a telomere-binding protein in the common stem lineage of marsupial and placental mammals. Phylointeractomics is a versatile and scalable approach to investigate evolutionary changes in protein function and thus can provide experimental evidence for phylogenomic relationships.
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Affiliation(s)
- Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.,Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstraße 74, Dresden D-01307, Germany
| | - Marion Scheibe
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, Mainz D-55128, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried D-82152, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstraße 74, Dresden D-01307, Germany
| | - Alina Bluhm
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, Mainz D-55128, Germany
| | - Toni Ingolf Gossmann
- Department of Animal &Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Sabrina Dietz
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, Mainz D-55128, Germany
| | - Mario Dejung
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, Mainz D-55128, Germany
| | - Holger Herlyn
- Institute of Anthropology, University of Mainz, Anselm-Franz-von-Bentzel-Weg 7, Mainz D-55099, Germany
| | - Frank Buchholz
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstraße 74, Dresden D-01307, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden D-01307, Germany.,German Cancer Research Center (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK) partner site, Fetscherstr. 74, 01307 Dresden Germany.,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden D-01307, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried D-82152, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, Mainz D-55128, Germany
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Ma H, Su L, Zhang S, Kung H, Miao J. Inhibition of ANXA7 GTPase activity by a small molecule promotes HMBOX1 translation of vascular endothelial cells in vitro and in vivo. Int J Biochem Cell Biol 2016; 79:33-40. [DOI: 10.1016/j.biocel.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/02/2016] [Accepted: 08/05/2016] [Indexed: 12/28/2022]
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Wierer M, Mann M. Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes. Hum Mol Genet 2016; 25:R106-R114. [PMID: 27402878 PMCID: PMC5036873 DOI: 10.1093/hmg/ddw208] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/24/2016] [Indexed: 01/30/2023] Open
Abstract
High-resolution mass spectrometry (MS)-based proteomics is a powerful method for the identification of soluble protein complexes and large-scale affinity purification screens can decode entire protein interaction networks. In contrast, protein complexes residing on chromatin have been much more challenging, because they are difficult to purify and often of very low abundance. However, this is changing due to recent methodological and technological advances in proteomics. Proteins interacting with chromatin marks can directly be identified by pulldowns with synthesized histone tails containing posttranslational modifications (PTMs). Similarly, pulldowns with DNA baits harbouring single nucleotide polymorphisms or DNA modifications reveal the impact of those DNA alterations on the recruitment of transcription factors. Accurate quantitation – either isotope-based or label free – unambiguously pinpoints proteins that are significantly enriched over control pulldowns. In addition, protocols that combine classical chromatin immunoprecipitation (ChIP) methods with mass spectrometry (ChIP-MS) target gene regulatory complexes in their in-vivo context. Similar to classical ChIP, cells are crosslinked with formaldehyde and chromatin sheared by sonication or nuclease digested. ChIP-MS baits can be proteins in tagged or endogenous form, histone PTMs, or lncRNAs. Locus-specific ChIP-MS methods would allow direct purification of a single genomic locus and the proteins associated with it. There, loci can be targeted either by artificial DNA-binding sites and corresponding binding proteins or via proteins with sequence specificity such as TAL or nuclease deficient Cas9 in combination with a specific guide RNA. We predict that advances in MS technology will soon make such approaches generally applicable tools in epigenetics.
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Affiliation(s)
- Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
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Dejung M, Subota I, Bucerius F, Dindar G, Freiwald A, Engstler M, Boshart M, Butter F, Janzen CJ. Quantitative Proteomics Uncovers Novel Factors Involved in Developmental Differentiation of Trypanosoma brucei. PLoS Pathog 2016; 12:e1005439. [PMID: 26910529 PMCID: PMC4765897 DOI: 10.1371/journal.ppat.1005439] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/15/2016] [Indexed: 11/18/2022] Open
Abstract
Developmental differentiation is a universal biological process that allows cells to adapt to different environments to perform specific functions. African trypanosomes progress through a tightly regulated life cycle in order to survive in different host environments when they shuttle between an insect vector and a vertebrate host. Transcriptomics has been useful to gain insight into RNA changes during stage transitions; however, RNA levels are only a moderate proxy for protein abundance in trypanosomes. We quantified 4270 protein groups during stage differentiation from the mammalian-infective to the insect form and provide classification for their expression profiles during development. Our label-free quantitative proteomics study revealed previously unknown components of the differentiation machinery that are involved in essential biological processes such as signaling, posttranslational protein modifications, trafficking and nuclear transport. Furthermore, guided by our proteomic survey, we identified the cause of the previously observed differentiation impairment in the histone methyltransferase DOT1B knock-out strain as it is required for accurate karyokinesis in the first cell division during differentiation. This epigenetic regulator is likely involved in essential chromatin restructuring during developmental differentiation, which might also be important for differentiation in higher eukaryotic cells. Our proteome dataset will serve as a resource for detailed investigations of cell differentiation to shed more light on the molecular mechanisms of this process in trypanosomes and other eukaryotes.
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Affiliation(s)
- Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
| | - Ines Subota
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Am Hubland, Wuerzburg, Germany
| | - Ferdinand Bucerius
- Department Biology I, Genetics, University of Munich (LMU), Großhaderner, Martinsried, Germany
| | - Gülcin Dindar
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Am Hubland, Wuerzburg, Germany
| | - Anja Freiwald
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Am Hubland, Wuerzburg, Germany
| | - Michael Boshart
- Department Biology I, Genetics, University of Munich (LMU), Großhaderner, Martinsried, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
- * E-mail: (FB); (CJJ)
| | - Christian J. Janzen
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Am Hubland, Wuerzburg, Germany
- * E-mail: (FB); (CJJ)
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Chu TW, MacNeil DE, Autexier C. Multiple Mechanisms Contribute to the Cell Growth Defects Imparted by Human Telomerase Insertion in Fingers Domain Mutations Associated with Premature Aging Diseases. J Biol Chem 2016; 291:8374-86. [PMID: 26887940 DOI: 10.1074/jbc.m116.714782] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Indexed: 11/06/2022] Open
Abstract
Normal human stem cells rely on low levels of active telomerase to sustain their high replicative requirements. Deficiency in telomere maintenance mechanisms leads to the development of premature aging diseases, such as dyskeratosis congenita and aplastic anemia. Mutations in the unique "insertion in fingers domain" (IFD) in the human telomerase reverse transcriptase catalytic subunit (hTERT) have previously been identified and shown to be associated with dyskeratosis congenita and aplastic anemia. However, little is known about the molecular mechanisms impacted by these IFD mutations. We performed comparative functional analyses of disease-associated IFD variants at the molecular and cellular levels. We report that hTERT-P721R- and hTERT-R811C-expressing cells exhibited growth defects likely due to impaired TPP1-mediated recruitment of these variant enzymes to telomeres. We showed that activity and processivity of hTERT-T726M failed to be stimulated by TPP1-POT1 overexpression and that dGTP usage by this variant was less efficient compared with the wild-type enzyme. hTERT-P785L-expressing cells did not show growth defects, and this variant likely confers cell survival through increased DNA synthesis and robust activity stimulation by TPP1-POT1. Altogether, our data suggest that multiple mechanisms contribute to cell growth defects conferred by the IFD variants.
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Affiliation(s)
- Tsz Wai Chu
- From the Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal H3T 1E2, Canada, Department of Medicine, McGill University, Montréal H4A 3J1, Canada, and
| | - Deanna Elise MacNeil
- From the Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal H3T 1E2, Canada, Department of Anatomy and Cell Biology, McGill University, Montréal H3A 0C7, Canada
| | - Chantal Autexier
- From the Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal H3T 1E2, Canada, Department of Medicine, McGill University, Montréal H4A 3J1, Canada, and Department of Anatomy and Cell Biology, McGill University, Montréal H3A 0C7, Canada
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Massad T, Papadopolos E, Stenmark P, Damberg P. The C repressor of the P2 bacteriophage. JOURNAL OF BIOMOLECULAR NMR 2016; 64:175-180. [PMID: 26695638 PMCID: PMC4752584 DOI: 10.1007/s10858-015-9999-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Tariq Massad
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Evangelos Papadopolos
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Av, Boston, MA, 02115, USA
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Peter Damberg
- Department of Clinical Neurosciences, Karolinska Institute, 171 77, Stockholm, Sweden.
- Karolinska Research and Imaging Center, Karolinska University Hospital, 171 76, Stockholm, Sweden.
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Zhang Y, Wu Y, Mao P, Li F, Han X, Zhang Y, Jiang S, Chen Y, Huang J, Liu D, Zhao Y, Ma W, Songyang Z. Cold-inducible RNA-binding protein CIRP/hnRNP A18 regulates telomerase activity in a temperature-dependent manner. Nucleic Acids Res 2015; 44:761-75. [PMID: 26673712 PMCID: PMC4737163 DOI: 10.1093/nar/gkv1465] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 12/01/2015] [Indexed: 01/22/2023] Open
Abstract
The telomerase is responsible for adding telomeric repeats to chromosomal ends and consists of the reverse transcriptase TERT and the RNA subunit TERC. The expression and activity of the telomerase are tightly regulated, and aberrant activation of the telomerase has been observed in >85% of human cancers. To better understand telomerase regulation, we performed immunoprecipitations coupled with mass spectrometry (IP-MS) and identified cold inducible RNA-binding protein (CIRP or hnRNP A18) as a telomerase-interacting factor. We have found that CIRP is necessary to maintain telomerase activities at both 32°C and 37°C. Furthermore, inhibition of CIRP by CRISPR-Cas9 or siRNA knockdown led to reduced telomerase activities and shortened telomere length, suggesting an important role of CIRP in telomere maintenance. We also provide evidence here that CIRP associates with the active telomerase complex through direct binding of TERC and regulates Cajal body localization of the telomerase. In addition, CIRP regulates the level of TERT mRNAs. At the lower temperature, TERT mRNA is upregulated in a CIRP-dependent manner to compensate for reduced telomerase activities. Taken together, these findings highlight the dual roles that CIRP plays in regulating TERT and TERC, and reveal a new class of telomerase modulators in response to hypothermia conditions.
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Affiliation(s)
- Youwei Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China Collaborative Innovation Center for Cancer Medicine, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Yangxiu Wu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Pingsu Mao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Feng Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xin Han
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yi Zhang
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Shuai Jiang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuxi Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Dan Liu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yong Zhao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenbin Ma
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China Collaborative Innovation Center for Cancer Medicine, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China Collaborative Innovation Center for Cancer Medicine, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou 510006, China Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Casas-Vila N, Scheibe M, Freiwald A, Kappei D, Butter F. Identification of TTAGGG-binding proteins in Neurospora crassa, a fungus with vertebrate-like telomere repeats. BMC Genomics 2015; 16:965. [PMID: 26577093 PMCID: PMC4650311 DOI: 10.1186/s12864-015-2158-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/27/2015] [Indexed: 11/23/2022] Open
Abstract
Background To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical TTAGGG motif found in vertebrates and also several other fungi. Results Using label-free quantitative proteomics, we here investigate the telosome of Neurospora crassa, a fungus with canonical telomeric repeats. We show that at least six of the candidates detected in our screen are direct TTAGGG-repeat binding proteins. While three of the direct interactors (NCU03416 [ncTbf1], NCU01991 [ncTbf2] and NCU02182 [ncTay1]) feature the known myb/homeobox DNA interaction domain also found in the vertebrate telomeric factors, we additionally show that a zinc-finger protein (NCU07846) and two proteins without any annotated DNA-binding domain (NCU02644 and NCU05718) are also direct double-strand TTAGGG binders. We further find two single-strand binders (NCU02404 [ncGbp2] and NCU07735 [ncTcg1]). Conclusion By quantitative label-free interactomics we identify TTAGGG-binding proteins in Neurospora crassa, suggesting candidates for telomeric factors that are supported by phylogenomic comparison with yeast species. Intriguingly, homologs in yeast species with degenerated telomeric repeats are also TTAGGG-binding proteins, e.g. in S. cerevisiae Tbf1 recognizes the TTAGGG motif found in its subtelomeres. However, there is also a subset of proteins that is not conserved. While a rudimentary core TTAGGG-recognition machinery may be conserved across yeast species, our data suggests Neurospora as an emerging model organism with unique features. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2158-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Núria Casas-Vila
- Quantitative Proteomics, Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Marion Scheibe
- Quantitative Proteomics, Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Anja Freiwald
- Quantitative Proteomics, Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, 117599, Singapore, Singapore
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany.
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The Insertion in Fingers Domain in Human Telomerase Can Mediate Enzyme Processivity and Telomerase Recruitment to Telomeres in a TPP1-Dependent Manner. Mol Cell Biol 2015; 36:210-22. [PMID: 26503784 DOI: 10.1128/mcb.00746-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/19/2015] [Indexed: 01/11/2023] Open
Abstract
In most human cancer cells, cellular immortalization relies on the activation and recruitment of telomerase to telomeres. The telomere-binding protein TPP1 and the TEN domain of the telomerase catalytic subunit TERT regulate telomerase recruitment. TERT contains a unique domain, called the insertion in fingers domain (IFD), located within the conserved reverse transcriptase domain. We report the role of specific hTERT IFD residues in the regulation of telomerase activity and processivity, recruitment to telomeres, and cell survival. One hTERT IFD variant, hTERT-L805A, with reduced activity and processivity showed impaired telomere association, which could be partially rescued by overexpression of TPP1-POT1. Another previously reported hTERT IFD mutant enzyme with similarly low levels of activity and processivity, hTERT-V791Y, displayed defects in telomere binding and was insensitive to TPP1-POT1 overexpression. Our results provide the first evidence that the IFD can mediate enzyme processivity and telomerase recruitment to telomeres in a TPP1-dependent manner. Moreover, unlike hTERT-V791Y, hTERT-V763S, a variant with reduced activity but increased processivity, and hTERT-L805A, could both immortalize limited-life-span cells, but cells expressing these two mutant enzymes displayed growth defects, increased apoptosis, DNA damage at telomeres, and short telomeres. Our results highlight the importance of the IFD in maintaining short telomeres and in cell survival.
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HMBOX1 interacts with MT2A to regulate autophagy and apoptosis in vascular endothelial cells. Sci Rep 2015; 5:15121. [PMID: 26456220 PMCID: PMC4600982 DOI: 10.1038/srep15121] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/16/2015] [Indexed: 12/03/2022] Open
Abstract
We previously found that Homeobox containing 1 (HMBOX1) was required for bone mesenchymal stem cell (BMSC) and mouse embryonic stem cell (ESC) differentiation into vascular endothelial cells (VECs). However, the function of HMBOX1 in VECs is still unknown. In this study, we found that HMBOX1 was abundantly expressed in the cytoplasm of human umbilical vascular endothelial cells (HUVECs). Knockdown of HMBOX1 induced apoptosis and inhibited autophagy. Overexpression of HMBOX1 inhibited apoptosis induced by fibroblast growth factor 2 deprivation and promoted autophagy. Metallothionein 2A (MT2A) was identified as an interaction protein with HMBOX1 by yeast two-hybrid assay, and confirmed by co-immunoprecipitation. Overexpression of HMBOX1 elevated intracellular free zinc level. Knockdown of MT2A inhibited this phenomenon. Moreover, N,N,N = ,N = -tetrakis (2-pyridylmethyl) ethylenediamine (TPEN), a zinc chelator, reversed the anti-apoptosis and pro-autophagy effects of HMBOX1. In conclusion, HMBOX1 regulated intracellular free zinc level by interacting with MT2A to inhibit apoptosis and promote autophagy in VECs.
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Grosbellet E, Zahn S, Arrivé M, Dumont S, Gourmelen S, Pévet P, Challet E, Criscuolo F. Circadian desynchronization triggers premature cellular aging in a diurnal rodent. FASEB J 2015; 29:4794-803. [PMID: 26260033 DOI: 10.1096/fj.14-266817] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/27/2015] [Indexed: 12/16/2022]
Abstract
Chronic jet lag or shift work is deleterious to human metabolic health, in that such circadian desynchronization is associated with being overweight and the prevalence of altered glucose metabolism. Similar metabolic changes are observed with age, suggesting that chronic jet lag and accelerated cell aging are intimately related, but the association remains to be determined. We addressed whether jet lag induces metabolic and cell aging impairments in young grass rats (2-3 mo old), using control old grass rats (12-18 mo old) as an aging reference. Desynchronized young and control old subjects had impaired glucose tolerance (+60 and +280%) when compared with control young animals. Despite no significant variation in liver DNA damage, shorter telomeres were characterized, not only in old animal liver cells (-18%), but also at an intermediate level in desynchronized young rats (-9%). The same pattern was found for deacetylase sirtuin (SIRT)-1 (-57 and -29%), confirming that jet-lagged young rats have an intermediate aging profile. Our data indicate that an experimental circadian desynchronization in young animals is associated with a precocious aging profile based on 3 well-known markers, as well as a prediabetic phenotype. Such chronic jet lag-induced alterations observed in a diurnal species constitute proof of principle of the need to develop preventive treatments in jet-lagged persons and shift workers.
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Affiliation(s)
- Edith Grosbellet
- *Institute of Cellular and Integrative Neurosciences, Unité Propres de Recherche 3212, and Department of Ecology, Physiology, and Ethology, Hubert Curien Pluridisciplinary Institute, Unité Mixte de Recherche 7178, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
| | - Sandrine Zahn
- *Institute of Cellular and Integrative Neurosciences, Unité Propres de Recherche 3212, and Department of Ecology, Physiology, and Ethology, Hubert Curien Pluridisciplinary Institute, Unité Mixte de Recherche 7178, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
| | - Mathilde Arrivé
- *Institute of Cellular and Integrative Neurosciences, Unité Propres de Recherche 3212, and Department of Ecology, Physiology, and Ethology, Hubert Curien Pluridisciplinary Institute, Unité Mixte de Recherche 7178, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
| | - Stéphanie Dumont
- *Institute of Cellular and Integrative Neurosciences, Unité Propres de Recherche 3212, and Department of Ecology, Physiology, and Ethology, Hubert Curien Pluridisciplinary Institute, Unité Mixte de Recherche 7178, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
| | - Sylviane Gourmelen
- *Institute of Cellular and Integrative Neurosciences, Unité Propres de Recherche 3212, and Department of Ecology, Physiology, and Ethology, Hubert Curien Pluridisciplinary Institute, Unité Mixte de Recherche 7178, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
| | - Paul Pévet
- *Institute of Cellular and Integrative Neurosciences, Unité Propres de Recherche 3212, and Department of Ecology, Physiology, and Ethology, Hubert Curien Pluridisciplinary Institute, Unité Mixte de Recherche 7178, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
| | - Etienne Challet
- *Institute of Cellular and Integrative Neurosciences, Unité Propres de Recherche 3212, and Department of Ecology, Physiology, and Ethology, Hubert Curien Pluridisciplinary Institute, Unité Mixte de Recherche 7178, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
| | - François Criscuolo
- *Institute of Cellular and Integrative Neurosciences, Unité Propres de Recherche 3212, and Department of Ecology, Physiology, and Ethology, Hubert Curien Pluridisciplinary Institute, Unité Mixte de Recherche 7178, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
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Tacconi EMC, Tarsounas M. How homologous recombination maintains telomere integrity. Chromosoma 2015; 124:119-30. [PMID: 25430998 DOI: 10.1007/s00412-014-0497-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 01/13/2023]
Abstract
Telomeres protect the ends of linear chromosomes against loss of genetic information and inappropriate processing as damaged DNA and are therefore crucial to the maintenance of chromosome integrity. In addition to providing a pathway for genome-wide DNA repair, homologous recombination (HR) plays a key role in telomere replication and capping. Consistent with this, the genomic instability characteristic of HR-deficient cells and tumours is driven in part by telomere dysfunction. Here, we discuss the mechanisms by which HR modulates the response to intrinsic cellular challenges that arise during telomere replication, as well as its impact on the assembly of telomere protective structures. How normal and tumour cells differ in their ability to maintain telomeres is deeply relevant to the search for treatments that would selectively eliminate cells whose capacity for HR-mediated repair has been compromised.
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Affiliation(s)
- Eliana M C Tacconi
- Telomere and Genome Stability Group, The CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
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Nuclear-receptor-mediated telomere insertion leads to genome instability in ALT cancers. Cell 2015; 160:913-927. [PMID: 25723166 DOI: 10.1016/j.cell.2015.01.044] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 11/18/2014] [Accepted: 01/27/2015] [Indexed: 01/26/2023]
Abstract
The breakage-fusion-bridge cycle is a classical mechanism of telomere-driven genome instability in which dysfunctional telomeres are fused to other chromosomal extremities, creating dicentric chromosomes that eventually break at mitosis. Here, we uncover a distinct pathway of telomere-driven genome instability, specifically occurring in cells that maintain telomeres with the alternative lengthening of telomeres mechanism. We show that, in these cells, telomeric DNA is added to multiple discrete sites throughout the genome, corresponding to regions regulated by NR2C/F transcription factors. These proteins drive local telomere DNA addition by recruiting telomeric chromatin. This mechanism, which we name targeted telomere insertion (TTI), generates potential common fragile sites that destabilize the genome. We propose that TTI driven by NR2C/F proteins contributes to the formation of complex karyotypes in ALT tumors.
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Luo Z, Dai Z, Xie X, Feng X, Liu D, Songyang Z, Xiong Y. TeloPIN: a database of telomeric proteins interaction network in mammalian cells. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav018. [PMID: 25792605 PMCID: PMC4365144 DOI: 10.1093/database/bav018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Interaction network surrounding telomeres has been intensively studied during the past two decades. However, no specific resource by integrating telomere interaction information data is currently available. To facilitate the understanding of the molecular interaction network by which telomeres are associated with biological process and diseases, we have developed TeloPIN (Telomeric Proteins Interaction Network) database (http://songyanglab.sysu.edu.cn/telopin/), a novel database that points to provide comprehensive information on protein–protein, protein–DNA and protein–RNA interaction of telomeres. TeloPIN database contains four types of interaction data, including (i) protein–protein interaction (PPI) data, (ii) telomeric proteins ChIP-seq data, (iii) telomere-associated proteins data and (iv) telomeric repeat-containing RNAs (TERRA)-interacting proteins data. By analyzing these four types of interaction data, we found that 358 and 199 proteins have more than one type of interaction information in human and mouse cells, respectively. We also developed table browser and TeloChIP genome browser to help researchers with better integrated visualization of interaction data from different studies. The current release of TeloPIN database includes 1111 PPI, eight telomeric protein ChIP-seq data sets, 1391 telomere-associated proteins and 183 TERRA-interacting proteins from 92 independent studies in mammalian cells. The interaction information provided by TeloPIN database will greatly expand our knowledge of telomeric proteins interaction network. Database URL: TeloPIN database address is http://songyanglab.sysu.edu.cn/telopin. TeloPIN database is freely available to non-commercial use.
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Affiliation(s)
- Zhenhua Luo
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China
| | - Zhiming Dai
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China
| | - Xiaowei Xie
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China
| | - Xuyang Feng
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China
| | - Dan Liu
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China, Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China; SYSU-CMU Shunde International Joint Research Institute (JRI) Shunde, Guangdong, China; Cell-Based Assay Screening Core, Dan L. Duncan Cancer Center, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, and Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China
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50
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Robles-Espinoza CD, Velasco-Herrera MDC, Hayward NK, Adams DJ. Telomere-regulating genes and the telomere interactome in familial cancers. Mol Cancer Res 2015; 13:211-22. [PMID: 25244922 PMCID: PMC4278843 DOI: 10.1158/1541-7786.mcr-14-0305] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Telomeres are repetitive sequence structures at the ends of linear chromosomes that consist of double-stranded DNA repeats followed by a short single-stranded DNA protrusion. Telomeres need to be replicated in each cell cycle and protected from DNA-processing enzymes, tasks that cells execute using specialized protein complexes such as telomerase (that includes TERT), which aids in telomere maintenance and replication, and the shelterin complex, which protects chromosome ends. These complexes are also able to interact with a variety of other proteins, referred to as the telomere interactome, to fulfill their biological functions and control signaling cascades originating from telomeres. Given their essential role in genomic maintenance and cell-cycle control, germline mutations in telomere-regulating proteins and their interacting partners have been found to underlie a variety of diseases and cancer-predisposition syndromes. These syndromes can be characterized by progressively shortening telomeres, in which carriers can present with organ failure due to stem cell senescence among other characteristics, or can also present with long or unprotected telomeres, providing an alternative route for cancer formation. This review summarizes the critical roles that telomere-regulating proteins play in cell-cycle control and cell fate and explores the current knowledge on different cancer-predisposing conditions that have been linked to germline defects in these proteins and their interacting partners.
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Affiliation(s)
| | | | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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