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Usmani MA, Ghaffar A, Shahzad M, Akram J, Majeed AI, Malik K, Fatima K, Khan AA, Ahmed ZM, Riazuddin S, Riazuddin S. A Missense Variant in HACE1 Is Associated with Intellectual Disability, Epilepsy, Spasticity, and Psychomotor Impairment in a Pakistani Kindred. Genes (Basel) 2024; 15:580. [PMID: 38790209 PMCID: PMC11121239 DOI: 10.3390/genes15050580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Intellectual disability (ID), which affects around 2% to 3% of the population, accounts for 0.63% of the overall prevalence of neurodevelopmental disorders (NDD). ID is characterized by limitations in a person's intellectual and adaptive functioning, and is caused by pathogenic variants in more than 1000 genes. Here, we report a rare missense variant (c.350T>C; p.(Leu117Ser)) in HACE1 segregating with NDD syndrome with clinical features including ID, epilepsy, spasticity, global developmental delay, and psychomotor impairment in two siblings of a consanguineous Pakistani kindred. HACE1 encodes a HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 (HACE1), which is involved in protein ubiquitination, localization, and cell division. HACE1 is also predicted to interact with several proteins that have been previously implicated in the ID phenotype in humans. The p.(Leu117Ser) variant replaces an evolutionarily conserved residue of HACE1 and is predicted to be deleterious by various in silico algorithms. Previously, eleven protein truncating variants of HACE1 have been reported in individuals with NDD. However, to our knowledge, p.(Leu117Ser) is the second missense variant in HACE1 found in an individual with NDD.
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Affiliation(s)
- Muhammad A. Usmani
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, University of Health Sciences, Lahore 54550, Pakistan
| | - Amama Ghaffar
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Mohsin Shahzad
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
| | - Javed Akram
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
| | - Aisha I. Majeed
- Department of Radiology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan;
| | - Kausar Malik
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Khushbakht Fatima
- Department of Applied Health Sciences, University of Management and Technology, Lahore 54500, Pakistan;
| | - Asma A. Khan
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Department of Molecular Biology and Biochemistry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Sheikh Riazuddin
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan; (M.S.); (J.A.); (S.R.)
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, University of Health Sciences, Lahore 54550, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (M.A.U.); (A.G.)
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
- Department of Molecular Biology and Biochemistry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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Chen S, Huang M, Xu D, Li M. Epigenetic regulation in epilepsy: A novel mechanism and therapeutic strategy for epilepsy. Neurochem Int 2024; 173:105657. [PMID: 38145842 DOI: 10.1016/j.neuint.2023.105657] [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: 08/23/2023] [Revised: 12/02/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023]
Abstract
Epilepsy is a common neurological disorder characterized by recurrent seizures with excessive and abnormal neuronal discharges. Epileptogenesis is usually involved in neuropathological processes such as ion channel dysfunction, neuronal injury, inflammatory response, synaptic plasticity, gliocyte proliferation and mossy fiber sprouting, currently the pathogenesis of epilepsy is not yet completely understood. A growing body of studies have shown that epigenetic regulation, such as histone modifications, DNA methylation, noncoding RNAs (ncRNAs), N6-methyladenosine (m6A) and restrictive element-1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) are also involved in epilepsy. Through epigenetic studies, we found that the synaptic dysfunction, nerve damage, cognitive dysfunction and brain development abnormalities are affected by epigenetic regulation of epilepsy-related genes in patients with epilepsy. However, the functional roles of epigenetics in pathogenesis and treatment of epilepsy are still to be explored. Therefore, profiling the array of genes that are epigenetically dysregulated in epileptogenesis is likely to advance our understanding of the mechanisms underlying the pathophysiology of epilepsy and may for the amelioration of these serious human conditions provide novel insight into therapeutic strategies and diagnostic biomarkers for epilepsy to improve serious human condition.
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Affiliation(s)
- Shuang Chen
- Department of Neurology, Hubei Provincial Hospital of Integrated Chinese and Western Medicine, Hubei University of Chinese Medicine, Wuhan, 430000, China
| | - Ming Huang
- Department of Neurology, Hubei Provincial Hospital of Integrated Chinese and Western Medicine, Hubei University of Chinese Medicine, Wuhan, 430000, China
| | - Da Xu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Man Li
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
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Barresi M, Hickmott RA, Bosakhar A, Quezada S, Quigley A, Kawasaki H, Walker D, Tolcos M. Toward a better understanding of how a gyrified brain develops. Cereb Cortex 2024; 34:bhae055. [PMID: 38425213 DOI: 10.1093/cercor/bhae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 03/02/2024] Open
Abstract
The size and shape of the cerebral cortex have changed dramatically across evolution. For some species, the cortex remains smooth (lissencephalic) throughout their lifetime, while for other species, including humans and other primates, the cortex increases substantially in size and becomes folded (gyrencephalic). A folded cortex boasts substantially increased surface area, cortical thickness, and neuronal density, and it is therefore associated with higher-order cognitive abilities. The mechanisms that drive gyrification in some species, while others remain lissencephalic despite many shared neurodevelopmental features, have been a topic of investigation for many decades, giving rise to multiple perspectives of how the gyrified cerebral cortex acquires its unique shape. Recently, a structurally unique germinal layer, known as the outer subventricular zone, and the specialized cell type that populates it, called basal radial glial cells, were identified, and these have been shown to be indispensable for cortical expansion and folding. Transcriptional analyses and gene manipulation models have provided an invaluable insight into many of the key cellular and genetic drivers of gyrification. However, the degree to which certain biomechanical, genetic, and cellular processes drive gyrification remains under investigation. This review considers the key aspects of cerebral expansion and folding that have been identified to date and how theories of gyrification have evolved to incorporate this new knowledge.
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Affiliation(s)
- Mikaela Barresi
- School of Health and Biomedical Sciences, RMIT University, Plenty Road, Bundoora, VIC 3083, Australia
- ACMD, St Vincent's Hospital Melbourne, Regent Street, Fitzroy, VIC 3065, Australia
| | - Ryan Alexander Hickmott
- School of Health and Biomedical Sciences, RMIT University, Plenty Road, Bundoora, VIC 3083, Australia
- ACMD, St Vincent's Hospital Melbourne, Regent Street, Fitzroy, VIC 3065, Australia
| | - Abdulhameed Bosakhar
- School of Health and Biomedical Sciences, RMIT University, Plenty Road, Bundoora, VIC 3083, Australia
| | - Sebastian Quezada
- School of Health and Biomedical Sciences, RMIT University, Plenty Road, Bundoora, VIC 3083, Australia
| | - Anita Quigley
- School of Health and Biomedical Sciences, RMIT University, Plenty Road, Bundoora, VIC 3083, Australia
- ACMD, St Vincent's Hospital Melbourne, Regent Street, Fitzroy, VIC 3065, Australia
- School of Engineering, RMIT University, La Trobe Street, Melbourne, VIC 3000, Australia
- Department of Medicine, University of Melbourne, St Vincent's Hospital, Regent Street, Fitzroy, VIC 3065, Australia
| | - Hiroshi Kawasaki
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Takara-machi 13-1, Kanazawa, Ishikawa 920-8640, Japan
| | - David Walker
- School of Health and Biomedical Sciences, RMIT University, Plenty Road, Bundoora, VIC 3083, Australia
| | - Mary Tolcos
- School of Health and Biomedical Sciences, RMIT University, Plenty Road, Bundoora, VIC 3083, Australia
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Banos A, Thomas K, Garantziotis P, Filia A, Malissovas N, Pieta A, Nikolakis D, Panagiotopoulos AG, Chalkia A, Petras D, Bertsias G, Boumpas DT, Vassilopoulos D. The genomic landscape of ANCA-associated vasculitis: Distinct transcriptional signatures, molecular endotypes and comparison with systemic lupus erythematosus. Front Immunol 2023; 14:1072598. [PMID: 37051253 PMCID: PMC10083368 DOI: 10.3389/fimmu.2023.1072598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
IntroductionAnti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAVs) present with a complex phenotype and are associated with high mortality and multi-organ involvement. We sought to define the transcriptional landscape and molecular endotypes of AAVs and compare it to systemic lupus erythematosus (SLE).MethodsWe performed whole blood mRNA sequencing from 30 patients with AAV (granulomatosis with polyangiitis/GPA and microscopic polyangiitis/MPA) combined with functional enrichment and network analysis for aberrant pathways. Key genes and pathways were validated in an independent cohort of 18 AAV patients. Co-expression network and hierarchical clustering analysis, identified molecular endotypes. Multi-level transcriptional overlap analysis to SLE was based on our published data from 142 patients.ResultsWe report here that “Pan-vasculitis” signature contained 1,982 differentially expressed genes, enriched in leukocyte differentiation, cytokine signaling, type I and type II IFN signaling and aberrant B-T cell immunity. Active disease was characterized by signatures linked to cell cycle checkpoints and metabolism pathways, whereas ANCA-positive patients exhibited a humoral immunity transcriptional fingerprint. Differential expression analysis of GPA and MPA yielded an IFN-g pathway (in addition to a type I IFN) in the former and aberrant expression of genes related to autophagy and mRNA splicing in the latter. Unsupervised molecular taxonomy analysis revealed four endotypes with neutrophil degranulation, aberrant metabolism and B-cell responses as potential mechanistic drivers. Transcriptional perturbations and molecular heterogeneity were more pronounced in SLE. Molecular analysis and data-driven clustering of AAV uncovered distinct transcriptional pathways that could be exploited for targeted therapy.DiscussionWe conclude that transcriptomic analysis of AAV reveals distinct endotypes and molecular pathways that could be targeted for therapy. The AAV transcriptome is more homogenous and less fragmented compared to the SLE which may account for its superior rates of response to therapy.
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Affiliation(s)
- Aggelos Banos
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Konstantinos Thomas
- Clinical Immunology- Rheumatology Unit, 2nd Department of Medicine and Laboratory, General Hospital of Athens Ippokrateio, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Garantziotis
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Department Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Anastasia Filia
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Nikolaos Malissovas
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Antigone Pieta
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Rheumatology and Clinical Immunology Unit, 4th Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | - Dimitrios Nikolakis
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Amsterdam Institute for Gastroenterology Endocrinology and Metabolism, Department of Gastroenterology, Academic Medical Center, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology & Immunology Center (ARC), Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection & Immunity, Department of Experimental Immunology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Alexandros G. Panagiotopoulos
- Clinical Immunology- Rheumatology Unit, 2nd Department of Medicine and Laboratory, General Hospital of Athens Ippokrateio, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Aglaia Chalkia
- Nephrology Department, General Hospital of Athens Ippokrateio, Athens, Greece
| | - Dimitrios Petras
- Nephrology Department, General Hospital of Athens Ippokrateio, Athens, Greece
| | - George Bertsias
- Department of Rheumatology and Clinical Immunology, University Hospital of Heraklion, Medical School, University of Crete, Heraklion, Greece
- Department of Immunity, Institute of Molecular Biology and Biotechnology-Foundation of Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Dimitrios T. Boumpas
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Rheumatology and Clinical Immunology Unit, 4th Department of Internal Medicine, Attikon University Hospital, Athens, Greece
- Joint Academic Rheumatology Program, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Vassilopoulos
- Clinical Immunology- Rheumatology Unit, 2nd Department of Medicine and Laboratory, General Hospital of Athens Ippokrateio, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Joint Academic Rheumatology Program, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- *Correspondence: Dimitrios Vassilopoulos,
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Leclerc K, Remark LH, Ramsukh M, Josephson AM, Palma L, Parente PEL, Sambon M, Lee S, Lopez EM, Morgani SM, Leucht P. Hox genes are crucial regulators of periosteal stem cell identity. Development 2023; 150:dev201391. [PMID: 36912250 PMCID: PMC10112919 DOI: 10.1242/dev.201391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/20/2023] [Indexed: 03/14/2023]
Abstract
Periosteal stem and progenitor cells (PSPCs) are major contributors to bone maintenance and repair. Deciphering the molecular mechanisms that regulate their function is crucial for the successful generation and application of future therapeutics. Here, we pinpoint Hox transcription factors as necessary and sufficient for periosteal stem cell function. Hox genes are transcriptionally enriched in periosteal stem cells and their overexpression in more committed progenitors drives reprogramming to a naïve, self-renewing stem cell-like state. Crucially, individual Hox family members are expressed in a location-specific manner and their stem cell-promoting activity is only observed when the Hox gene is matched to the anatomical origin of the PSPC, demonstrating a role for the embryonic Hox code in adult stem cells. Finally, we demonstrate that Hoxa10 overexpression partially restores the age-related decline in fracture repair. Together, our data highlight the importance of Hox genes as key regulators of PSPC identity in skeletal homeostasis and repair.
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Affiliation(s)
- Kevin Leclerc
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Lindsey H. Remark
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Malissa Ramsukh
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Anne Marie Josephson
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Laura Palma
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Paulo E. L. Parente
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Margaux Sambon
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Sooyeon Lee
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Institute of Comparative Molecular Endocrinology, Ulm University, Ulm 89081, Germany
| | - Emma Muiños Lopez
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Cell Therapy Area, Clínica Universidad de Navarra, Pamplona 31008, Spain
| | - Sophie M. Morgani
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
| | - Philipp Leucht
- Department of Orthopedic Surgery, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, NYU Robert I. Grossman School of Medicine, New York, NY 10016, USA
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Ruthig VA, Hatkevich T, Hardy J, Friedersdorf MB, Mayère C, Nef S, Keene JD, Capel B. The RNA binding protein DND1 is elevated in a subpopulation of pro-spermatogonia and targets chromatin modifiers and translational machinery during late gestation. PLoS Genet 2023; 19:e1010656. [PMID: 36857387 PMCID: PMC10010562 DOI: 10.1371/journal.pgen.1010656] [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: 07/01/2022] [Revised: 03/13/2023] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
DND1 is essential to maintain germ cell identity. Loss of Dnd1 function results in germ cell differentiation to teratomas in some inbred strains of mice or to somatic fates in zebrafish. Using our knock-in mouse line in which a functional fusion protein between DND1 and GFP is expressed from the endogenous locus (Dnd1GFP), we distinguished two male germ cell (MGC) populations during late gestation cell cycle arrest (G0), consistent with recent reports of heterogeneity among MGCs. Most MGCs express lower levels of DND1-GFP (DND1-GFP-lo), but some MGCs express elevated levels of DND1-GFP (DND1-GFP-hi). A RNA-seq time course confirmed high Dnd1 transcript levels in DND1-GFP-hi cells along with 5-10-fold higher levels for multiple epigenetic regulators. Using antibodies against DND1-GFP for RNA immunoprecipitation (RIP)-sequencing, we identified multiple epigenetic and translational regulators that are binding targets of DND1 during G0 including DNA methyltransferases (Dnmts), histone deacetylases (Hdacs), Tudor domain proteins (Tdrds), actin dependent regulators (Smarcs), and a group of ribosomal and Golgi proteins. These data suggest that in DND1-GFP-hi cells, DND1 hosts coordinating mRNA regulons that consist of functionally related and localized groups of epigenetic enzymes and translational components.
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Affiliation(s)
- Victor A. Ruthig
- Sexual Medicine Lab, Department of Urology, Weill Cornell Medicine, New York, New York, United States of America
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Talia Hatkevich
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Josiah Hardy
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthew B. Friedersdorf
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Chloé Mayère
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | - Jack D. Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
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Tominaga K, Sakashita E, Kasashima K, Kuroiwa K, Nagao Y, Iwamori N, Endo H. Tip60/KAT5 Histone Acetyltransferase Is Required for Maintenance and Neurogenesis of Embryonic Neural Stem Cells. Int J Mol Sci 2023; 24:ijms24032113. [PMID: 36768434 PMCID: PMC9916716 DOI: 10.3390/ijms24032113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Epigenetic regulation via epigenetic factors in collaboration with tissue-specific transcription factors is curtail for establishing functional organ systems during development. Brain development is tightly regulated by epigenetic factors, which are coordinately activated or inactivated during processes, and their dysregulation is linked to brain abnormalities and intellectual disability. However, the precise mechanism of epigenetic regulation in brain development and neurogenesis remains largely unknown. Here, we show that Tip60/KAT5 deletion in neural stem/progenitor cells (NSCs) in mice results in multiple abnormalities of brain development. Tip60-deficient embryonic brain led to microcephaly, and proliferating cells in the developing brain were reduced by Tip60 deficiency. In addition, neural differentiation and neuronal migration were severely affected in Tip60-deficient brains. Following neurogenesis in developing brains, gliogenesis started from the earlier stage of development in Tip60-deficient brains, indicating that Tip60 is involved in switching from neurogenesis to gliogenesis during brain development. It was also confirmed in vitro that poor neurosphere formation, proliferation defects, neural differentiation defects, and accelerated astrocytic differentiation in mutant NSCs are derived from Tip60-deficient embryonic brains. This study uncovers the critical role of Tip60 in brain development and NSC maintenance and function in vivo and in vitro.
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Affiliation(s)
- Kaoru Tominaga
- Division of Structural Biochemistry, Department of Biochemistry, Jichi Medical University, Tochigi 321-0498, Japan
- Division of Functional Biochemistry, Department of Biochemistry, Jichi Medical University, Tochigi 321-0498, Japan
- Correspondence: (K.T.); (N.I.)
| | - Eiji Sakashita
- Division of Functional Biochemistry, Department of Biochemistry, Jichi Medical University, Tochigi 321-0498, Japan
| | - Katsumi Kasashima
- Division of Functional Biochemistry, Department of Biochemistry, Jichi Medical University, Tochigi 321-0498, Japan
| | - Kenji Kuroiwa
- Division of Functional Biochemistry, Department of Biochemistry, Jichi Medical University, Tochigi 321-0498, Japan
| | - Yasumitsu Nagao
- Center for Experimental Medicine, Jichi Medical University, Tochigi 321-0498, Japan
| | - Naoki Iwamori
- Department of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence: (K.T.); (N.I.)
| | - Hitoshi Endo
- Division of Functional Biochemistry, Department of Biochemistry, Jichi Medical University, Tochigi 321-0498, Japan
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Jiang D, Li T, Guo C, Tang TS, Liu H. Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration. Cell Biosci 2023; 13:10. [PMID: 36647159 PMCID: PMC9841685 DOI: 10.1186/s13578-023-00953-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes. Recent studies have shown that chromatin remodeling is essential in different stages of postnatal and adult neurogenesis. Chromatin deregulation, which leads to defects in epigenetic gene regulation and further pathological gene expression programs, often causes a wide range of pathologies. This review first gives an overview of the regulatory mechanisms of chromatin remodeling. We then focus mainly on discussing the physiological functions of chromatin remodeling, particularly histone and DNA modifications and the four classes of ATP-dependent chromatin-remodeling enzymes, in the central and peripheral nervous systems under healthy and pathological conditions, that is, in neurodegenerative disorders. Finally, we provide an update on the development of potent and selective small molecule modulators targeting various chromatin-modifying proteins commonly associated with neurodegenerative diseases and their potential clinical applications.
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Affiliation(s)
- Dongfang Jiang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingting Li
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Caixia Guo
- grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tie-Shan Tang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Liu
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
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9
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Yin BK, Lázaro D, Wang ZQ. TRRAP-mediated acetylation on Sp1 regulates adult neurogenesis. Comput Struct Biotechnol J 2022; 21:472-484. [PMID: 36618986 PMCID: PMC9804013 DOI: 10.1016/j.csbj.2022.12.024] [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: 10/25/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The adult hippocampal neurogenesis plays a vital role in the function of the central nervous system (CNS), including memory consolidation, cognitive flexibility, emotional function, and social behavior. The deficiency of adult neural stem cells (aNSCs) in maintaining the quiescence and entering cell cycle, self-renewal and differentiation capacity is detrimental to the functional integrity of neurons and cognition of the adult brain. Histone acetyltransferase (HAT) and histone deacetylase (HDAC) have been shown to modulate brain functionality and are important for embryonic neurogenesis via regulation of gene transcription. We showed previously that Trrap, an adapter for several HAT complexes, is required for Sp1 transcriptional control of the microtubule dynamics in neuronal cells. Here, we find that Trrap deletion compromises self-renewal and differentiation of aNSCs in mice and in cultures. We find that the acetylation status of lysine residues K16, K19, K703 and K639 all fail to overcome Trrap-deficiency-incurred instability of Sp1, indicating a scaffold role of Trrap. Interestingly, the deacetylation of Sp1 at K639 and K703 greatly increases Sp1 binding to the promoter of target genes, which antagonizes Trrap binding, and thereby elevates Sp1 activity. However, only deacetylated K639 is refractory to Trrap deficiency and corrects the differentiation defects of Trrap-deleted aNSCs. We demonstrate that the acetylation pattern at K639 by HATs dictates the role of Sp1 in the regulation of adult neurogenesis.
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Affiliation(s)
- Bo-Kun Yin
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - David Lázaro
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany,Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, Bachstrasse 18k, 07743 Jena, Germany,Corresponding author at: Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany,.
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10
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Zhang D, Hugo W, Bergsneider M, Wang MB, Kim W, Vinters HV, Heaney AP. Single-cell RNA sequencing in silent corticotroph tumors confirms impaired POMC processing and provides new insights into their invasive behavior. Eur J Endocrinol 2022; 187:49-64. [PMID: 35521707 PMCID: PMC9248914 DOI: 10.1530/eje-21-1183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/21/2022] [Indexed: 11/08/2022]
Abstract
Objective Provide insights into the defective POMC processing and invasive behavior in silent pituitary corticotroph tumors. Design and methods Single-cell RNAseq was used to compare the cellular makeup and transcriptome of silent and active corticotroph tumors. Results A series of transcripts related to hormone processing peptidases and genes involved in the structural organization of secretory vesicles were reduced in silent compared to active corticotroph tumors. Most relevant to their invasive behavior, silent corticotroph tumors exhibited several features of epithelial-to-mesenchymal transition, with increased expression of mesenchymal genes along with the loss of transcripts that regulate hormonal biogenesis and secretion. Silent corticotroph tumor vascular smooth muscle cell and pericyte stromal cell populations also exhibited plasticity in their mesenchymal features. Conclusions Our findings provide novel insights into the mechanisms of impaired POMC processing and invasion in silent corticotroph tumors and suggest that a common transcriptional reprogramming mechanism simultaneously impairs POMC processing and activates tumor invasion.
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Affiliation(s)
- Dongyun Zhang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Willy Hugo
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Marvin Bergsneider
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles
| | - Marilene B. Wang
- Department of Head and Neck Surgery, David Geffen School of Medicine, University of California, Los Angeles
| | - Won Kim
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles
| | - Harry V. Vinters
- Department of Pathology and Lab Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Anthony P. Heaney
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles
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11
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Detilleux D, Raynaud P, Pradet-Balade B, Helmlinger D. The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells. eLife 2022; 11:69705. [PMID: 35244540 PMCID: PMC8926402 DOI: 10.7554/elife.69705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/03/2022] [Indexed: 11/30/2022] Open
Abstract
Transcription is essential for cells to respond to signaling cues and involves factors with multiple distinct activities. One such factor, TRRAP, functions as part of two large complexes, SAGA and TIP60, which have crucial roles during transcription activation. Structurally, TRRAP belongs to the phosphoinositide 3 kinase-related kinases (PIKK) family but is the only member classified as a pseudokinase. Recent studies established that a dedicated HSP90 co-chaperone, the triple T (TTT) complex, is essential for PIKK stabilization and activity. Here, using endogenous auxin-inducible degron alleles, we show that the TTT subunit TELO2 promotes TRRAP assembly into SAGA and TIP60 in human colorectal cancer cells (CRCs). Transcriptomic analysis revealed that TELO2 contributes to TRRAP regulatory roles in CRC cells, most notably of MYC target genes. Surprisingly, TELO2 and TRRAP depletion also induced the expression of type I interferon genes. Using a combination of nascent RNA, antibody-targeted chromatin profiling (CUT&RUN), ChIP, and kinetic analyses, we propose a model by which TRRAP directly represses the transcription of IRF9, which encodes a master regulator of interferon-stimulated genes. We have therefore uncovered an unexpected transcriptional repressor role for TRRAP, which we propose contributes to its tumorigenic activity.
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Affiliation(s)
| | - Peggy Raynaud
- CRBM, University of Montpellier, CNRS, Montpellier, France
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12
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Suzuki T, Hirai Y, Uehara T, Ohga R, Kosaki K, Kawahara A. Involvement of the zebrafish trrap gene in craniofacial development. Sci Rep 2021; 11:24166. [PMID: 34934055 PMCID: PMC8692476 DOI: 10.1038/s41598-021-03123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Trrap (transformation/transcription domain-associated protein) is a component shared by several histone acetyltransferase (HAT) complexes and participates in transcriptional regulation and DNA repair; however, the developmental functions of Trrap in vertebrates are not fully understood. Recently, it has been reported that human patients with genetic mutations in the TRRAP gene show various symptoms, including facial dysmorphisms, microcephaly and global developmental delay. To investigate the physiological functions of Trrap, we established trrap gene-knockout zebrafish and examined loss-of-function phenotypes in the mutants. The trrap zebrafish mutants exhibited smaller eyes and heads than the wild-type zebrafish. The size of the ventral pharyngeal arches was reduced and the mineralization of teeth was impaired in the trrap mutants. Whole-mount in situ hybridization analysis revealed that dlx3 expression was narrowly restricted in the developing ventral pharyngeal arches, while dlx2b expression was diminished in the trrap mutants. These results suggest that trrap zebrafish mutants are useful model organisms for a human disorder associated with genetic mutations in the human TRRAP gene.
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Affiliation(s)
- Taichi Suzuki
- Laboratory for Developmental Biology, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Yo Hirai
- Laboratory for Developmental Biology, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.,Department of Clinical Genetics, Central Hospital, Adachi Developmental Disability Center, Aichi, Japan
| | - Rie Ohga
- Laboratory for Developmental Biology, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
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13
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Yin BK, Wang ZQ. Beyond HAT Adaptor: TRRAP Liaisons with Sp1-Mediated Transcription. Int J Mol Sci 2021; 22:12445. [PMID: 34830324 PMCID: PMC8625110 DOI: 10.3390/ijms222212445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 12/19/2022] Open
Abstract
The members of the phosphatidylinositol 3-kinase-related kinase (PIKK) family play vital roles in multiple biological processes, including DNA damage response, metabolism, cell growth, mRNA decay, and transcription. TRRAP, as the only member lacking the enzymatic activity in this family, is an adaptor protein for several histone acetyltransferase (HAT) complexes and a scaffold protein for multiple transcription factors. TRRAP has been demonstrated to regulate various cellular functions in cell cycle progression, cell stemness maintenance and differentiation, as well as neural homeostasis. TRRAP is known to be an important orchestrator of many molecular machineries in gene transcription by modulating the activity of some key transcription factors, including E2F1, c-Myc, p53, and recently, Sp1. This review summarizes the biological and biochemical studies on the action mode of TRRAP together with the transcription factors, focusing on how TRRAP-HAT mediates the transactivation of Sp1-governing biological processes, including neurodegeneration.
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Affiliation(s)
- Bo-Kun Yin
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany;
| | - Zhao-Qi Wang
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany;
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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14
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Gupta R, Jha A, Ambasta RK, Kumar P. Regulatory mechanism of cyclins and cyclin-dependent kinases in post-mitotic neuronal cell division. Life Sci 2021; 285:120006. [PMID: 34606852 DOI: 10.1016/j.lfs.2021.120006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases (NDDs) are the most common life-threatening disease of the central nervous system and it cause the progressive loss of neuronal cells. The exact mechanism of the disease's progression is not clear and thus line of treatment for NDDs is a baffling issue. During the progression of NDDs, oxidative stress and DNA damage play an important regulatory function, and ultimately induces neurodegeneration. Recently, aberrant cell cycle events have been demonstrated in the progression of different NDDs. However, the pertinent role of signaling mechanism, for instance, post-translational modifications, oxidative stress, DNA damage response pathway, JNK/p38 MAPK, MEK/ERK cascade, actively participated in the aberrant cell cycle reentry induced neuronal cell death. Mounting evidence has demonstrated that aberrant cell cycle re-entry is a major contributing factor in the pathogenesis of NDDs rather than a secondary phenomenon. In the brain of AD patients with mild cognitive impairment, post miotic cell division can be seen in the early stage of the disease. However, in the brain of PD patients, response to various neurotoxic signals, the cell cycle re-entry has been observed that causes neuronal apoptosis. On contrary, the contributing factors that leads to the induction of cell cycle events in mature neurons in HD and ALS brain pathology is remain unclear. Various pharmacological drugs have been developed to reduce the pathogenesis of NDDs, but they are still not helpful in eliminating the cause of these NDDs.
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Affiliation(s)
- Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Ankita Jha
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India.
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15
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D'Souza L, Channakkar AS, Muralidharan B. Chromatin remodelling complexes in cerebral cortex development and neurodevelopmental disorders. Neurochem Int 2021; 147:105055. [PMID: 33964373 PMCID: PMC7611358 DOI: 10.1016/j.neuint.2021.105055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/11/2021] [Accepted: 04/24/2021] [Indexed: 12/19/2022]
Abstract
The diverse number of neurons in the cerebral cortex are generated during development by neural stem cells lining the ventricle, and they continue maturing postnatally. Dynamic chromatin regulation in these neural stem cells is a fundamental determinant of the emerging property of the functional neural network, and the chromatin remodellers are critical determinants of this process. Chromatin remodellers participate in several steps of this process from proliferation, differentiation, migration leading to complex network formation which forms the basis of higher-order functions of cognition and behaviour. Here we review the role of these ATP-dependent chromatin remodellers in cortical development in health and disease and highlight several key mouse mutants of the subunits of the complexes which have revealed how the remodelling mechanisms control the cortical stem cell chromatin landscape for expression of stage-specific transcripts. Consistent with their role in cortical development, several putative risk variants in the subunits of the remodelling complexes have been identified as the underlying causes of several neurodevelopmental disorders. A basic understanding of the detailed molecular mechanism of their action is key to understating how mutations in the same networks lead to disease pathologies and perhaps pave the way for therapeutic development for these complex multifactorial disorders.
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Affiliation(s)
- Leora D'Souza
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India
| | - Asha S Channakkar
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India
| | - Bhavana Muralidharan
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India.
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16
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Abbey D, Conlon D, Rainville C, Elwyn S, Quiroz-Figueroa K, Billheimer J, Schultz DC, Hand NJ, Cherry S, Rader DJ. Lipid droplet screen in human hepatocytes identifies TRRAP as a regulator of cellular triglyceride metabolism. Clin Transl Sci 2021; 14:1369-1379. [PMID: 34156146 PMCID: PMC8301584 DOI: 10.1111/cts.12988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Hepatocytes store triglycerides (TGs) in the form of lipid droplets (LDs), which are increased in hepatosteatosis. The regulation of hepatic LDs is poorly understood and new therapies to reduce hepatosteatosis are needed. We performed a siRNA kinase and phosphatase screen in HuH‐7 cells using high‐content automated imaging of LDs. Changes in accumulated lipids were quantified with developed pipeline that measures intensity, area, and number of LDs. Selected “hits,” which reduced lipid accumulation, were further validated with other lipid and expression assays. Among several siRNAs that resulted in significantly reduced LDs, one was targeted to the nuclear adapter protein, transformation/transcription domain‐associated protein (TRRAP). Knockdown of TRRAP reduced triglyceride accumulation in HuH‐7 hepatocytes, in part by reducing C/EBPα‐mediated de novo synthesis of TGs. These findings implicate TRRAP as a novel regulator of hepatic TG metabolism and nominate it as a potential drug target for hepatosteatosis.
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Affiliation(s)
- Deepti Abbey
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Donna Conlon
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher Rainville
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susannah Elwyn
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine Quiroz-Figueroa
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jeffrey Billheimer
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas J Hand
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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17
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Tapias A, Lázaro D, Yin BK, Rasa SMM, Krepelova A, Kelmer Sacramento E, Grigaravicius P, Koch P, Kirkpatrick J, Ori A, Neri F, Wang ZQ. HAT cofactor TRRAP modulates microtubule dynamics via SP1 signaling to prevent neurodegeneration. eLife 2021; 10:61531. [PMID: 33594975 PMCID: PMC7939550 DOI: 10.7554/elife.61531] [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: 07/28/2020] [Accepted: 02/16/2021] [Indexed: 01/22/2023] Open
Abstract
Brain homeostasis is regulated by the viability and functionality of neurons. HAT (histone acetyltransferase) and HDAC (histone deacetylase) inhibitors have been applied to treat neurological deficits in humans; yet, the epigenetic regulation in neurodegeneration remains elusive. Mutations of HAT cofactor TRRAP (transformation/transcription domain-associated protein) cause human neuropathies, including psychosis, intellectual disability, autism, and epilepsy, with unknown mechanism. Here we show that Trrap deletion in Purkinje neurons results in neurodegeneration of old mice. Integrated transcriptomics, epigenomics, and proteomics reveal that TRRAP via SP1 conducts a conserved transcriptomic program. TRRAP is required for SP1 binding at the promoter proximity of target genes, especially microtubule dynamics. The ectopic expression of Stathmin3/4 ameliorates defects of TRRAP-deficient neurons, indicating that the microtubule dynamics is particularly vulnerable to the action of SP1 activity. This study unravels a network linking three well-known, but up-to-date unconnected, signaling pathways, namely TRRAP, HAT, and SP1 with microtubule dynamics, in neuroprotection.
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Affiliation(s)
- Alicia Tapias
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - David Lázaro
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bo-Kun Yin
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Anna Krepelova
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | | | - Philipp Koch
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Joanna Kirkpatrick
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.,Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, Jena, Germany
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18
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Yoo DY, Jung HY, Kim W, Hahn KR, Kwon HJ, Nam SM, Chung JY, Yoon YS, Kim DW, Hwang IK. Entacapone Treatment Modulates Hippocampal Proteins Related to Synaptic Vehicle Trafficking. Cells 2020; 9:cells9122712. [PMID: 33352833 PMCID: PMC7765944 DOI: 10.3390/cells9122712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 11/29/2022] Open
Abstract
Entacapone, a reversible inhibitor of catechol-O-methyl transferase, is used for patients in Parkinson’s disease because it increases the bioavailability and effectiveness of levodopa. In the present study, we observed that entacapone increases novel object recognition and neuroblasts in the hippocampus. In the present study, two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry were performed to compare the abundance profiles of proteins expressed in the hippocampus after entacapone treatment in mice. Results of 2-DE, MALDI-TOF mass spectrometry, and subsequent proteomic analysis revealed an altered protein expression profile in the hippocampus after entacapone treatment. Based on proteomic analysis, 556 spots were paired during the image analysis of 2-DE gels and 76 proteins were significantly changed more than two-fold among identified proteins. Proteomic analysis indicated that treatment with entacapone induced expressional changes in proteins involved in synaptic transmission, cellular processes, cellular signaling, the regulation of cytoskeletal structure, energy metabolism, and various subcellular enzymatic reactions. In particular, entacapone significantly increased proteins related to synaptic trafficking and plasticity, such as dynamin 1, synapsin I, and Munc18-1. Immunohistochemical staining showed the localization of the proteins, and western blot confirmed the significant increases in dynamin I (203.5% of control) in the hippocampus as well as synapsin I (254.0% of control) and Munc18-1 (167.1% of control) in the synaptic vesicle fraction of hippocampus after entacapone treatment. These results suggest that entacapone can enhance hippocampal synaptic trafficking and plasticity against various neurological diseases related to hippocampal dysfunction.
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Affiliation(s)
- Dae Young Yoo
- Department of Anatomy and Cell Biology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (D.Y.Y.); (H.Y.J.); (W.K.); (K.R.H.); (Y.S.Y.)
- Department of Anatomy, College of Medicine, Soonchunhyang University, Cheonan 31151, Korea
| | - Hyo Young Jung
- Department of Anatomy and Cell Biology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (D.Y.Y.); (H.Y.J.); (W.K.); (K.R.H.); (Y.S.Y.)
| | - Woosuk Kim
- Department of Anatomy and Cell Biology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (D.Y.Y.); (H.Y.J.); (W.K.); (K.R.H.); (Y.S.Y.)
- Department of Biomedical Sciences, Research Institute for Bioscience and Biotechnology, Hallym University, Chuncheon 24252, Korea
| | - Kyu Ri Hahn
- Department of Anatomy and Cell Biology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (D.Y.Y.); (H.Y.J.); (W.K.); (K.R.H.); (Y.S.Y.)
| | - Hyun Jung Kwon
- Department of Biochemistry and Molecular Biology, Research Institute of Oral Sciences, College of Dentistry, Gangneung-Wonju National University, Gangneung 25457, Korea;
| | - Sung Min Nam
- Department of Anatomy, School of Medicine and Institute for Environmental Science, Wonkwang University, Iksan 54538, Korea;
| | - Jin Young Chung
- Department of Veterinary Internal Medicine and Geriatrics, College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Yeo Sung Yoon
- Department of Anatomy and Cell Biology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (D.Y.Y.); (H.Y.J.); (W.K.); (K.R.H.); (Y.S.Y.)
| | - Dae Won Kim
- Department of Biochemistry and Molecular Biology, Research Institute of Oral Sciences, College of Dentistry, Gangneung-Wonju National University, Gangneung 25457, Korea;
- Correspondence: (D.W.K.); (I.K.H.)
| | - In Koo Hwang
- Department of Anatomy and Cell Biology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (D.Y.Y.); (H.Y.J.); (W.K.); (K.R.H.); (Y.S.Y.)
- Correspondence: (D.W.K.); (I.K.H.)
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19
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Kwan SY, Sheel A, Song CQ, Zhang XO, Jiang T, Dang H, Cao Y, Ozata DM, Mou H, Yin H, Weng Z, Wang XW, Xue W. Depletion of TRRAP Induces p53-Independent Senescence in Liver Cancer by Down-Regulating Mitotic Genes. Hepatology 2020; 71:275-290. [PMID: 31188495 PMCID: PMC6906267 DOI: 10.1002/hep.30807] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/27/2019] [Indexed: 01/10/2023]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive subtype of liver cancer with few effective treatments, and the underlying mechanisms that drive HCC pathogenesis remain poorly characterized. Identifying genes and pathways essential for HCC cell growth will aid the development of new targeted therapies for HCC. Using a kinome CRISPR screen in three human HCC cell lines, we identified transformation/transcription domain-associated protein (TRRAP) as an essential gene for HCC cell proliferation. TRRAP has been implicated in oncogenic transformation, but how it functions in cancer cell proliferation is not established. Here, we show that depletion of TRRAP or its co-factor, histone acetyltransferase KAT5, inhibits HCC cell growth through induction of p53-independent and p21-independent senescence. Integrated cancer genomics analyses using patient data and RNA sequencing identified mitotic genes as key TRRAP/KAT5 targets in HCC, and subsequent cell cycle analyses revealed that TRRAP-depleted and KAT5-depleted cells are arrested at the G2/M phase. Depletion of topoisomerase II alpha (TOP2A), a mitotic gene and TRRAP/KAT5 target, was sufficient to recapitulate the senescent phenotype of TRRAP/KAT5 knockdown. Conclusion: Our results uncover a role for TRRAP/KAT5 in promoting HCC cell proliferation by activating mitotic genes. Targeting the TRRAP/KAT5 complex is a potential therapeutic strategy for HCC.
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Affiliation(s)
- Suet-Yan Kwan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Ankur Sheel
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Chun-Qing Song
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Tingting Jiang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Hien Dang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Yueying Cao
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Deniz M. Ozata
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Hao Yin
- Medical research institute, Wuhan University, Wuhan, PR China
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, P. R. China
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
- Program in Molecular Medicine, Department of Molecular, Cell and Cancer Biology, and Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605
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20
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Chen P, Guo Z, Chen C, Tian S, Bai X, Zhai G, Ma Z, Wu H, Zhang K. Identification of dual histone modification-binding protein interaction by combining mass spectrometry and isothermal titration calorimetric analysis. J Adv Res 2019; 22:35-46. [PMID: 31956440 PMCID: PMC6961217 DOI: 10.1016/j.jare.2019.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/29/2019] [Accepted: 11/10/2019] [Indexed: 12/13/2022] Open
Abstract
The interaction between combinatorial histone modifications and tandem-domain reader proteins was identified. Four tandem-domain proteins (BPTF-PB, CBP-BP, TRIM24-PB, TAF1-BB) could read the peptides with dual-modifications. The binding affinities were detected by isothermal titration calorimetry. The interaction between BPTF-PB and peptides with PTMs is the strongest. The binding proteins to the tandem-domains were quantified. 78 enriched proteins were further characterized. The molecule network of “histone modification-reader-binding proteins” was analyzed.
Histone posttranslational modifications (HPTMs) play important roles in eukaryotic transcriptional regulation. Recently, it has been suggested that combinatorial modification codes that comprise two or more HPTMs can recruit readers of HPTMs, performing complex regulation of gene expression. However, the characterization of the multiplex interactions remains challenging, especially for the molecular network of histone PTMs, readers and binding complexes. Here, we developed an integrated method that combines a peptide library, affinity enrichment, mass spectrometry (MS) and bioinformatics analysis for the identification of the interaction between HPTMs and their binding proteins. Five tandem-domain-reader proteins (BPTF, CBP, TAF1, TRIM24 and TRIM33) were designed and prepared as the enriched probes, and a group of histone peptides with multiple PTMs were synthesized as the target peptide library. First, the domain probes were used to pull down the PTM peptides from the library, and then the resulting product was characterized by MS. The binding interactions between PTM peptides and domains were further validated and measured by isothermal titration calorimetry analysis (ITC). Meanwhile, the binding proteins were enriched by domain probes and identified by HPLC-MS/MS. The interaction network of histone PTMs-readers-binding complexes was finally analyzed via informatics tools. Our results showed that the integrated approach combining MS analysis with ITC assay enables us to understand the interaction between the combinatorial HPTMs and reading domains. The identified network of “HPTMs-reader proteins-binding complexes” provided potential clues to reveal HPTM functions and their regulatory mechanisms.
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Affiliation(s)
- Pu Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Zhenchang Guo
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Cong Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xue Bai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Guijin Zhai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Zhenyi Ma
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Huiyuan Wu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
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21
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Pseudokinases: From Allosteric Regulation of Catalytic Domains and the Formation of Macromolecular Assemblies to Emerging Drug Targets. Catalysts 2019. [DOI: 10.3390/catal9090778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pseudokinases are a member of the kinase superfamily that lack one or more of the canonical residues required for catalysis. Protein pseudokinases are widely distributed across species and are present in proteins that perform a great diversity of roles in the cell. They represent approximately 10% to 40% of the kinome of a multicellular organism. In the human, the pseudokinase subfamily consists of approximately 60 unique proteins. Despite their lack of one or more of the amino acid residues typically required for the productive interaction with ATP and metal ions, which is essential for the phosphorylation of specific substrates, pseudokinases are important functional molecules that can act as dynamic scaffolds, competitors, or modulators of protein–protein interactions. Indeed, pseudokinase misfunctions occur in diverse diseases and represent a new therapeutic window for the development of innovative therapeutic approaches. In this contribution, we describe the structural features of pseudokinases that are used as the basis of their classification; analyse the interactome space of human pseudokinases and discuss their potential as suitable drug targets for the treatment of various diseases, including metabolic, neurological, autoimmune, and cell proliferation disorders.
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22
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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23
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Cogné B, Ehresmann S, Beauregard-Lacroix E, Rousseau J, Besnard T, Garcia T, Petrovski S, Avni S, McWalter K, Blackburn PR, Sanders SJ, Uguen K, Harris J, Cohen JS, Blyth M, Lehman A, Berg J, Li MH, Kini U, Joss S, von der Lippe C, Gordon CT, Humberson JB, Robak L, Scott DA, Sutton VR, Skraban CM, Johnston JJ, Poduri A, Nordenskjöld M, Shashi V, Gerkes EH, Bongers EM, Gilissen C, Zarate YA, Kvarnung M, Lally KP, Kulch PA, Daniels B, Hernandez-Garcia A, Stong N, McGaughran J, Retterer K, Tveten K, Sullivan J, Geisheker MR, Stray-Pedersen A, Tarpinian JM, Klee EW, Sapp JC, Zyskind J, Holla ØL, Bedoukian E, Filippini F, Guimier A, Picard A, Busk ØL, Punetha J, Pfundt R, Lindstrand A, Nordgren A, Kalb F, Desai M, Ebanks AH, Jhangiani SN, Dewan T, Coban Akdemir ZH, Telegrafi A, Zackai EH, Begtrup A, Song X, Toutain A, Wentzensen IM, Odent S, Bonneau D, Latypova X, Deb W, Redon S, Bilan F, Legendre M, Troyer C, Whitlock K, Caluseriu O, Murphree MI, Pichurin PN, Agre K, Gavrilova R, Rinne T, Park M, Shain C, Heinzen EL, Xiao R, Amiel J, Lyonnet S, Isidor B, Biesecker LG, Lowenstein D, Posey JE, Denommé-Pichon AS, Férec C, Yang XJ, Rosenfeld JA, Gilbert-Dussardier B, Audebert-Bellanger S, Redon R, Stessman HA, Nellaker C, Yang Y, Lupski JR, Goldstein DB, Eichler EE, Bolduc F, Bézieau S, Küry S, Campeau PM, Küry S, Campeau PM. Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability. Am J Hum Genet 2019; 104:530-541. [PMID: 30827496 DOI: 10.1016/j.ajhg.2019.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sébastien Küry
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France; INSERM, CNRS, UNIV Nantes, l'institut du thorax, 44007 Nantes, France.
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H3T1J4, Canada.
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24
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Kang KT, Kwon YW, Kim DK, Lee SI, Kim KH, Suh DS, Kim JH. TRRAP stimulates the tumorigenic potential of ovarian cancer stem cells. BMB Rep 2019. [PMID: 29936929 PMCID: PMC6235085 DOI: 10.5483/bmbrep.2018.51.10.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ovarian cancer is the most fatal gynecological malignancy in women and identification of new therapeutic targets is essential for the continued development of therapy for ovarian cancer. TRRAP (transformation/transcription domain-associated protein) is an adaptor protein and a component of histone acetyltransferase complex. The present study was undertaken to investigate the roles played by TRRAP in the proliferation and tumorigenicity of ovarian cancer stem cells. TRRAP expression was found to be up-regulated in the sphere cultures of A2780 ovarian cancer cells. Knockdown of TRRAP significantly decreased cell proliferation and the number of A2780 spheroids. In addition, TRRAP knockdown induced cell cycle arrest and increased apoptotic percentages of A2780 sphere cells. Notably, the mRNA levels of stemness-associated markers, that is, OCT4, SOX2, and NANOG, were suppressed in TRRAP-silenced A2780 sphere cells. In addition, TRRAP overexpression increased the mRNA level of NANOG and the transcriptional activity of NANOG promoter in these cells. Furthermore, TRRAP knockdown significantly reduced tumor growth in a murine xenograft transplantation model. Taken together, the findings of the present study suggest that TRRAP plays an important role in the regulation of the proliferation and stemness of ovarian cancer stem cells.
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Affiliation(s)
- Kyung Taek Kang
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Yang Woo Kwon
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Dae Kyoung Kim
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Su In Lee
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Ki-Hyung Kim
- Obstetrics and Gynecology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Dong-Soo Suh
- Obstetrics and Gynecology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Jae Ho Kim
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea; Research Institute of Convergence Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Korea
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25
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McCarthy A, Deiulio A, Martin ET, Upadhyay M, Rangan P. Tip60 complex promotes expression of a differentiation factor to regulate germline differentiation in female Drosophila. Mol Biol Cell 2018; 29:2933-2945. [PMID: 30230973 PMCID: PMC6329907 DOI: 10.1091/mbc.e18-06-0385] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/06/2018] [Accepted: 09/13/2018] [Indexed: 01/23/2023] Open
Abstract
Germline stem cells (GSCs) self-renew and differentiate to sustain a continuous production of gametes. In the female Drosophila germ line, two differentiation factors, bag of marbles ( bam) and benign gonial cell neoplasm ( bgcn), work in concert in the stem cell daughter to promote the generation of eggs. In GSCs, bam transcription is repressed by signaling from the niche and is activated in stem cell daughters. In contrast, bgcn is transcribed in both the GSCs and stem cell daughters, but little is known about how bgcn is transcriptionally modulated. Here we find that the conserved protein Nipped-A acts through the Tat interactive protein 60-kDa (Tip60) histone acetyl transferase complex in the germ line to promote GSC daughter differentiation. We find that Nipped-A is required for efficient exit from the gap phase 2 (G2) of cell cycle of the GSC daughter and for expression of a differentiation factor, bgcn. Loss of Nipped-A results in accumulation of GSC daughters . Forced expression of bgcn in Nipped-A germline-depleted ovaries rescues this differentiation defect. Together, our results indicate that Tip60 complex coordinates cell cycle progression and expression of bgcn to help drive GSC daughters toward a differentiation program.
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Affiliation(s)
- Alicia McCarthy
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
| | - Aron Deiulio
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
| | - Elliot Todd Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
| | - Maitreyi Upadhyay
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222
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26
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Mavros CF, Brownstein CA, Thyagrajan R, Genetti CA, Tembulkar S, Graber K, Murphy Q, Cabral K, VanNoy GE, Bainbridge M, Shi J, Agrawal PB, Beggs AH, D’Angelo E, Gonzalez-Heydrich J. De novo variant of TRRAP in a patient with very early onset psychosis in the context of non-verbal learning disability and obsessive-compulsive disorder: a case report. BMC MEDICAL GENETICS 2018; 19:197. [PMID: 30424743 PMCID: PMC6234620 DOI: 10.1186/s12881-018-0711-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/25/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND TRRAP encodes a multidomain protein kinase that works as a genetic cofactor to influence DNA methylation patterns, DNA damage repair, and chromatin remodeling. TRRAP protein is vital to early neural developmental processes, and variants in this gene have been associated with schizophrenia and childhood disintegrative disorder. CASE PRESENTATION Here, we report on a patient with a de novo nonsynonymous TRRAP single-nucleotide variant (EST00000355540.3:c.5957G > A, p.Arg1986Gln) and early onset major depression accompanied by a psychotic episode (before age 10) that occurred in the context of longer standing nonverbal learning disability and a past history of obsessions and compulsions. CONCLUSIONS The de novo variant and presentation of very early onset psychosis indicate a rare Mendelian disorder inheritance model. The genotype and behavioral abnormalities of this patient are reviewed.
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Affiliation(s)
- Chrystal F. Mavros
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | - Catherine A. Brownstein
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | - Roshni Thyagrajan
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | - Casie A. Genetti
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | - Sahil Tembulkar
- Developmental Neuropsychiatry Program, Department of Psychiatry, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Kelsey Graber
- Developmental Neuropsychiatry Program, Department of Psychiatry, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Quinn Murphy
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | - Kristin Cabral
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | - Grace E. VanNoy
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | | | - Jiahai Shi
- Department of Biomedical Sciences, City University of Hong Kong, 1/F, Block 1, To Yuen Building, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Pankaj B. Agrawal
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | - Alan H. Beggs
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle CLS 16009, 300 Longwood Avenue, Boston, MA 02115 USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
| | - Eugene D’Angelo
- Developmental Neuropsychiatry Program, Department of Psychiatry, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Joseph Gonzalez-Heydrich
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, 3 Blackfan Circle, CLSB 15031, Boston, MA 02115 USA
- Developmental Neuropsychiatry Program, Department of Psychiatry, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 USA
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27
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Sokpor G, Castro-Hernandez R, Rosenbusch J, Staiger JF, Tuoc T. ATP-Dependent Chromatin Remodeling During Cortical Neurogenesis. Front Neurosci 2018; 12:226. [PMID: 29686607 PMCID: PMC5900035 DOI: 10.3389/fnins.2018.00226] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
The generation of individual neurons (neurogenesis) during cortical development occurs in discrete steps that are subtly regulated and orchestrated to ensure normal histogenesis and function of the cortex. Notably, various gene expression programs are known to critically drive many facets of neurogenesis with a high level of specificity during brain development. Typically, precise regulation of gene expression patterns ensures that key events like proliferation and differentiation of neural progenitors, specification of neuronal subtypes, as well as migration and maturation of neurons in the developing cortex occur properly. ATP-dependent chromatin remodeling complexes regulate gene expression through utilization of energy from ATP hydrolysis to reorganize chromatin structure. These chromatin remodeling complexes are characteristically multimeric, with some capable of adopting functionally distinct conformations via subunit reconstitution to perform specific roles in major aspects of cortical neurogenesis. In this review, we highlight the functions of such chromatin remodelers during cortical development. We also bring together various proposed mechanisms by which ATP-dependent chromatin remodelers function individually or in concert, to specifically modulate vital steps in cortical neurogenesis.
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Affiliation(s)
- Godwin Sokpor
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Ricardo Castro-Hernandez
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Joachim Rosenbusch
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Tran Tuoc
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
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28
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Wang Z, Plasschaert LW, Aryal S, Renaud NA, Yang Z, Choo-Wing R, Pessotti AD, Kirkpatrick ND, Cochran NR, Carbone W, Maher R, Lindeman A, Russ C, Reece-Hoyes J, McAllister G, Hoffman GR, Roma G, Jaffe AB. TRRAP is a central regulator of human multiciliated cell formation. J Cell Biol 2018; 217:1941-1955. [PMID: 29588376 PMCID: PMC5987713 DOI: 10.1083/jcb.201706106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/24/2022] Open
Abstract
Multiciliated cells (MCCs) function to promote directional fluid flow across epithelial tissues. Wang et al. show that TRRAP, a component of multiple histone acetyltransferase complexes, is required for airway MCC formation and regulates a network of genes involved in MCC differentiation and function. The multiciliated cell (MCC) is an evolutionarily conserved cell type, which in vertebrates functions to promote directional fluid flow across epithelial tissues. In the conducting airway, MCCs are generated by basal stem/progenitor cells and act in concert with secretory cells to perform mucociliary clearance to expel pathogens from the lung. Studies in multiple systems, including Xenopus laevis epidermis, murine trachea, and zebrafish kidney, have uncovered a transcriptional network that regulates multiple steps of multiciliogenesis, ultimately leading to an MCC with hundreds of motile cilia extended from their apical surface, which beat in a coordinated fashion. Here, we used a pool-based short hairpin RNA screening approach and identified TRRAP, an essential component of multiple histone acetyltransferase complexes, as a central regulator of MCC formation. Using a combination of immunofluorescence, signaling pathway modulation, and genomic approaches, we show that (a) TRRAP acts downstream of the Notch2-mediated basal progenitor cell fate decision and upstream of Multicilin to control MCC differentiation; and (b) TRRAP binds to the promoters and regulates the expression of a network of genes involved in MCC differentiation and function, including several genes associated with human ciliopathies.
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Affiliation(s)
- Zhao Wang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Lindsey W Plasschaert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Shivani Aryal
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Nicole A Renaud
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Zinger Yang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Rayman Choo-Wing
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Angelica D Pessotti
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Nadire R Cochran
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Rob Maher
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Alicia Lindeman
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Carsten Russ
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - John Reece-Hoyes
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Gregory McAllister
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Gregory R Hoffman
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Aron B Jaffe
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
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Liu X, Zong W, Li T, Wang Y, Xu X, Zhou ZW, Wang ZQ. The E3 ubiquitin ligase APC/C Cdh1 degrades MCPH1 after MCPH1-βTrCP2-Cdc25A-mediated mitotic entry to ensure neurogenesis. EMBO J 2017; 36:3666-3681. [PMID: 29150431 DOI: 10.15252/embj.201694443] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 12/20/2022] Open
Abstract
Mutations of microcephalin (MCPH1) can cause the neurodevelopmental disorder primary microcephaly type 1. We previously showed that MCPH1 deletion in neural stem cells results in early mitotic entry that distracts cell division mode, leading to exhaustion of the progenitor pool. Here, we show that MCPH1 interacts with and promotes the E3 ligase βTrCP2 to degrade Cdc25A independent of DNA damage. Overexpression of βTrCP2 or the knockdown of Cdc25A remedies the high mitotic index and rescues the premature differentiation of Mcph1-deficient neuroprogenitors in vivo MCPH1 itself is degraded by APC/CCdh1, but not APC/CCdc20, in late mitosis and G1 phase. Forced MCPH1 expression causes cell death, underlining the importance of MCPH1 turnover after mitosis. Ectopic expression of Cdh1 leads to premature differentiation of neuroprogenitors, mimicking differentiation defects of Mcph1-knockout neuroprogenitors. The homeostasis of MCPH1 in association with the ubiquitin-proteasome system ensures mitotic entry independent of cell cycle checkpoint. This study provides a mechanistic understanding of how MCPH1 controls neural stem cell fate and brain development.
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Affiliation(s)
- Xiaoqian Liu
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Wen Zong
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Tangliang Li
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.,Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Yujun Wang
- Division of Biology, City of Hope National Medical Center/Beckman Research Institute, Duarte, CA, USA
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response, College of Life Sciences, Capital Normal University, Beijing, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Zhong-Wei Zhou
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany .,Faculty of Biology and Pharmacy, Friedrich-Schiller University of Jena, Jena, Germany
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30
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Tauc HM, Tasdogan A, Meyer P, Pandur P. Nipped-A regulates intestinal stem cell proliferation in Drosophila. Development 2017; 144:612-623. [PMID: 28196804 DOI: 10.1242/dev.142703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/30/2016] [Indexed: 12/11/2022]
Abstract
Adult stem cells uphold a delicate balance between quiescent and active states, a deregulation of which can lead to age-associated diseases such as cancer. In Drosophila, intestinal stem cell (ISC) proliferation is tightly regulated and mis-regulation is detrimental to intestinal homeostasis. Various factors are known to govern ISC behavior; however, transcriptional changes in ISCs during aging are still unclear. RNA sequencing of young and old ISCs newly identified Nipped-A, a subunit of histone acetyltransferase complexes, as a regulator of ISC proliferation that is upregulated in old ISCs. We show that Nipped-A is required for maintaining the proliferative capacity of ISCs during aging and in response to tissue-damaging or tumorigenic stimuli. Interestingly, Drosophila Myc cannot compensate for the effect of the loss of Nipped-A on ISC proliferation. Nipped-A seems to be a superordinate regulator of ISC proliferation, possibly by coordinating different processes including modifying the chromatin landscape of ISCs and progenitors.
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Affiliation(s)
- Helen Marie Tauc
- Institut für Biochemie und Molekulare Biologie, Universität Ulm, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Alpaslan Tasdogan
- Institut für Immunologie, Universitätsklinikum Ulm, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Patrick Meyer
- Institut für Dermatologie, Universität Ulm, Life Science Building N27, James Franck-Ring/Meyerhofstrasse 11c, Ulm 89081, Germany
| | - Petra Pandur
- Institut für Biochemie und Molekulare Biologie, Universität Ulm, Albert-Einstein-Allee 11, Ulm 89081, Germany
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31
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The secret life of kinases: insights into non-catalytic signalling functions from pseudokinases. Biochem Soc Trans 2017; 45:665-681. [PMID: 28620028 DOI: 10.1042/bst20160331] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/31/2022]
Abstract
Over the past decade, our understanding of the mechanisms by which pseudokinases, which comprise ∼10% of the human and mouse kinomes, mediate signal transduction has advanced rapidly with increasing structural, biochemical, cellular and genetic studies. Pseudokinases are the catalytically defective counterparts of conventional, active protein kinases and have been attributed functions as protein interaction domains acting variously as allosteric modulators of conventional protein kinases and other enzymes, as regulators of protein trafficking or localisation, as hubs to nucleate assembly of signalling complexes, and as transmembrane effectors of such functions. Here, by categorising mammalian pseudokinases based on their known functions, we illustrate the mechanistic diversity among these proteins, which can be viewed as a window into understanding the non-catalytic functions that can be exerted by conventional protein kinases.
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32
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In Utero Exposure to Valproic Acid Induces Neocortical Dysgenesis via Dysregulation of Neural Progenitor Cell Proliferation/Differentiation. J Neurosci 2017; 36:10908-10919. [PMID: 27798144 DOI: 10.1523/jneurosci.0229-16.2016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 09/12/2016] [Indexed: 11/21/2022] Open
Abstract
Valproic acid (VPA), a widely used antiepileptic drug, is an inhibitor of histone deacetylases, which epigenetically modify cell proliferation/differentiation in developing tissues. A series of recent clinical studies in humans reported that VPA exposure in utero impaired histogenesis and the development of the central nervous system, leading to increased risks of congenital malformation and the impairment of higher brain functions in children. In the present study conducted in mice, we report that VPA exposure in utero (1) increases the amount of acetylated histone proteins, (2) alters the expression of G1-phase regulatory proteins, (3) inhibits the cell cycle exit of neural progenitor cells during the early stage of neocortical histogenesis, and (4) increases the production of projection neurons distributed in the superficial neocortical layers in embryonic brains. Together, our findings show that VPA exposure in utero alters proliferation/differentiation characteristics of neural progenitor cells and hence leads to the neocortical dysgenesis. SIGNIFICANCE STATEMENT This study provides new insight into the mechanisms of how an altered in utero environment, such as drug exposure, affects the generation of neurons prenatally. The antiepileptic drug valproic acid (VPA) is a good target molecule as in utero exposure to VPA has been repeatedly reported to increase the risk of nervous system malformations and to impair higher brain functions in children. We show that VPA decreases the probability of differentiation of the neural progenitor cells (NPCs) in mice, resulting in an abnormally increased number of projection neurons in the superficial layers of the neocortex. Further, we suggest that histone deacetylase inhibition by VPA may be involved in the dysregulation of proliferation/differentiation characteristics of NPCs.
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33
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Zhang CU, Cadigan KM. The matrix protein Tiggrin regulates plasmatocyte maturation in Drosophila larva. Development 2017; 144:2415-2427. [PMID: 28526755 DOI: 10.1242/dev.149641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 01/24/2023]
Abstract
The lymph gland (LG) is a major source of hematopoiesis during Drosophila development. In this tissue, prohemocytes differentiate into multiple lineages, including macrophage-like plasmatocytes, which comprise the vast majority of mature hemocytes. Previous studies have uncovered genetic pathways that regulate prohemocyte maintenance and some cell fate choices between hemocyte lineages. However, less is known about how the plasmatocyte pool of the LG is established and matures. Here, we report that Tiggrin, a matrix protein expressed in the LG, is a specific regulator of plasmatocyte maturation. Tiggrin mutants exhibit precocious maturation of plasmatocytes, whereas Tiggrin overexpression blocks this process, resulting in a buildup of intermediate progenitors (IPs) expressing prohemocyte and hemocyte markers. These IPs likely represent a transitory state in prohemocyte to plasmatocyte differentiation. We also found that overexpression of Wee1 kinase, which slows G2/M progression, results in a phenotype similar to Tiggrin overexpression, whereas String/Cdc25 expression phenocopies Tiggrin mutants. Further analysis revealed that Wee1 inhibits plasmatocyte maturation through upregulation of Tiggrin transcription. Our results elucidate connections between the extracellular matrix and cell cycle regulators in the regulation of hematopoiesis.
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Affiliation(s)
- Chen U Zhang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ken M Cadigan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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34
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Lysine Acetylation and Deacetylation in Brain Development and Neuropathies. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:19-36. [PMID: 28161493 PMCID: PMC5339409 DOI: 10.1016/j.gpb.2016.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/11/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022]
Abstract
Embryonic development is critical for the final functionality and maintenance of the adult brain. Brain development is tightly regulated by intracellular and extracellular signaling. Lysine acetylation and deacetylation are posttranslational modifications that are able to link extracellular signals to intracellular responses. A wealth of evidence indicates that lysine acetylation and deacetylation are critical for brain development and functionality. Indeed, mutations of the enzymes and cofactors responsible for these processes are often associated with neurodevelopmental and psychiatric disorders. Lysine acetylation and deacetylation are involved in all levels of brain development, starting from neuroprogenitor survival and proliferation, cell fate decisions, neuronal maturation, migration, and synaptogenesis, as well as differentiation and maturation of astrocytes and oligodendrocytes, to the establishment of neuronal circuits. Hence, fluctuations in the balance between lysine acetylation and deacetylation contribute to the final shape and performance of the brain. In this review, we summarize the current basic knowledge on the specific roles of lysine acetyltransferase (KAT) and lysine deacetylase (KDAC) complexes in brain development and the different neurodevelopmental disorders that are associated with dysfunctional lysine (de)acetylation machineries.
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35
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Recent Zika Virus Isolates Induce Premature Differentiation of Neural Progenitors in Human Brain Organoids. Cell Stem Cell 2017; 20:397-406.e5. [PMID: 28132835 DOI: 10.1016/j.stem.2016.12.005] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/05/2016] [Accepted: 12/14/2016] [Indexed: 01/12/2023]
Abstract
The recent Zika virus (ZIKV) epidemic is associated with microcephaly in newborns. Although the connection between ZIKV and neurodevelopmental defects is widely recognized, the underlying mechanisms are poorly understood. Here we show that two recently isolated strains of ZIKV, an American strain from an infected fetal brain (FB-GWUH-2016) and a closely-related Asian strain (H/PF/2013), productively infect human iPSC-derived brain organoids. Both of these strains readily target to and replicate in proliferating ventricular zone (VZ) apical progenitors. The main phenotypic effect was premature differentiation of neural progenitors associated with centrosome perturbation, even during early stages of infection, leading to progenitor depletion, disruption of the VZ, impaired neurogenesis, and cortical thinning. The infection pattern and cellular outcome differ from those seen with the extensively passaged ZIKV strain MR766. The structural changes we see after infection with these more recently isolated viral strains closely resemble those seen in ZIKV-associated microcephaly.
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36
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Dee A, Li K, Heng X, Guo Q, Li JYH. Regulation of self-renewing neural progenitors by FGF/ERK signaling controls formation of the inferior colliculus. Development 2016; 143:3661-3673. [PMID: 27578777 DOI: 10.1242/dev.138537] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/22/2016] [Indexed: 11/20/2022]
Abstract
The embryonic tectum displays an anteroposterior gradient in development and produces the superior colliculus and inferior colliculus. Studies suggest that partition of the tectum is controlled by different strengths and durations of FGF signals originated from the so-called isthmic organizer at the mid/hindbrain junction; however, the underlying mechanism is unclear. We show that deleting Ptpn11, which links FGF with the ERK pathway, prevents inferior colliculus formation by depleting a previously uncharacterized stem cell zone. The stem-zone loss is attributed to shortening of S phase and acceleration of cell cycle exit and neurogenesis. Expression of a constitutively active Mek1 (Mek1DD), the known ERK activator, restores the tectal stem zone and the inferior colliculus without Ptpn11. By contrast, Mek1DD expression fails to rescue the tectal stem zone and the inferior colliculus in the absence of Fgf8 and the isthmic organizer, indicating that FGF and Mek1DD initiate qualitatively and/or quantitatively distinctive signaling. Together, our data show that the formation of the inferior colliculus relies on the provision of new cells from the tectal stem zone. Furthermore, distinctive ERK signaling mediates Fgf8 in the control of cell survival, tissue polarity and cytogenetic gradient during the development of the tectum.
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Affiliation(s)
- Alexander Dee
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Kairong Li
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Xin Heng
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Qiuxia Guo
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - James Y H Li
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA .,Institute for Systems Genomics, School of Medicine, University of Connecticut Health, Farmington, CT 06030, USA
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37
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GCN5 modulates osteogenic differentiation of periodontal ligament stem cells through DKK1 acetylation in inflammatory microenvironment. Sci Rep 2016; 6:26542. [PMID: 27216891 PMCID: PMC4877597 DOI: 10.1038/srep26542] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/04/2016] [Indexed: 12/21/2022] Open
Abstract
Periodontal ligament stem cells (PDLSCs) from periodontitis patients showed defective osteogenic differentiation. However, the mechanism of impaired osteogenic differentiation of PDLSCs in inflammatory microenvironments is still unclear. In this study, we found that inflammation in the microenvironment resulted in downregulation of histone acetyltransferase GCN5 expression and lack of GCN5 caused decreased osteogenic differentiation of PDLSCs. Previous study showed activated Wnt/β-cateinin pathway of PDLSCs resulted in defective osteogenic differentiation. Here we found knockdown of GCN5 decreased the expression of DKK1, an inhibitor of Wnt/β-cateinin pathway, thus activated Wnt/β-catenin pathway of PDLSCs. Mechanistically, GCN5 regulated DKK1 expression by acetylation of Histone H3 lysine 9 (H3K9) and Histone H3 lysine 14 (H3K14) at its promoter region. Interestingly, we found that in vivo injection of aspirin rescued the periodontitis of rats through inhibiting inflammation and upregulating GCN5 expression. Furthermore, aspirin treatment of PDLSCs upregulated GCN5 expression and increased osteogenic differentiation of PDLSCs. In conclusion, GCN5 plays a protective role in periodontitis through acetylation of DKK1 and applying drugs targeting GCN5, such as aspirin, could be a new approach for periodontitis treatment.
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38
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Roles for the Histone Modifying and Exchange Complex NuA4 in Cell Cycle Progression in Drosophila melanogaster. Genetics 2016; 203:1265-81. [PMID: 27184390 DOI: 10.1534/genetics.116.188581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/04/2016] [Indexed: 11/18/2022] Open
Abstract
Robust and synchronous repression of E2F-dependent gene expression is critical to the proper timing of cell cycle exit when cells transition to a postmitotic state. Previously NuA4 was suggested to act as a barrier to proliferation in Drosophila by repressing E2F-dependent gene expression. Here we show that NuA4 activity is required for proper cell cycle exit and the repression of cell cycle genes during the transition to a postmitotic state in vivo However, the delay of cell cycle exit caused by compromising NuA4 is not due to additional proliferation or effects on E2F activity. Instead NuA4 inhibition results in slowed cell cycle progression through late S and G2 phases due to aberrant activation of an intrinsic p53-independent DNA damage response. A reduction in NuA4 function ultimately produces a paradoxical cell cycle gene expression program, where certain cell cycle genes become derepressed in cells that are delayed during the G2 phase of the final cell cycle. Bypassing the G2 delay when NuA4 is inhibited leads to abnormal mitoses and results in severe tissue defects. NuA4 physically and genetically interacts with components of the E2F complex termed D: rosophila, R: bf, E: 2F A: nd M: yb/ M: ulti-vulva class B: (DREAM/MMB), and modulates a DREAM/MMB-dependent ectopic neuron phenotype in the posterior wing margin. However, this effect is also likely due to the cell cycle delay, as simply reducing Cdk1 is sufficient to generate a similar phenotype. Our work reveals that the major requirement for NuA4 in the cell cycle in vivo is to suppress an endogenous DNA damage response, which is required to coordinate proper S and G2 cell cycle progression with differentiation and cell cycle gene expression.
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Gabriel E, Wason A, Ramani A, Gooi LM, Keller P, Pozniakovsky A, Poser I, Noack F, Telugu NS, Calegari F, Šarić T, Hescheler J, Hyman AA, Gottardo M, Callaini G, Alkuraya FS, Gopalakrishnan J. CPAP promotes timely cilium disassembly to maintain neural progenitor pool. EMBO J 2016; 35:803-19. [PMID: 26929011 PMCID: PMC4972140 DOI: 10.15252/embj.201593679] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/05/2016] [Indexed: 12/28/2022] Open
Abstract
A mutation in the centrosomal‐P4.1‐associated protein (CPAP) causes Seckel syndrome with microcephaly, which is suggested to arise from a decline in neural progenitor cells (NPCs) during development. However, mechanisms of NPCs maintenance remain unclear. Here, we report an unexpected role for the cilium in NPCs maintenance and identify CPAP as a negative regulator of ciliary length independent of its role in centrosome biogenesis. At the onset of cilium disassembly, CPAP provides a scaffold for the cilium disassembly complex (CDC), which includes Nde1, Aurora A, and OFD1, recruited to the ciliary base for timely cilium disassembly. In contrast, mutated CPAP fails to localize at the ciliary base associated with inefficient CDC recruitment, long cilia, retarded cilium disassembly, and delayed cell cycle re‐entry leading to premature differentiation of patient iPS‐derived NPCs. Aberrant CDC function also promotes premature differentiation of NPCs in Seckel iPS‐derived organoids. Thus, our results suggest a role for cilia in microcephaly and its involvement during neurogenesis and brain size control.
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Affiliation(s)
- Elke Gabriel
- Center for Molecular Medicine and Institute for Biochemistry I of the University of Cologne, Cologne, Germany
| | - Arpit Wason
- Center for Molecular Medicine and Institute for Biochemistry I of the University of Cologne, Cologne, Germany
| | - Anand Ramani
- Center for Molecular Medicine and Institute for Biochemistry I of the University of Cologne, Cologne, Germany
| | - Li Ming Gooi
- Center for Molecular Medicine and Institute for Biochemistry I of the University of Cologne, Cologne, Germany
| | - Patrick Keller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrei Pozniakovsky
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Florian Noack
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies, TU-Dresden, Dresden, Germany
| | - Narasimha Swamy Telugu
- Center for Physiology and Pathophysiology, Institute for Neurophysiology Medical Faculty University of Cologne, Cologne, Germany
| | - Federico Calegari
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies, TU-Dresden, Dresden, Germany
| | - Tomo Šarić
- Center for Physiology and Pathophysiology, Institute for Neurophysiology Medical Faculty University of Cologne, Cologne, Germany
| | - Jürgen Hescheler
- Center for Physiology and Pathophysiology, Institute for Neurophysiology Medical Faculty University of Cologne, Cologne, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marco Gottardo
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Fowzan Sami Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center Alfasial University, Riyadh, Saudi Arabia Department of Anatomy and Cell Biology, College of Medicine Alfasial University, Riyadh, Saudi Arabia
| | - Jay Gopalakrishnan
- Center for Molecular Medicine and Institute for Biochemistry I of the University of Cologne, Cologne, Germany
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41
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Abstract
Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues. Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging. Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions. This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.
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42
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Dehay C, Kennedy H, Kosik KS. The outer subventricular zone and primate-specific cortical complexification. Neuron 2015; 85:683-94. [PMID: 25695268 DOI: 10.1016/j.neuron.2014.12.060] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Evolutionary expansion and complexification of the primate cerebral cortex are largely linked to the emergence of the outer subventricular zone (OSVZ), a uniquely structured germinal zone that generates the expanded primate supragranular layers. The primate OSVZ departs from rodent germinal zones in that it includes a higher diversity of precursor types, inter-related in bidirectional non-hierarchical lineages. In addition, primate-specific regulatory mechanisms are operating in primate cortical precursors via the occurrence of novel miRNAs. Here, we propose that the origin and evolutionary importance of the OSVZ is related to genetic changes in multiple regulatory loops and that cell-cycle regulation is a favored target for evolutionary adaptation of the cortex.
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Affiliation(s)
- Colette Dehay
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003, Lyon, France.
| | - Henry Kennedy
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003, Lyon, France.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Dept Cellular Molecular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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Davis WJ, Lehmann PZ, Li W. Nuclear PI3K signaling in cell growth and tumorigenesis. Front Cell Dev Biol 2015; 3:24. [PMID: 25918701 PMCID: PMC4394695 DOI: 10.3389/fcell.2015.00024] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/27/2015] [Indexed: 12/12/2022] Open
Abstract
The PI3K/Akt signaling pathway is a major driving force in a variety of cellular functions. Dysregulation of this pathway has been implicated in many human diseases including cancer. While the activity of the cytoplasmic PI3K/Akt pathway has been extensively studied, the functions of these molecules and their effector proteins within the nucleus are poorly understood. Harboring key cellular processes such as DNA replication and repair as well as nascent messenger RNA transcription, the nucleus provides a unique compartmental environment for protein–protein and protein–DNA/RNA interactions required for cell survival, growth, and proliferation. Here we summarize recent advances made toward elucidating the nuclear PI3K/Akt signaling cascade and its key components within the nucleus as they pertain to cell growth and tumorigenesis. This review covers the spatial and temporal localization of the major nuclear kinases having PI3K activities and the counteracting phosphatases as well as the role of nuclear PI3K/Akt signaling in mRNA processing and exportation, DNA replication and repair, ribosome biogenesis, cell survival, and tumorigenesis.
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Affiliation(s)
- William J Davis
- College of Medical Sciences, Washington State University Spokane, WA, USA
| | - Peter Z Lehmann
- College of Medical Sciences, Washington State University Spokane, WA, USA
| | - Weimin Li
- College of Medical Sciences, Washington State University Spokane, WA, USA
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Ma Y, Kanakousaki K, Buttitta L. How the cell cycle impacts chromatin architecture and influences cell fate. Front Genet 2015; 6:19. [PMID: 25691891 PMCID: PMC4315090 DOI: 10.3389/fgene.2015.00019] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/14/2015] [Indexed: 01/17/2023] Open
Abstract
Since the earliest observations of cells undergoing mitosis, it has been clear that there is an intimate relationship between the cell cycle and nuclear chromatin architecture. The nuclear envelope and chromatin undergo robust assembly and disassembly during the cell cycle, and transcriptional and post-transcriptional regulation of histone biogenesis and chromatin modification is controlled in a cell cycle-dependent manner. Chromatin binding proteins and chromatin modifications in turn influence the expression of critical cell cycle regulators, the accessibility of origins for DNA replication, DNA repair, and cell fate. In this review we aim to provide an integrated discussion of how the cell cycle machinery impacts nuclear architecture and vice-versa. We highlight recent advances in understanding cell cycle-dependent histone biogenesis and histone modification deposition, how cell cycle regulators control histone modifier activities, the contribution of chromatin modifications to origin firing for DNA replication, and newly identified roles for nucleoporins in regulating cell cycle gene expression, gene expression memory and differentiation. We close with a discussion of how cell cycle status may impact chromatin to influence cell fate decisions, under normal contexts of differentiation as well as in instances of cell fate reprogramming.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Kiriaki Kanakousaki
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Laura Buttitta
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
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Yang J, Tang Y, Liu H, Guo F, Ni J, Le W. Suppression of histone deacetylation promotes the differentiation of human pluripotent stem cells towards neural progenitor cells. BMC Biol 2014; 12:95. [PMID: 25406762 PMCID: PMC4254204 DOI: 10.1186/s12915-014-0095-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 10/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Emerging studies of human pluripotent stem cells (hPSCs) raise new prospects for neurodegenerative disease modeling and cell replacement therapies. Therefore, understanding the mechanisms underlying the commitment of neural progenitor cells (NPCs) is important for the application of hPSCs in neurodegenerative disease therapies. It has been reported that epigenetic modifications of histones play important roles in neural differentiation, but the exact mechanisms in regulating hPSC differentiation towards NPCs are not fully elucidated. RESULTS We demonstrated that suppression of histone deacetylases (HDACs) promoted the differentiation of hPSCs towards NPCs. Application of HDAC inhibitors (HDACi) increased the expression of neuroectodermal markers and enhanced the neuroectodermal specification once neural differentiation was initiated, thereby leading to more NPC generation. Similarly, the transcriptome analysis showed that HDACi increased the expression levels of ectodermal markers and triggered the NPC differentiation related pathways, while decreasing the expression levels of endodermal and mesodermal markers. Furthermore, we documented that HDAC3 but not HDAC1 or HDAC2 was the critical regulator participating in NPC differentiation, and knockdown of HDAC3's cofactor SMRT exhibited a similar effect as HDAC3 on NPC generation. CONCLUSIONS Our study reveals that HDACs, especially HDAC3, negatively regulate the differentiation of hPSCs towards NPCs at an earlier stage of neural differentiation. Moreover, HDAC3 might function by forming a repressor complex with its cofactor SMRT during this process. Thus, our findings uncover an important epigenetic mechanism of HDAC3 in the differentiation of hPSCs towards NPCs.
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Affiliation(s)
- Juan Yang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yu Tang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hui Liu
- Center for Translational Research of Neurology Disease, The 1st Affiliated Hospital, Dalian Medical University, Dalian, China.
| | - Fang Guo
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jun Ni
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Weidong Le
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Center for Translational Research of Neurology Disease, The 1st Affiliated Hospital, Dalian Medical University, Dalian, China.
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