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Stabile R, Cabezas MR, Verhagen MP, Tucci FA, van den Bosch TPP, De Herdt MJ, van der Steen B, Nigg AL, Chen M, Ivan C, Shimizu M, Koljenović S, Hardillo JA, Verrijzer CP, Baatenburg de Jong RJ, Calin GA, Fodde R. The deleted in oral cancer (DOC1 aka CDK2AP1) tumor suppressor gene is downregulated in oral squamous cell carcinoma by multiple microRNAs. Cell Death Dis 2023; 14:337. [PMID: 37217493 DOI: 10.1038/s41419-023-05857-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Cyclin-dependent kinase 2-associated protein 1 (CDK2AP1; also known as deleted in oral cancer or DOC1) is a tumor suppressor gene known to play functional roles in both cell cycle regulation and in the epigenetic control of embryonic stem cell differentiation, the latter as a core subunit of the nucleosome remodeling and histone deacetylation (NuRD) complex. In the vast majority of oral squamous cell carcinomas (OSCC), expression of the CDK2AP1 protein is reduced or lost. Notwithstanding the latter (and the DOC1 acronym), mutations or deletions in its coding sequence are extremely rare. Accordingly, CDK2AP1 protein-deficient oral cancer cell lines express as much CDK2AP1 mRNA as proficient cell lines. Here, by combining in silico and in vitro approaches, and by taking advantage of patient-derived data and tumor material in the analysis of loss of CDK2AP1 expression, we identified a set of microRNAs, namely miR-21-5p, miR-23b-3p, miR-26b-5p, miR-93-5p, and miR-155-5p, which inhibit its translation in both cell lines and patient-derived OSCCs. Of note, no synergistic effects were observed of the different miRs on the CDK2AP1-3-UTR common target. We also developed a novel approach to the combined ISH/IF tissue microarray analysis to study the expression patterns of miRs and their target genes in the context of tumor architecture. Last, we show that CDK2AP1 loss, as the result of miRNA expression, correlates with overall survival, thus highlighting the clinical relevance of these processes for carcinomas of the oral cavity.
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Affiliation(s)
- Roberto Stabile
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mario Román Cabezas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mathijs P Verhagen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Francesco A Tucci
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | | | - Maria J De Herdt
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Berdine van der Steen
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alex L Nigg
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Meng Chen
- Department of Translational Molecular Pathology and Center of Department of Translational Molecular Pathology, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cristina Ivan
- Department of Translational Molecular Pathology and Center of Department of Translational Molecular Pathology, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Caris Life Science, Irving, TX, USA
| | - Masayoshi Shimizu
- Department of Translational Molecular Pathology and Center of Department of Translational Molecular Pathology, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Senada Koljenović
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Antwerp University Hospital, 2650, Edegem, Belgium
| | - Jose A Hardillo
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert J Baatenburg de Jong
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - George A Calin
- Department of Translational Molecular Pathology and Center of Department of Translational Molecular Pathology, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Riccardo Fodde
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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Li QS, De Muynck L. Differentially expressed genes in Alzheimer's disease highlighting the roles of microglia genes including OLR1 and astrocyte gene CDK2AP1. Brain Behav Immun Health 2021; 13:100227. [PMID: 34589742 PMCID: PMC8474442 DOI: 10.1016/j.bbih.2021.100227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is associated with abnormal tau and amyloid-β accumulation in the brain, leading to neurofibrillary tangles, neuropil threads and extracellular amyloid-β plaques. Treatment is limited to symptom management, a disease-modifying therapy is not available. To advance search of therapy approaches, there is a continued need to identify targets for disease intervention both by confirming existing hypotheses and generating new hypotheses. METHODS We conducted a mRNA-seq study to identify genes associated with AD in post-mortem brain samples from the superior temporal gyrus (STG, n = 76), and inferior frontal gyrus (IFG, n = 65) brain regions. Differentially expressed genes (DEGs) were identified correcting for gender and surrogate variables to capture hidden variation not accounted for by pre-planned covariates. The results from this study were compared with the transcriptome studies from the Accelerated Medicine Partnership - Alzheimer's Disease (AMP-AD) initiative. Over-representation and gene set enrichment analysis (GSEA) was used to identify disease-associated pathways. Protein-protein interaction (PPI) and weighted gene co-expression network analysis (WGCNA) analyses were carried out and co-expressed gene modules and their hub genes were identified and associated with additional phenotypic traits of interest. RESULTS Several hundred mRNAs were differentially expressed between AD cases and cognitively normal controls in the STG, while no and few transcripts met the same criteria (adjusted p less than 0.05 and fold change greater than 1.2) in the IFG. The findings were consistent at the gene set level with two out of three cohorts from AMP-AD. PPI analysis suggested that the DEGs were enriched in protein-protein interactions than expected by random chance. Over-representation and GSEA analysis suggested genes playing roles in neuroinflammation, amyloid-β, autophagy and trafficking being important for the AD disease process. At the gene level, 10 genes from the STG that were consistently differentially expressed in this study and in the MSBB study (one of the three cohorts within the AMP-AD initiative) were enriched in microglial genes (TREM2, C3AR1, ITGAX, OLR1, CD74, and HLA-DRA), but also included genes with a broader cell type expression pattern such as CDK2AP1. Among the DEGs with supporting evidence from an independent study, CDK2AP1 (most abundantly expressed in astrocyte) was the transcript with strongest association with antemortem cognitive measure (last Mini-Mental State Examination score) and neurofibril tangle burden but also associated with amyloid plaque burden, while OLR1 was the transcript with strongest association with amyloid plaque burden. GSEA and over-representation analyses revealed gene sets related to immune processes including neutrophil degranulation, interleukin 10 signaling, and interferon gamma signaling, complement and coagulation cascades, phosphatidylinositol signaling system, phagosome and neurotransmitter receptors and postsynaptic signal transmission were enriched from this study and replicated in an independent study. CONCLUSION This study identified differential gene sets, common with two out of three AMP-AD cohorts (ROSMAP and MSBB) and highlights microglia and astrocyte as the key cell-types with DGEs associated with AD clinical diagnosis, and/or antemortem cognitive measure as well as neuropathological indices. Future meta-analysis and causal inferential analysis will be helpful in pinpointing the most relevant pathways and genes to intervene.
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Affiliation(s)
- Qingqin S. Li
- Neuroscience Department, Janssen Research & Development, LLC, 1125 Trenton-Harbourton Road, Titusville, NJ, 08560, USA
| | - Louis De Muynck
- Neuroscience Department, Janssen Research & Development, a Division of Janssen Pharmaceutica NV, 2340, Beerse, Belgium
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3
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Tinarelli F, Ivanova E, Colombi I, Barini E, Balzani E, Garcia CG, Gasparini L, Chiappalone M, Kelsey G, Tucci V. Cell-cell coupling and DNA methylation abnormal phenotypes in the after-hours mice. Epigenetics Chromatin 2021; 14:1. [PMID: 33407878 PMCID: PMC7789812 DOI: 10.1186/s13072-020-00373-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 11/13/2020] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation has emerged as an important epigenetic regulator of brain processes, including circadian rhythms. However, how DNA methylation intervenes between environmental signals, such as light entrainment, and the transcriptional and translational molecular mechanisms of the cellular clock is currently unknown. Here, we studied the after-hours mice, which have a point mutation in the Fbxl3 gene and a lengthened circadian period. Methods In this study, we used a combination of in vivo, ex vivo and in vitro approaches. We measured retinal responses in Afh animals and we have run reduced representation bisulphite sequencing (RRBS), pyrosequencing and gene expression analysis in a variety of brain tissues ex vivo. In vitro, we used primary neuronal cultures combined to micro electrode array (MEA) technology and gene expression. Results We observed functional impairments in mutant neuronal networks, and a reduction in the retinal responses to light-dependent stimuli. We detected abnormalities in the expression of photoreceptive melanopsin (OPN4). Furthermore, we identified alterations in the DNA methylation pathways throughout the retinohypothalamic tract terminals and links between the transcription factor Rev-Erbα and Fbxl3. Conclusions The results of this study, primarily represent a contribution towards an understanding of electrophysiological and molecular phenotypic responses to external stimuli in the Afh model. Moreover, as DNA methylation has recently emerged as a new regulator of neuronal networks with important consequences for circadian behaviour, we discuss the impact of the Afh mutation on the epigenetic landscape of circadian biology.
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Affiliation(s)
- Federico Tinarelli
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,BioMed X Innovation Center, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
| | - Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Ilaria Colombi
- Neuroscience and Brain Technologies, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,Brain Development and Disease, NBT, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Erica Barini
- Neurodevelopmental and Neurodegenerative Disease Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,AbbVie Deutschland GmbH & Co, Knollstr, 67061, Ludwigshafen, Germany
| | - Edoardo Balzani
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,Center for Neural Science, New York University, New York, NY, 10006, USA
| | - Celina Garcia Garcia
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Laura Gasparini
- Neurodevelopmental and Neurodegenerative Disease Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,AbbVie Deutschland GmbH & Co, Knollstr, 67061, Ludwigshafen, Germany
| | - Michela Chiappalone
- Neuroscience and Brain Technologies, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,Rehab Technologies, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Valter Tucci
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.
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Alsayegh KN, Sheridan SD, Iyer S, Rao RR. Knockdown of CDK2AP1 in human embryonic stem cells reduces the threshold of differentiation. PLoS One 2018; 13:e0196817. [PMID: 29734353 PMCID: PMC5937771 DOI: 10.1371/journal.pone.0196817] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/22/2018] [Indexed: 01/08/2023] Open
Abstract
Recent studies have suggested a role for the Cyclin Dependent Kinase-2 Associated Protein 1 (CDK2AP1) in stem cell differentiation and self-renewal. In studies with mouse embryonic stem cells (mESCs) derived from generated mice embryos with targeted deletion of the Cdk2ap1 gene, CDK2AP1 was shown to be required for epigenetic silencing of Oct4 during differentiation, with deletion resulting in persistent self-renewal and reduced differentiation potential. Differentiation capacity was restored in these cells following the introduction of a non-phosphorylatible form of the retinoblastoma protein (pRb) or exogenous Cdk2ap1. In this study, we investigated the role of CDK2AP1 in human embryonic stem cells (hESCs). Using a shRNA to reduce its expression in hESCs, we found that CDK2AP1 knockdown resulted in a significant reduction in the expression of the pluripotency genes, OCT4 and NANOG. We also found that CDK2AP1 knockdown increased the number of embryoid bodies (EBs) formed when differentiation was induced. In addition, the generated EBs had significantly higher expression of markers of all three germ layers, indicating that CDK2AP1 knockdown enhanced differentiation. CDK2AP1 knockdown also resulted in reduced proliferation and reduced the percentage of cells in the S phase and increased cells in the G2/M phase of the cell cycle. Further investigation revealed that a higher level of p53 protein was present in the CDK2AP1 knockdown hESCs. In hESCs in which p53 and CDK2AP1 were simultaneously downregulated, OCT4 and NANOG expression was not affected and percentage of cells in the S phase of the cell cycle was not reduced. Taken together, our results indicate that the knockdown of CDK2AP1 in hESCs results in increased p53 and enhances differentiation and favors it over a self-renewal fate.
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Affiliation(s)
- Khaled N. Alsayegh
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States of America
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Steven D. Sheridan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Shilpa Iyer
- Department of Biological Sciences, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, AR, United States of America
- * E-mail: (RR); (SI)
| | - Raj Raghavendra Rao
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, AR, United States of America
- * E-mail: (RR); (SI)
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5
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Kar S, Patra SK. Overexpression of OCT4 induced by modulation of histone marks plays crucial role in breast cancer progression. Gene 2018; 643:35-45. [DOI: 10.1016/j.gene.2017.11.077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/17/2017] [Accepted: 11/30/2017] [Indexed: 02/08/2023]
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6
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Afonso MB, Rodrigues PM, Simão AL, Gaspar MM, Carvalho T, Borralho P, Bañales JM, Castro RE, Rodrigues CMP. miRNA-21 ablation protects against liver injury and necroptosis in cholestasis. Cell Death Differ 2017; 25:857-872. [PMID: 29229992 DOI: 10.1038/s41418-017-0019-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/10/2017] [Accepted: 10/20/2017] [Indexed: 01/04/2023] Open
Abstract
Inhibition of microRNA-21 (miR-21) prevents necroptosis in the mouse pancreas. Necroptosis contributes to hepatic necro-inflammation in the common bile duct ligation (BDL) murine model. We aimed to evaluate the role of miR-21 in mediating deleterious processes associated with cholestasis. Mechanistic studies established a functional link between miR-21 and necroptosis through cyclin-dependent kinase 2-associated protein 1 (CDK2AP1). miR-21 expression increased in the liver of primary biliary cholangitis (PBC) patients and BDL wild-type (WT) mice at both 3 and 14 days. Notably, under BDL, miR-21 -/- mice displayed decreased liver injury markers in serum compared with WT mice, accompanied by reduced hepatocellular degeneration, oxidative stress and fibrosis. Hallmarks of necroptosis were decreased in the liver of BDL miR-21 -/- mice, via relieved repression of CDK2AP1. Further, miR-21 -/- mice displayed improved adaptive response of bile acid homeostasis. In conclusion, miR-21 ablation ameliorates liver damage and necroptosis in BDL mice. Inhibition of miR-21 should arise as a promising approach to treat cholestasis.
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Affiliation(s)
- Marta B Afonso
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro M Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - André L Simão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Maria M Gaspar
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Tânia Carvalho
- Histology and Comparative Pathology Laboratory, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Paula Borralho
- Escola Superior de Tecnologia da Saúde de Lisboa (ESTEsL), Lisbon, Portugal.,Instituto de Anatomia Patológica, Universidade de Lisboa, Lisbon, Portugal.,Hospital Cuf Descobertas, Lisbon, Portugal
| | - Jesús M Bañales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute - Donostia University Hospital - University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Rui E Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Cecília M P Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
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She S, Wei Q, Kang B, Wang YJ. Cell cycle and pluripotency: Convergence on octamer‑binding transcription factor 4 (Review). Mol Med Rep 2017; 16:6459-6466. [PMID: 28901500 PMCID: PMC5865814 DOI: 10.3892/mmr.2017.7489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
Abstract
Embryonic stem cells (ESCs) have unlimited expansion potential and the ability to differentiate into all somatic cell types for regenerative medicine and disease model studies. Octamer-binding transcription factor 4 (OCT4), encoded by the POU domain, class 5, transcription factor 1 gene, is a transcription factor vital for maintaining ESC pluripotency and somatic reprogramming. Many studies have established that the cell cycle of ESCs is featured with an abbreviated G1 phase and a prolonged S phase. Changes in cell cycle dynamics are intimately associated with the state of ESC pluripotency, and manipulating cell-cycle regulators could enable a controlled differentiation of ESCs. The present review focused primarily on the emerging roles of OCT4 in coordinating the cell cycle progression, the maintenance of pluripotency and the glycolytic metabolism in ESCs.
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Affiliation(s)
- Shiqi She
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Qucheng Wei
- Cardiovascular Key Lab of Zhejiang, Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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8
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Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets. Genes (Basel) 2017; 8:genes8080196. [PMID: 28783137 PMCID: PMC5575660 DOI: 10.3390/genes8080196] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/19/2017] [Accepted: 07/31/2017] [Indexed: 12/19/2022] Open
Abstract
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed “epigenetics”. These modifications play critical roles, either by affecting non-histone protein recruitment to chromatin or by disturbing chromatin contacts. Their presence dictates the condensed packaging of DNA and can coordinate the orderly recruitment of various enzyme complexes for DNA manipulation. This genetic modification machinery involves various writers, readers, and erasers that have unique structures, functions, and modes of action. Regarding human disease, studies have mainly focused on the genetic mechanisms; however, alteration in the balance of epigenetic networks can result in major pathologies including mental retardation, chromosome instability syndromes, and various types of cancers. Owing to its critical influence, great potential lies in developing epigenetic therapies. In this regard, this review has highlighted mechanistic and structural interactions of the main epigenetic families with their targets, which will help to identify more efficient and safe drugs against several diseases.
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9
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Bode D, Yu L, Tate P, Pardo M, Choudhary J. Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells. Mol Cell Proteomics 2015; 15:878-91. [PMID: 26714524 PMCID: PMC4813707 DOI: 10.1074/mcp.m115.053207] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/26/2022] Open
Abstract
Pluripotency and self-renewal, the defining properties of embryonic stem cells, are brought about by transcriptional programs involving an intricate network of transcription factors and chromatin remodeling complexes. The Nucleosome Remodeling and Deacetylase (NuRD) complex plays a crucial and dynamic role in the regulation of stemness and differentiation. Several NuRD-associated factors have been reported but how they are organized has not been investigated in detail. Here, we have combined affinity purification and blue native polyacrylamide gel electrophoresis followed by protein identification by mass spectrometry and protein correlation profiling to characterize the topology of the NuRD complex. Our data show that in mouse embryonic stem cells the NuRD complex is present as two distinct assemblies of differing topology with different binding partners. Cell cycle regulator Cdk2ap1 and transcription factor Sall4 associate only with the higher mass NuRD assembly. We further establish that only isoform Sall4a, and not Sall4b, associates with NuRD. By contrast, Suz12, a component of the PRC2 Polycomb repressor complex, associates with the lower mass entity. In addition, we identify and validate a novel NuRD-associated protein, Wdr5, a regulatory subunit of the MLL histone methyltransferase complex, which associates with both NuRD entities. Bioinformatic analyses of published target gene sets of these chromatin binding proteins are in agreement with these structural observations. In summary, this study provides an interesting insight into mechanistic aspects of NuRD function in stem cell biology. The relevance of our work has broader implications because of the ubiquitous nature of the NuRD complex. The strategy described here can be more broadly applicable to investigate the topology of the multiple complexes an individual protein can participate in.
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Affiliation(s)
- Daniel Bode
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Lu Yu
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Peri Tate
- §Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Mercedes Pardo
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK;
| | - Jyoti Choudhary
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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10
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Wille A, Maurer V, Piatti P, Whittle N, Rieder D, Singewald N, Lusser A. Impaired Contextual Fear Extinction Learning is Associated with Aberrant Regulation of CHD-Type Chromatin Remodeling Factors. Front Behav Neurosci 2015; 9:313. [PMID: 26635563 PMCID: PMC4649039 DOI: 10.3389/fnbeh.2015.00313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/03/2015] [Indexed: 02/04/2023] Open
Abstract
Successful attenuation of fearful memories is a cognitive process requiring initiation of highly coordinated transcription programs. Chromatin-modulating mechanisms such as DNA methylation and histone modifications, including acetylation, are key regulators of these processes. However, knowledge concerning the role of ATP-dependent chromatin remodeling factors (ChRFs) being required for successful fear extinction is lacking. Underscoring the potential importance of these factors that alter histone-DNA contacts within nucleosomes are recent genome-wide association studies linking several ChRFs to various human cognitive and psychiatric disorders. To better understand the role of ChRFs in the brain, and since to date little is known about ChRF expression in the brain, we performed a comprehensive survey of expression levels of 24 ATP-dependent remodelers across different brain areas, and we identified several distinct high molecular weight complexes by chromatographic methods. We next aimed to gain novel insight into the potential regulation of ChRFs in different brain regions in association with normal and impaired fear extinction learning. To this end, we established the 129S1/SvImJ (S1) laboratory mouse strain as a model for compromised contextual fear extinction learning that can be rescued by dietary zinc restriction (ZnR). Using this model along with genetically related but fear extinction-competent 129S6/SvEv (S6) mice as controls, we found that impaired fear extinction in S1 was associated with enhanced ventral hippocampal expression of CHD1 and reduced expression of CHD5 that was normalized following successful rescue of impaired fear extinction. Moreover, a select reduction in CHD3 expression was observed in the ventral hippocampus (vHC) following successful rescue of fear extinction in S1 mice. Taken together, these data provide novel insight into the regulation of specific ChRFs following an impaired cognitive process and its rescue, and they suggest that imbalance of CHD-type remodeler levels, which consequently may lead to changes of transcriptional programs, may be an underlying mechanism involved in impaired fear extinction learning and its therapeutic rescue.
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Affiliation(s)
- Alexandra Wille
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Verena Maurer
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Paolo Piatti
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Nigel Whittle
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
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Alsayegh KN, Gadepalli VS, Iyer S, Rao RR. Knockdown of CDK2AP1 in primary human fibroblasts induces p53 dependent senescence. PLoS One 2015; 10:e0120782. [PMID: 25785833 PMCID: PMC4365013 DOI: 10.1371/journal.pone.0120782] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/06/2015] [Indexed: 12/30/2022] Open
Abstract
Cyclin Dependent Kinase-2 Associated Protein-1 (CDK2AP1) is known to be a tumor suppressor that plays a role in cell cycle regulation by sequestering monomeric CDK2, and targeting it for proteolysis. A reduction of CDK2AP1 expression is considered to be a negative prognostic indicator in patients with oral squamous cell carcinoma and also associated with increased invasion in human gastric cancer tissue. CDK2AP1 overexpression was shown to inhibit growth, reduce invasion and increase apoptosis in prostate cancer cell lines. In this study, we investigated the effect of CDK2AP1 downregulation in primary human dermal fibroblasts. Using a short-hairpin RNA to reduce its expression, we found that knockdown of CDK2AP1in primary human fibroblasts resulted in reduced proliferation and in the induction of senescence associated beta-galactosidase activity. CDK2AP1 knockdown also resulted in a significant reduction in the percentage of cells in the S phase and an accumulation of cells in the G1 phase of the cell cycle. Immunocytochemical analysis also revealed that the CDK2AP1 knockdown significantly increased the percentage of cells that exhibited γ-H2AX foci, which could indicate presence of DNA damage. CDK2AP1 knockdown also resulted in increased mRNA levels of p53, p21, BAX and PUMA and p53 protein levels. In primary human fibroblasts in which p53 and CDK2AP1 were simultaneously downregulated, there was: (a) no increase in senescence associated beta-galactosidase activity, (b) decrease in the number of cells in the G1-phase and increase in number of cells in the S-phase of the cell cycle, and (c) decrease in the mRNA levels of p21, BAX and PUMA when compared with CDK2AP1 knockdown only fibroblasts. Taken together, this suggests that the observed phenotype is p53 dependent. We also observed a prominent increase in the levels of ARF protein in the CDK2AP1 knockdown cells, which suggests a possible role of ARF in p53 stabilization following CDK2AP1 knockdown. Altogether, our results show that knockdown of CDK2AP1 in primary human fibroblasts reduced proliferation and induced premature senescence, with the observed phenotype being p53 dependent.
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Affiliation(s)
- Khaled N. Alsayegh
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, United States of America
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Venkat S. Gadepalli
- Integrated Life Sciences Program, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Shilpa Iyer
- Center for the Study of Biological Complexity, Life Sciences Program, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Chemical and Life Sciences Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Raj R. Rao
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, United States of America
- Integrated Life Sciences Program, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Center for the Study of Biological Complexity, Life Sciences Program, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Chemical and Life Sciences Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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12
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Re A, Workman CT, Waldron L, Quattrone A, Brunak S. Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells. Stem Cell Res 2014; 13:316-28. [PMID: 25173649 DOI: 10.1016/j.scr.2014.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/25/2014] [Accepted: 07/26/2014] [Indexed: 11/25/2022] Open
Abstract
The shortage of molecular information on cell cycle changes along embryonic stem cell (ESC) differentiation prompts an in silico approach, which may provide a novel way to identify candidate genes or mechanisms acting in coordinating the two programs. We analyzed germ layer specific gene expression changes during the cell cycle and ESC differentiation by combining four human cell cycle transcriptome profiles with thirteen in vitro human ESC differentiation studies. To detect cross-talk mechanisms we then integrated the transcriptome data that displayed differential regulation with protein interaction data. A new class of non-transcriptionally regulated genes was identified, encoding proteins which interact systematically with proteins corresponding to genes regulated during the cell cycle or cell differentiation, and which therefore can be seen as interface proteins coordinating the two programs. Functional analysis gathered insights in fate-specific candidates of interface functionalities. The non-transcriptionally regulated interface proteins were found to be highly regulated by post-translational ubiquitylation modification, which may synchronize the transition between cell proliferation and differentiation in ESCs.
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Affiliation(s)
- Angela Re
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via delle Regole 101, I38123 Trento, Italy; Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark
| | - Christopher T Workman
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark
| | - Levi Waldron
- City University of New York School of Public Health, Hunter College, 2180 3rd Avenue, NY 10035, USA
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via delle Regole 101, I38123 Trento, Italy.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK2200 Copenhagen, Denmark.
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13
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Liu L, Yang X, Ni Q, Xiao Z, Zhao Y, Han J, Sun M, Chen B. Interaction between p12CDK2AP1 and a novel unnamed protein product inhibits cell proliferation by regulating the cell cycle. Mol Med Rep 2013; 9:156-62. [PMID: 24248101 DOI: 10.3892/mmr.2013.1801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 10/16/2013] [Indexed: 11/05/2022] Open
Abstract
Human p12CDK2AP1 protein is encoded by the cyclin‑dependent kinase 2‑associated protein 1 (CDK2AP1) gene. This protein suppresses cell growth, differentiation and angiogenesis in numerous types of carcinoma by interacting with certain cell cycle proteins, including CDK2 and DNA polymerase α/primase. p12CDK2AP1 exerts its functions predominantly through protein‑protein interactions. Therefore, the identification of other p12CDK2AP1‑interacting proteins may clarify its role in cell cycle regulation and carcinogenesis. The aim of this study was to identify additional p12CDK2AP1‑interacting proteins. A novel unnamed protein product (UPP, BC006130) was identified through using a yeast two‑hybrid system. The interaction of p12CDK2AP1 with the UPP was further verified by glutathione S-transferase pull‑down and co‑immunoprecipitation experiments in vitro. The qPCR results following overexpression and siRNA assays demonstrated that the expression levels of the UPP were mediated by the CDK2AP1 gene. Furthermore, overexpression of the UPP gene was shown to shorten the length of the G2/M phase of the cell cycle in normal and tumor cell lines in a flow cytometry assay. The results of human tumor xenografts experiments in Balb/c nude mice indicated that stable transfection with the UPP gene was able to inhibit tumor cell proliferation in vivo. Overall, this study identified and characterized a novel interactive protein of p12CDK2AP1, which may inhibit cell proliferation by mediating the cell cycle. It expands the understanding of the mechanisms of p12CDK2AP1 and its potential as a cancer therapeutic target.
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Affiliation(s)
- Lijun Liu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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14
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Jerabek S, Merino F, Schöler HR, Cojocaru V. OCT4: dynamic DNA binding pioneers stem cell pluripotency. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1839:138-54. [PMID: 24145198 DOI: 10.1016/j.bbagrm.2013.10.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/02/2013] [Accepted: 10/06/2013] [Indexed: 12/12/2022]
Abstract
OCT4 was discovered more than two decades ago as a transcription factor specific to early embryonic development. Early studies with OCT4 were descriptive and looked at determining the functional roles of OCT4 in the embryo as well as in pluripotent cell lines derived from embryos. Later studies showed that OCT4 was one of the transcription factors in the four-factor cocktail required for reprogramming somatic cells into induced pluripotent stem cells (iPSCs) and that it is the only factor that cannot be substituted in this process by other members of the same protein family. In recent years, OCT4 has emerged as a master regulator of the induction and maintenance of cellular pluripotency, with crucial roles in the early stages of differentiation. Currently, mechanistic studies look at elucidating the molecular details of how OCT4 contributes to establishing selective gene expression programs that define different developmental stages of pluripotent cells. OCT4 belongs to the POU family of proteins, which have two conserved DNA-binding domains connected by a variable linker region. The functions of OCT4 depend on its ability to recognize and bind to DNA regulatory regions alone or in cooperation with other transcription factors and on its capacity to recruit other factors required to regulate the expression of specific sets of genes. Undoubtedly, future iPSC-based applications in regenerative medicine will benefit from understanding how OCT4 functions. Here we provide an integrated view of OCT4 research conducted to date by reviewing the different functional roles for OCT4 and discussing the current progress in understanding their underlying molecular mechanisms. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Stepan Jerabek
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Felipe Merino
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Hans Robert Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany.
| | - Vlad Cojocaru
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany.
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15
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Jiao F, Wang X, Yan Z, Liu C, Yue Z, Li Z, Ma Y, Li Y, Wang J. Effect of dynamic DNA methylation and histone acetylation on cPouV expression in differentiation of chick embryonic germ cells. Stem Cells Dev 2013; 22:2725-35. [PMID: 23750509 DOI: 10.1089/scd.2013.0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As a crucial pluripotency-related factor, the epigenetic regulation of Oct4 has been studied intensively in mammalians. However, its dynamic changes of DNA methylation and histone modification in avians remain poorly understood. In the present study, we first described the alterations of DNA methylation and histone acetylation in the promoter of chicken PouV (cPouV; the homologue of Oct4 in avian) during chick embryonic germ (EG) cell differentiation. The epigenetic modification analysis showed that DNA methylation in the cPouV promoter increased obviously, while histone acetylation decreased dramatically detected by chromatin immunoprecipitation assay in the process of differentiation. Gene expression analysis detection indicated that the levels of DNA methyltransferase 3a (Dnmt 3a), Dnmt 3b, and histone deacetylase 3 (HDAC 3) transcripts were significantly high, whereas the relative abundance of Dnmt 1, histone acetyltransferase (HAT), and cPouV mRNA was significantly decreased during the conversion of EG to embryoid body-like structures (EBs), which was correlated with the increased level of methylation and reduced level of H3 acetylation. Moreover, in vitro methylation assay indicated that the reporter gene was remarkably inhibited by the methylated promoter of cPouV. To further understand the effect of epigenetic modifiers on cPouV expression, we performed an analysis of EB cells treated with trichostatin A (TSA), Aza-2'-deoxycytidine (Aza), or TSA plus Aza (TSA/Aza). We observed that the effect of TSA/Aza is more sensitive to the reactivation of cPouV compared with TSA or Aza, indicating that these epigenetic inhibitors can function synergistically to facilitate the reprogramming process. The present study provided evidences that a critical role for cPouV activation/repression by DNA methylation and/or histone modifications is involved in the pluripotency maintenance and differentiation process of chick EG.
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Affiliation(s)
- Fei Jiao
- 1 Department of Biochemistry and Molecular Biology, Binzhou Medical College , Yantai, Shandong Province, People's Republic of China
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16
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Abstract
PSCs (pluripotent stem cells) possess two key properties that have made them the focus of global research efforts in regenerative medicine: they have unlimited expansion potential under conditions which favour their preservation as PSCs and they have the ability to generate all somatic cell types upon differentiation (pluripotency). Conditions have been defined in vitro in which pluripotency is maintained, or else differentiation is favoured and is directed towards specific somatic cell types. However, an unanswered question is whether or not the core cell cycle machinery directly regulates the pluripotency and differentiation properties of PSCs. If so, then manipulation of the cell cycle may represent an additional tool by which in vitro maintenance or differentiation of PSCs may be controlled in regenerative medicine. The present review aims to summarize our current understanding of links between the core cell cycle machinery and the maintenance of pluripotency in ESCs (embryonic stem cells) and iPSCs (induced PSCs).
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17
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Luo M, Liu Z, Hao H, Lu T, Chen M, Lei M, Verfaillie CM, Liu Z. High glucose facilitates cell cycle arrest of rat bone marrow multipotent adult progenitor cells through transforming growth factor-β1 and extracellular signal-regulated kinase 1/2 signalling without changing Oct4 expression. Clin Exp Pharmacol Physiol 2013; 39:843-51. [PMID: 22804759 DOI: 10.1111/j.1440-1681.2012.05747.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
1. The transcription factor Oct4 is critical to the pluripotency, self-renewal and differentiation of stem cells. The aim of the present study was to investigate the effects of high glucose (HG) on the cell cycle progression of bone marrow multipotent adult progenitor cells (MAPC) and Oct4 expression, as well as the underlying mechanisms. 2. Rat MAPC were cultured in normal (5.5 mmol/L D-glucose) and HG (25.5 mmol/L D-glucose) media for up to 14 days. L-Glucose served as a high osmolarity control. Culture in HG media substantially increased the number of cells in the G(0)/G(1) phase and decreased the number in the S phase without changing the cell population in the G(2) phase. Expression of the cell cycle regulatory protein p21CIP/WAF-1 (p21), but not that of p27KIP-1 (p27), was significantly upregulated in cells cultured in HG media. Significant increases were seen in transforming growth factor (TGF)-β1 levels in cells and MAPC-conditioned medium in the presence of HG, and extracellular signal-regulated kinase (ERK) 1/2 phosphorylation was enhanced in cells cultured in the presence of HG medium without any changes in Akt phosphorylation. 3. Neutralizing TGF-β1 antibody effectively prevented HG-induced increases in ERK1/2 phosphorylation, p21 expression and suppression of cell cycle progression of MAPC. Inhibiting ERK1/2 phosphorylation with PD98059 completely blocked HG-induced p21 expression and markedly reversed HG-induced inhibition of cell cycle progression in MAPC. The HG-induced suppression of cell cycle progression was not accompanied by inhibition of cell proliferation or Oct4 expression in these cells. 4. The data indicate that HG facilitates cell cycle arrest of rat MAPC through TGF-β1-induced activation of ERK1/2 signalling and p21 expression, and that Oct4 expression in MAPC is independent of the cell cycle and/or TGF-β1 or ERK1/2 signalling in HG medium.
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Affiliation(s)
- Min Luo
- Xiangya Hospital of Central South University, Changsha, Hunan, China
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18
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Kim JJ, Khalid O, Vo S, Sun HH, Wong DTW, Kim Y. A novel regulatory factor recruits the nucleosome remodeling complex to wingless integrated (Wnt) signaling gene promoters in mouse embryonic stem cells. J Biol Chem 2012; 287:41103-17. [PMID: 23074223 DOI: 10.1074/jbc.m112.416545] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nucleosome remodeling and deacetylation (NuRD) complex is required for modulating the transcription of essential pluripotency genes in ESC self-renewal. MBD3 is considered a key player in the formation of a functional NuRD complex. The recruitment of MBD3 to methylated promoters may require other prerequisite factors. We show that cyclin-dependent kinase 2-associated protein 1 (CDK2AP1), an essential gene for early embryonic development, plays a role in pluripotency of ESC by engaging MBD3 to the promoter region of Wnt signaling genes. The occupancy of MBD3 on several promoters of Wnt genes was significantly lost in the absence of CDK2AP1, resulting in hyperactivation of Wnt. We propose that the transcriptional modulation of the Wnt pathway mediated by NuRD requires the presence of essential auxiliary components such as CDK2AP1, which may aid the association of the complex with specific focal regions of the target promoters.
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Affiliation(s)
- Jeffrey J Kim
- Laboratory of Stem Cell and Cancer Epigenetic Research, UCLA, Los Angeles, California 90095, USA
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19
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Chaerkady R, Letzen B, Renuse S, Sahasrabuddhe NA, Kumar P, All AH, Thakor NV, Delanghe B, Gearhart JD, Pandey A, Kerr CL. Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. Proteomics 2011; 11:4007-20. [PMID: 21770034 DOI: 10.1002/pmic.201100107] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 06/19/2011] [Accepted: 07/01/2011] [Indexed: 11/11/2022]
Abstract
Oligodendrocytes (OLs) are glial cells of the central nervous system, which produce myelin. Cultured OLs provide immense therapeutic opportunities for treating a variety of neurological conditions. One of the most promising sources for such therapies is human embryonic stem cells (ESCs) as well as providing a model to study human OL development. For these purposes, an investigation of proteome level changes is critical for understanding the process of OL differentiation. In this report, an iTRAQ-based quantitative proteomic approach was used to study multiple steps during OL differentiation including neural progenitor cells, glial progenitor cells and oligodendrocyte progenitor cells (OPCs) compared to undifferentiated ESCs. Using a 1% false discovery rate cutoff, ∼3145 proteins were quantitated and several demonstrated progressive stage-specific expression. Proteins such as transferrin, neural cell adhesion molecule 1, apolipoprotein E and wingless-related MMTV integration site 5A showed increased expression from the neural progenitor cell to the OPC stage. Several proteins that have demonstrated evidence or been suspected in OL maturation were also found upregulated in OPCs including fatty acid-binding protein 4, THBS1, bone morphogenetic protein 1, CRYAB, transferrin, tenascin C, COL3A1, TGFBI and EPB41L3. Thus, by providing the first extensive proteomic profiling of human ESC differentiation into OPCs, this study provides many novel proteins that are potentially involved in OL development.
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Affiliation(s)
- Raghothama Chaerkady
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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20
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Wong DTW, Kim JJ, Khalid O, Sun HH, Kim Y. Double edge: CDK2AP1 in cell-cycle regulation and epigenetic regulation. J Dent Res 2011; 91:235-41. [PMID: 21865592 DOI: 10.1177/0022034511420723] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cancer research has been devoted toward an understanding of the molecular regulation and functional significance of cell-cycle regulators in the pathogenesis and development of cancers. Cyclin-dependent Kinase 2-associated Protein 1 (CDK2AP1) is one such cell-cycle regulator, originally identified as a growth suppressor and a prognostic marker for human oral/head and neck cancers. Functional importance and the molecular mechanism of CDK2AP1-mediated cell-cycle regulation have been documented over the years. Recent progress has shown that CDK2AP1 is a competency factor in embryonic stem cell differentiation. Deletion of CDK2AP1 leads to early embryonic lethality, potentially through altered differentiation capability of embryonic stem cells. More intriguingly, CDK2AP1 exerts its effect on stem cell maintenance/differentiation through epigenetic regulation. Cancer cells and stem cells share common cellular characteristics, most prominently in maintaining high proliferative potential through an unconventional cell-cycle regulatory mechanism. Cross-talk between cellular processes and molecular signaling pathways is frequent in any biological system. Currently, it remains largely elusive how cell-cycle regulation is mechanistically linked to epigenetic control. Understanding the molecular mechanism underlying CDK2AP1-mediated cell-cycle regulation and epigenetic control will set an example for establishing a novel and effective molecular link between these two important regulatory mechanisms.
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Affiliation(s)
- D T W Wong
- UCLA School of Dentistry and Dental Research Institute, 10833 Le Conte Ave., 73-017 CHS, Los Angeles, CA 90095, USA
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21
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Zhang Y. Biology of the Mi-2/NuRD Complex in SLAC (Stemness, Longevity/Ageing, and Cancer). GENE REGULATION AND SYSTEMS BIOLOGY 2011; 5:1-26. [PMID: 21523247 PMCID: PMC3080740 DOI: 10.4137/grsb.s6510] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The dynamic chromatin activities of Mi-2/Nucleosome Remodeling and Histone deacetylation (Mi-2/NuRD) complexes in mammals are at the basis of current research on stemness, longevity/ageing, and cancer (4-2-1/SLAC), and have been widely studied over the past decade in mammals and the elegant model organism, Caenorhabditis elegans. Interestingly, a common emergent theme from these studies is that of distinct coregulator-recruited Mi-2/NuRD complexes largely orchestrating the 4-2-1/SLAC within a unique paradigm by maintaining genome stability via DNA repair and controlling three types of transcriptional programs in concert in a number of cellular, tissue, and organism contexts. Thus, the core Mi-2/NuRD complex plays a central role in 4-2-1/SLAC. The plasticity and robustness of 4-2-1/SLAC can be interpreted as modulation of specific coregulator(s) within cell-specific, tissue-specific, stage-specific, or organism-specific niches during stress induction, ie, a functional module and its networking, thereby conferring differential responses to different environmental cues. According to “Occam’s razor”, a simple theory is preferable to a complex one, so this simplified notion might be useful for exploring 4-2-1/SLAC with a holistic view. This thought could also be valuable in forming strategies for future research, and could open up avenues for cancer prevention and antiageing strategies.
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Affiliation(s)
- Yue Zhang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA
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22
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Abstract
Pluripotency, a characteristic of cells in the inner cell mass of the mammalian preimplantation blastocyst as well as of embryonic stem cells, is defined as the ability of a cell to generate all of the cell types of an organism. A group of transcription factors is essential for the establishment and maintenance of the pluripotent state. Recent studies have demonstrated that differentiated somatic cells could be reverted to a pluripotent state by the overexpression of a set of transcription factors, further highlighting the significance of transcription factors in the control of pluripotency. Among these factors, a member of the POU transcription factor family, Oct4, is central to the machinery governing pluripotency. Oct4 is highly expressed in pluripotent cells and becomes silenced upon differentiation. Interestingly, the precise expression level of Oct4 determines the fate of embryonic stem cells. Therefore, to control the expression of Oct4 precisely, a variety of regulators function at multiple levels, including transcription, translation of mRNA and post-translational modification. Additionally, in cooperation with Sox2, Nanog and other members of the core transcriptional regulatory circuitry, Oct4 activates both protein-coding genes and noncoding RNAs necessary for pluripotency. Simultaneously, in association with transcriptional repressive complexes, Oct4 represses another set of targets involved in developmental processes. Importantly, Oct4 can re-establish pluripotency in somatic cells, and proper reprogramming of Oct4 expression is indispensable for deriving genuine induced pluripotent stem cell lines. In the past several years, genome-wide identification of Oct4 target genes and Oct4-centered protein interactomes has been reported, indicating that Oct4 exerts tight control over pluripotency regulator expression and protects embryonic stem cells in an undifferentiated state. Nevertheless, further investigation is required to fully elucidate the underlying molecular mechanisms through which Oct4 maintains and reinitiates pluripotency. Systemic and dynamic exploration of the protein complexes and target genes associated with Oct4 will help to elucidate the role of Oct4 more comprehensively.
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Affiliation(s)
- Guilai Shi
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, Shanghai 200025, China.
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23
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Cheon YP, Kim CH. Progesterone is primary regulator of Cdk2ap1 gene expression and tissue-specific expression in the uterus. J Endocrinol Invest 2010; 33:650-6. [PMID: 20354353 DOI: 10.1007/bf03346665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Proliferation of endometrial cells is a prerequisite step for functional differentiation in the uterus. A tumor suppressor gene, Cyclin-dependent kinase 2-associated protein 1 (Cdk2ap1) mRNA was detected in the pregnant uterus and was suggested to be involved in cell proliferation. However, its roles and the mechanisms regulating its expression are largely unknown. In this study, the role of steroid hormones in the expression of Cdk2ap1 was examined using RT-PCR, Northern blotting and in situ hybridization methods. Cdk2ap1 mRNA was highly expressed during the proestrus phase and was mainly localized in the epithelium and subepithelium. Its expression was induced by a single injection of estradiol and progesterone, but the effect of progesterone was stronger than that of estradiol. Injections of progesterone (P1,2) on 2 consecutive days induced Cdk2ap1 expression in the endometrium with the same patterns observed in the proestrus phase, but injections of estradiol (E1,2) on 2 consecutive days did not induce expression. The Cdk2ap1 mRNA level was decreased by combined treatment of progesterone and estradiol (E1+P2,3). RU486 suppressed completely the Cdk2ap1 mRNA expression in P1,2 while ICI 182,780 did not in E1+P2,3. In the uteri on day 4 of gestation, expression of Cdk2ap1 also was regulated by progesterone as expected. Cdk2ap1 mRNA expression was totally suppressed by RU486 but not by ICI 182,780. Thus, it is suggested that Cdk2ap1 expression is primarily regulated by progesterone and the progesterone receptor in uterus and is mainly localized to proliferating tissues.
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Affiliation(s)
- Y P Cheon
- Division of Development and Physiology, School of Biological Sciences and Chemistry, Institute for Basic Sciences, College of Natural Sciences, Sungshin Women's University, Seongbukgu, Seoul, Korea.
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24
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Fazzio TG, Panning B. Control of embryonic stem cell identity by nucleosome remodeling enzymes. Curr Opin Genet Dev 2010; 20:500-4. [PMID: 20800472 DOI: 10.1016/j.gde.2010.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 08/04/2010] [Indexed: 11/19/2022]
Abstract
Embryonic stem (ES) cells are pluripotent cells that can self-renew indefinitely or be induced to differentiate into multiple cell lineages, and thus have the potential to be used in regenerative medicine. Pluripotency transcription factors (TFs), such as Oct4, Sox2, and Nanog, function in a regulatory circuit that silences the expression of key TFs required for differentiation and activates the expression of genes important for maintenance of pluripotency. In addition, proteins that remodel chromatin structure also play important roles in determining the ES cell-specific gene expression pattern. Here we review recent studies demonstrating the roles of enzymes that carry out one facet of chromatin regulation, nucleosome remodeling, in control of ES cell self-renewal and differentiation.
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Affiliation(s)
- Thomas G Fazzio
- Program in Gene Function and Expression, University of Massachusetts Medical School, United States
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25
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Spruijt CG, Bartels SJJ, Brinkman AB, Tjeertes JV, Poser I, Stunnenberg HG, Vermeulen M. CDK2AP1/DOC-1 is a bona fide subunit of the Mi-2/NuRD complex. MOLECULAR BIOSYSTEMS 2010; 6:1700-6. [PMID: 20523938 DOI: 10.1039/c004108d] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The Mi-2/NuRD (NUcleosome Remodeling and histone Deacetylase) chromatin remodeling complex is a large heterogeneous multiprotein complex associated with transcriptional repression. Here we apply a SILAC based quantitative proteomics approach to show that all known Mi-2/NuRD complex subunits co-purify with Cyclin Dependent Kinase 2 Associated Protein1 (CDK2AP1), also known as Deleted in Oral Cancer 1 (DOC-1). DOC-1 displays in vitro binding affinity for methylated DNA as part of the meCpG binding MBD2/NuRD complex. In luciferase reporter assays, DOC-1 is a potent repressor of transcription. Finally, immunofluorescence experiments reveal co-localization between MBD2 and DOC-1 in mouse NIH-3T3 nuclei. Collectively, these results indicate that DOC-1 is a bona fide subunit of the Mi-2/NuRD chromatin remodeling complex.
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Affiliation(s)
- Cornelia G Spruijt
- Department of Physiological Chemistry and Cancer Genomics Centre, University Medical Center Utrecht, Utrecht, The Netherlands
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Jung M, Peterson H, Chavez L, Kahlem P, Lehrach H, Vilo J, Adjaye J. A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS One 2010; 5:e10709. [PMID: 20505756 PMCID: PMC2873957 DOI: 10.1371/journal.pone.0010709] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 04/25/2010] [Indexed: 01/06/2023] Open
Abstract
It is essential to understand the network of transcription factors controlling self-renewal of human embryonic stem cells (ESCs) and human embryonal carcinoma cells (ECs) if we are to exploit these cells in regenerative medicine regimes. Correlating gene expression levels after RNAi-based ablation of OCT4 function with its downstream targets enables a better prediction of motif-specific driven expression modules pertinent for self-renewal and differentiation of embryonic stem cells and induced pluripotent stem cells.We initially identified putative direct downstream targets of OCT4 by employing CHIP-on-chip analysis. A comparison of three peak analysis programs revealed a refined list of OCT4 targets in the human EC cell line NCCIT, this list was then compared to previously published OCT4 CHIP-on-chip datasets derived from both ES and EC cells. We have verified an enriched POU-motif, discovered by a de novo approach, thus enabling us to define six distinct modules of OCT4 binding and regulation of its target genes.A selection of these targets has been validated, like NANOG, which harbours the evolutionarily conserved OCT4-SOX2 binding motif within its proximal promoter. Other validated targets, which do not harbour the classical HMG motif are USP44 and GADD45G, a key regulator of the cell cycle. Over-expression of GADD45G in NCCIT cells resulted in an enrichment and up-regulation of genes associated with the cell cycle (CDKN1B, CDKN1C, CDK6 and MAPK4) and developmental processes (BMP4, HAND1, EOMES, ID2, GATA4, GATA5, ISL1 and MSX1). A comparison of positively regulated OCT4 targets common to EC and ES cells identified genes such as NANOG, PHC1, USP44, SOX2, PHF17 and OCT4, thus further confirming their universal role in maintaining self-renewal in both cell types. Finally we have created a user-friendly database (http://biit.cs.ut.ee/escd/), integrating all OCT4 and stem cell related datasets in both human and mouse ES and EC cells.In the current era of systems biology driven research, we envisage that our integrated embryonic stem cell database will prove beneficial to the booming field of ES, iPS and cancer research.
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Affiliation(s)
- Marc Jung
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail: (JA); (MJ)
| | - Hedi Peterson
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Quretec Ltd., Tartu, Estonia
| | - Lukas Chavez
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Pascal Kahlem
- EMBL - European Bioinformatics Institute, Cambridge, United Kingdom
| | - Hans Lehrach
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jaak Vilo
- Quretec Ltd., Tartu, Estonia
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - James Adjaye
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail: (JA); (MJ)
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Streamlined analysis schema for high-throughput identification of endogenous protein complexes. Proc Natl Acad Sci U S A 2010; 107:2431-6. [PMID: 20133760 DOI: 10.1073/pnas.0912599106] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Immunoprecipitation followed by mass spectrometry (IP/MS) has recently emerged as a preferred method in the analysis of protein complex components and cellular protein networks. Targeting endogenous protein complexes of higher eukaryotes, particularly in large-scale efforts, has been challenging due to cellular heterogeneity, high proteome complexity, and, compared to lower organisms, lack of efficient in-locus epitope-tagging techniques. It is further complicated by variability in nonspecific identifications and cross-reactivity of primary antibodies. Still, the study of endogenous human protein networks is highly desired despite its challenges. Here we describe a streamlined IP/MS protocol for the purification and identification of extended endogenous protein complexes. We investigate the sources of nonspecific protein binding and develop semiquantitative specificity filters that are based on peptide spectral count measurements. We also outline logical constraints for the derivation of accurate complex composition from IP/MS data and demonstrate the effectiveness of this approach by presenting our analyses of different transcriptional coregulator complexes. We show consistent purification of novel components for the Integrator complex, analyze the composition of the Mediator complex solely from our data to demonstrate the wide usability of spectral counts, and deconvolute heterogeneous HDAC1/2 networks into core complex modules and several novel subcomplex interactions.
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Mahapatra S, Firpo MT, Bacanamwo M. Inhibition of DNA methyltransferases and histone deacetylases induces bone marrow-derived multipotent adult progenitor cells to differentiate into endothelial cells. Ethn Dis 2010; 20:S1-64. [PMID: 20521387 PMCID: PMC5702555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
INTRODUCTION Endothelial dysfunction plays a critical role in the pathogenesis of cardiovascular diseases and cancer. Bone marrow-derived multipotent adult progenitor cells (MAPC) have the potential to differentiate, at the single cell level, toward the three embryonic germ layers and may be the progenitors of the other tissue-specific stem cells. However, molecular mechanisms of endothelial differentiation from MAPC have not been defined. The importance of epigenetic changes such as DNA methylation and histone acetylation in gene regulatory networks during embryonic stem cell (ESC) differentiation has been documented. We postulated that endothelial cell (EC) differentiation from MAPC could be enhanced by inhibiting DNA methylation and histone deacetylation, reversing the repression of genes that specify EC fate. METHODS MAPCs were derived from rat bone marrow and differentiated into EC by vascular endothelial growth factor (VEGF) treatment in the presence or absence of the specific DNA methyltransferase (DNMT) inhibitor 5'-aza-2'-deoxycytidine (aza-dC) and the histone deacetylase (HDAC) inhibitor trichostatin A (TSA). Expression of the endothelial marker genes was assessed by real time quantitative PCR and angiogenic potential of the differentiated EC was assessed by analysis of vascular network formation on fibronectin. RESULTS Both aza-dC and TSA induced at least a three-fold increase in the expression of the EC marker genes VE-cadherin, vWF, and Flk1. This increase was also observed in the presence of the EC differentiation inducer VEGF, suggesting that factors other than VEGF mediate the response to the epigenetic agents. Both DNMT and HDAC inhibition stimulated vascular network formation. CONCLUSION Epigenetic therapy holds a potential in inducing self-repair, vascular tissue regeneration, controlling angiogenesis and endothelial dysfunction.
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Affiliation(s)
- Saswati Mahapatra
- Department of Medicine, Division of Endocrinology and Stem Cell Institute, University of Minnesota, Minneapolis, USA
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Kang J, Shakya A, Tantin D. Stem cells, stress, metabolism and cancer: a drama in two Octs. Trends Biochem Sci 2009; 34:491-9. [PMID: 19733480 DOI: 10.1016/j.tibs.2009.06.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 05/30/2009] [Accepted: 06/03/2009] [Indexed: 01/16/2023]
Abstract
It is a classic story of two related transcription factors. Oct4 is a potent regulator of pluripotency during early mammalian embryonic development, and is notable for its ability to convert adult somatic cells to pluripotency. The widely expressed Oct1 protein shares significant homology with Oct4, binds to the same sequences, regulates common target genes, and shares common modes of upstream regulation, including the ability to respond to cellular stress. Both proteins are also associated with malignancy, yet Oct1 cannot substitute for Oct4 in the generation of pluripotency. The molecular underpinnings of these phenomena are emerging, as are the consequences for adult stem cells and cancer, and thereby hangs a tale.
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Affiliation(s)
- Jinsuk Kang
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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Kim Y, Deshpande A, Dai Y, Kim JJ, Lindgren A, Conway A, Clark AT, Wong DT. Cyclin-dependent kinase 2-associating protein 1 commits murine embryonic stem cell differentiation through retinoblastoma protein regulation. J Biol Chem 2009; 284:23405-14. [PMID: 19564334 DOI: 10.1074/jbc.m109.026088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) maintain pluripotency and indefinite self-renewal through yet to be defined molecular mechanisms. Leukemia inhibitory factor has been utilized to maintain the symmetrical self-renewal and pluripotency of mESCs in culture. It has been suggested that molecules with significant cellular effects on retinoblastoma protein (pRb) or its related pathways should have functional impact on mESC proliferation and differentiation. However, the involvement of pRb in pluripotent differentiation of mESCs has not been extensively elaborated. In this paper, we present novel experimental data indicating that Cdk2ap1 (cyclin-dependent kinase 2-associating protein 1), an inhibitor of G(1)/S transition through down-regulation of CDK2 and an essential gene for early embryonic development, confers competency for mESC differentiation. Targeted disruption of Cdk2ap1 in mESCs resulted in abrogation of leukemia inhibitory factor withdrawal-induced differentiation, along with altered pRb phosphorylation. The differentiation competency of the Cdk2ap1(-/-) mESCs was restored upon the ectopic expression of Cdk2ap1 or a nonphosphorylatable pRb mutant (mouse Ser(788) --> Ala), suggesting that the CDK2AP1-mediated differentiation of mESCs was elicited through the regulation of pRb. Further analysis on mESC maintenance or differentiation-related gene expression supports the phosphorylation at serine 788 in pRb plays a significant role for the CDK2AP1-mediated differentiation of mESCs. These data clearly demonstrate that CDK2AP1 is a competency factor in the proper differentiation of mESCs by modulating the phosphorylation level of pRb. This sheds light on the role of the establishment of the proper somatic cell type cell cycle regulation for mESCs to enter into the differentiation process.
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Affiliation(s)
- Yong Kim
- School of Dentistry and Dental Research Institute, UCLA, Los Angeles, CA 90095, USA.
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Bogdanović O, Veenstra GJC. DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 2009; 118:549-65. [PMID: 19506892 PMCID: PMC2729420 DOI: 10.1007/s00412-009-0221-9] [Citation(s) in RCA: 320] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/19/2009] [Accepted: 05/27/2009] [Indexed: 02/06/2023]
Abstract
DNA methylation is a major epigenetic modification in the genomes of higher eukaryotes. In vertebrates, DNA methylation occurs predominantly on the CpG dinucleotide, and approximately 60% to 90% of these dinucleotides are modified. Distinct DNA methylation patterns, which can vary between different tissues and developmental stages, exist on specific loci. Sites of DNA methylation are occupied by various proteins, including methyl-CpG binding domain (MBD) proteins which recruit the enzymatic machinery to establish silent chromatin. Mutations in the MBD family member MeCP2 are the cause of Rett syndrome, a severe neurodevelopmental disorder, whereas other MBDs are known to bind sites of hypermethylation in human cancer cell lines. Here, we review the advances in our understanding of the function of DNA methylation, DNA methyltransferases, and methyl-CpG binding proteins in vertebrate embryonic development. MBDs function in transcriptional repression and long-range interactions in chromatin and also appear to play a role in genomic stability, neural signaling, and transcriptional activation. DNA methylation makes an essential and versatile epigenetic contribution to genome integrity and function.
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Affiliation(s)
- Ozren Bogdanović
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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