1
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Pathania AS, Chava H, Balusu R, Pasupulati AK, Coulter DW, Challagundla KB. The crosstalk between non-coding RNAs and cell-cycle events: A new frontier in cancer therapy. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200785. [PMID: 38595981 PMCID: PMC10973673 DOI: 10.1016/j.omton.2024.200785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The cell cycle comprises sequential events during which a cell duplicates its genome and divides it into two daughter cells. This process is tightly regulated to ensure that the daughter cell receives identical copied chromosomal DNA and that any errors in the DNA during replication are correctly repaired. Cyclins and their enzyme partners, cyclin-dependent kinases (CDKs), are critical regulators of G- to M-phase transitions during the cell cycle. Mitogenic signals induce the formation of the cyclin/CDK complexes, resulting in phosphorylation and activation of the CDKs. Once activated, cyclin/CDK complexes phosphorylate specific substrates that drive the cell cycle forward. The sequential activation and inactivation of cyclin-CDK complexes are tightly controlled by activating and inactivating phosphorylation events induced by cell-cycle proteins. The non-coding RNAs (ncRNAs), which do not code for proteins, regulate cell-cycle proteins at the transcriptional and translational levels, thereby controlling their expression at different cell-cycle phases. Deregulation of ncRNAs can cause abnormal expression patterns of cell-cycle-regulating proteins, resulting in abnormalities in cell-cycle regulation and cancer development. This review explores how ncRNA dysregulation can disrupt cell division balance and discusses potential therapeutic approaches targeting these ncRNAs to control cell-cycle events in cancer treatment.
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Affiliation(s)
- Anup S. Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Haritha Chava
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ramesh Balusu
- Department of Hematologic Malignancies and Cellular Therapeutics, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Anil K. Pasupulati
- Department of Biochemistry, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Don W. Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishore B. Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- The Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
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2
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Liu W, Liu X, Li L, Tai Z, Li G, Liu JX. EPC1/2 regulate hematopoietic stem and progenitor cell proliferation by modulating H3 acetylation and DLST. iScience 2024; 27:109263. [PMID: 38439957 PMCID: PMC10910311 DOI: 10.1016/j.isci.2024.109263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/21/2023] [Accepted: 02/14/2024] [Indexed: 03/06/2024] Open
Abstract
Enhancers of polycomb 1 (EPC1) and 2 (EPC2) are involved in multiple biological processes as components of histone acetyltransferases/deacetylase complexes and transcriptional cofactors, and their dysfunction was associated with developmental defects and diseases. However, it remains unknown how their dysfunction induces hematopoietic stem and progenitor cell (HSPC) defects. Here, we show that depletion of EPC1/2 significantly reduced the number of hematopoietic stem and progenitor cells (HSPCs) in the aorta-gonad mesonephros and caudal hematopoietic tissue regions by impairing HSPC proliferation, and consistently downregulated the expression of HSPC genes in K562 cells. This study demonstrates the functions of EPC1/2 in regulating histone H3 acetylation, and in regulating DLST (dihydrolipoamide S-succinyltransferase) via H3 acetylation and cooperating with transcription factors serum response factor and FOXR2 together, and in the subsequent HSPC emergence and proliferation. Our results demonstrate the essential roles of EPC1/2 in regulating H3 acetylation, and DLST as a linkage between EPC1 and EPC2 with mitochondria metabolism, in HSPC emergence and proliferation.
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Affiliation(s)
- WenYe Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - LingYa Li
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - ZhiPeng Tai
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - GuoLiang Li
- College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing-Xia Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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Gawriyski L, Tan Z, Liu X, Chowdhury I, Malaymar Pinar D, Zhang Q, Weltner J, Jouhilahti EM, Wei GH, Kere J, Varjosalo M. Interaction network of human early embryonic transcription factors. EMBO Rep 2024; 25:1589-1622. [PMID: 38297188 PMCID: PMC10933267 DOI: 10.1038/s44319-024-00074-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Embryonic genome activation (EGA) occurs during preimplantation development and is characterized by the initiation of de novo transcription from the embryonic genome. Despite its importance, the regulation of EGA and the transcription factors involved in this process are poorly understood. Paired-like homeobox (PRDL) family proteins are implicated as potential transcriptional regulators of EGA, yet the PRDL-mediated gene regulatory networks remain uncharacterized. To investigate the function of PRDL proteins, we are identifying the molecular interactions and the functions of a subset family of the Eutherian Totipotent Cell Homeobox (ETCHbox) proteins, seven PRDL family proteins and six other transcription factors (TFs), all suggested to participate in transcriptional regulation during preimplantation. Using mass spectrometry-based interactomics methods, AP-MS and proximity-dependent biotin labeling, and chromatin immunoprecipitation sequencing we derive the comprehensive regulatory networks of these preimplantation TFs. By these interactomics tools we identify more than a thousand high-confidence interactions for the 21 studied bait proteins with more than 300 interacting proteins. We also establish that TPRX2, currently assigned as pseudogene, is a transcriptional activator.
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Affiliation(s)
- Lisa Gawriyski
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiaonan Liu
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | | | - Dicle Malaymar Pinar
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Qin Zhang
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Juha Kere
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Markku Varjosalo
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
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4
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Shirahama Y, Yamamoto K. The E2F6 Transcription Factor is Associated with the Mammalian SUZ12-Containing Polycomb Complex. Kurume Med J 2023; 67:171-183. [PMID: 36464274 DOI: 10.2739/kurumemedj.ms674006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The Polycomb group protein (PcG) SUZ12 forms Polycomb repressive complexes together with histone methyltransferase EZH2. Although the complexes have been demonstrated to be involved in epigenetic maintenance of gene expression in a transcriptional repressive state, it is unclear how they are recruited to the target genes. Here we report that SUZ12 directly interacts with site-specific transcriptional repressor E2F6 and forms a complex together with EZH2. SUZ12 interacts with E2F6 selectively among the E2F family proteins and E2F6- containing SUZ12-EZH2 complex was biochemically purified from HEK293 cells stably expressing Flag-tagged SUZ12. Chromatin immunoprecipitation assays revealed the target genes of the E2F6-SUZ12-EZH2 complex. Contrary to expectation, the promoter regions of these genes are not or only weakly tri-methylated at histone H3-K27, and their expression is down-regulated by depletion of EZH2. Given that the transactivation function of SUZ12-EZH2 has been previously reported, the inhibitory effect on E2F6-mediated transcriptional repression by physical interaction can be considered a candidate mechanism of gene activation by these PcGs.
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Affiliation(s)
- Yuko Shirahama
- Department of Medical Biochemistry, Kurume University School of Medicine
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine
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5
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Mäkelä JA, Toppari J. Retinoblastoma-E2F Transcription Factor Interplay Is Essential for Testicular Development and Male Fertility. Front Endocrinol (Lausanne) 2022; 13:903684. [PMID: 35663332 PMCID: PMC9161260 DOI: 10.3389/fendo.2022.903684] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 01/11/2023] Open
Abstract
The retinoblastoma (RB) protein family members (pRB, p107 and p130) are key regulators of cell cycle progression, but also play crucial roles in apoptosis, and stem cell self-renewal and differentiation. RB proteins exert their effects through binding to E2F transcription factors, which are essential developmental and physiological regulators of tissue and organ homeostasis. According to the canonical view, phosphorylation of RB results in release of E2Fs and induction of genes needed for progress of the cell cycle. However, there are eight members in the E2F transcription factor family with both activator (E2F1-3a) and repressor (E2F3b-E2F8) roles, highlighting the functional diversity of RB-E2F pathway. In this review article we summarize the data showing that RB-E2F interaction is a key cell-autonomous mechanism responsible for establishment and maintenance of lifelong male fertility. We also review the expression pattern of RB proteins and E2F transcription factors in the testis and male germ cells. The available evidence supports that RB and E2F family members are widely and dynamically expressed in the testis, and they are known to have versatile roles during spermatogenesis. Knowledge of the function and significance of RB-E2F interplay for testicular development and spermatogenesis comes primarily from gene knock-out (KO) studies. Several studies conducted in Sertoli cell-specific pRB-KO mice have demonstrated that pRB-mediated inhibition of E2F3 is essential for Sertoli cell functional maturation and cell cycle exit, highlighting that RB-E2F interaction in Sertoli cells is paramount to male fertility. Similarly, ablation of either pRB or E2F1 in the germline results in progressive testicular atrophy due to germline stem cell (GSC) depletion, emphasizing the importance of proper RB-E2F interplay for germline maintenance and lifelong sperm production. In summary, while balanced RB-E2F interplay is essential for cell-autonomous maintenance of GSCs and, the pRB-E2F3 system in Sertoli cells is critical for providing GSC niche thus laying the basis for spermatogenesis.
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Affiliation(s)
- Juho-Antti Mäkelä
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Jorma Toppari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- *Correspondence: Jorma Toppari,
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6
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Utsunomiya S, Kishi Y, Tsuboi M, Kawaguchi D, Gotoh Y, Abe M, Sakimura K, Maeda K, Takemoto H. Ezh1 regulates expression of Cpg15/Neuritin in mouse cortical neurons. Drug Discov Ther 2021; 15:55-65. [PMID: 33678755 DOI: 10.5582/ddt.2021.01017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Immature neurons undergo morphological and physiological maturation in order to establish neuronal networks. During neuronal maturation, a large number of genes change their transcriptional levels, and these changes may be mediated by chromatin modifiers. In this study, we found that the level of Ezh1, a component of Polycomb repressive complex 2 (PRC2), increases during neuronal maturation in mouse neocortical culture. In addition, conditional knockout of Ezh1 in post-mitotic excitatory neurons leads to downregulation of a set of genes related to neuronal maturation. Moreover, the locus encoding Cpg15/Neuritin (Nrn1), which is regulated by neuronal activity and implicated in stabilization and maturation of excitatory synapses, is a direct target of Ezh1 in cortical neurons. Together, these results suggest that elevated expression of Ezh1 contributes to maturation of cortical neurons.
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Affiliation(s)
- Shun Utsunomiya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.,Neuroscience 2, Laboratory for Drug Discovery and Disease Research, Shionogi & Co. Ltd., Toyonaka, Osaka, Japan.,Business-Academia Collaborative Laboratory (Shionogi), Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke Kishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Masafumi Tsuboi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Daichi Kawaguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kazuma Maeda
- Neuroscience 2, Laboratory for Drug Discovery and Disease Research, Shionogi & Co. Ltd., Toyonaka, Osaka, Japan.,Business-Academia Collaborative Laboratory (Shionogi), Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Takemoto
- Neuroscience 2, Laboratory for Drug Discovery and Disease Research, Shionogi & Co. Ltd., Toyonaka, Osaka, Japan.,Business-Academia Collaborative Laboratory (Shionogi), Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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7
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Scarth JA, Patterson MR, Morgan EL, Macdonald A. The human papillomavirus oncoproteins: a review of the host pathways targeted on the road to transformation. J Gen Virol 2021; 102:001540. [PMID: 33427604 PMCID: PMC8148304 DOI: 10.1099/jgv.0.001540] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022] Open
Abstract
Persistent infection with high-risk human papillomaviruses (HR-HPVs) is the causal factor in over 99 % of cervical cancer cases, and a significant proportion of oropharyngeal and anogenital cancers. The key drivers of HPV-mediated transformation are the oncoproteins E5, E6 and E7. Together, they act to prolong cell-cycle progression, delay differentiation and inhibit apoptosis in the host keratinocyte cell in order to generate an environment permissive for viral replication. The oncoproteins also have key roles in mediating evasion of the host immune response, enabling infection to persist. Moreover, prolonged infection within the cellular environment established by the HR-HPV oncoproteins can lead to the acquisition of host genetic mutations, eventually culminating in transformation to malignancy. In this review, we outline the many ways in which the HR-HPV oncoproteins manipulate the host cellular environment, focusing on how these activities can contribute to carcinogenesis.
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Affiliation(s)
- James A. Scarth
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
| | - Molly R. Patterson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
| | - Ethan L. Morgan
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
- Present address: Tumour Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institute of Health, Bethesda, MD 20892, USA
| | - Andrew Macdonald
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
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8
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The role of HOPX in normal tissues and tumor progression. Biosci Rep 2020; 40:221873. [PMID: 31934721 PMCID: PMC6997107 DOI: 10.1042/bsr20191953] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/03/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
The homeodomain-only protein homeobox (HOPX) as the smallest homeodomain protein, lacks certain conserved residues required for DNA binding. Through our literature search, we reviewed the current understandings of HOPX in normal tissues and tumor progression. HOPX was initially identified as a critical transcription factor in various normal tissues, which interacted with serum response factor (SRF) or other substance to regulate normal physiological function. However, HOPX is at a low expression or methylation level in tumors. These data indicated that HOPX may play a very important role in regulating differentiation phenotype and tumor suppressive function. We predicted the prognosis of HOPX in tumors from TCGA database and discussed the downstream genes of HOPX. To understand how HOPX is involved in the mechanisms between physical and pathological conditions could lead to novel therapeutic strategies for treatment.
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9
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Ashok C, Selvam M, Ponne S, Parcha PK, Raja KMP, Baluchamy S. CREB acts as a common transcription factor for major epigenetic repressors; DNMT3B, EZH2, CUL4B and E2F6. Med Oncol 2020; 37:68. [PMID: 32710193 DOI: 10.1007/s12032-020-01395-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/16/2020] [Indexed: 12/28/2022]
Abstract
CREB signaling is known for several decades, but how it regulates both positive and negative regulators of cell proliferation is not well understood. On the other hand functions of major epigenetic repressors such as DNMT3B, EZH2 and CUL4B for their repressive epigenetic modifications on chromatin have also been well studied. However, there is very limited information available on how these repressors are regulated at their transcriptional level. Here, using computational tools and molecular techniques including site directed mutagenesis, promoter reporter assay, chromatin immunoprecipitation (ChIP), we identified that CREB acts as a common transcription factor for DNMT3B, EZH2, CUL4B and E2F6. ChIP assay revealed that pCREB binds to promoters of these repressors at CREs and induce their transcription. As expected, the expression of these repressors and their associated repressive marks particularly H3K27me3 and H2AK119ub are increased and decreased upon CREB overexpression and knock-down conditions respectively in the cancer cells indicating that CREB regulates the functions of these repressors by activating their transcription. Since CREB and these epigenetic repressors are overexpressed in various cancer types, our findings showed the molecular relationship between them and indicate that CREB is an important therapeutic target for cancer therapy.
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Affiliation(s)
- Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Saravanaraman Ponne
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Phani K Parcha
- Department of Biochemistry and Molecular Biology, Pondicherry Central University, Pondicherry, 605014, India
| | | | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India.
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10
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Bernitz JM, Rapp K, Daniel MG, Shcherbinin D, Yuan Y, Gomes A, Waghray A, Brosh R, Lachmann A, Ma'ayan A, Papatsenko D, Moore KA. Memory of Divisional History Directs the Continuous Process of Primitive Hematopoietic Lineage Commitment. Stem Cell Reports 2020; 14:561-574. [PMID: 32243840 PMCID: PMC7160360 DOI: 10.1016/j.stemcr.2020.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic stem cells (HSCs) exist in a dormant state and progressively lose regenerative potency as they undergo successive divisions. Why this functional decline occurs and how this information is encoded is unclear. To better understand how this information is stored, we performed RNA sequencing on HSC populations differing only in their divisional history. Comparative analysis revealed that genes upregulated with divisions are enriched for lineage genes and regulated by cell-cycle-associated transcription factors, suggesting that proliferation itself drives lineage priming. Downregulated genes are, however, associated with an HSC signature and targeted by the Polycomb Repressive Complex 2 (PRC2). The PRC2 catalytic subunits Ezh1 and Ezh2 promote and suppress the HSC state, respectively, and successive divisions cause a switch from Ezh1 to Ezh2 dominance. We propose that cell divisions drive lineage priming and Ezh2 accumulation, which represses HSC signature genes to consolidate information on divisional history into memory. Divisional history is a major source of gene expression variation across HSCs Cell divisions themselves appear to drive lineage priming in HSCs Comparative analysis suggests that chromatin marks are dynamic with cell divisions An Ezh1-to-Ezh2 switch consolidates HSC divisional history information into memory
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Affiliation(s)
- Jeffrey M Bernitz
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; The Graduate School of Biomedical Sciences; Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA
| | - Katrina Rapp
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA
| | - Michael G Daniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; The Graduate School of Biomedical Sciences; Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA
| | - Dmitrii Shcherbinin
- Skoltech Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia
| | - Ye Yuan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; The Graduate School of Biomedical Sciences; Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA
| | - Andreia Gomes
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Avinash Waghray
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; The Graduate School of Biomedical Sciences; Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA
| | - Ran Brosh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitri Papatsenko
- Skoltech Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Kateri A Moore
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA.
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11
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Raby L, Völkel P, Le Bourhis X, Angrand PO. The Polycomb Orthologues in Teleost Fishes and Their Expression in the Zebrafish Model. Genes (Basel) 2020; 11:genes11040362. [PMID: 32230868 PMCID: PMC7230241 DOI: 10.3390/genes11040362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 01/25/2023] Open
Abstract
The Polycomb Repressive Complex 1 (PRC1) is a chromatin-associated protein complex involved in transcriptional repression of hundreds of genes controlling development and differentiation processes, but also involved in cancer and stem cell biology. Within the canonical PRC1, members of Pc/CBX protein family are responsible for the targeting of the complex to specific gene loci. In mammals, the Pc/CBX protein family is composed of five members generating, through mutual exclusion, different PRC1 complexes with potentially distinct cellular functions. Here, we performed a global analysis of the cbx gene family in 68 teleost species and traced the distribution of the cbx genes through teleost evolution in six fish super-orders. We showed that after the teleost-specific whole genome duplication, cbx4, cbx7 and cbx8 are retained as pairs of ohnologues. In contrast, cbx2 and cbx6 are present as pairs of ohnologues in the genome of several teleost clades but as singletons in others. Furthermore, since zebrafish is a widely used vertebrate model for studying development, we report on the expression of the cbx family members during zebrafish development and in adult tissues. We showed that all cbx genes are ubiquitously expressed with some variations during early development.
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12
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Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, Meyerson M, Zhang X. Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma. Mol Cancer Res 2019; 18:574-584. [PMID: 31862696 DOI: 10.1158/1541-7786.mcr-19-0657] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/25/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023]
Abstract
Genomic analysis of lung adenocarcinomas has revealed that the MGA gene, which encodes a heterodimeric partner of the MYC-interacting protein MAX, is significantly mutated or deleted in lung adenocarcinomas. Most of the mutations are loss of function for MGA, suggesting that MGA may act as a tumor suppressor. Here, we characterize both the molecular and cellular role of MGA in lung adenocarcinomas and illustrate its functional relevance in the MYC pathway. Although MGA and MYC interact with the same binding partner, MAX, and recognize the same E-box DNA motif, we show that the molecular function of MGA appears to be antagonistic to that of MYC. Using mass spectrometry-based affinity proteomics, we demonstrate that MGA interacts with a noncanonical PCGF6-PRC1 complex containing MAX and E2F6 that is involved in gene repression, while MYC is not part of this MGA complex, in agreement with previous studies describing the interactomes of E2F6 and PCGF6. Chromatin immunoprecipitation-sequencing and RNA sequencing assays show that MGA binds to and represses genes that are bound and activated by MYC. In addition, we show that, as opposed to the MYC oncoprotein, MGA acts as a negative regulator for cancer cell proliferation. Our study defines a novel MYC/MAX/MGA pathway, in which MYC and MGA play opposite roles in protein interaction, transcriptional regulation, and cellular proliferation. IMPLICATIONS: This study expands the range of key cancer-associated genes whose dysregulation is functionally equivalent to MYC activation and places MYC within a linear pathway analogous to cell-cycle or receptor tyrosine kinase/RAS/RAF pathways in lung adenocarcinomas.
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Affiliation(s)
- Paula Llabata
- Cancer Epigenetics and Biology Program-PEBC (IDIBELL), Barcelona, Spain
| | - Yoichiro Mitsuishi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Peter S Choi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Diana Cai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Joshua M Francis
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Manuel Torres-Diz
- Cancer Epigenetics and Biology Program-PEBC (IDIBELL), Barcelona, Spain
| | - Namrata D Udeshi
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Lior Golomb
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Zhong Wu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jin Zhou
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Tanya Svinkina
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Estrella Aguilera-Jimenez
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Yanli Liu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Steven A Carr
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Matthew Meyerson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts. .,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
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13
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Lafta IJ. E2F6 is essential for cell viability in breast cancer cells during replication stress. ACTA ACUST UNITED AC 2019; 43:293-304. [PMID: 31768102 PMCID: PMC6823915 DOI: 10.3906/biy-1905-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
E2F6 is a member of the E2F family of transcription factors involved in regulation of a wide variety of genes through both activation and repression. E2F6 has been reported as overexpressed in breast cancers but whether or not this is important for tumor development is unclear. We first checked E2F6 expression in tumor cDNAs and the protein level in a range of breast cancer cell lines. RNA interference-mediated depletion was then used to assess the importance of E2F6 expression in cell lines with regard to cell cycle profile using fluorescence-activated cell sorting and a cell survival assay using (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The overexpression of E2F6 was confirmed in breast tumor cDNA samples and breast cancer cell lines. Depletion of E2F6 in the breast cancer cells reduced cell viability in MCF-7, T-47D, and MDA-MB-231 cells. There was little effect in the nontumor breast cell line MCF-10A. The deleterious effect on cancer cells was greater during replication stress, leading to an increase in the proportion of breast cancer cells with sub-G1 DNA content. These results suggest that E2F6 might be essential for the survival of breast cancer cells experiencing replication stress, and therefore it could be a target for combined therapy.
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Affiliation(s)
- Inam Jasim Lafta
- Department of Microbiology, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
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14
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Panas MW, Naor A, Cygan AM, Boothroyd JC. Toxoplasma Controls Host Cyclin E Expression through the Use of a Novel MYR1-Dependent Effector Protein, HCE1. mBio 2019; 10:e00674-19. [PMID: 31040242 PMCID: PMC6495377 DOI: 10.1128/mbio.00674-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 01/27/2023] Open
Abstract
Toxoplasma gondii is an obligate intracellular parasite that establishes a favorable environment in the host cells in which it replicates. We have previously reported that it uses MYR-dependent translocation of dense granule proteins to elicit a key set of host responses related to the cell cycle, specifically, E2F transcription factor targets, including cyclin E. We report here the identification of a novel Toxoplasma effector protein that is exported from the parasitophorous vacuole in a MYR1-dependent manner and localizes to the host's nucleus. Parasites lacking this inducer of host cyclin E (HCE1) are unable to modulate E2F transcription factor target genes and exhibit a substantial growth defect. Immunoprecipitation of HCE1 from infected host cells showed that HCE1 efficiently binds elements of the cyclin E regulatory complex, namely, DP1 and its partners E2F3 and E2F4. Expression of HCE1 in Neospora caninum, or in uninfected human foreskin fibroblasts (HFFs), showed localization of the expressed protein to the host nuclei and strong cyclin E upregulation. Thus, HCE1 is a novel effector protein that is necessary and sufficient to impact the E2F axis of transcription, resulting in co-opting of host functions to the advantage of ToxoplasmaIMPORTANCE Like most Apicomplexan parasites, Toxoplasma gondii has the remarkable ability to invade and establish a replicative niche within another eukaryotic cell, in this case, any of a large number of cell types in almost any warm-blooded animals. Part of the process of establishing this niche is the export of effector proteins to co-opt host cell functions in favor of the parasite. Here we identify a novel effector protein, HCE1, that the parasites export into the nucleus of human cells, where it modulates the expression of multiple genes, including the gene encoding cyclin E, one of the most crucial proteins involved in controlling when and whether a human cell divides. We show that HCE1 works through binding to specific transcription factors, namely, E2F3, E2F4, and DP1, that normally carefully regulate these all-important pathways. This represents a new way in which these consummately efficient infectious agents co-opt the human cells that they so efficiently grow within.
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Affiliation(s)
- Michael W Panas
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, USA
| | - Adit Naor
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, USA
| | - Alicja M Cygan
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, USA
| | - John C Boothroyd
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, USA
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15
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Lukoseviciute M, Gavriouchkina D, Williams RM, Hochgreb-Hagele T, Senanayake U, Chong-Morrison V, Thongjuea S, Repapi E, Mead A, Sauka-Spengler T. From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo. Dev Cell 2019; 47:608-628.e6. [PMID: 30513303 PMCID: PMC6286384 DOI: 10.1016/j.devcel.2018.11.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 08/15/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023]
Abstract
The neural crest (NC) is a transient embryonic stem cell-like population characterized by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that, during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes. Strikingly, foxd3 then gradually switches from an activator to its well-described role as a transcriptional repressor and potentially uses differential partners for each role. Taken together, these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from “permissive” to “repressive” nucleosome and chromatin organization to maintain multipotency and define cell fates. FoxD3 primes neural crest specification by modulating distal enhancers FoxD3 represses a number of neural crest migration and differentiation genes In neural crest, FoxD3 acts to switch chromatin from “permissive” to “repressive” Distinctive gene regulatory mechanisms underlie the bimodal action of FoxD3
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Affiliation(s)
- Martyna Lukoseviciute
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ruth M Williams
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatiana Hochgreb-Hagele
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Supat Thongjuea
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam Mead
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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16
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Cheng FHC, Lin HY, Hwang TW, Chen YC, Huang RL, Chang CB, Yang W, Lin RI, Lin CW, Chen GCW, Mai SY, Lin JMJ, Chuang YM, Chou JL, Kuo LW, Li C, Cheng ASL, Lai HC, Wu SF, Tsai JC, Chan MWY. E2F6 functions as a competing endogenous RNA, and transcriptional repressor, to promote ovarian cancer stemness. Cancer Sci 2019; 110:1085-1095. [PMID: 30582655 PMCID: PMC6398890 DOI: 10.1111/cas.13920] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/20/2022] Open
Abstract
Ovarian cancer is the most lethal cancer of the female reproductive system. In that regard, several epidemiological studies suggest that long‐term exposure to estrogen could increase ovarian cancer risk, although its precise role remains controversial. To decipher a mechanism for this, we previously generated a mathematical model of how estrogen‐mediated upregulation of the transcription factor, E2F6, upregulates the ovarian cancer stem/initiating cell marker, c‐Kit, by epigenetic silencing the tumor suppressor miR‐193a, and a competing endogenous (ceRNA) mechanism. In this study, we tested that previous mathematical model, showing that estrogen treatment of immortalized ovarian surface epithelial cells upregulated both E2F6 and c‐KIT, but downregulated miR‐193a. Luciferase assays further confirmed that microRNA‐193a targets both E2F6 and c‐Kit. Interestingly, ChIP‐PCR and bisulphite pyrosequencing showed that E2F6 also epigenetically suppresses miR‐193a, through recruitment of EZH2, and by a complex ceRNA mechanism in ovarian cancer cell lines. Importantly, cell line and animal experiments both confirmed that E2F6 promotes ovarian cancer stemness, whereas E2F6 or EZH2 depletion derepressed miR‐193a, which opposes cancer stemness, by alleviating DNA methylation and repressive chromatin. Finally, 118 ovarian cancer patients with miR‐193a promoter hypermethylation had poorer survival than those without hypermethylation. These results suggest that an estrogen‐mediated E2F6 ceRNA network epigenetically and competitively inhibits microRNA‐193a activity, promoting ovarian cancer stemness and tumorigenesis.
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Affiliation(s)
- Frank H C Cheng
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Hon-Yi Lin
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi, Taiwan.,School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Tzy-Wei Hwang
- Department of Mathematics, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yin-Chen Chen
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine and Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Chia-Bin Chang
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Weiqin Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ru-Inn Lin
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi, Taiwan
| | - Ching-Wen Lin
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Gary C W Chen
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Shu-Yuan Mai
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jora M J Lin
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yu-Ming Chuang
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jian-Liang Chou
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Li-Wei Kuo
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Chin Li
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
| | - Alfred S L Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine and Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Shu-Fen Wu
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan
| | - Je-Chiang Tsai
- Department of Mathematics, National Tsing Hua University, Hsin-Chu, Taiwan
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan.,Epigenomics and Human Disease Research Center, National Chung Cheng University, Chia-Yi, Taiwan.,Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chia-Yi, Taiwan.,Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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17
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Lan W, Bian B, Xia Y, Dou S, Gayet O, Bigonnet M, Santofimia-Castaño P, Cong M, Peng L, Dusetti N, Iovanna J. E2F signature is predictive for the pancreatic adenocarcinoma clinical outcome and sensitivity to E2F inhibitors, but not for the response to cytotoxic-based treatments. Sci Rep 2018; 8:8330. [PMID: 29844366 PMCID: PMC5974374 DOI: 10.1038/s41598-018-26613-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/14/2018] [Indexed: 12/26/2022] Open
Abstract
The main goal of this study was to find out strategies of clinical relevance to classify patients with a pancreatic ductal adenocarcinoma (PDAC) for individualized treatments. In the present study a set of 55 patient-derived xenografts (PDX) were obtained and their transcriptome were analyzed by using an Affymetrix approach. A supervised bioinformatics-based analysis let us to classify these PDX in two main groups named E2F-highly dependent and E2F-lowly dependent. Afterwards their characterization by using a Kaplan-Meier analysis demonstrated that E2F high patients survived significantly less than E2F low patients (9.5 months vs. 16.8 months; p = 0.0066). Then we tried to establish if E2F transcriptional target levels were associated to the response to cytotoxic treatments by comparing the IC50 values of E2F high and E2F low cells after gemcitabine, 5-fluorouracil, oxaliplatin, docetaxel or irinotecan treatment, and no association was found. Then we identified an E2F inhibitor compound, named ly101-4B, and we observed that E2F-higly dependent cells were more sensitive to its treatment (IC50 of 19.4 ± 1.8 µM vs. 44.1 ± 4.4 µM; p = 0.0061). In conclusion, in this work we describe an E2F target expression-based classification that could be predictive for patient outcome, but more important, for the sensitivity of tumors to the E2F inhibitors as a treatment. Finally, we can assume that phenotypic characterization, essentially by an RNA expression analysis of the PDAC, can help to predict their clinical outcome and their response to some treatments when are rationally selected.
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Affiliation(s)
- Wenjun Lan
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», Marseille, France
| | - Benjamin Bian
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Yi Xia
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Samir Dou
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Odile Gayet
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Martin Bigonnet
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Mei Cong
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», Marseille, France
| | - Ling Peng
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», Marseille, France
| | - Nelson Dusetti
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France.
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France.
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18
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Wang X, Xu H. Potential Epigenetic Regulation in the Germinal Center Reaction of Lymphoid Tissues in HIV/SIV Infection. Front Immunol 2018; 9:159. [PMID: 29449847 PMCID: PMC5799247 DOI: 10.3389/fimmu.2018.00159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/18/2018] [Indexed: 01/08/2023] Open
Abstract
The production of high-affinity and broadly neutralizing antibodies plays a key role in the defense against pathogens. These antibody responses require effective germinal center (GC) reaction within anatomical niches of GCs, where follicular helper T (Tfh) cells provide cognate help to B cells for T cell-dependent antibody responses. Emerging evidences indicate that GC reaction in normal state and perhaps establishment of latent Tfh cell reservoir in HIV/SIV infection are tightly regulated by epigenetic histone modifications, which are responsible for activating or silencing chromatin. A better understanding of the mechanisms behind GC responses at cellular and molecular levels thus provides necessary knowledge for vaccination and immunotherapy. In this review, we discussed the epigenetic regulation of GC responses, especially for GC B and Tfh cell under normal state or HIV/SIV infection.
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Affiliation(s)
- Xiaolei Wang
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States
| | - Huanbin Xu
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States
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19
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McNair C, Xu K, Mandigo AC, Benelli M, Leiby B, Rodrigues D, Lindberg J, Gronberg H, Crespo M, De Laere B, Dirix L, Visakorpi T, Li F, Feng FY, de Bono J, Demichelis F, Rubin MA, Brown M, Knudsen KE. Differential impact of RB status on E2F1 reprogramming in human cancer. J Clin Invest 2017; 128:341-358. [PMID: 29202480 DOI: 10.1172/jci93566] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 10/24/2017] [Indexed: 01/03/2023] Open
Abstract
The tumor suppressor protein retinoblastoma (RB) is mechanistically linked to suppression of transcription factor E2F1-mediated cell cycle regulation. For multiple tumor types, loss of RB function is associated with poor clinical outcome. RB action is abrogated either by direct depletion or through inactivation of RB function; however, the basis for this selectivity is unknown. Here, analysis of tumor samples and cell-free DNA from patients with advanced prostate cancer showed that direct RB loss was the preferred pathway of disruption in human disease. While RB loss was associated with lethal disease, RB-deficient tumors had no proliferative advantage and exhibited downstream effects distinct from cell cycle control. Mechanistically, RB loss led to E2F1 cistrome expansion and different binding specificity, alterations distinct from those observed after functional RB inactivation. Additionally, identification of protumorigenic transcriptional networks specific to RB loss that were validated in clinical samples demonstrated the ability of RB loss to differentially reprogram E2F1 in human cancers. Together, these findings not only identify tumor-suppressive functions of RB that are distinct from cell cycle control, but also demonstrate that the molecular consequence of RB loss is distinct from RB inactivation. Thus, these studies provide insight into how RB loss promotes disease progression, and identify new nodes for therapeutic intervention.
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Affiliation(s)
- Christopher McNair
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kexin Xu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Amy C Mandigo
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Matteo Benelli
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Benjamin Leiby
- Department of Pharmacology and Experimental Therapeutics, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Daniel Rodrigues
- Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mateus Crespo
- Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Bram De Laere
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium
| | - Luc Dirix
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium.,Department of Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Tapio Visakorpi
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Fugen Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Felix Y Feng
- Department of Radiation Oncology, Urology, and Medicine and Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Johann de Bono
- Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Francesca Demichelis
- Centre for Integrative Biology, University of Trento, Trento, Italy.,Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian Hospital, New York, New York, USA
| | - Mark A Rubin
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian Hospital, New York, New York, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York, New York, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Karen E Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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20
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EPC1/TIP60-Mediated Histone Acetylation Facilitates Spermiogenesis in Mice. Mol Cell Biol 2017; 37:MCB.00082-17. [PMID: 28694333 DOI: 10.1128/mcb.00082-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022] Open
Abstract
Global histone hyperacetylation is suggested to play a critical role for replacement of histones by transition proteins and protamines to compact the genome during spermiogenesis. However, the underlying mechanisms for hyperacetylation-mediated histone replacement remains poorly understood. Here, we report that EPC1 and TIP60, two critical components of the mammalian nucleosome acetyltransferase of H4 (NuA4) complexes, are coexpressed in male germ cells. Strikingly, genetic ablation of either Epc1 or Tip60 disrupts hyperacetylation and impairs histone replacement, in turn causing aberrant spermatid development. Taking these observations together, we reveal an essential role of the NuA4 complexes for histone hyperacetylation and subsequent compaction of the spermatid genome.
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21
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Searle NE, Pillus L. Critical genomic regulation mediated by Enhancer of Polycomb. Curr Genet 2017; 64:147-154. [PMID: 28884217 DOI: 10.1007/s00294-017-0742-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/28/2023]
Abstract
Enhancer of Polycomb (EPC) was first identified for its contributions to development in Drosophila and was soon-thereafter purified as a subunit of the NuA4/TIP60 acetyltransferase complex. Since then, EPC has often been left in the shadows as an essential, yet non-catalytic subunit of NuA4/TIP60; however, its deep conservation and disease association make clear that it warrants additional attention. In fact, recent studies in yeast demonstrated that its Enhancer of Polycomb, Epl1, was just as important for gene expression and acetylation as is the catalytic subunit of NuA4. Despite its conservation, studies of EPC have often remained siloed between organisms. Here, our goal is to provide a cohesive view of the current state of the EPC literature as it stands among the major model organisms in which it has been studied. EPC is involved in multiple processes, beginning with its cardinal role in regulating global and targeted histone acetylation. EPC also frequently serves as an important interaction partner in these basic cellular functions, as well as in multicellular development, such as in hematopoiesis and skeletal muscle differentiation, and in human disease. Taken together, a unifying theme from these studies highlights EPC as a critical genomic regulator.
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Affiliation(s)
- Naomi E Searle
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, UC San Diego Moores Cancer Center, 9500 Gilman Drive, La Jolla, CA, 92093-0347, USA.,UC San Diego Biomedical Sciences, La Jolla, CA, 92093-0685, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, UC San Diego Moores Cancer Center, 9500 Gilman Drive, La Jolla, CA, 92093-0347, USA.
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22
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Fischer M, Müller GA. Cell cycle transcription control: DREAM/MuvB and RB-E2F complexes. Crit Rev Biochem Mol Biol 2017; 52:638-662. [PMID: 28799433 DOI: 10.1080/10409238.2017.1360836] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The precise timing of cell cycle gene expression is critical for the control of cell proliferation; de-regulation of this timing promotes the formation of cancer and leads to defects during differentiation and development. Entry into and progression through S phase requires expression of genes coding for proteins that function in DNA replication. Expression of a distinct set of genes is essential to pass through mitosis and cytokinesis. Expression of these groups of cell cycle-dependent genes is regulated by the RB pocket protein family, the E2F transcription factor family, and MuvB complexes together with B-MYB and FOXM1. Distinct combinations of these transcription factors promote the transcription of the two major groups of cell cycle genes that are maximally expressed either in S phase (G1/S) or in mitosis (G2/M). In this review, we discuss recent work that has started to uncover the molecular mechanisms controlling the precisely timed expression of these genes at specific cell cycle phases, as well as the repression of the genes when a cell exits the cell cycle.
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Affiliation(s)
- Martin Fischer
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany.,b Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA.,c Department of Medicine, Brigham and Women's Hospital , Harvard Medical School , Boston , MA , USA
| | - Gerd A Müller
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany
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23
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Molecular mechanisms of human papillomavirus-related carcinogenesis in head and neck cancer. Microbes Infect 2017; 19:464-475. [PMID: 28619685 DOI: 10.1016/j.micinf.2017.06.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 01/04/2023]
Abstract
This review examines the general cellular and molecular underpinnings of human papillomavirus (HPV)-related carcinogenesis in the context of head and neck squamous cell carcinoma (HNSCC) and focuses on HPV-positive oropharyngeal squamous cell carcinoma in areas for which specific data is available. It covers the major pathways dysregulated in HPV-positive HNSCC and the genome-wide changes associated with this disease.
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24
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Chromatin Regulation by the NuA4 Acetyltransferase Complex Is Mediated by Essential Interactions Between Enhancer of Polycomb (Epl1) and Esa1. Genetics 2017; 205:1125-1137. [PMID: 28108589 DOI: 10.1534/genetics.116.197830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/16/2017] [Indexed: 12/20/2022] Open
Abstract
Enzymes that modify and remodel chromatin act in broadly conserved macromolecular complexes. One key modification is the dynamic acetylation of histones and other chromatin proteins by opposing activities of acetyltransferase and deacetylase complexes. Among acetyltransferases, the NuA4 complex containing Tip60 or its Saccharomyces cerevisiae ortholog Esa1 is of particular significance because of its roles in crucial genomic processes including DNA damage repair and transcription. The catalytic subunit Esa1 is essential, as are five noncatalytic NuA4 subunits. We found that of the noncatalytic subunits, deletion of Enhancer of polycomb (Epl1), but not the others, can be bypassed by loss of a major deacetylase complex, a property shared by Esa1 Noncatalytic complex subunits can be critical for complex assembly, stability, genomic targeting, substrate specificity, and regulation. Understanding the essential role of Epl1 has been previously limited, a limitation now overcome by the discovery of its bypass suppression. Here, we present a comprehensive in vivo study of Epl1 using the powerful tool of suppression combined with transcriptional and mutational analyses. Our results highlight functional parallels between Epl1 and Esa1 and further illustrate that the structural role of Epl1 is important for promotion of Esa1 activity. This conclusion is strengthened by our dissection of Epl1 domains required in vivo for interaction with specific NuA4 subunits, histone acetylation, and chromatin targeting. These results provide new insights for the conserved, essential nature of Epl1 and its homologs, such as EPC1/2 in humans, which is frequently altered in cancers.
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25
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Entrevan M, Schuettengruber B, Cavalli G. Regulation of Genome Architecture and Function by Polycomb Proteins. Trends Cell Biol 2016; 26:511-525. [PMID: 27198635 DOI: 10.1016/j.tcb.2016.04.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/13/2022]
Abstract
Polycomb group (PcG) proteins dynamically define cellular identities through the epigenetic repression of key developmental regulatory genes. PcG proteins are recruited to specific regulatory elements to modify the chromatin surrounding them. In addition, they regulate the organization of their target genes in the 3D space of the nucleus, and this regulatory function of the 3D genome architecture is involved in cell differentiation and the maintenance of cellular memory. In this review we discuss recent advances in our understanding of how PcG proteins are recruited to chromatin to induce local and global changes in chromosome conformation and regulate their target genes.
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Affiliation(s)
- Marianne Entrevan
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Bernd Schuettengruber
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
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26
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Mariotto A, Pavlova O, Park HS, Huber M, Hohl D. HOPX: The Unusual Homeodomain-Containing Protein. J Invest Dermatol 2016; 136:905-911. [PMID: 27017330 DOI: 10.1016/j.jid.2016.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/23/2015] [Accepted: 01/04/2016] [Indexed: 01/15/2023]
Abstract
The homeodomain-only protein homeobox (HOPX) is the smallest known member of the homeodomain-containing protein family, atypically unable to bind DNA. HOPX is widely expressed in diverse tissues, where it is critically involved in the regulation of proliferation and differentiation. In human skin, HOPX controls epidermal formation through the regulation of late differentiation markers, and HOPX expression correlates with the level of differentiation in cutaneous pathologies. In mouse skin, Hopx was additionally identified as a lineage tracing marker of quiescent hair follicle stem cells. This review discusses current knowledge of HOPX structure and function in normal and pathological conditions.
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Affiliation(s)
- Anita Mariotto
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Olesya Pavlova
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Hyun-Sook Park
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Marcel Huber
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Daniel Hohl
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.
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27
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Aranda S, Mas G, Di Croce L. Regulation of gene transcription by Polycomb proteins. SCIENCE ADVANCES 2015; 1:e1500737. [PMID: 26665172 PMCID: PMC4672759 DOI: 10.1126/sciadv.1500737] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/17/2015] [Indexed: 05/14/2023]
Abstract
The Polycomb group (PcG) of proteins defines a subset of factors that physically associate and function to maintain the positional identity of cells from the embryo to adult stages. PcG has long been considered a paradigmatic model for epigenetic maintenance of gene transcription programs. Despite intensive research efforts to unveil the molecular mechanisms of action of PcG proteins, several fundamental questions remain unresolved: How many different PcG complexes exist in mammalian cells? How are PcG complexes targeted to specific loci? How does PcG regulate transcription? In this review, we discuss the diversity of PcG complexes in mammalian cells, examine newly identified modes of recruitment to chromatin, and highlight the latest insights into the molecular mechanisms underlying the function of PcGs in transcription regulation and three-dimensional chromatin conformation.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Gloria Mas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author. E-mail:
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28
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Wang Y, Alla V, Goody D, Gupta SK, Spitschak A, Wolkenhauer O, Pützer BM, Engelmann D. Epigenetic factor EPC1 is a master regulator of DNA damage response by interacting with E2F1 to silence death and activate metastasis-related gene signatures. Nucleic Acids Res 2015; 44:117-33. [PMID: 26350215 PMCID: PMC4705687 DOI: 10.1093/nar/gkv885] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/24/2015] [Indexed: 12/31/2022] Open
Abstract
Transcription factor E2F1 is a key regulator of cell proliferation and apoptosis. Recently, it has been shown that aberrant E2F1 expression often detectable in advanced cancers contributes essentially to cancer cell propagation and characterizes the aggressive potential of a tumor. Conceptually, this requires a subset of malignant cells capable of evading apoptotic death through anticancer drugs. The molecular mechanism by which the pro-apoptotic activity of E2F1 is antagonized is widely unclear. Here we report a novel function for EPC1 (enhancer of polycomb homolog 1) in DNA damage protection. Depletion of EPC1 potentiates E2F1-mediated apoptosis in response to genotoxic treatment and abolishes tumor cell motility. We found that E2F1 directly binds to the EPC1 promoter and EPC1 vice versa physically interacts with bifunctional E2F1 to modulate its transcriptional activity in a target gene-specific manner. Remarkably, nuclear-colocalized EPC1 activates E2F1 to upregulate the expression of anti-apoptotic survival genes such as BCL-2 or Survivin/BIRC5 and inhibits death-inducing targets. The uncovered cooperativity between EPC1 and E2F1 triggers a metastasis-related gene signature in advanced cancers that predicts poor patient survival. These findings unveil a novel oncogenic function of EPC1 for inducing the switch into tumor progression-relevant gene expression that may help to set novel therapies.
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Affiliation(s)
- Yajie Wang
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Vijay Alla
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Deborah Goody
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Shailendra K Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Alf Spitschak
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Brigitte M Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - David Engelmann
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
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29
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Maternal Plane of Nutrition during Late Gestation and Weaning Age Alter Angus × Simmental Offspring Longissimus Muscle Transcriptome and Intramuscular Fat. PLoS One 2015; 10:e0131478. [PMID: 26153887 PMCID: PMC4496061 DOI: 10.1371/journal.pone.0131478] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/01/2015] [Indexed: 12/29/2022] Open
Abstract
In model organisms both the nutrition of the mother and the young offspring could induce long-lasting transcriptional changes in tissues. In livestock, such changes could have important roles in determining nutrient use and meat quality. The main objective was to evaluate if plane of maternal nutrition during late-gestation and weaning age alter the offspring's Longissimus muscle (LM) transcriptome, animal performance, and metabolic hormones. Whole-transcriptome microarray analysis was performed on LM samples of early (EW) and normal weaned (NW) Angus × Simmental calves born to grazing cows receiving no supplement [low plane of nutrition (LPN)] or 2.3 kg high-grain mix/day [medium plane of nutrition (MPN)] during the last 105 days of gestation. Biopsies of LM were harvested at 78 (EW), 187 (NW) and 354 (before slaughter) days of age. Despite greater feed intake in MPN offspring, blood insulin was greater in LPN offspring. Carcass intramuscular fat content was greater in EW offspring. Bioinformatics analysis of the transcriptome highlighted a modest overall response to maternal plane of nutrition, resulting in only 35 differentially expressed genes (DEG). However, weaning age and a high-grain diet (EW) strongly impacted the transcriptome (DEG = 167), especially causing a lipogenic program activation. In addition, between 78 and 187 days of age, EW steers had an activation of the innate immune system due presumably to macrophage infiltration of intramuscular fat. Between 187 and 354 days of age (the "finishing" phase), NW steers had an activation of the lipogenic transcriptome machinery, while EW steers had a clear inhibition through the epigenetic control of histone acetylases. Results underscored the need to conduct further studies to understand better the functional outcome of transcriptome changes induced in the offspring by pre- and post-natal nutrition. Additional knowledge on molecular and functional outcomes would help produce more efficient beef cattle.
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30
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Cheng FHC, Aguda BD, Tsai JC, Kochańczyk M, Lin JMJ, Chen GCW, Lai HC, Nephew KP, Hwang TW, Chan MWY. A mathematical model of bimodal epigenetic control of miR-193a in ovarian cancer stem cells. PLoS One 2014; 9:e116050. [PMID: 25545504 PMCID: PMC4278842 DOI: 10.1371/journal.pone.0116050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/30/2014] [Indexed: 12/31/2022] Open
Abstract
Accumulating data indicate that cancer stem cells contribute to tumor chemoresistance and their persistence alters clinical outcome. Our previous study has shown that ovarian cancer may be initiated by ovarian cancer initiating cells (OCIC) characterized by surface antigen CD44 and c-KIT (CD117). It has been experimentally demonstrated that a microRNA, namely miR-193a, targets c-KIT mRNA for degradation and could play a crucial role in ovarian cancer development. How miR-193a is regulated is poorly understood and the emerging picture is complex. To unravel this complexity, we propose a mathematical model to explore how estrogen-mediated up-regulation of another target of miR-193a, namely E2F6, can attenuate the function of miR-193a in two ways, one through a competition of E2F6 and c-KIT transcripts for miR-193a, and second by binding of E2F6 protein, in association with a polycomb complex, to the promoter of miR-193a to down-regulate its transcription. Our model predicts that this bimodal control increases the expression of c-KIT and that the second mode of epigenetic regulation is required to generate a switching behavior in c-KIT and E2F6 expressions. Additional analysis of the TCGA ovarian cancer dataset demonstrates that ovarian cancer patients with low expression of EZH2, a polycomb-group family protein, show positive correlation between E2F6 and c-KIT. We conjecture that a simultaneous EZH2 inhibition and anti-estrogen therapy can constitute an effective combined therapeutic strategy against ovarian cancer.
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Affiliation(s)
- Frank H. C. Cheng
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
| | | | - Je-Chiang Tsai
- Department of Mathematics, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
| | - Marek Kochańczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Jora M. J. Lin
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
| | - Gary C. W. Chen
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, Republic of China
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan, Republic of China
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
- Institute of Clinical Pharmacology, Central South University, Changsha, People's Republic of China
- Hunan Key Laboratory of Pharmacogenetics, Changsha, People's Republic of China
| | - Kenneth P. Nephew
- Medical Sciences, Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Tzy-Wei Hwang
- Department of Mathematics, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
- * E-mail: (MWYC); (TWH)
| | - Michael W. Y. Chan
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, Republic of China
- * E-mail: (MWYC); (TWH)
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31
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Bonnici V, Russo F, Bombieri N, Pulvirenti A, Giugno R. Comprehensive reconstruction and visualization of non-coding regulatory networks in human. Front Bioeng Biotechnol 2014; 2:69. [PMID: 25540777 PMCID: PMC4261811 DOI: 10.3389/fbioe.2014.00069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 11/24/2014] [Indexed: 11/16/2022] Open
Abstract
Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.
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Affiliation(s)
- Vincenzo Bonnici
- Department of Computer Science, University of Verona , Verona , Italy
| | - Francesco Russo
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics (IIT) and Institute of Clinical Physiology (IFC), National Research Council (CNR) , Pisa , Italy ; Department of Computer Science, University of Pisa , Pisa , Italy
| | - Nicola Bombieri
- Department of Computer Science, University of Verona , Verona , Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy
| | - Rosalba Giugno
- Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy
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32
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Scelfo A, Piunti A, Pasini D. The controversial role of the Polycomb group proteins in transcription and cancer: how much do we not understand Polycomb proteins? FEBS J 2014; 282:1703-22. [PMID: 25315766 DOI: 10.1111/febs.13112] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/03/2014] [Accepted: 10/14/2014] [Indexed: 12/21/2022]
Abstract
Polycomb group proteins (PcGs) are a large protein family that includes diverse biochemical features assembled together in two large multiprotein complexes. These complexes maintain gene transcriptional repression in a cell type specific manner by modifying the surrounding chromatin to control development, differentiation and cell proliferation. PcGs are also involved in several diseases. PcGs are often directly or indirectly implicated in cancer development for which they have been proposed as potential targets for cancer therapeutic strategies. However, in the last few years a series of discoveries about the basic properties of PcGs and the identification of specific genetic alterations affecting specific Polycomb proteins in different tumours have converged to challenge old dogmas about PcG biological and molecular functions. In this review, we analyse these new data in the context of the old knowledge, highlighting the controversies and providing new models of interpretation and ideas that will perhaps bring some order among apparently contradicting observations.
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Affiliation(s)
- Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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33
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Neo WH, Lim JF, Grumont R, Gerondakis S, Su IH. c-Rel regulates Ezh2 expression in activated lymphocytes and malignant lymphoid cells. J Biol Chem 2014; 289:31693-31707. [PMID: 25266721 DOI: 10.1074/jbc.m114.574517] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The polycomb group protein Ezh2 is a histone methyltransferase that modifies chromatin structure to alter gene expression during embryonic development, lymphocyte activation, and tumorigenesis. The mechanism by which Ezh2 expression is regulated is not well defined. In the current study, we report that c-Rel is a critical activator of Ezh2 transcription in lymphoid cells. In activated primary murine B and T cells, plus human leukemia and multiple myeloma cell lines, recruitment of c-Rel to the first intron of the Ezh2 locus promoted Ezh2 mRNA expression. This up-regulation was abolished in activated c-Rel-deficient lymphocytes and by c-Rel knockdown in Jurkat T cells. Treatment of malignant cells with the c-Rel inhibitor pentoxifylline not only reduced c-Rel nuclear translocation and Ezh2 expression, but also enhanced their sensitivity to the Ezh2-specific drug, GSK126 through increased growth inhibition and cell death. In summary, our demonstration that c-Rel regulates Ezh2 expression in lymphocytes and malignant lymphoid cells reveals a novel transcriptional network in transformed lymphoid cells expressing high levels of Ezh2 that provides a molecular justification for combinatorial drug therapy.
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Affiliation(s)
- Wen Hao Neo
- School of Biological Sciences, College of Science, Nanyang Technological University, Singapore 637551, Republic of Singapore and
| | - Jun Feng Lim
- School of Biological Sciences, College of Science, Nanyang Technological University, Singapore 637551, Republic of Singapore and
| | - Raelene Grumont
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Steve Gerondakis
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - I-Hsin Su
- School of Biological Sciences, College of Science, Nanyang Technological University, Singapore 637551, Republic of Singapore and.
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Raynaud C, Mallory AC, Latrasse D, Jégu T, Bruggeman Q, Delarue M, Bergounioux C, Benhamed M. Chromatin meets the cell cycle. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2677-89. [PMID: 24497647 DOI: 10.1093/jxb/ert433] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The cell cycle is one of the most comprehensively studied biological processes, due primarily to its significance in growth and development, and its deregulation in many human disorders. Studies using a diverse set of model organisms, including yeast, worms, flies, frogs, mammals, and plants, have greatly expanded our knowledge of the cell cycle and have contributed to the universally accepted view of how the basic cell cycle machinery is regulated. In addition to the oscillating activity of various cyclin-dependent kinase (CDK)-cyclin complexes, a plethora of proteins affecting various aspects of chromatin dynamics has been shown to be essential for cell proliferation during plant development. Furthermore, it was reported recently that core cell cycle regulators control gene expression by modifying histone patterns. This review focuses on the intimate relationship between the cell cycle and chromatin. It describes the dynamics and functions of chromatin structures throughout cell cycle progression and discusses the role of heterochromatin as a barrier against re-replication and endoreduplication. It also proposes that core plant cell cycle regulators control gene expression in a manner similar to that described in mammals. At present, our challenge in plants is to define the complete set of effectors and actors that coordinate cell cycle progression and chromatin structure and to understand better the functional interplay between these two processes.
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Affiliation(s)
- Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Allison C Mallory
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - David Latrasse
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Quentin Bruggeman
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Marianne Delarue
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
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Huang X, Spencer GJ, Lynch JT, Ciceri F, Somerville TDD, Somervaille TCP. Enhancers of Polycomb EPC1 and EPC2 sustain the oncogenic potential of MLL leukemia stem cells. Leukemia 2014; 28:1081-91. [PMID: 24166297 PMCID: PMC3998875 DOI: 10.1038/leu.2013.316] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/30/2013] [Accepted: 10/22/2013] [Indexed: 01/21/2023]
Abstract
Through a targeted knockdown (KD) screen of chromatin regulatory genes, we identified the EP400 complex components EPC1 and EPC2 as critical oncogenic cofactors in acute myeloid leukemia (AML). EPC1 and EPC2 were required for the clonogenic potential of human AML cells of multiple molecular subtypes. Focusing on MLL-mutated AML as an exemplar, Epc1 or Epc2 KD-induced apoptosis of murine MLL-AF9 AML cells and abolished leukemia stem cell potential. By contrast, normal hematopoietic stem and progenitor cells (HSPC) were spared. Similar selectivity was observed for human primary AML cells versus normal CD34(+) HSPC. In keeping with these distinct functional consequences, Epc1 or Epc2 KD-induced divergent transcriptional consequences in murine MLL-AF9 granulocyte-macrophage progenitor-like (GMP) cells versus normal GMP, with a signature of increased MYC activity in leukemic but not normal cells. This was caused by accumulation of MYC protein and was also observed following KD of other EP400 complex genes. Pharmacological inhibition of MYC:MAX dimerization, or concomitant MYC KD, reduced apoptosis following EPC1 KD, linking the accumulation of MYC to cell death. Therefore, EPC1 and EPC2 are components of a complex that directly or indirectly serves to prevent MYC accumulation and AML cell apoptosis, thus sustaining oncogenic potential.
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Affiliation(s)
- Xu Huang
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Gary J Spencer
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - James T Lynch
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Filippo Ciceri
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Tim D D Somerville
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
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Tooze RM. A replicative self-renewal model for long-lived plasma cells: questioning irreversible cell cycle exit. Front Immunol 2013; 4:460. [PMID: 24385976 PMCID: PMC3866514 DOI: 10.3389/fimmu.2013.00460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/02/2013] [Indexed: 12/23/2022] Open
Abstract
Plasma cells are heterogenous in terms of their origins, secretory products, and lifespan. A current paradigm is that cell cycle exit in plasma cell differentiation is irreversible, following a pattern familiar in short-lived effector populations in other hemopoietic lineages. This paradigm no doubt holds true for many plasma cells whose lifespan can be measured in days following the completion of differentiation. Whether this holds true for long-lived bone marrow plasma cells that are potentially maintained for the lifespan of the organism is less apparent. Added to this the mechanisms that establish and maintain cell cycle quiescence in plasma cells are incompletely defined. Gene expression profiling indicates that in the transition of human plasmablasts to long-lived plasma cells a range of cell cycle regulators are induced in a pattern that suggests a quiescence program with potential for cell cycle re-entry. Here a model of relative quiescence with the potential for replicative self-renewal amongst long-lived plasma cells is explored. The implications of such a mechanism would be diverse, and the argument is made here that current evidence is not sufficiently strong that the possibility should be disregarded.
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Affiliation(s)
- Reuben M Tooze
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds , Leeds , UK ; Haematological Malignancy Diagnostic Service, Leeds Teaching Hospitals NHS Trust , Leeds , UK
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Tommasino M. The human papillomavirus family and its role in carcinogenesis. Semin Cancer Biol 2013; 26:13-21. [PMID: 24316445 DOI: 10.1016/j.semcancer.2013.11.002] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/22/2013] [Accepted: 11/27/2013] [Indexed: 01/17/2023]
Abstract
Human papillomaviruses (HPVs) are a family of small double-stranded DNA viruses that have a tropism for the epithelia of the genital and upper respiratory tracts and for the skin. Approximately 150 HPV types have been discovered so far, which are classified into several genera based on their DNA sequence. Approximately 15 high-risk mucosal HPV types are clearly associated with cervical cancer; HPV16 and HPV18 are the most carcinogenic since they are responsible for approximately 50% and 20% of all cervical cancers worldwide, respectively. It is now also clear that these viruses are linked to a subset of other genital cancers, as well as head and neck cancers. Due to their high level of carcinogenic activity, HPV16 and HPV18 are the most studied HPV types so far. Biological studies have highlighted the key roles in cellular transformation of the products of two viral early genes, E6 and E7. Many of the mechanisms of E6 and E7 in subverting the regulation of fundamental cellular events have been fully characterized, contributing not only to our knowledge of how the oncogenic viruses promote cancer development but also to our understanding of basic cell biology. Despite HPV research resulting in extraordinary achievements in the last four decades, significantly improving the screening and prophylaxis of HPV-induced lesions, additional research is necessary to characterize the biology and epidemiology of the vast number of HPV types that have been poorly investigated so far, with a final aim of clarifying their potential roles in other human diseases.
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Affiliation(s)
- Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer - World Health Organization, 150 Cours Albert-Thomas, 69372 Lyon cedex 08, France.
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Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol 2013; 20:1147-55. [PMID: 24096405 DOI: 10.1038/nsmb.2669] [Citation(s) in RCA: 645] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/12/2013] [Indexed: 12/12/2022]
Abstract
Polycomb group (PcG) proteins are epigenetic regulators of transcription that have key roles in stem-cell identity, differentiation and disease. Mechanistically, they function within multiprotein complexes, called Polycomb repressive complexes (PRCs), which modify histones (and other proteins) and silence target genes. The dynamics of PRC1 and PRC2 components has been the focus of recent research. Here we discuss our current knowledge of the PRC complexes, how they are targeted to chromatin and how the high diversity of the PcG proteins allows these complexes to influence cell identity.
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Wang X, Choi JH, Ding J, Yang L, Ngoka LC, Lee EJ, Zha Y, Mao L, Jin B, Ren M, Cowell J, Huang S, Shi H, Cui H, Ding HF. HOXC9 directly regulates distinct sets of genes to coordinate diverse cellular processes during neuronal differentiation. BMC Genomics 2013; 14:830. [PMID: 24274069 PMCID: PMC3906982 DOI: 10.1186/1471-2164-14-830] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/20/2013] [Indexed: 01/06/2023] Open
Abstract
Background Cellular differentiation is characterized by the acquisition of specialized structures and functions, cell cycle exit, and global attenuation of the DNA damage response. It is largely unknown how these diverse cellular events are coordinated at the molecular level during differentiation. We addressed this question in a model system of neuroblastoma cell differentiation induced by HOXC9. Results We conducted a genome-wide analysis of the HOXC9-induced neuronal differentiation program. Microarray gene expression profiling revealed that HOXC9-induced differentiation was associated with transcriptional regulation of 2,370 genes, characterized by global upregulation of neuronal genes and downregulation of cell cycle and DNA repair genes. Remarkably, genome-wide mapping by ChIP-seq demonstrated that HOXC9 bound to 40% of these genes, including a large number of genes involved in neuronal differentiation, cell cycle progression and the DNA damage response. Moreover, we showed that HOXC9 interacted with the transcriptional repressor E2F6 and recruited it to the promoters of cell cycle genes for repressing their expression. Conclusions Our results demonstrate that HOXC9 coordinates diverse cellular processes associated with differentiation by directly activating and repressing the transcription of distinct sets of genes.
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Affiliation(s)
- Xiangwei Wang
- Cancer Center, Georgia Regents University, Augusta, GA 30912, USA.
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Leseva M, Santostefano KE, Rosenbluth AL, Hamazaki T, Terada N. E2f6-mediated repression of the meiotic Stag3 and Smc1β genes during early embryonic development requires Ezh2 and not the de novo methyltransferase Dnmt3b. Epigenetics 2013; 8:873-84. [PMID: 23880518 PMCID: PMC3883790 DOI: 10.4161/epi.25522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/12/2013] [Accepted: 06/24/2013] [Indexed: 12/31/2022] Open
Abstract
The E2f6 transcriptional repressor is an E2F-family member essential for the silencing of a group of meiosis-specific genes in somatic tissues. Although E2f6 has been shown to associate with both polycomb repressive complexes (PRC) and the methyltransferase Dnmt3b, the cross-talk between these repressive machineries during E2f6-mediated gene silencing has not been clearly demonstrated yet. In particular, it remains largely undetermined when and how E2f6 establishes repression of meiotic genes during embryonic development. We demonstrate here that the inactivation of a group of E2f6 targeted genes, including Stag3 and Smc1β, first occurs at the transition from mouse embryonic stem cells (ESCs) to epiblast stem cells (EpiSCs), which represent pre- and post-implantation stages, respectively. This process was accompanied by de novo methylation of their promoters. Of interest, despite a clear difference in DNA methylation status, E2f6 was similarly bound to the proximal promoter regions both in ESCs and EpiSCs. Neither E2f6 nor Dnmt3b overexpression in ESCs decreased meiotic gene expression or increased DNA methylation, indicating that additional factors are required for E2f6-mediated repression during the transition. When the SET domain of Ezh2, a core subunit of the PRC2 complex, was deleted, however, repression of Stag3 and Smc1β during embryoid body differentiation was largely impaired, indicating that the event required the enzymatic activity of Ezh2. In addition, repression of Stag3 and Smc1β occurred in the absence of Dnmt3b. The data presented here suggest a primary role of PRC2 in E2f6-mediated gene silencing of the meiotic genes.
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Affiliation(s)
- Milena Leseva
- Department of Pathology; University of Florida College of Medicine; Gainesville, FL USA
| | | | - Amy L Rosenbluth
- Department of Pathology; University of Florida College of Medicine; Gainesville, FL USA
| | - Takashi Hamazaki
- Department of Pathology; University of Florida College of Medicine; Gainesville, FL USA
- Department of Pediatrics; Osaka City University Graduate School of Medicine; Osaka, Japan
| | - Naohiro Terada
- Department of Pathology; University of Florida College of Medicine; Gainesville, FL USA
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Di Fiore R, D'Anneo A, Tesoriere G, Vento R. RB1 in cancer: different mechanisms of RB1 inactivation and alterations of pRb pathway in tumorigenesis. J Cell Physiol 2013; 228:1676-87. [PMID: 23359405 DOI: 10.1002/jcp.24329] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 01/15/2013] [Indexed: 12/14/2022]
Abstract
Loss of RB1 gene is considered either a causal or an accelerating event in retinoblastoma. A variety of mechanisms inactivates RB1 gene, including intragenic mutations, loss of expression by methylation and chromosomal deletions, with effects which are species-and cell type-specific. RB1 deletion can even lead to aneuploidy thus greatly increasing cancer risk. The RB1gene is part of a larger gene family that includes RBL1 and RBL2, each of the three encoding structurally related proteins indicated as pRb, p107, and p130, respectively. The great interest in these genes and proteins springs from their ability to slow down neoplastic growth. pRb can associate with various proteins by which it can regulate a great number of cellular activities. In particular, its association with the E2F transcription factor family allows the control of the main pRb functions, while the loss of these interactions greatly enhances cancer development. As RB1 gene, also pRb can be functionally inactivated through disparate mechanisms which are often tissue specific and dependent on the scenario of the involved tumor suppressors and oncogenes. The critical role of the context is complicated by the different functions played by the RB proteins and the E2F family members. In this review, we want to emphasize the importance of the mechanisms of RB1/pRb inactivation in inducing cancer cell development. The review is divided in three chapters describing in succession the mechanisms of RB1 inactivation in cancer cells, the alterations of pRb pathway in tumorigenesis and the RB protein and E2F family in cancer.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Polyclinic, University of Palermo, Palermo, Italy
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Biochemical and functional interactions of human papillomavirus proteins with polycomb group proteins. Viruses 2013; 5:1231-49. [PMID: 23673719 PMCID: PMC3712305 DOI: 10.3390/v5051231] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 04/23/2013] [Accepted: 04/27/2013] [Indexed: 12/22/2022] Open
Abstract
The role of enzymes involved in polycomb repression of gene transcription has been studied extensively in human cancer. Polycomb repressive complexes mediate oncogene-induced senescence, a principal innate cell-intrinsic tumor suppressor pathway that thwarts expansion of cells that have suffered oncogenic hits. Infections with human cancer viruses including human papillomaviruses (HPVs) and Epstein-Barr virus can trigger oncogene-induced senescence, and the viruses have evolved strategies to abrogate this response in order to establish an infection and reprogram their host cells to establish a long-term persistent infection. As a consequence of inhibiting polycomb repression and evading oncogene induced-senescence, HPV infected cells have an altered epigenetic program as evidenced by aberrant homeobox gene expression. Similar alterations are frequently observed in non-virus associated human cancers and may be harnessed for diagnosis and therapy.
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Nagel S, Ehrentraut S, Tomasch J, Quentmeier H, Meyer C, Kaufmann M, Drexler HG, MacLeod RAF. Ectopic expression of homeobox gene NKX2-1 in diffuse large B-cell lymphoma is mediated by aberrant chromatin modifications. PLoS One 2013; 8:e61447. [PMID: 23637834 PMCID: PMC3639244 DOI: 10.1371/journal.pone.0061447] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/08/2013] [Indexed: 12/01/2022] Open
Abstract
Homeobox genes encode transcription factors ubiquitously involved in basic developmental processes, deregulation of which promotes cell transformation in multiple cancers including hematopoietic malignancies. In particular, NKL-family homeobox genes TLX1, TLX3 and NKX2-5 are ectopically activated by chromosomal rearrangements in T-cell neoplasias. Here, using transcriptional microarray profiling and RQ-PCR we identified ectopic expression of NKL-family member NKX2-1, in a diffuse large B-cell lymphoma (DLBCL) cell line SU-DHL-5. Moreover, in silico analysis demonstrated NKX2-1 overexpression in 5% of examined DLBCL patient samples. NKX2-1 is physiologically expressed in lung and thyroid tissues where it regulates differentiation. Chromosomal and genomic analyses excluded rearrangements at the NKX2-1 locus in SU-DHL-5, implying alternative activation. Comparative expression profiling implicated several candidate genes in NKX2-1 regulation, variously encoding transcription factors, chromatin modifiers and signaling components. Accordingly, siRNA-mediated knockdown and overexpression studies confirmed involvement of transcription factor HEY1, histone methyltransferase MLL and ubiquitinated histone H2B in NKX2-1 deregulation. Chromosomal aberrations targeting MLL at 11q23 and the histone gene cluster HIST1 at 6p22 which we observed in SU-DHL-5 may, therefore, represent fundamental mutations mediating an aberrant chromatin structure at NKX2-1. Taken together, we identified ectopic expression of NKX2-1 in DLBCL cells, representing the central player in an oncogenic regulative network compromising B-cell differentiation. Thus, our data extend the paradigm of NKL homeobox gene deregulation in lymphoid malignancies.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
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Nara M, Teshima K, Watanabe A, Ito M, Iwamoto K, Kitabayashi A, Kume M, Hatano Y, Takahashi N, Iida S, Sawada K, Tagawa H. Bortezomib reduces the tumorigenicity of multiple myeloma via downregulation of upregulated targets in clonogenic side population cells. PLoS One 2013; 8:e56954. [PMID: 23469177 PMCID: PMC3587640 DOI: 10.1371/journal.pone.0056954] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 01/16/2013] [Indexed: 11/19/2022] Open
Abstract
Side population (SP) cells in cancers, including multiple myeloma, exhibit tumor-initiating characteristics. In the present study, we isolated SP cells from human myeloma cell lines and primary tumors to detect potential therapeutic targets specifically expressed in SP cells. We found that SP cells from myeloma cell lines (RPMI 8226, AMO1, KMS-12-BM, KMS-11) express CD138 and that non-SP cells include a CD138-negative population. Serial transplantation of SP and non-SP cells into NOD/Shi-scid IL-2γnul mice revealed that clonogenic myeloma SP cells are highly tumorigenic and possess a capacity for self-renewal. Gene expression analysis showed that SP cells from five MM cell lines (RPMI 8226, AMO1, KMS-12-BM, KMS-11, JJN3) express genes involved in the cell cycle and mitosis (e.g., CCNB1, CDC25C, CDC2, BIRC5, CENPE, SKA1, AURKB, KIFs, TOP2A, ASPM), polycomb (e.g., EZH2, EPC1) and ubiquitin-proteasome (e.g., UBE2D3, UBE3C, PSMA5) more strongly than do non-SP cells. Moreover, CCNB1, AURKB, EZH2 and PSMA5 were also upregulated in the SPs from eight primary myeloma samples. On that basis, we used an aurora kinase inhibitor (VX-680) and a proteasome inhibitor (bortezomib) with RPMI 8226 and AMO1 cells to determine whether these agents could be used to selectively target the myeloma SP. We found that both these drugs reduced the SP fraction, though bortezomib did so more effectively than VX-680 due to its ability to reduce levels of both phospho-histone H3 (p-hist. H3) and EZH2; VX-680 reduced only p-hist. H3. This is the first report to show that certain oncogenes are specifically expressed in the myeloma SP, and that bortezomib effectively downregulates expression of their products. Our approach may be useful for screening new agents with which to target a cell population possessing strong tumor initiating potential in multiple myeloma.
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Affiliation(s)
- Miho Nara
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Kazuaki Teshima
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Atsushi Watanabe
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Mitsugu Ito
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Keiko Iwamoto
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Atsushi Kitabayashi
- Department of Internal Medicine, Akita Kumiai General Hospital, Akita, Japan
| | - Masaaki Kume
- Department of Internal Medicine, Hiraka General Hospital, Yokote, Japan
| | - Yoshiaki Hatano
- Department of Internal Medicine, Yamamoto Kumiai General Hospital, Noshiro, Japan
| | - Naoto Takahashi
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Shinsuke Iida
- Department of Medical Oncology and Immunology, Nagoya City University School of Medical Science, Nagoya, Japan
| | - Kenichi Sawada
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroyuki Tagawa
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
- * E-mail:
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Yachida S, Iacobuzio-Donahue CA. Evolution and dynamics of pancreatic cancer progression. Oncogene 2013; 32:5253-60. [PMID: 23416985 DOI: 10.1038/onc.2013.29] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/02/2013] [Accepted: 01/03/2013] [Indexed: 02/08/2023]
Abstract
Efficient metastasis is believed as the result of multiple genetic, epigenetic and/or post-translational events in the lifetime of a carcinoma. At the genetic level, these events may be categorized into those that occur during carcinogenesis, and those that occur during subclonal evolution. This review summarizes current knowledge of the genetics of pancreatic cancer from its initiation within a normal cell until the time that is has disseminated to distant organs, many features of which can be extrapolated to other solid tumor types. The implications of these findings to personalize genome analyses of an individual patient's tumor are also discussed.
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Affiliation(s)
- S Yachida
- 1] Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA [2] Division of Refractory Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
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In vivo regulation of E2F1 by Polycomb group genes in Drosophila. G3-GENES GENOMES GENETICS 2012; 2:1651-60. [PMID: 23275887 PMCID: PMC3516486 DOI: 10.1534/g3.112.004333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 10/24/2012] [Indexed: 01/17/2023]
Abstract
The E2F transcription factors are important regulators of the cell cycle whose function is commonly misregulated in cancer. To identify novel regulators of E2F1 activity in vivo, we used Drosophila to conduct genetic screens. For this, we generated transgenic lines that allow the tissue-specific depletion of dE2F1 by RNAi. Expression of these transgenes using Gal4 drivers in the eyes and wings generated reliable and modifiable phenotypes. We then conducted genetic screens testing the capacity of Exelixis deficiencies to modify these E2F1-RNAi phenotypes. From these screens, we identified mutant alleles of Suppressor of zeste 2 [Su(z)2] and multiple Polycomb group genes as strong suppressors of the E2F1-RNA interference phenotypes. In validation of our genetic data, we find that depleting Su(z)2 in cultured Drosophila cells restores the cell-proliferation defects caused by reduction of dE2F1 by elevating the level of dE2f1. Furthermore, analyses of methylation status of histone H3 lysine 27 (H3K27me) from the published modENCODE data sets suggest that the genomic regions harboring dE2f1 gene and certain dE2f1 target genes display H3K27me during development and in several Drosophila cell lines. These in vivo observations suggest that the Polycomb group may regulate cell proliferation by repressing the transcription of dE2f1 and certain dE2F1 target genes. This mechanism may play an important role in coordinating cellular differentiation and proliferation during Drosophila development.
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Aksoy O, Chicas A, Zeng T, Zhao Z, McCurrach M, Wang X, Lowe SW. The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence. Genes Dev 2012; 26:1546-57. [PMID: 22802529 DOI: 10.1101/gad.196238.112] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Oncogene-induced senescence is an anti-proliferative stress response program that acts as a fail-safe mechanism to limit oncogenic transformation and is regulated by the retinoblastoma protein (RB) and p53 tumor suppressor pathways. We identify the atypical E2F family member E2F7 as the only E2F transcription factor potently up-regulated during oncogene-induced senescence, a setting where it acts in response to p53 as a direct transcriptional target. Once induced, E2F7 binds and represses a series of E2F target genes and cooperates with RB to efficiently promote cell cycle arrest and limit oncogenic transformation. Disruption of RB triggers a further increase in E2F7, which induces a second cell cycle checkpoint that prevents unconstrained cell division despite aberrant DNA replication. Mechanistically, E2F7 compensates for the loss of RB in repressing mitotic E2F target genes. Together, our results identify a causal role for E2F7 in cellular senescence and uncover a novel link between the RB and p53 pathways.
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Affiliation(s)
- Ozlem Aksoy
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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Waraya M, Yamashita K, Katoh H, Ooki A, Kawamata H, Nishimiya H, Nakamura K, Ema A, Watanabe M. Cancer specific promoter CpG Islands hypermethylation of HOP homeobox (HOPX) gene and its potential tumor suppressive role in pancreatic carcinogenesis. BMC Cancer 2012; 12:397. [PMID: 22958219 PMCID: PMC3488580 DOI: 10.1186/1471-2407-12-397] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Accepted: 08/31/2012] [Indexed: 12/25/2022] Open
Abstract
Background We have recently identified HOP hoemobox (HOPX) as a tumor suppressor gene candidate, characterized by tumor-specific promoter DNA hypermethylation in human cancers, and it can remarkably inhibit tumors’ aggressive phenotypes. In this current study, we for the first time examined methylation level of HOPX and tested the functional relevance in pancreatic cancer (PC). Methods Clinical features of HOPX promoter hypermethylation was investigated in 89 PC tissues, and immunohistochemistry was added. We also examined its functional relevance in phenotype assays such as soft agar, proliferation, invasion, and cell cycle analysis. Results PC tissues had HOPX gene hypermethylation as compared to the corresponding normal pancreas tissues, and its uniqueness was robust to discriminate tumor from normal tissues (AUC = 0.85, P < 0.0001). Unexpectedly, HOPX was increased in expression in tumor tissues, and immunohistochemistry revealed its predominant expression in the Langerhans islet cells, where HOPX was reduced in expression for PC cells with promoter hypermethylation. HOPX transfectants exhibited G1 arrest with subG1 accumulation, and inhibited tumor forming and invasive ability. Conclusion Defective expression of HOPX which is consistent with promoter DNA hypermethylation may explain aggressive phenotype of pancreatic cancer, and intense expression of HOPX in the Langerhans cells may in turn uniquely contribute to pancreatic carcinogenesis.
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Affiliation(s)
- Mina Waraya
- Department of Surgery, Kitasato University Hospital, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0375, Japan.
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David G. Regulation of oncogene-induced cell cycle exit and senescence by chromatin modifiers. Cancer Biol Ther 2012; 13:992-1000. [PMID: 22825329 DOI: 10.4161/cbt.21116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Oncogene activation leads to dramatic changes in numerous biological pathways controlling cellular division, and results in the initiation of a transcriptional program that promotes transformation. Conversely, it also triggers an irreversible cell cycle exit called cellular senescence, which allows the organism to counteract the potentially detrimental uncontrolled proliferation of damaged cells. Therefore, a tight transcriptional control is required at the onset of oncogenic signal, coordinating both positive and negative regulation of gene expression. Not surprisingly, numerous chromatin modifiers contribute to the cellular response to oncogenic stress. While these chromatin modifiers were initially thought of as mere mediators of the cellular response to oncogenic stress, recent studies have uncovered a direct and specific regulation of chromatin modifiers by oncogenic signals. We review here the diverse functions of chromatin modifiers in the cellular response to oncogenic stress, and discuss the implications of these findings on the regulation of cell cycle progression and proliferation by activated oncogenes.
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Affiliation(s)
- Gregory David
- Department of Pharmacology and NYU Cancer Institute, NYU Langone Medical Center, New York, NY, USA.
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Dietrich N, Lerdrup M, Landt E, Agrawal-Singh S, Bak M, Tommerup N, Rappsilber J, Södersten E, Hansen K. REST-mediated recruitment of polycomb repressor complexes in mammalian cells. PLoS Genet 2012; 8:e1002494. [PMID: 22396653 PMCID: PMC3291536 DOI: 10.1371/journal.pgen.1002494] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 12/07/2011] [Indexed: 12/02/2022] Open
Abstract
Polycomb Repressive Complex (PRC) 1 and PRC2 regulate genes involved in differentiation and development. However, the mechanism for how PRC1 and PRC2 are recruited to genes in mammalian cells is unclear. Here we present evidence for an interaction between the transcription factor REST, PRC1, and PRC2 and show that RNF2 and REST co-regulate a number of neuronal genes in human teratocarcinoma cells (NT2-D1). Using NT2-D1 cells as a model of neuronal differentiation, we furthermore showed that retinoic-acid stimulation led to displacement of PRC1 at REST binding sites, reduced H3K27Me3, and increased gene expression. Genome-wide analysis of Polycomb binding in Rest−/− and Eed−/− mouse embryonic stem (mES) cells showed that Rest was required for PRC1 recruitment to a subset of Polycomb regulated neuronal genes. Furthermore, we found that PRC1 can be recruited to Rest binding sites independently of CpG islands and the H3K27Me3 mark. Surprisingly, PRC2 was frequently increased around Rest binding sites located in CpG-rich regions in the Rest−/− mES cells, indicating a more complex interplay where Rest also can limit PRC2 recruitment. Therefore, we propose that Rest has context-dependent functions for PRC1- and PRC2- recruitment, which allows this transcription factor to act both as a recruiter of Polycomb as well as a limiting factor for PRC2 recruitment at CpG islands. Multicellular organisms are composed of a large number of specialized cell types that all originate from the Embryonic Stem cell (ES cell). It is crucial for the maintenance of naïve ES cells that developmental genes are kept in an off-state until appropriate differentiation stimuli are received. Polycomb Repressive Complexes, PRC1 and PRC2, are bound at and repress the activity of a large number of key developmental genes in ES cells and at different stages of differentiation. While in Drosophila the PRC complexes are recruited to DNA elements called Polycomb Response Elements (PREs), through the interaction with transcription factors; examples of such factors remain poorly characterized in mammals. We here demonstrate that the transcription factor Rest interacts with and is required for recruitment of PRC1 and PRC2 to a subset of Rest target genes in mouse embryonic stem (mES) cells. In line with REST being a repressor of neuronal genes, we found that PRC1 and PRC2 co-localized with REST at genes involved in neuronal development and got displaced during neuronal differentiation. Based on our data we propose that the PRC1 and PRC2 complexes function as co-repressors for Rest to control the timed expression of developmental genes in the process of cellular differentiation.
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Affiliation(s)
- Nikolaj Dietrich
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Mads Lerdrup
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Eskild Landt
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Shuchi Agrawal-Singh
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Mads Bak
- Wilhelm Johannsen Centre For Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Centre For Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Erik Södersten
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Hansen
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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