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Tran NT, Graf R, Acevedo-Ochoa E, Trombke J, Weber T, Sommermann T, Salomon C, Kühn R, Rajewsky K, Chu VT. In vivo CRISPR/Cas9-mediated screen reveals a critical function of TFDP1 and E2F4 transcription factors in hematopoiesis. Leukemia 2024; 38:2003-2015. [PMID: 39043964 PMCID: PMC11347378 DOI: 10.1038/s41375-024-02357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
Hematopoiesis is a continuous process of blood cell production driven by hematopoietic stem and progenitor cells (HSPCs) in the bone marrow. Proliferation and differentiation of HSPCs are regulated by complex transcriptional networks. In order to identify transcription factors with key roles in HSPC-mediated hematopoietic reconstitution, we developed an efficient and robust CRISPR/Cas9-based in vivo genetic screen. Using this experimental system, we identified the TFDP1 transcription factor to be essential for HSPC proliferation and post-transplant hematopoiesis. We further discovered that E2F4, an E2F transcription factor, serves as a binding partner of TFDP1 and is required for HSPC proliferation. Deletion of TFDP1 caused downregulation of genes associated with the cell cycle, with around 50% of these genes being identified as direct targets of TFDP1 and E2F4. Thus, our study expands the transcriptional network governing hematopoietic development through an in vivo CRISPR/Cas9-based genetic screen and identifies TFDP1/E2F4 as positive regulators of cell cycle genes in HSPCs.
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Affiliation(s)
- Ngoc Tung Tran
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Robin Graf
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin, Berlin, Germany
| | - Ernesto Acevedo-Ochoa
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Janine Trombke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Timm Weber
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Biobank OWL (BOWL), Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Thomas Sommermann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Dynamic42 GmbH, Jena, Germany
| | - Claudia Salomon
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Genome Engineering & Disease Models, Berlin, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
| | - Van Trung Chu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Genome Engineering & Disease Models, Berlin, Germany.
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2
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Zhou Y, Nakajima R, Shirasawa M, Fikriyanti M, Zhao L, Iwanaga R, Bradford AP, Kurayoshi K, Araki K, Ohtani K. Expanding Roles of the E2F-RB-p53 Pathway in Tumor Suppression. BIOLOGY 2023; 12:1511. [PMID: 38132337 PMCID: PMC10740672 DOI: 10.3390/biology12121511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The transcription factor E2F links the RB pathway to the p53 pathway upon loss of function of pRB, thereby playing a pivotal role in the suppression of tumorigenesis. E2F fulfills a major role in cell proliferation by controlling a variety of growth-associated genes. The activity of E2F is controlled by the tumor suppressor pRB, which binds to E2F and actively suppresses target gene expression, thereby restraining cell proliferation. Signaling pathways originating from growth stimulative and growth suppressive signals converge on pRB (the RB pathway) to regulate E2F activity. In most cancers, the function of pRB is compromised by oncogenic mutations, and E2F activity is enhanced, thereby facilitating cell proliferation to promote tumorigenesis. Upon such events, E2F activates the Arf tumor suppressor gene, leading to activation of the tumor suppressor p53 to protect cells from tumorigenesis. ARF inactivates MDM2, which facilitates degradation of p53 through proteasome by ubiquitination (the p53 pathway). P53 suppresses tumorigenesis by inducing cellular senescence or apoptosis. Hence, in almost all cancers, the p53 pathway is also disabled. Here we will introduce the canonical functions of the RB-E2F-p53 pathway first and then the non-classical functions of each component, which may be relevant to cancer biology.
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Affiliation(s)
- Yaxuan Zhou
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Rinka Nakajima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mashiro Shirasawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mariana Fikriyanti
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Lin Zhao
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Ritsuko Iwanaga
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Andrew P. Bradford
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Kenta Kurayoshi
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan;
| | - Keigo Araki
- Department of Morphological Biology, Ohu University School of Dentistry, 31-1 Misumido Tomitamachi, Koriyama, Fukushima 963-8611, Japan;
| | - Kiyoshi Ohtani
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
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3
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Li K, Huang Z, Liu C, Xu Y, Chen W, Shi L, Li C, Zhou F, Zhou F. Transcriptomic analysis of human pulmonary microvascular endothelial cells treated with LPS. Cell Signal 2023; 111:110870. [PMID: 37633475 DOI: 10.1016/j.cellsig.2023.110870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Acute respiratory distress syndrome (ARDS) has a rapid onset and progression, which lead to the severity and complexity of the primary disease and significantly increase the fatality rate of patients. Transcriptomics provides some ideas for clarifying the mechanism of ARDS, exploring prevention and treatment targets, and searching for related specific markers. In this study, RNA-Seq technology was used to observe the gene expression of human pulmonary microvascular endothelial cells (PMVECs) induced by LPS, and to excavate the key genes and signaling pathways in ARDS process. A total of 2300 up-regulated genes were detected, and a corresponding 1696 down-regulated genes were screened. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and protein-protein interaction (PPI) were also used for functional annotation of key genes. TFDP1 was identified as a cell cycle-dependent differentially expressed gene, and its reduced expression was verified in LPS-treated PMVECs and lung tissues of CLP-induced mice. In addition, the inhibition of TFDP1 on inflammation and apoptosis, and the promotion of proliferation were confirmed. The decreased expression of E2F1, Rb, CDK1 and the activation of MAPK signaling pathway were substantiated in the in vivo and in vitro models of ARDS. Moreover, SREBF1 has been demonstrated to be involved in cell cycle arrest in PMVECs by inhibiting CDK1. Our study shows that transcriptomics combined with basic research can broaden the investigation of ARDS mechanisms and may provide a basis for future mechanistic innovations.
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Affiliation(s)
- Kaili Li
- Department of Emergency, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China.
| | - Zuotian Huang
- Department of Hepatobiliary Pancreatic Tumor Center, Chongqing University Cancer Hospital, 400030 Chongqing Municipality, China
| | - Chang Liu
- Department of Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China.
| | - Yuanyuan Xu
- Department of Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Wei Chen
- Department of Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Lu Shi
- Department of Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Can Li
- Department of Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Fawei Zhou
- Department of Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Fachun Zhou
- Department of Emergency, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China; Department of Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China.
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4
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Zhao J, Xu Y. PITX1 plays essential functions in cancer. Front Oncol 2023; 13:1253238. [PMID: 37841446 PMCID: PMC10570508 DOI: 10.3389/fonc.2023.1253238] [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: 07/05/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023] Open
Abstract
PITX1, also known as the pituitary homeobox 1 gene, has emerged as a key regulator in animal growth and development, attracting significant research attention. Recent investigations have revealed the implication of dysregulated PITX1 expression in tumorigenesis, highlighting its involvement in cancer development. Notably, PITX1 interacts with p53 and exerts control over crucial cellular processes including cell cycle progression, apoptosis, and chemotherapy resistance. Its influence extends to various tumors, such as esophageal, colorectal, gastric, and liver cancer, contributing to tumor progression and metastasis. Despite its significance, a comprehensive review examining PITX1's role in oncology remains lacking. This review aims to address this gap by providing a comprehensive overview of PITX1 in different cancer types, with a particular focus on its clinicopathological significance.
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Affiliation(s)
- Jingpu Zhao
- Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Yongfeng Xu
- Abdominal Oncology Ward, Cancer Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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5
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Sun N, Victor MB, Park YP, Xiong X, Scannail AN, Leary N, Prosper S, Viswanathan S, Luna X, Boix CA, James BT, Tanigawa Y, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M. Human microglial state dynamics in Alzheimer's disease progression. Cell 2023; 186:4386-4403.e29. [PMID: 37774678 PMCID: PMC10644954 DOI: 10.1016/j.cell.2023.08.037] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/21/2023] [Accepted: 08/29/2023] [Indexed: 10/01/2023]
Abstract
Altered microglial states affect neuroinflammation, neurodegeneration, and disease but remain poorly understood. Here, we report 194,000 single-nucleus microglial transcriptomes and epigenomes across 443 human subjects and diverse Alzheimer's disease (AD) pathological phenotypes. We annotate 12 microglial transcriptional states, including AD-dysregulated homeostatic, inflammatory, and lipid-processing states. We identify 1,542 AD-differentially-expressed genes, including both microglia-state-specific and disease-stage-specific alterations. By integrating epigenomic, transcriptomic, and motif information, we infer upstream regulators of microglial cell states, gene-regulatory networks, enhancer-gene links, and transcription-factor-driven microglial state transitions. We demonstrate that ectopic expression of our predicted homeostatic-state activators induces homeostatic features in human iPSC-derived microglia-like cells, while inhibiting activators of inflammation can block inflammatory progression. Lastly, we pinpoint the expression of AD-risk genes in microglial states and differential expression of AD-risk genes and their regulators during AD progression. Overall, we provide insights underlying microglial states, including state-specific and AD-stage-specific microglial alterations at unprecedented resolution.
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Affiliation(s)
- Na Sun
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matheus B Victor
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yongjin P Park
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology and Laboratory Medicine, Department of Statistics, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Xushen Xiong
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aine Ni Scannail
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Noelle Leary
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shaniah Prosper
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Soujanya Viswanathan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xochitl Luna
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carles A Boix
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin T James
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yosuke Tanigawa
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyriaki Galani
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hansruedi Mathys
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Xueqiao Jiang
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ayesha P Ng
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Li-Huei Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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6
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Militi S, Nibhani R, Jalali M, Pauklin S. RBL2-E2F-GCN5 guide cell fate decisions during tissue specification by regulating cell-cycle-dependent fluctuations of non-cell-autonomous signaling. Cell Rep 2023; 42:113146. [PMID: 37725511 DOI: 10.1016/j.celrep.2023.113146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/30/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
The retinoblastoma family proteins (RBs) and E2F transcription factors are cell-autonomous regulators of cell-cycle progression, but they also impact fate choice in addition to tumor suppression. The range of mechanisms involved remains to be uncovered. Here, we show that RBs, particularly RBL2/p130, repress WNT ligands such as WNT4 and WNT8A, thereby directing ectoderm specification between neural crest to neuroepithelium. RBL2 achieves this function through cell-cycle-dependent cooperation with E2Fs and GCN5 on the regulatory regions of WNT loci, which direct neuroepithelial versus neural crest specification by temporal fluctuations of WNT/β-catenin and DLL/NOTCH signaling activity. Thus, the RB-E2F bona fide cell-autonomous axis controls cell fate decisions, and RBL2 regulates field effects via WNT ligands. This reveals a non-cell-autonomous function of RBL2-E2F in stem cell and tissue progenitor differentiation that has broader implications for cell-cycle-dependent cell fate specification in organogenesis, adult stem cells, tissue homeostasis, and tumorigenesis.
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Affiliation(s)
- Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford OX3 7LD, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford OX3 7LD, UK
| | - Morteza Jalali
- Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford OX3 7LD, UK.
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7
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Aubry A, Pearson JD, Charish J, Yu T, Sivak JM, Xirodimas DP, Avet-Loiseau H, Corre J, Monnier PP, Bremner R. Deneddylation of ribosomal proteins promotes synergy between MLN4924 and chemotherapy to elicit complete therapeutic responses. Cell Rep 2023; 42:112925. [PMID: 37552601 DOI: 10.1016/j.celrep.2023.112925] [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: 11/14/2022] [Revised: 05/29/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
The neddylation inhibitor MLN4924/Pevonedistat is in clinical trials for multiple cancers. Efficacy is generally attributed to cullin RING ligase (CRL) inhibition, but the contribution of non-CRL targets is unknown. Here, CRISPR screens map MLN4924-monotherapy sensitivity in retinoblastoma to a classic DNA damage-induced p53/E2F3/BAX-dependent death effector network, which synergizes with Nutlin3a or Navitoclax. In monotherapy-resistant cells, MLN4924 plus standard-of-care topotecan overcomes resistance, but reduces DNA damage, instead harnessing ribosomal protein nucleolar-expulsion to engage an RPL11/p21/MYCN/E2F3/p53/BAX synergy network that exhibits extensive cross-regulation. Strikingly, unneddylatable RPL11 substitutes for MLN4924 to perturb nucleolar function and enhance topotecan efficacy. Orthotopic tumors exhibit complete responses while preserving visual function. Moreover, MLN4924 plus melphalan deploy this DNA damage-independent strategy to synergistically kill multiple myeloma cells. Thus, MLN4924 synergizes with standard-of-care drugs to unlock a nucleolar death effector network across cancer types implying broad therapeutic relevance.
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Affiliation(s)
- Arthur Aubry
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada; Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France
| | - Joel D Pearson
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jason Charish
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Tao Yu
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jeremy M Sivak
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Hervé Avet-Loiseau
- Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM, Toulouse, France
| | - Jill Corre
- Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM, Toulouse, France
| | - Philippe P Monnier
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada; Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada.
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8
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Nakajima R, Deguchi R, Komori H, Zhao L, Zhou Y, Shirasawa M, Angelina A, Goto Y, Tohjo F, Nakahashi K, Nakata K, Iwanaga R, Bradford AP, Araki K, Warita T, Ohtani K. The TFDP1 gene coding for DP1, the heterodimeric partner of the transcription factor E2F, is a target of deregulated E2F. Biochem Biophys Res Commun 2023; 663:154-162. [PMID: 37141667 DOI: 10.1016/j.bbrc.2023.04.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
The TFDP1 gene codes for the heterodimeric partner DP1 of the transcription factor E2F. E2F, principal target of the tumor suppressor pRB, plays central roles in cell proliferation by activating a group of growth-related genes. E2F also mediates tumor suppression by activating tumor suppressor genes such as ARF, an upstream activator of the tumor suppressor p53, when deregulated from pRB upon oncogenic changes. Among 8 E2F family members (E2F1∼E2F8), expression of activator E2Fs (E2F1∼E2F3a) is induced at the G1/S boundary of the cell cycle after growth stimulation by E2F itself. However, mechanisms regulating DP1 expression are not known. We show here that over-expression of E2F1 and forced inactivation of pRB, by adenovirus E1a, induced TFDP1 gene expression in human normal fibroblast HFFs, suggesting that the TFDP1 gene is a target of E2F. Serum stimulation of HFFs also induced TFDP1 gene expression, but with different kinetics from that of the CDC6 gene, a typical growth-related E2F target. Both over-expression of E2F1 and serum stimulation activated the TFDP1 promoter. We searched for E2F1-responsive regions by 5' and 3' deletion of the TFDP1 promoter and by introducing point mutations in putative E2F1-responsive elements. Promoter analysis identified several GC-rich elements, mutation of which reduced E2F1-responsiveness but not serum-responsiveness. ChIP assays showed that the GC-rich elements bound deregulated E2F1 but not physiological E2F1 induced by serum stimulation. These results suggest that the TFDP1 gene is a target of deregulated E2F. In addition, knockdown of DP1 expression by shRNA enhanced ARF gene expression, which is specifically induced by deregulated E2F activity, suggesting that activation of the TFDP1 gene by deregulated E2F may function as a failsafe feedback mechanism to suppress deregulated E2F and maintain normal cell growth in the event that DP1 expression is insufficient relative to that of its partner activator E2Fs. a maximum of 6 keywords: E2F, DP1, TFDP1 gene, pRB, gene expression.
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Affiliation(s)
- Rinka Nakajima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Reika Deguchi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Hideyuki Komori
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Lin Zhao
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Yaxuan Zhou
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Mashiro Shirasawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Arlene Angelina
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Yasuko Goto
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Fumiya Tohjo
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Kengo Nakahashi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Kimi Nakata
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Ritsuko Iwanaga
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Andrew P Bradford
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Keigo Araki
- Department of Morphological Biology, Ohu University School of Dentistry, 31-1 Misumido Tomitamachi, Koriyama, Fukushima, 963-8611, Japan
| | - Tomoko Warita
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan
| | - Kiyoshi Ohtani
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1337, Japan.
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9
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Zhu X, Guo L, Zhu R, Zhou X, Zhang J, Li D, He S, Qiao Y. Phytophthora sojae effector PsAvh113 associates with the soybean transcription factor GmDPB to inhibit catalase-mediated immunity. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 36972124 DOI: 10.1111/pbi.14043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Phytophthora species are the most destructive plant pathogens worldwide and the main threat to agricultural and natural ecosystems; however, their pathogenic mechanism remains largely unknown. Here, we show that Avh113 effector is required for the virulence of Phytophthora sojae and is important for development of Phytophthora root and stem rot (PRSR) in soybean (Glycine max). Ectopic expression of PsAvh113 enhanced viral and Phytophthora infection in Nicotiana benthamiana. PsAvh113 directly associated with the soybean transcription factor GmDPB, inducing its degradation by the 26S proteasome. The internal repeat 2 (IR2) motif of PsAvh113 was important for its virulence and interaction with GmDPB, while silencing and overexpression of GmDPB in soybean hairy roots altered the resistance to P. sojae. Upon binding to GmDPB, PsAvh113 decreased the transcription of the downstream gene GmCAT1, which acts as a positive regulator of plant immunity. Furthermore, we revealed that PsAvh113 suppressed the GmCAT1-induced cell death by associating with GmDPB, thereby enhancing plant susceptibility to Phytophthora. Together, our findings reveal a vital role of PsAvh113 in inducing PRSR in soybean and offer a novel insight into the interplay between defence and counter-defence during the P. sojae infection of soybean.
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Affiliation(s)
- Xiaoguo Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Liang Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ruiqing Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoyi Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jianing Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Die Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shidan He
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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10
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Deregulated E2F Activity as a Cancer-Cell Specific Therapeutic Tool. Genes (Basel) 2023; 14:genes14020393. [PMID: 36833320 PMCID: PMC9956157 DOI: 10.3390/genes14020393] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The transcription factor E2F, the principal target of the tumor suppressor pRB, plays crucial roles in cell proliferation and tumor suppression. In almost all cancers, pRB function is disabled, and E2F activity is enhanced. To specifically target cancer cells, trials have been undertaken to suppress enhanced E2F activity to restrain cell proliferation or selectively kill cancer cells, utilizing enhanced E2F activity. However, these approaches may also impact normal growing cells, since growth stimulation also inactivates pRB and enhances E2F activity. E2F activated upon the loss of pRB control (deregulated E2F) activates tumor suppressor genes, which are not activated by E2F induced by growth stimulation, inducing cellular senescence or apoptosis to protect cells from tumorigenesis. Deregulated E2F activity is tolerated in cancer cells due to inactivation of the ARF-p53 pathway, thus representing a feature unique to cancer cells. Deregulated E2F activity, which activates tumor suppressor genes, is distinct from enhanced E2F activity, which activates growth-related genes, in that deregulated E2F activity does not depend on the heterodimeric partner DP. Indeed, the ARF promoter, which is specifically activated by deregulated E2F, showed higher cancer-cell specific activity, compared to the E2F1 promoter, which is also activated by E2F induced by growth stimulation. Thus, deregulated E2F activity is an attractive potential therapeutic tool to specifically target cancer cells.
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11
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Han Z, Wang L, Wang D, Zhang L, Bi Y, Zheng X, Liu W, Bai G, Wang Z, Wan W, Ma Y, Cai X, Liu T, Jia Q. DJ-1 promotes osteosarcoma progression through activating CDK4/RB/E2F1 signaling pathway. Front Oncol 2022; 12:1036401. [PMID: 36408174 PMCID: PMC9671360 DOI: 10.3389/fonc.2022.1036401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2023] Open
Abstract
Osteosarcoma (OS) is a primary malignant tumor of the bone characterized by poor prognosis due to chemotherapy resistance and high recurrence rates. DJ-1 (PARK7) is known as an oncogene and its abnormal expression is related to the poor prognosis of various types of malignant tumors. It was found in this study that upregulated expression of DJ-1 was closely correlated with the prognosis of OS patients by promoting the proliferation, migration and chemotherapy resistance of OS cells in vitro through regulating the activity of CDK4 but not through the oxidation mechanism or AKT pathway. The combination of DJ-1 and CDK4 promoted RB phosphorylation, leading to the dissociation of E2F1 into the nucleus to regulate the expression of cell cycle-related genes. The tumor xenograft mouse model demonstrated that DJ-1 knockout suppressed tumor growth in vivo. All these findings indicate that DJ-1 can affect the occurrence and progression of OS by regulating the CDK/RB/E2F1axis, suggesting a novel therapeutic opportunity for OS patients.
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Affiliation(s)
- Zhitao Han
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Lining Wang
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Laboratory of New Techniques of Restoration & Reconstruction, Institute of Traumatology & Orthopedics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Dongshuo Wang
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Luosheng Zhang
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yifeng Bi
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xinlei Zheng
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Weibo Liu
- Department of Orthopaedics, the Fourth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Guangjian Bai
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhenhua Wang
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Wei Wan
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yong Ma
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xiaopan Cai
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Tielong Liu
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Qi Jia
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
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12
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Liu Y, Guo S, He X, Jiang Y, Hong Q, Lan R, Chu M. Effect of Upregulation of Transcription Factor TFDP1 Binding Promoter Activity Due to RBP4 g.36491960G>C Mutation on the Proliferation of Goat Granulosa Cells. Cells 2022; 11:cells11142148. [PMID: 35883591 PMCID: PMC9321149 DOI: 10.3390/cells11142148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 01/27/2023] Open
Abstract
Retinol-binding protein 4 (RBP4), a member of the lipocalin family, is a specific carrier of retinol (vitamin A) in the blood. Numerous studies have shown that RBP4 plays an important role in mammalian embryonic development and that mutations in RBP4 can be used for the marker-assisted selection of animal reproductive traits. However, there are few studies on the regulation of reproduction and high-prolificacy traits by RBP4 in goats. In this study, the 5′ flanking sequence of RBP4 was amplified, and a G>C polymorphism in the promoter region -211 bp (g.36491960) was detected. An association analysis revealed that the respective first, second and third kidding number and mean kidding number of nanny goats with CC and GC genotypes (2.167 ± 0.085, 2.341 ± 0.104, 2.529 ± 0.107 and 2.189 ± 0.070 for CC and 2.052 ± 0.047, 2.206 ± 0.057, 2.341 ± 0.056 and 2.160 ± 0.039 for GC) were significantly higher (p < 0.05) than those with the GG genotype (1.893 ± 0.051, 2.027 ± 0.064, 2.107 ± 0.061 and 1.74 ± 0.05). The luciferase assay showed that luciferase activity was increased in C allele individuals compared with that in G allele individuals. A competitive electrophoretic mobility shift assay (EMSA) showed that individuals with the CC genotype had a stronger promoter region binding capacity than those with the GG genotype. In addition, transcription factor prediction software showed that the RBP4 g.36491960G>C mutation added a novel binding site for transcription factor DP-1 (TFDP1). RT−qPCR results showed that the expression of TFDP1 was significantly higher in the high-prolificacy group than in the low-prolificacy group, and the expression of RBP4 was higher in both the CC and GC genotypes than that in the GG genotype. TFDP1 overexpression significantly increased the expression of RBP4 mRNA (p < 0.05) and the expression of the cell proliferation factors cyclin-D1, cyclin-D2 and CDK4 (p < 0.05). The opposite trend was observed after interference with TFDP1. Both the EdU and CCK-8 results showed that TFDP1 expression could regulate the proliferation of goat ovarian granulosa cells. In summary, our results showed that RBP4 g.36491960G>C was significantly associated with fecundity traits in goats. The g.36491960G>C mutation enhanced the transcriptional activity of RBP4 and increased the expression of RBP4, thus improving the fertility of Yunshang black goats.
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Affiliation(s)
- Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (S.G.); (X.H.)
| | - Siwu Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (S.G.); (X.H.)
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (S.G.); (X.H.)
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Q.H.); (R.L.)
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Q.H.); (R.L.)
| | - Rong Lan
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Q.H.); (R.L.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (S.G.); (X.H.)
- Correspondence: ; Tel.: +86-10-62819850; Fax: +86-10-62895351
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13
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Bakr A, Hey J, Sigismondo G, Liu CS, Sadik A, Goyal A, Cross A, Iyer RL, Müller P, Trauernicht M, Breuer K, Lutsik P, Opitz C, Krijgsveld J, Weichenhan D, Plass C, Popanda O, Schmezer P. ID3 promotes homologous recombination via non-transcriptional and transcriptional mechanisms and its loss confers sensitivity to PARP inhibition. Nucleic Acids Res 2021; 49:11666-11689. [PMID: 34718742 PMCID: PMC8599806 DOI: 10.1093/nar/gkab964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
The inhibitor of DNA-binding 3 (ID3) is a transcriptional regulator that limits interaction of basic helix-loop-helix transcription factors with their target DNA sequences. We previously reported that ID3 loss is associated with mutational signatures linked to DNA repair defects. Here we demonstrate that ID3 exhibits a dual role to promote DNA double-strand break (DSB) repair, particularly homologous recombination (HR). ID3 interacts with the MRN complex and RECQL helicase to activate DSB repair and it facilitates RAD51 loading and downstream steps of HR. In addition, ID3 promotes the expression of HR genes in response to ionizing radiation by regulating both chromatin accessibility and activity of the transcription factor E2F1. Consistently, analyses of TCGA cancer patient data demonstrate that low ID3 expression is associated with impaired HR. The loss of ID3 leads to sensitivity of tumor cells to PARP inhibition, offering new therapeutic opportunities in ID3-deficient tumors.
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Affiliation(s)
- Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
| | - Chun-Shan Liu
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Ahmed Sadik
- DKTK Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ashish Goyal
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Alice Cross
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- Imperial College London, London, SW7 2AZ, UK
| | - Ramya Lakshmana Iyer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Patrick Müller
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Max Trauernicht
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Kersten Breuer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Christiane A Opitz
- DKTK Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Neurology Clinic and National Center for Tumor Diseases, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
- Heidelberg University, Medical Faculty, INF672, 69120, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), INF280, 69120 Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
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14
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Huang J, Wang Y, Liu J, Chu M, Wang Y. TFDP3 as E2F Unique Partner, Has Crucial Roles in Cancer Cells and Testis. Front Oncol 2021; 11:742462. [PMID: 34745961 PMCID: PMC8564135 DOI: 10.3389/fonc.2021.742462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/30/2021] [Indexed: 12/03/2022] Open
Abstract
Transcription factor DP family member 3 (TFDP3) is a cancer-testis antigen, mainly expressed in normal testis and multiple cancers. TFDP3 gene (Gene ID: 51270) is located on the chromosome X and shares a high degree of sequence homology with TFDP1 and TFDP2, which can form heterodimers with E2F family members and enhance DNA-binding activity of E2Fs. In contrast to TFDP1 and TFDP2, TFDP3 downregulates E2F-mediated transcriptional activation. During DNA damage response in cancer cells, TFDP3 is induced and can inhibit E2F1-mediated apoptosis. Moreover, TFDP3 is involved in cell autophagy and epithelial-mesenchymal transition. Regarding cancer therapy opportunity, the transduction of dendritic cells with recombinant adenovirus-encoding TFDP3 can activate autologous cytotoxic T lymphocytes to target hepatoma cells. Here, we review the characterization of TFDP3, with an emphasis on the biological function and molecular mechanism. A better understanding of TFDP3 will provide new insights into the pathological mechanisms and therapeutic strategies for cancers.
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Affiliation(s)
- Jiahao Huang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yini Wang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Jinlong Liu
- Department of Basic Medicine and Forensic Medicine, Baotou Medical College, Baotou, China
| | - Ming Chu
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yuedan Wang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
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15
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Takouda J, Katada S, Imamura T, Sanosaka T, Nakashima K. SoxE group transcription factor Sox8 promotes astrocytic differentiation of neural stem/precursor cells downstream of Nfia. Pharmacol Res Perspect 2021; 9:e00749. [PMID: 34677001 PMCID: PMC8532136 DOI: 10.1002/prp2.749] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/13/2022] Open
Abstract
The brain consists of three major cell types: neurons and two glial cell types (astrocytes and oligodendrocytes). Although they are generated from common multipotent neural stem/precursor cells (NS/PCs), embryonic NS/PCs cannot generate all of the cell types at the beginning of brain development. NS/PCs first undergo extensive self-renewal to expand their pools, and then acquire the potential to produce neurons, followed by glial cells. Astrocytes are the most frequently found cell type in the central nervous system (CNS), and play important roles in brain development and functions. Although it has been shown that nuclear factor IA (Nfia) is a pivotal transcription factor for conferring gliogenic potential on neurogenic NS/PCs by sequestering DNA methyltransferase 1 (Dnmt1) from astrocyte-specific genes, direct targets of Nfia that participate in astrocytic differentiation have yet to be completely identified. Here we show that SRY-box transcription factor 8 (Sox8) is a direct target gene of Nfia at the initiation of the gliogenic phase. We found that expression of Sox8 augmented leukemia inhibitory factor (LIF)-induced astrocytic differentiation, while Sox8 knockdown inhibited Nfia-enhanced astrocytic differentiation of NS/PCs. In contrast to Nfia, Sox8 did not induce DNA demethylation of an astrocyte-specific marker gene, glial fibrillary acidic protein (Gfap), but instead associated with LIF downstream transcription factor STAT3 through transcriptional coactivator p300, explaining how Sox8 expression further facilitated LIF-induced Gfap expression. Taken together, these results suggest that Sox8 is a crucial Nfia downstream transcription factor for the astrocytic differentiation of NS/PCs in the developing brain.
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Affiliation(s)
- Jun Takouda
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sayako Katada
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takuya Imamura
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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16
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Zhang J, Hu C, Hu D, Fan Z. MicroRNA-1298-5p inhibits the tumorigenesis of breast cancer by targeting E2F1. Oncol Lett 2021; 22:660. [PMID: 34386082 PMCID: PMC8299007 DOI: 10.3892/ol.2021.12921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 06/03/2021] [Indexed: 12/24/2022] Open
Abstract
Studies performed in the last two decades have identified microRNA (miR)-1298-5p to display tumor-suppressive functions in several types of malignancy. In addition, the regulatory role of E2F transcription factor 1 (E2F1) has been reported in multiple types of cancer, including breast cancer (BC). However, whether miR-1298-5p participates in BC progression and whether a regulatory association exists between miR-1298-5p and E2F1 remains to be explored. The present study aimed to determine the role of miR-1298-5p and its interaction with E2F1 in BC. The expression of miR-1298-5p and E2F1 was examined by reverse transcription-quantitative PCR and western blot assays. The viability and proliferative capacity of BC cells were evaluated by Cell Counting Kit-8 and 5-bromo-2'-deoxyuridine assays, respectively. The apoptotic rate was assessed by the caspase-3 activity assay and flow cytometry; the protein expression levels of vimentin and E-cadherin were evaluated by western blotting. In addition, the adhesive and migratory abilities of BC cells were determined by conducting cell adhesion and wound healing assay, respectively. The target relationship between miR-1298-5p and E2F1 was validated by the luciferase reporter assay. The results of the present study revealed that the levels of miR-1298-5p were downregulated in BC tissues and cells compared with those in normal breast tissues and cells, respectively. In addition, miR-1298-5p was demonstrated to inhibit the proliferation, adhesion and migration of BC cells and to promote BC cell apoptosis. E2F1 was verified as a target gene of miR-1298-5p using the luciferase reporter assay. Additionally, E2F1 exhibited an opposite expression pattern compared with that of miR-1298-5p in BC tissues. Furthermore, the downregulation of miR-1298-5p in BC cells was reversed by silencing E2F1. Overall, the results of the present study suggested that miR-1298-5p repressed BC cell proliferation, adhesion and migration, and enhanced BC cell apoptosis by downregulating E2F1.
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Affiliation(s)
- Jie Zhang
- Department of Breast Surgery, The Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, P.R. China
| | - Chenyang Hu
- Department of Breast Surgery, The First Bethune Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Dawei Hu
- Department of Breast Surgery, The Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, P.R. China
| | - Zhimin Fan
- Department of Breast Surgery, The First Bethune Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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17
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Yao Q, Ferragina P, Reshef Y, Lettre G, Bauer DE, Pinello L. Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators. Bioinformatics 2021; 37:2103-2111. [PMID: 33532840 PMCID: PMC11025460 DOI: 10.1093/bioinformatics/btab072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 11/30/2020] [Accepted: 01/28/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Genome-wide association studies (GWASs) have identified thousands of common trait-associated genetic variants but interpretation of their function remains challenging. These genetic variants can overlap the binding sites of transcription factors (TFs) and therefore could alter gene expression. However, we currently lack a systematic understanding on how this mechanism contributes to phenotype. RESULTS We present Motif-Raptor, a TF-centric computational tool that integrates sequence-based predictive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants. Given trait-associated non-coding variants, Motif-Raptor can recover relevant cell types and critical TFs to drive hypotheses regarding their mechanism of action. We tested Motif-Raptor on complex traits such as rheumatoid arthritis and red blood cell count and demonstrated its ability to prioritize relevant cell types, potential regulatory TFs and non-coding SNPs which have been previously characterized and validated. AVAILABILITY AND IMPLEMENTATION Motif-Raptor is freely available as a Python package at: https://github.com/pinellolab/MotifRaptor. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qiuming Yao
- Department of Pathology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Paolo Ferragina
- Department of Computer Science, University of Pisa, Pisa 56128, Italy
| | - Yakir Reshef
- Department of Computer Science, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Guillaume Lettre
- Faculty of Medicine, Université de Montréal, Montreal, Quebec H3C3J7, Canada
- Montreal Heart Institute, Montreal, Quebec H1T1C8, Canada
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Luca Pinello
- Department of Pathology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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18
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Shen D, Gao Y, Huang Q, Xuan Y, Yao Y, Gu L, Huang Y, Zhang Y, Li P, Fan Y, Tang L, Du S, Wu S, Wang H, Wang C, Gong H, Pang Y, Ma X, Wang B, Zhang X. E2F1 promotes proliferation and metastasis of clear cell renal cell carcinoma via activation of SREBP1-dependent fatty acid biosynthesis. Cancer Lett 2021; 514:48-62. [PMID: 34019961 DOI: 10.1016/j.canlet.2021.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 11/18/2022]
Abstract
Enhanced synthesis or uptake of lipids contributes to rapid cancer cell proliferation and tumor progression. In recent years, cell cycle regulators have been shown to be involved in the control of lipid synthesis, in addition to their classical function of controlling the cell cycle. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer and is characterized by lipid-rich cytoplasmic deposition. However, the relationship between altered lipid metabolism and tumor progression in ccRCC is poorly understood. Here, we demonstrated that E2F transcription factor 1 (E2F1), in addition to its key role in regulating the cell cycle, induces extensive lipid accumulation and elevated levels of lipogenic enzymes in ccRCC cells by upregulating sterol regulatory element-binding protein 1 (SREBP1). E2F1 knockdown or SREBP1 suppression attenuated fatty acid (FA) de novo synthesis, cell proliferation and epithelial-mesenchymal transition (EMT) in ccRCC cells. Furthermore, overexpression of E2F1 promoted lipid storage, tumor growth and metastasis in a mouse xenograft model, whereas E2F1 downregulation or SREBP1 inhibition reversed these effects. In ccRCC patients, high levels of E2F1 and SREBP1 were associated with increased lipid accumulation and correlated with poor prognosis. Our results demonstrate that E2F1 can increase proliferation and metastasis through SREBP1-induced aberrant lipid metabolism, which is a novel critical signaling mechanism driving human ccRCC progression.
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Affiliation(s)
- Donglai Shen
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Yu Gao
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Qingbo Huang
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Yundong Xuan
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Yuanxin Yao
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Liangyou Gu
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China.
| | - Yan Huang
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Yu Zhang
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Pin Li
- Department of Pediatric Urology, Bayi Children's Hospital Affiliated to the Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100007, PR China.
| | - Yang Fan
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Lu Tang
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Songliang Du
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China; School of Medicine, Nankai University, Tianjin, 300071, PR China.
| | - Shengpan Wu
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Hanfeng Wang
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Chenfeng Wang
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Huijie Gong
- Department of Urology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, 100700, PR China.
| | - Yuewen Pang
- Department of Urology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, 100700, PR China.
| | - Xin Ma
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Baojun Wang
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
| | - Xu Zhang
- Department of Urology, Chinese PLA General Hospita l, Beijing, 100853, PR China; State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital/Chinese PLA Medical School, Beijing, 100853, PR China.
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19
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Identification and functional characterization of the transcription factor coding Dp1 gene in large yellow croaker Pseudosciaena crocea. Heliyon 2021; 7:e06299. [PMID: 33718639 PMCID: PMC7921785 DOI: 10.1016/j.heliyon.2021.e06299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/09/2020] [Accepted: 02/12/2021] [Indexed: 11/24/2022] Open
Abstract
The transcription factor Dp1, as a binding partner, often forms a dimerization complex with typical E2F to play a central role in regulating gene expression during G1/S cell cycle progression. In this study, a full-length dp1 cDNA (Pcdp1) was successfully cloned and characterized from the large yellow croaker Pseudosciaena crocea. The nucleotidic sequence of Pcdp1 is 1,427 bp long with an open reading frame (ORF) of 1,239 bp encoding a putative protein of 412 amino acids, a 5′-untranslated region of 116 bp and a 3′-untranslated region of 70 bp. Prediction of protein domains showed that PcDp1 contains a DNA-binding domain (DBD) with a DEF box, a dimerization domain and an acidic region at C terminus with transcription activity. Homology comparisons indicated that PcDp1 shared the highest sequence identity of 98.55% with Oreochromis niloticus dp1, followed by 88.72% identity with Danio rerio dp1 and a relatively low identity of 78.91–80.55% with its mammalian and amphibian counterparts. The mRNA of Pcdp1 showed ubiquitously expression in all analyzed tissues, with the highest level of expression in the body kidney. Moderate expression levels of Pcdp1 was found in several immune-related tissues including the gills, head kidney and liver, indicating that PcDp1 might play an important role in osmotic pressure regulation and immune response of the large yellow croaker. The subcellular localization of PcDp1 revealed that it is mainly distributed in the cytoplasm both in COS-7 and parenchymal cells of the spleen, head kidney and kidney tissues. Furthermore, the recombinant PcDp1 exhibited DNA-binding activity to E2F site in vitro. In conclusion, these results indicated that PcDp1 may participate in immune regulation and provide a foundation for further study of the regulatory mechanism of Dp1 in teleosts.
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20
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Miyokawa R, Kanaya HJ, Itoh TQ, Kobayakawa Y, Kusumi J. Immature symbiotic system between horizontally transmitted green algae and brown hydra. Sci Rep 2021; 11:2921. [PMID: 33536483 PMCID: PMC7859245 DOI: 10.1038/s41598-021-82489-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Some strains of brown hydra (Hydra vulgaris) are able to harbor the green algae Chlorococcum in their endodermal epithelial cells as symbionts. However, the relationship between brown hydra and chlorococcum is considered to be incipient symbiosis because most artificially introduced symbionts are not stable and because symbiotic H. vulgaris strains are rare in the wild. In this study, we compared the gene expression levels of the newly established symbiotic hydra (strain 105G), the native symbiotic strain (J7), and their non-symbiotic polyps to determine what changes would occur at the early stage of the evolution of symbiosis. We found that both the 105G and J7 strains showed comparable expression patterns, exhibiting upregulation of lysosomal enzymes and downregulation of genes related to nematocyte development and function. Meanwhile, genes involved in translation and the respiratory chain were upregulated only in strain 105G. Furthermore, treatment with rapamycin, which inhibits translation activity, induced the degeneration of the symbiotic strains (105G and J7). This effect was severe in strain 105G. Our results suggested that evolving the ability to balance the cellular metabolism between the host and the symbiont is a key requirement for adapting to endosymbiosis with chlorococcum.
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Affiliation(s)
- Ryo Miyokawa
- grid.177174.30000 0001 2242 4849Graduate School of Integrated Science for Global Society, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395 Japan
| | - Hiroyuki J. Kanaya
- grid.177174.30000 0001 2242 4849School of Science, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395 Japan
| | - Taichi Q. Itoh
- grid.177174.30000 0001 2242 4849Faculty of Arts and Science, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395 Japan
| | - Yoshitaka Kobayakawa
- grid.177174.30000 0001 2242 4849Faculty of Arts and Science, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395 Japan
| | - Junko Kusumi
- grid.177174.30000 0001 2242 4849Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395 Japan
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21
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Kan L, Cui D, Chai Y, Ma L, Li X, Zhao M. TMT-based quantitative proteomic analysis of antitumor mechanism of Sporisorium reilianum polysaccharide WM-NP-60 against HCT116 cells. Int J Biol Macromol 2020; 165:1755-1764. [PMID: 33068624 DOI: 10.1016/j.ijbiomac.2020.10.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/29/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022]
Abstract
Sporisorium reilianum is an active edible and medicinal phytopathogenic fungus. Our study indicated that the S. reilianum polysaccharide WM-NP-60 could inhibit the growth of HCT116 cells in a dose-dependent manner. In addition, WM-NP-60 could trigger the cell cycle of HCT116 arrest at the G1 phase and induce its apoptosis. In order to explore the anti-tumor mechanism of WM-NP-60, TMT-based quantitative proteomic analysis was used. Results indicated that 369 differentially expressed proteins including 240 up-regulated and 129 down-regulated proteins in WM-NP-60 treated HCT116 cells compared with normal HCT116 cells. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that 192 pathways were enriched containing 15 metabolic pathways with significant difference (P < 0.05). The levels of mRNA and protein up-regulated TGFβR1, P107, DP1 and down-regulated THBS1 related to TGF-β signaling pathway were verified with qRT-PCR and Western Blot (WB). These findings will provide theoretical basis for the important role of fungal polysaccharides in the field of tumor treatment.
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Affiliation(s)
- Lianbao Kan
- School of Life Sciences, Northeast Forestry University, Harbin 150040, PR China; Northeast Petroleum University, Daqing 163318, PR China
| | - Daizong Cui
- School of Life Sciences, Northeast Forestry University, Harbin 150040, PR China
| | - Yangyang Chai
- School of Forestry, Northeast Forestry University, Harbin 150040, PR China
| | - Ling Ma
- School of Forestry, Northeast Forestry University, Harbin 150040, PR China.
| | - Xiaoyan Li
- School of Life Sciences, Northeast Forestry University, Harbin 150040, PR China.
| | - Min Zhao
- School of Life Sciences, Northeast Forestry University, Harbin 150040, PR China.
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22
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Emanuele MJ, Enrico TP, Mouery RD, Wasserman D, Nachum S, Tzur A. Complex Cartography: Regulation of E2F Transcription Factors by Cyclin F and Ubiquitin. Trends Cell Biol 2020; 30:640-652. [PMID: 32513610 PMCID: PMC7859860 DOI: 10.1016/j.tcb.2020.05.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
The E2F family of transcriptional regulators sits at the center of cell cycle gene expression and plays vital roles in normal and cancer cell cycles. Whereas control of E2Fs by the retinoblastoma family of proteins is well established, much less is known about their regulation by ubiquitin pathways. Recent studies placed the Skp1-Cul1-F-box-protein (SCF) family of E3 ubiquitin ligases with the F-box protein Cyclin F at the center of E2F regulation, demonstrating temporal proteolysis of both activator and atypical repressor E2Fs. Importantly, these E2F members, in particular activator E2F1 and repressors E2F7 and E2F8, form a feedback circuit at the crossroads of cell cycle and cell death. Moreover, Cyclin F functions in a reciprocal circuit with the cell cycle E3 ligase anaphase-promoting complex/cyclosome (APC/C), which also controls E2F7 and E2F8. This review focuses on the complex contours of feedback within this circuit, highlighting the deep crosstalk between E2F, SCF-Cyclin F, and APC/C in regulating the oscillator underlying human cell cycles.
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Affiliation(s)
- Michael J Emanuele
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Taylor P Enrico
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D Mouery
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Genetics and Molecular Biology Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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23
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The Role of Crosstalk between AR3 and E2F1 in Drug Resistance in Prostate Cancer Cells. Cells 2020; 9:cells9051094. [PMID: 32354165 PMCID: PMC7290672 DOI: 10.3390/cells9051094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 01/20/2023] Open
Abstract
Background: Drug resistance is one of the most prevalent causes of death in advanced prostate cancer patients. Combination therapies that target cancer cells via different mechanisms to overcome resistance have gained increased attention in recent years. However, the optimal drug combinations and the underlying mechanisms are yet to be fully explored. Aim and methods: The aim of this study is to investigate drug combinations that inhibit the growth of drug-resistant cells and determine the underlying mechanisms of their actions. In addition, we also established cell lines that are resistant to combination treatments and tested new compounds to overcome the phenomenon of double drug-resistance. Results: Our results show that the combination of enzalutamide (ENZ) and docetaxel (DTX) effectively inhibit the growth of prostate cancer cells that are resistant to either drug alone. The downregulation of transcription factor E2F1 plays a crucial role in cellular inhibition in response to the combined therapy. Notably, we found that the androgen receptor (AR) variant AR3 (a.k.a. AR-V7), but not AR full length (AR-FL), positively regulates E2F1 expression in these cells. E2F1 in turn regulates AR3 and forms a positive regulatory feedforward loop. We also established double drug-resistant cell lines that are resistant to ENZ+DTX combination therapy and found that the expression of both AR3 and E2F1 was restored in these cells. Furthermore, we identified that auranofin, an FDA-approved drug for the treatment of rheumatoid arthritis, overcame drug resistance and inhibited the growth of drug-resistant prostate cancer cells both in vitro and in vivo. Conclusion and significance: This proof-of-principle study demonstrates that targeting the E2F1/AR3 feedforward loop via a combination therapy or a multi-targeting drug could circumvent castration resistance in prostate cancer.
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24
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Schmidt F, Kern F, Schulz MH. Integrative prediction of gene expression with chromatin accessibility and conformation data. Epigenetics Chromatin 2020; 13:4. [PMID: 32029002 PMCID: PMC7003490 DOI: 10.1186/s13072-020-0327-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Enhancers play a fundamental role in orchestrating cell state and development. Although several methods have been developed to identify enhancers, linking them to their target genes is still an open problem. Several theories have been proposed on the functional mechanisms of enhancers, which triggered the development of various methods to infer promoter-enhancer interactions (PEIs). The advancement of high-throughput techniques describing the three-dimensional organization of the chromatin, paved the way to pinpoint long-range PEIs. Here we investigated whether including PEIs in computational models for the prediction of gene expression improves performance and interpretability. RESULTS We have extended our [Formula: see text] framework to include DNA contacts deduced from chromatin conformation capture experiments and compared various methods to determine PEIs using predictive modelling of gene expression from chromatin accessibility data and predicted transcription factor (TF) motif data. We designed a novel machine learning approach that allows the prioritization of TFs binding to distal loop and promoter regions with respect to their importance for gene expression regulation. Our analysis revealed a set of core TFs that are part of enhancer-promoter loops involving YY1 in different cell lines. CONCLUSION We present a novel approach that can be used to prioritize TFs involved in distal and promoter-proximal regulatory events by integrating chromatin accessibility, conformation, and gene expression data. We show that the integration of chromatin conformation data can improve gene expression prediction and aids model interpretability.
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Affiliation(s)
- Florian Schmidt
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max-Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672 Singapore
| | - Fabian Kern
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Marcel H. Schulz
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max-Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Institute of Cardiovascular Regeneration, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner Site Rhein-Main, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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25
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Uxa S, Bernhart SH, Mages CFS, Fischer M, Kohler R, Hoffmann S, Stadler PF, Engeland K, Müller GA. DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation. Nucleic Acids Res 2019; 47:9087-9103. [PMID: 31400114 PMCID: PMC6753476 DOI: 10.1093/nar/gkz635] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/07/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
Most human cancers acquire mutations causing defects in the p53 signaling pathway. The tumor suppressor p53 becomes activated in response to genotoxic stress and is essential for arresting the cell cycle to facilitate DNA repair or to initiate apoptosis. p53-induced cell cycle-arrest is mediated by expression of the CDK inhibitor p21WAF1/Cip1, which prevents phosphorylation and inactivation of the pocket proteins RB, p130, and p107. In a hypophosphorylated state, pocket proteins bind to E2F factors forming RB-E2F and DREAM transcriptional repressor complexes. Here, we analyze the influence of RB and DREAM on p53-induced gene repression and cell-cycle arrest. We show that abrogation of DREAM function by knockout of the DREAM component LIN37 results in a reduced repression of cell-cycle genes. We identify the genes repressed by the p53-DREAM pathway and describe a set of genes that is downregulated by p53 independent of LIN37/DREAM. Most strikingly, p53-dependent repression of cell-cycle genes is completely abrogated in LIN37-/-;RB-/- cells leading to a loss of the G1/S checkpoint. Taken together, we show that DREAM and RB are key factors in the p53 signaling pathway to downregulate a large number of cell-cycle genes and to arrest the cell cycle at the G1/S transition.
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Affiliation(s)
- Sigrid Uxa
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany
| | - Christina F S Mages
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Robin Kohler
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Peter F Stadler
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Research Center for Civilization Diseases; and Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Leipzig University, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, A-1090 Wien, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogota, Colombia.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Kurt Engeland
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Gerd A Müller
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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26
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Lavitrano M, Ianzano L, Bonomo S, Cialdella A, Cerrito MG, Pisano F, Missaglia C, Giovannoni R, Romano G, McLean CM, Voest EE, D'Amato F, Noli B, Ferri GL, Agostini M, Pucciarelli S, Helin K, Leone BE, Canzonieri V, Grassilli E. BTK inhibitors synergise with 5-FU to treat drug-resistant TP53-null colon cancers. J Pathol 2019; 250:134-147. [PMID: 31518438 DOI: 10.1002/path.5347] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/05/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022]
Abstract
Colorectal cancer (CRC) is the fourth cause of death from cancer worldwide mainly due to the high incidence of drug-resistance. During a screen for new actionable targets in drug-resistant tumours we recently identified p65BTK - a novel oncogenic isoform of Bruton's tyrosine kinase. Studying three different cohorts of patients here we show that p65BTK expression correlates with histotype and cancer progression. Using drug-resistant TP53-null colon cancer cells as a model we demonstrated that p65BTK silencing or chemical inhibition overcame the 5-fluorouracil resistance of CRC cell lines and patient-derived organoids and significantly reduced the growth of xenografted tumours. Mechanistically, we show that blocking p65BTK in drug-resistant cells abolished a 5-FU-elicited TGFB1 protective response and triggered E2F-dependent apoptosis. Taken together, our data demonstrated that targeting p65BTK restores the apoptotic response to chemotherapy of drug-resistant CRCs and gives a proof-of-concept for suggesting the use of BTK inhibitors in combination with 5-FU as a novel therapeutic approach in CRC patients. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Leonarda Ianzano
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Sara Bonomo
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | | | - Fabio Pisano
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Carola Missaglia
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Roberto Giovannoni
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Gabriele Romano
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Chelsea M McLean
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emile E Voest
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Filomena D'Amato
- NEF-Laboratory, Department of Biomedical Science, University of Cagliari, Cagliari, Italy
| | - Barbara Noli
- NEF-Laboratory, Department of Biomedical Science, University of Cagliari, Cagliari, Italy
| | - Gian Luca Ferri
- NEF-Laboratory, Department of Biomedical Science, University of Cagliari, Cagliari, Italy
| | - Marco Agostini
- First Surgical Clinic Section, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy.,Department of Nanomedicine, The Methodist Hospital Research Institute, Houston, TX, USA
| | - Salvatore Pucciarelli
- First Surgical Clinic Section, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Kristian Helin
- Center for Epigenetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Biagio E Leone
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Vincenzo Canzonieri
- Pathology Unit and CRO Biobank, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Emanuela Grassilli
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
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27
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Masnadi-Shirazi M, Maurya MR, Pao G, Ke E, Verma IM, Subramaniam S. Time varying causal network reconstruction of a mouse cell cycle. BMC Bioinformatics 2019; 20:294. [PMID: 31142274 PMCID: PMC6542064 DOI: 10.1186/s12859-019-2895-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 12/21/2022] Open
Abstract
Background Biochemical networks are often described through static or time-averaged measurements of the component macromolecules. Temporal variation in these components plays an important role in both describing the dynamical nature of the network as well as providing insights into causal mechanisms. Few methods exist, specifically for systems with many variables, for analyzing time series data to identify distinct temporal regimes and the corresponding time-varying causal networks and mechanisms. Results In this study, we use well-constructed temporal transcriptional measurements in a mammalian cell during a cell cycle, to identify dynamical networks and mechanisms describing the cell cycle. The methods we have used and developed in part deal with Granger causality, Vector Autoregression, Estimation Stability with Cross Validation and a nonparametric change point detection algorithm that enable estimating temporally evolving directed networks that provide a comprehensive picture of the crosstalk among different molecular components. We applied our approach to RNA-seq time-course data spanning nearly two cell cycles from Mouse Embryonic Fibroblast (MEF) primary cells. The change-point detection algorithm is able to extract precise information on the duration and timing of cell cycle phases. Using Least Absolute Shrinkage and Selection Operator (LASSO) and Estimation Stability with Cross Validation (ES-CV), we were able to, without any prior biological knowledge, extract information on the phase-specific causal interaction of cell cycle genes, as well as temporal interdependencies of biological mechanisms through a complete cell cycle. Conclusions The temporal dependence of cellular components we provide in our model goes beyond what is known in the literature. Furthermore, our inference of dynamic interplay of multiple intracellular mechanisms and their temporal dependence on one another can be used to predict time-varying cellular responses, and provide insight on the design of precise experiments for modulating the regulation of the cell cycle. Electronic supplementary material The online version of this article (10.1186/s12859-019-2895-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maryam Masnadi-Shirazi
- Department of Electrical and Computer Engineering and Bioengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Mano R Maurya
- Department of Bioengineering and San Diego Supercomputer center, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Gerald Pao
- Salk institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Eugene Ke
- Salk institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Inder M Verma
- Salk institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Shankar Subramaniam
- Department of Bioengineering, Departments of Computer Science and Engineering, Cellular and Molecular Medicine, and the Graduate Program in Bioinformatics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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28
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Moody L, Hernández-Saavedra D, Kougias DG, Chen H, Juraska JM, Pan YX. Tissue-specific changes in Srebf1 and Srebf2 expression and DNA methylation with perinatal phthalate exposure. ENVIRONMENTAL EPIGENETICS 2019; 5:dvz009. [PMID: 31240115 PMCID: PMC6586200 DOI: 10.1093/eep/dvz009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 05/30/2023]
Abstract
Perinatal exposure to endocrine disrupting chemicals negatively impacts health, but the mechanism by which such toxicants damage long-term reproductive and metabolic function is unknown. Lipid metabolism plays a pivotal role in steroid hormone synthesis as well as energy utilization and storage; thus, aberrant lipid regulation may contribute to phthalate-driven health impairments. In order to test this hypothesis, we specifically examined epigenetic disruptions in lipid metabolism pathways after perinatal phthalate exposure. During gestation and lactation, pregnant Long-Evans rat dams were fed environmentally relevant doses of phthalate mixture: 0 (CON), 200 (LO), or 1000 (HI) µg/kg body weight/day. On PND90, male offspring in the LO and HI groups had higher body weights than CON rats. Gene expression of lipid metabolism pathways was altered in testis and adipose tissue of males exposed to the HI phthalate dosage. Specifically, Srebf1 was downregulated in testis and Srebf2 was upregulated in adipose tissue. In testis of HI rats, DNA methylation was increased at two loci and reduced at one other site surrounding Srebf1 transcription start site. In adipose tissue of HI rats, we observed increased DNA methylation at one region within the first intron of Srebf2. Computational analysis revealed several potential transcriptional regulator binding sites, suggesting functional relevance of the identified differentially methylated CpGs. Overall, we show that perinatal phthalate exposure affects lipid metabolism gene expression in a tissue-specific manner possibly through altering DNA methylation of Srebf1 and Srebf2.
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Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Daniel G Kougias
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hong Chen
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Janice M Juraska
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Psychology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yuan-Xiang Pan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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29
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Huang H, Luo B, Wang B, Wu Q, Liang Y, He Y. Identification of Potential Gene Interactions in Heart Failure Caused by Idiopathic Dilated Cardiomyopathy. Med Sci Monit 2018; 24:7697-7709. [PMID: 30368515 PMCID: PMC6216482 DOI: 10.12659/msm.912984] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Many heart failure (HF) cases are caused by idiopathic dilated cardiomyopathy (iDCM). This study explored the mechanisms of the development and progression of HF caused by iDCM. Material/Methods The gene expression profiles of 102 samples were downloaded from the GEO database (GSE5406). Differentially expressed genes (DEGs) were identified through GO analysis and a KEGG pathway analysis, respectively. A protein–protein interaction (PPI) network was constructed and analyzed to screen potential regulatory proteins. In addition, MCODE and a cytoHubba plugin were used to identify the module and hub genes of DEGs. Finally, transcription factors (TFs) were predicted using PASTAA. We did not perform whole-exome sequencing (WES) for detecting mitochondrial DNA (mtDNA). Results A total of 197 DEGs were screened, and 3 modules, and 4 upregulated and 11 downregulated hub genes were screened. The GO analysis focused on the terms and 12 KEGG pathways were enriched. The FOS, TIMP1, and SERPINE1 hub genes, as well as some key TFs, demonstrated important roles in the progression of HF caused by iDCM. CEBPD, CEBOB, CDC37L1, and SRGN may be new targets for HF in iDCM patients. Conclusions The identified DEGs and their enriched pathways provide references for exploring the mechanisms of the development and progression of HF patients with iDCM. Moreover, modules, hub genes, and TFs may be useful in the treatment and diagnosis of HF patients with iDCM. However, mtDNA was not investigated.
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Affiliation(s)
- Huijuan Huang
- Department of Geriatric Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Beibei Luo
- Department of Geriatric Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Boqun Wang
- Department of Geriatric Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Qianwen Wu
- Department of Geriatric Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Yuming Liang
- Department of Geriatric Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Yan He
- Department of Geriatric Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
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E2F1 and E2F7 differentially regulate KPNA2 to promote the development of gallbladder cancer. Oncogene 2018; 38:1269-1281. [PMID: 30254209 DOI: 10.1038/s41388-018-0494-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/29/2018] [Accepted: 08/15/2018] [Indexed: 12/14/2022]
Abstract
Karyopherin alpha 2 (KPNA2) is a nuclear import factor that is elevated in multiple cancers. However, its molecular regulation at the transcriptional levels is poorly understood. Here we found that KPNA2 was significantly upregulated in gallbladder cancer (GBC), and the increased levels were correlated with short survival of patients. Gene knocking down of KPNA2 inhibited tumor cell proliferation and migration in vitro as well as xenografted tumor development in vivo. A typical transcription factor E2F1 associated with its DNA-binding partner DP1 bond to the promoter region of KPNA2 and induced KPNA2 expression. In contrast, an atypical transcription factor E2F7 competed against DP1 and blocked E2F1-induced KPNA2 gene activation. Mutation of the dimerization residues of E2F7 or DNA-binding domain of E2F1 abolished the suppressive effects of E2F7 on KPNA2 gene expression. In addition, KPNA2 mediated nuclear localization of E2F1 and E2F7, where they in turn controlled KPNA2 expression. Taken together, our data provided mechanistic insights into divergently transcriptional regulation of KPNA2, thus pointing to KPNA2 as a potential target for cancer therapy.
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31
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Disproportionate feedback interactions govern cell‐type specific proliferation in mammalian cells. FEBS Lett 2018; 592:3248-3263. [DOI: 10.1002/1873-3468.13241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/17/2018] [Accepted: 09/03/2018] [Indexed: 11/07/2022]
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32
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Differential requirement for dimerization partner DP between E2F-dependent activation of tumor suppressor and growth-related genes. Sci Rep 2018; 8:8438. [PMID: 29855511 PMCID: PMC5981219 DOI: 10.1038/s41598-018-26860-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/31/2018] [Indexed: 01/17/2023] Open
Abstract
The transcription factor E2F plays crucial roles in cell proliferation and tumor suppression by activating growth-related genes and pro-apoptotic tumor suppressor genes, respectively. It is generally accepted that E2F binds to target sequences with its heterodimeric partner DP. Here we show that, while knockdown of DP1 expression inhibited ectopic E2F1- or adenovirus E1a-induced expression of the CDC6 gene and cell proliferation, knockdown of DP1 and DP2 expression did not affect ectopic E2F1- or E1a-induced expression of the tumor suppressor ARF gene, an upstream activator of the tumor suppressor p53, activation of p53 or apoptosis. These observations suggest that growth related and pro-apoptotic E2F targets are regulated by distinct molecular mechanisms and contradict the threshold model, which postulates that E2F activation of pro-apoptotic genes requires a higher total activity of activator E2Fs, above that necessary for E2F-dependent activation of growth-related genes.
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33
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Onsbring H, Jamy M, Ettema TJG. RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration. Curr Biol 2018; 28:1281-1288.e3. [PMID: 29628369 DOI: 10.1016/j.cub.2018.02.055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/08/2018] [Accepted: 02/20/2018] [Indexed: 01/05/2023]
Abstract
While ciliates of the genus Stentor are known for their ability to regenerate when their cells are damaged or even fragmented, the physical and molecular mechanisms underlying this process are poorly understood. To identify genes involved in the regenerative capability of Stentor cells, RNA sequencing of individual Stentor polymorphus cell fragments was performed. After splitting a cell over the anterior-posterior axis, the posterior fragment has to regenerate the oral apparatus, while the anterior part needs to regenerate the hold fast. Altogether, differential expression analysis of both posterior and anterior S. polymorphus cell fragments for four different post-split time points revealed over 10,000 upregulated genes throughout the regeneration process. Among these, genes involved in cell signaling, microtubule-based movement, and cell cycle regulation seemed to be particularly important during cellular regeneration. We identified roughly nine times as many upregulated genes in regenerating S. polymorphus posterior fragments as compared to anterior fragments, indicating that regeneration of the anterior oral apparatus is a complex process that involves many genes. Our analyses identified several expanded groups of genes, such as dual-specific tyrosine-(Y)-phosphorylation-regulated kinases and MORN domain-containing proteins that seemingly act as key regulators of cellular regeneration. In agreement with earlier morphological and cell biological studies [1, 2], our differential expression analyses indicate that cellular regeneration and vegetative division share many similarities.
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Affiliation(s)
- Henning Onsbring
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden
| | - Mahwash Jamy
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden.
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34
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Zhang J, Yan G, Tian M, Ma Y, Xiong J, Miao W. A DP-like transcription factor protein interacts with E2fl1 to regulate meiosis in Tetrahymena thermophila. Cell Cycle 2018; 17:634-642. [PMID: 29417875 DOI: 10.1080/15384101.2018.1431595] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Evolutionarily conserved E2F family transcription factors regulate the cell cycle via controlling gene expression in a wide range of eukaryotes. We previously demonstrated that the meiosis-specific transcription factor E2fl1 had an important role in meiosis in the model ciliate Tetrahymena thermophila. Here, we report that expression of another E2F family transcription factor gene DPL2 correlates highly with that of E2FL1. Similar to e2fl1Δ cells, dpl2Δ cells undergo meiotic arrest prior to anaphase I, with the five chromosomes adopting an abnormal tandem arrangement. Immunofluorescence staining and immunoprecipitation experiments demonstrate that Dpl2 and E2fl1 form a complex during meiosis. We previously identified several meiotic regulatory proteins in T. thermophila. Cyc2 and Tcdk3 may cooperate to initiate meiosis and Cyc17 is essential for initiating meiotic anaphase. We investigate the relationship of these regulators with Dpl2 and E2fl1, and then construct a meiotic regulatory network by measuring changes in meiotic genes expression in knockout cells. We conclude that the E2fl1/Dpl2 complex plays a central role in meiosis in T. thermophila.
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Affiliation(s)
- Jing Zhang
- a Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology , Chinese Academy of Sciences , Wuhan , People's Republic of China.,b University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Guanxiong Yan
- a Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology , Chinese Academy of Sciences , Wuhan , People's Republic of China.,b University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Miao Tian
- a Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology , Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Yang Ma
- a Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology , Chinese Academy of Sciences , Wuhan , People's Republic of China.,b University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Jie Xiong
- a Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology , Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Wei Miao
- a Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology , Chinese Academy of Sciences , Wuhan , People's Republic of China
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35
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From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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36
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Sengupta D, Govindaraj V, Kar S. Alteration in microRNA-17-92 dynamics accounts for differential nature of cellular proliferation. FEBS Lett 2018; 592:446-458. [PMID: 29331028 DOI: 10.1002/1873-3468.12974] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 12/19/2022]
Abstract
MicroRNAs associated with the mir-17-92 cluster are crucial regulators of the mammalian cell cycle, as they inhibit transcription factors related to the E2F family that tightly control decision-making events for a cell to commit for active cellular proliferation. Intriguingly, in many solid cancers, these mir-17-92 cluster members are overexpressed, whereas in some hematopoietic cancers they are down-regulated. Our proposed model of the Myc/E2F/mir-17-92 network demonstrates that the differential expression pattern of mir-17-92 in different cell types can be conceived due to having a contrasting E2F dynamics induced by mir-17-92. The model predicts that by explicitly altering the mir-17-92-related part of the network, experimentally it is possible to control cellular proliferation in a cell type-dependent manner for therapeutic intervention.
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Affiliation(s)
| | | | - Sandip Kar
- Department of Chemistry, IIT Bombay, Mumbai, India
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37
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Iwahori S, Kalejta RF. Phosphorylation of transcriptional regulators in the retinoblastoma protein pathway by UL97, the viral cyclin-dependent kinase encoded by human cytomegalovirus. Virology 2017; 512:95-103. [PMID: 28946006 DOI: 10.1016/j.virol.2017.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 01/11/2023]
Abstract
Human cytomegalovirus (HCMV) encodes a viral cyclin-dependent kinase (v-CDK), the UL97 protein. UL97 phosphorylates Rb, p107 and p130, thereby inactivating all three retinoblastoma (Rb) family members. Rb proteins function through regulating the activity of transcription factors to which they bind. Therefore, we examined whether the UL97-mediated regulation of the Rb tumor suppressors also extended to their binding partners. We observed that UL97 phosphorylates LIN52, a component of p107- and p130-assembled transcriptionally repressive DREAM complexes that control transcription during the G0/G1 phases, and the Rb-associated E2F3 protein that activates transcription through G1 and S phases. Intriguingly, we also identified FoxM1B, a transcriptional regulator during the S and G2 phases, as a UL97 substrate. This survey extends the influence of UL97 beyond simply the Rb proteins themselves to their binding partners, as well as past the G1/S transition into later stages of the cell cycle.
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Affiliation(s)
- Satoko Iwahori
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, United States
| | - Robert F Kalejta
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, United States.
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38
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Xie Y, Si J, Wang Y, Li H, Di C, Yan J, Ye Y, Zhang Y, Zhang H. E2F is involved in radioresistance of carbon ion induced apoptosis via Bax/caspase 3 signal pathway in human hepatoma cell. J Cell Physiol 2017; 233:1312-1320. [DOI: 10.1002/jcp.26005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/11/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Yi Xie
- Institute of Modern PhysicsChinese Academy of SciencesLanzhouChina
- CAS Key Laboratory of Heavy Ion Radiation Biology and MedicineInstitute of Modern PhysicsLanzhouGansuChina
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in MedicineGansu ProvinceLanzhouChina
| | - Jing Si
- Institute of Modern PhysicsChinese Academy of SciencesLanzhouChina
- CAS Key Laboratory of Heavy Ion Radiation Biology and MedicineInstitute of Modern PhysicsLanzhouGansuChina
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in MedicineGansu ProvinceLanzhouChina
| | - Yu‐Pei Wang
- Institute of Modern PhysicsChinese Academy of SciencesLanzhouChina
- CAS Key Laboratory of Heavy Ion Radiation Biology and MedicineInstitute of Modern PhysicsLanzhouGansuChina
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in MedicineGansu ProvinceLanzhouChina
- Graduate School of University of Chinese Academy of SciencesBeijingChina
| | - Hong‐Yan Li
- Institute of Modern PhysicsChinese Academy of SciencesLanzhouChina
- CAS Key Laboratory of Heavy Ion Radiation Biology and MedicineInstitute of Modern PhysicsLanzhouGansuChina
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in MedicineGansu ProvinceLanzhouChina
- Graduate School of University of Chinese Academy of SciencesBeijingChina
| | - Cui‐Xia Di
- Institute of Modern PhysicsChinese Academy of SciencesLanzhouChina
- CAS Key Laboratory of Heavy Ion Radiation Biology and MedicineInstitute of Modern PhysicsLanzhouGansuChina
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in MedicineGansu ProvinceLanzhouChina
| | - Jun‐Fang Yan
- Institute of Modern PhysicsChinese Academy of SciencesLanzhouChina
- CAS Key Laboratory of Heavy Ion Radiation Biology and MedicineInstitute of Modern PhysicsLanzhouGansuChina
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in MedicineGansu ProvinceLanzhouChina
- Graduate School of University of Chinese Academy of SciencesBeijingChina
| | | | | | - Hong Zhang
- Institute of Modern PhysicsChinese Academy of SciencesLanzhouChina
- CAS Key Laboratory of Heavy Ion Radiation Biology and MedicineInstitute of Modern PhysicsLanzhouGansuChina
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in MedicineGansu ProvinceLanzhouChina
- Gansu Wuwei Tumor HospitalWuweiChina
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Thwaites MJ, Cecchini MJ, Talluri S, Passos DT, Carnevale J, Dick FA. Multiple molecular interactions redundantly contribute to RB-mediated cell cycle control. Cell Div 2017; 12:3. [PMID: 28293272 PMCID: PMC5348811 DOI: 10.1186/s13008-017-0029-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/28/2017] [Indexed: 02/07/2023] Open
Abstract
Background The G1-S phase transition is critical to maintaining proliferative control and preventing carcinogenesis. The retinoblastoma tumor suppressor is a key regulator of this step in the cell cycle. Results Here we use a structure–function approach to evaluate the contributions of multiple protein interaction surfaces on pRB towards cell cycle regulation. SAOS2 cell cycle arrest assays showed that disruption of three separate binding surfaces were necessary to inhibit pRB-mediated cell cycle control. Surprisingly, mutation of some interaction surfaces had no effect on their own. Rather, they only contributed to cell cycle arrest in the absence of other pRB dependent arrest functions. Specifically, our data shows that pRB–E2F interactions are competitive with pRB–CDH1 interactions, implying that interchangeable growth arrest functions underlie pRB’s ability to block proliferation. Additionally, disruption of similar cell cycle control mechanisms in genetically modified mutant mice results in ectopic DNA synthesis in the liver. Conclusions Our work demonstrates that pRB utilizes a network of mechanisms to prevent cell cycle entry. This has important implications for the use of new CDK4/6 inhibitors that aim to activate this proliferative control network.
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Affiliation(s)
- Michael J Thwaites
- London Regional Cancer Program, London, Canada.,Department of Biochemistry, Western University, London, ON Canada
| | - Matthew J Cecchini
- London Regional Cancer Program, London, Canada.,Department of Biochemistry, Western University, London, ON Canada
| | - Srikanth Talluri
- London Regional Cancer Program, London, Canada.,Department of Biochemistry, Western University, London, ON Canada
| | - Daniel T Passos
- London Regional Cancer Program, London, Canada.,Department of Biochemistry, Western University, London, ON Canada
| | - Jasmyne Carnevale
- London Regional Cancer Program, London, Canada.,Department of Biochemistry, Western University, London, ON Canada
| | - Frederick A Dick
- London Regional Cancer Program, London, Canada.,Children's Health Research Institute, London, Canada.,Department of Biochemistry, Western University, London, ON Canada
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COMMD9 promotes TFDP1/E2F1 transcriptional activity via interaction with TFDP1 in non-small cell lung cancer. Cell Signal 2017; 30:59-66. [DOI: 10.1016/j.cellsig.2016.11.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/07/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022]
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41
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Okuda M, Araki K, Ohtani K, Nishimura Y. The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH. J Mol Biol 2016; 428:4993-5006. [DOI: 10.1016/j.jmb.2016.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/27/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
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42
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BGRMI: A method for inferring gene regulatory networks from time-course gene expression data and its application in breast cancer research. Sci Rep 2016; 6:37140. [PMID: 27876826 PMCID: PMC5120305 DOI: 10.1038/srep37140] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/24/2016] [Indexed: 02/06/2023] Open
Abstract
Reconstructing gene regulatory networks (GRNs) from gene expression data is a challenging problem. Existing GRN reconstruction algorithms can be broadly divided into model-free and model–based methods. Typically, model-free methods have high accuracy but are computation intensive whereas model-based methods are fast but less accurate. We propose Bayesian Gene Regulation Model Inference (BGRMI), a model-based method for inferring GRNs from time-course gene expression data. BGRMI uses a Bayesian framework to calculate the probability of different models of GRNs and a heuristic search strategy to scan the model space efficiently. Using benchmark datasets, we show that BGRMI has higher/comparable accuracy at a fraction of the computational cost of competing algorithms. Additionally, it can incorporate prior knowledge of potential gene regulation mechanisms and TF hetero-dimerization processes in the GRN reconstruction process. We incorporated existing ChIP-seq data and known protein interactions between TFs in BGRMI as sources of prior knowledge to reconstruct transcription regulatory networks of proliferating and differentiating breast cancer (BC) cells from time-course gene expression data. The reconstructed networks revealed key driver genes of proliferation and differentiation in BC cells. Some of these genes were not previously studied in the context of BC, but may have clinical relevance in BC treatment.
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Pellicelli M, Picard C, Wang D, Lavigne P, Moreau A. E2F1 and TFDP1 Regulate PITX1 Expression in Normal and Osteoarthritic Articular Chondrocytes. PLoS One 2016; 11:e0165951. [PMID: 27802335 PMCID: PMC5089553 DOI: 10.1371/journal.pone.0165951] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/20/2016] [Indexed: 12/19/2022] Open
Abstract
We previously reported a loss-of-PITX1 expression in patients suffering of knee/hip osteoarthritis (OA). Search for the mechanism underlying this event led us to discover that PITX1 repression was triggered by the aberrant nuclear accumulation of Prohibitin (PHB1), an E2F1 co-repressor, in OA articular chondrocytes. In the current study, we assessed in details the involvement of E2F transcription factors in regulating PITX1 expression. We also analyzed other genes that are similarly regulated by E2F in regard to osteoarthritis. The transcriptional regulation of the PITX1 promoter by E2F1 was analyzed with the luciferase reporter assay, and chromatin immunoprecipitation assays, which confirmed direct E2F1-PITX1 interactions. The probable binding sites for E2F1 in the PITX1 promoter were identified by DNA pulldown experiments. In silico and in vitro analyses show that the PITX1 proximal promoter region contains 2 specific sequences that are bound by E2F1. Overexpression of E2F1 enhances PITX1 promoter activity and mRNA transcription. In primary control and osteoarthritis chondrocytes, real time RT-PCR was used to measure the mRNA expression levels of candidate genes under E2F1 transcriptional control. Transcription Factor Dp-1 (TFDP1) knockdown experiments confirmed that the E2F1-TFDP1 complex regulates PITX1. Knockdown of TFDP1, an E2F1 dimerization partner, inhibits the activating effect of E2F1 and reduces both PITX1 promoter activity and mRNA transcription. Real time RT-PCR results reveal reduced expression of TFDP1 and a similar downregulation of their targets PITX1, BRCA1, CDKN1A, and RAD51 in mid-stage OA chondrocytes. Collectively, our data define a previously uncharacterized role for E2F1 and TFDP1 in the transcriptional regulation of PITX1 in articular chondrocytes. Additional E2F1 targets may be affected in OA pathogenesis.
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Affiliation(s)
- Martin Pellicelli
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Cynthia Picard
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - DaShen Wang
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada
| | - Patrick Lavigne
- Orthopedic Division, Maisonneuve-Rosemont Hospital, Montréal, Québec, Canada and Department of Surgery, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Alain Moreau
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Stomatology, Faculty of Dentistry, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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44
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Liu Y, Lai J, Yu M, Wang F, Zhang J, Jiang J, Hu H, Wu Q, Lu G, Xu P, Yang C. The Arabidopsis SUMO E3 Ligase AtMMS21 Dissociates the E2Fa/DPa Complex in Cell Cycle Regulation. THE PLANT CELL 2016; 28:2225-2237. [PMID: 27492969 PMCID: PMC5059808 DOI: 10.1105/tpc.16.00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/22/2016] [Accepted: 08/01/2016] [Indexed: 05/03/2023]
Abstract
Development requires the proper execution and regulation of the cell cycle via precise, conserved mechanisms. Critically, the E2F/DP complex controls the expression of essential genes during cell cycle transitions. Here, we discovered the molecular function of the Arabidopsis thaliana SUMO E3 ligase METHYL METHANESULFONATE SENSITIVITY GENE21 (AtMMS21) in regulating the cell cycle via the E2Fa/DPa pathway. DPa was identified as an AtMMS21-interacting protein and AtMMS21 competes with E2Fa for interaction with DPa. Moreover, DPa is a substrate for SUMOylation mediated by AtMMS21, and this SUMOylation enhances the dissociation of the E2Fa/DPa complex. AtMMS21 also affects the subcellular localization of E2Fa/DPa. The E2Fa/DPa target genes are upregulated in the root of mms21-1 and mms21-1 mutants showed increased endoreplication. Overexpression of DPa affected the root development of mms21-1, and overexpression of AtMMS21 completely recovered the abnormal phenotypes of 35S:E2Fa-DPa plants. Our results suggest that AtMMS21 dissociates the E2Fa/DPa complex via competition and SUMOylation in the regulation of plant cell cycle.
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Affiliation(s)
- Yiyang Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Mengyuan Yu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Feige Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Juanjuan Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jieming Jiang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Huan Hu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Qian Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Guohui Lu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Panglian Xu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
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Wang Y, Zheng Z, Zhang J, Wang Y, Kong R, Liu J, Zhang Y, Deng H, Du X, Ke Y. A Novel Retinoblastoma Protein (RB) E3 Ubiquitin Ligase (NRBE3) Promotes RB Degradation and Is Transcriptionally Regulated by E2F1 Transcription Factor. J Biol Chem 2015; 290:28200-28213. [PMID: 26442585 DOI: 10.1074/jbc.m115.655597] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Indexed: 12/25/2022] Open
Abstract
Retinoblastoma protein (RB) plays critical roles in tumor suppression and is degraded through the proteasomal pathway. However, E3 ubiquitin ligases responsible for proteasome-mediated degradation of RB are largely unknown. Here we characterize a novel RB E3 ubiquitin ligase (NRBE3) that binds RB and promotes RB degradation. NRBE3 contains an LXCXE motif and bound RB in vitro. NRBE3 interacted with RB in cells when proteasome activity was inhibited. NRBE3 promoted RB ubiquitination and degradation via the ubiquitin-proteasome pathway. Importantly, purified NRBE3 ubiquitinated recombinant RB in vitro, and a U-box was identified as essential for its E3 activity. Surprisingly, NRBE3 was transcriptionally activated by E2F1/DP1. Consequently, NRBE3 affected the cell cycle by promoting G1/S transition. Moreover, NRBE3 was up-regulated in breast cancer tissues. Taken together, we identified NRBE3 as a novel ubiquitin E3 ligase for RB that might play a role as a potential oncoprotein in human cancers.
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Affiliation(s)
- Yingshuang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Zongfang Zheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Jingyi Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education)
| | - You Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Ruirui Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Jiangying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Ying Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
| | - Hongkui Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaojuan Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Genetics Laboratory, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, China
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Mahanic CS, Budhavarapu V, Graves JD, Li G, Lin WC. Regulation of E2 promoter binding factor 1 (E2F1) transcriptional activity through a deubiquitinating enzyme, UCH37. J Biol Chem 2015; 290:26508-22. [PMID: 26396186 DOI: 10.1074/jbc.m115.659425] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 01/27/2023] Open
Abstract
E2F1 is tightly controlled by multiple mechanisms, but whether ubiquitination regulates its transcriptional activity remains unknown. Here we identify UCH37 as the first, to our knowledge, deubiquitinating enzyme for E2F1. UCH37 does not deubiquitinate UbK48 chains or affect E2F1 protein stability. Instead, UCH37, but not a catalytically dead mutant, decreases the Lys-63-linked ubiquitination of E2F1 and activates its transcriptional activity. UCH37 depletion reduces the gene expression of both proliferative and pro-apoptotic E2F1 target genes. UCH37 depletion also decreases both cell proliferation and apoptosis induction in functional assays. Interestingly, UCH37 expression is induced by E2F1, and its level rises in G1/S transition and S phase, suggesting a positive feedback loop between UCH37 and E2F1. UCH37 protein and mRNA levels are also induced after DNA damage. UCH37 localizes to the promoters of E2F1 pro-apoptotic target genes such as caspase 3, caspase 7, PARP1, and Apaf-1 and activates their expression after DNA damage. Moreover, the expression of E2F1 proliferative and pro-apoptotic genes is correlated with the levels of UCH37 in many primary tumors. These results uncover a novel mechanism for E2F1 transcriptional activation through removal of its Lys-63-linked ubiquitination by UCH37.
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Affiliation(s)
- Christina S Mahanic
- From the Section of Hematology/Oncology and Integrative Molecular and Biomedical Sciences Graduate Program, Departments of Medicine and Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | | | - Joshua D Graves
- From the Section of Hematology/Oncology and Integrative Molecular and Biomedical Sciences Graduate Program, Departments of Medicine and Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Gang Li
- From the Section of Hematology/Oncology and
| | - Weei-Chin Lin
- From the Section of Hematology/Oncology and Integrative Molecular and Biomedical Sciences Graduate Program, Departments of Medicine and Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
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Wu J, Lv Q, He J, Zhang H, Mei X, Cui K, Huang N, Xie W, Xu N, Zhang Y. MicroRNA-188 suppresses G1/S transition by targeting multiple cyclin/CDK complexes. Cell Commun Signal 2014; 12:66. [PMID: 25304455 PMCID: PMC4200121 DOI: 10.1186/s12964-014-0066-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/30/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Accelerated cell cycle progression is the common feature of most cancers. MiRNAs can act as oncogenes or tumor suppressors by directly modulating cell cycle machinery. It has been shown that miR-188 is upregulated in UVB-irradiated mouse skin and human nasopharyngeal carcinoma CNE cells under hypoxic stress. However, little is known about the function of miR-188 in cell proliferation and growth control. RESULTS Overexpression of miR-188 inhibits cell proliferation, tumor colony formation and G1/S cell cycle transition in human nasopharyngeal carcinoma CNE cells. Using bioinformatics approach, we identify a series of genes regulating G1/S transition as putative miR-188 targets. MiR-188 inhibits both mRNA and protein expression of CCND1, CCND3, CCNE1, CCNA2, CDK4 and CDK2, suppresses Rb phosphorylation and downregulates E2F transcriptional activity. The expression level of miR-188 also inversely correlates with the expression of miR-188 targets in human nasopharyngeal carcinoma (NPC) tissues. Moreover, studies in xenograft mouse model reveal that miR-188 is capable of inhibiting tumor initiation and progression by suppressing target genes expression and Rb phosphorylation. CONCLUSIONS This study demonstrates that miR-188 exerts anticancer effects, via downregulation of multiple G1/S related cyclin/CDKs and Rb/E2F signaling pathway.
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Affiliation(s)
- Jiangbin Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Qing Lv
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Jie He
- Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Haoxiang Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Xueshuang Mei
- ENT Department, Peking University Shenzhen Hospital, Shenzhen, 518055, PR China.
| | - Kai Cui
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Nunu Huang
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Weidong Xie
- Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Naihan Xu
- Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Yaou Zhang
- Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
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48
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Karwaciak I, Pulaski L, Ratajewski M. Regulation of the human ABCB10 gene by E2F transcription factors. Genomics 2014; 104:520-9. [PMID: 25220178 DOI: 10.1016/j.ygeno.2014.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/20/2014] [Accepted: 08/26/2014] [Indexed: 12/12/2022]
Abstract
Here, we report for the first time a functional study of transcriptional regulation of the human ABCB10 gene. We cloned a functional promoter sequence, and then showed that E2F2, E2F3 and E2F4 can activate transcription from the ABCB10 promoter. We identified sites responsible for this activation and confirmed direct binding of E2F4 to these sites in EMSA and ChIP assays. Finally, by silencing the expression of E2F factors we demonstrated their importance in maintenance of the basal ABCB10 expression. This study provides important atypical examples of E2F4 being a transcriptional activator rather than repressor as well as directly binding to a promoter and regulating it through an alternative and classical DNA consensus response element sequences. It also provides a mechanistic link between E2F4 and ABCB10, both of which are involved in the same physiological phenomena: erythroid lineage differentiation and maturation as well as protection against cardiomyocyte cell death.
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Affiliation(s)
- Iwona Karwaciak
- Laboratory of Transcriptional Regulation, Institute of Medical Biology, Polish Academy of Sciences, Poland
| | - Lukasz Pulaski
- Laboratory of Transcriptional Regulation, Institute of Medical Biology, Polish Academy of Sciences, Poland
| | - Marcin Ratajewski
- Laboratory of Transcriptional Regulation, Institute of Medical Biology, Polish Academy of Sciences, Poland.
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49
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Watnick RS, Rodriguez RK, Wang S, Blois AL, Rangarajan A, Ince T, Weinberg RA. Thrombospondin-1 repression is mediated via distinct mechanisms in fibroblasts and epithelial cells. Oncogene 2014; 34:2823-35. [PMID: 25109329 DOI: 10.1038/onc.2014.228] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 06/03/2014] [Accepted: 06/21/2014] [Indexed: 12/27/2022]
Abstract
Tumor-associated angiogenesis is postulated to be regulated by the balance between pro- and anti-angiogenic factors. We demonstrate here that the critical step in establishing the angiogenic capability of human tumor cells is the repression of a key secreted anti-angiogenic factor, thrombospondin-1 (Tsp-1). This repression is essential for tumor formation by mammary epithelial cells and kidney cells engineered to express SV40 early region proteins, hTERT, and H-RasV12. In transformed epithelial cells, a signaling pathway leading from Ras to Tsp-1 repression induces the sequential activation of PI3 kinase, Rho and ROCK, leading to activation of Myc through phosphorylation, thereby enabling Myc to repress Tsp-1 transcription. In transformed fibroblasts, however, the repression of Tsp-1 can be achieved by an alternative mechanism involving inactivation of both p53 and pRb. We thus describe novel mechanisms by which the activation of oncogenes in epithelial cells and the inactivation of tumor suppressors in fibroblasts permits angiogenesis and, in turn, tumor formation.
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Affiliation(s)
- R S Watnick
- 1] Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA [2] Department of Surgery, Harvard Medical School, Boston, MA, USA [3] Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - R K Rodriguez
- 1] Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA [2] Department of Surgery, Harvard Medical School, Boston, MA, USA [3] Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - S Wang
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA
| | - A L Blois
- 1] Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA [2] Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - A Rangarajan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - T Ince
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - R A Weinberg
- 1] Whitehead Institute for Biomedical Research, Cambridge, MA, USA [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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50
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LIN-35/Rb causes starvation-induced germ cell apoptosis via CED-9/Bcl2 downregulation in Caenorhabditis elegans. Mol Cell Biol 2014; 34:2499-516. [PMID: 24752899 DOI: 10.1128/mcb.01532-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Apoptosis is an important mechanism for maintaining germ line health. In Caenorhabditis elegans, germ cell apoptosis occurs under normal conditions to sustain gonad homeostasis and oocyte quality. Under stress, germ cell apoptosis can be triggered via different pathways, including the following: (i) the CEP-1/p53 pathway, which induces germ cell apoptosis when animals are exposed to DNA damage; (ii) the mitogen-activated protein kinase kinase (MAPKK) pathway, which triggers germ cell apoptosis when animals are exposed to heat shock, oxidative stress, or osmotic stress; and (iii) an unknown mechanism that triggers germ cell apoptosis during starvation. Here, we address how starvation induces germ cell apoptosis. Using polysomal profiling, we found that starvation for 6 h reduces the translationally active ribosomes, which differentially affect the mRNAs of the core apoptotic machinery and some of its regulators. During starvation, lin-35/Rb mRNA increases its expression, resulting in the accumulation of this protein. As a consequence, LIN-35 downregulates the expression of the antiapoptotic gene ced-9/Bcl-2. We observed that the reduced translation of ced-9/Bcl-2 mRNA during food deprivation together with its downregulation drastically affects its protein accumulation. We propose that CED-9/Bcl-2 downregulation via LIN-35/Rb triggers germ cell apoptosis in C. elegans in response to starvation.
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