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Abstract
The transition between proliferating and quiescent states must be carefully regulated to ensure that cells divide to create the cells an organism needs only at the appropriate time and place. Cyclin-dependent kinases (CDKs) are critical for both transitioning cells from one cell cycle state to the next, and for regulating whether cells are proliferating or quiescent. CDKs are regulated by association with cognate cyclins, activating and inhibitory phosphorylation events, and proteins that bind to them and inhibit their activity. The substrates of these kinases, including the retinoblastoma protein, enforce the changes in cell cycle status. Single cell analysis has clarified that competition among factors that activate and inhibit CDK activity leads to the cell's decision to enter the cell cycle, a decision the cell makes before S phase. Signaling pathways that control the activity of CDKs regulate the transition between quiescence and proliferation in stem cells, including stem cells that generate muscle and neurons. © 2020 American Physiological Society. Compr Physiol 10:317-344, 2020.
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Affiliation(s)
- Hilary A Coller
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, and the Molecular Biology Institute, University of California, Los Angeles, California, USA.,Molecular Biology Institute, University of California, Los Angeles, California, USA
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52
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Non-overlapping Control of Transcriptome by Promoter- and Super-Enhancer-Associated Dependencies in Multiple Myeloma. Cell Rep 2019; 25:3693-3705.e6. [PMID: 30590042 PMCID: PMC6407615 DOI: 10.1016/j.celrep.2018.12.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 10/04/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022] Open
Abstract
The relationship between promoter proximal transcription
factor-associated gene expression and super-enhancer-driven transcriptional
programs are not well defined. However, their distinct genomic occupancy
suggests a mechanism for specific and separable gene control. We explored the
transcriptional and functional interrelationship between E2F transcription
factors and BET transcriptional co-activators in multiple myeloma. We found that
the transcription factor E2F1 and its heterodimerization partner DP1 represent a
dependency in multiple myeloma cells. Global chromatin analysis reveals distinct
regulatory axes for E2F and BETs, with E2F predominantly localized to active
gene promoters of growth and/or proliferation genes and BETs disproportionately
at enhancer-regulated tissue-specific genes. These two separate gene regulatory
axes can be simultaneously targeted to impair the myeloma proliferative program,
providing an important molecular mechanism for combination therapy. This study
therefore suggests a sequestered cellular functional control that may be
perturbed in cancer with potential for development of a promising therapeutic
strategy. Uncontrolled proliferation is a hallmark of tumorigenesis and is
associated with perturbed transcriptomic profile. Fulciniti et al. explored the
interrelationship between E2F transcription factors and BET transcriptional
co-activators in multiple myeloma, reporting the existence of two distinct
regulatory axes that can be synergistically targeted to impact myeloma growth
and survival.
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53
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Choi EH, Kim KP. E2F1 facilitates DNA break repair by localizing to break sites and enhancing the expression of homologous recombination factors. Exp Mol Med 2019; 51:1-12. [PMID: 31534120 PMCID: PMC6802646 DOI: 10.1038/s12276-019-0307-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/16/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
The human genome is constantly exposed to both endogenous and exogenous stresses, which can lead to errors in DNA replication and the accumulation of DNA mutations, thereby increasing the risk of cancer development. The transcription factor E2F1 is a key regulator of DNA repair. E2F1 also has defined roles in the replication of many cell cycle-related genes and is highly expressed in cancer cells, and its abundance is strongly associated with poor prognosis in cancers. Studies on colon cancer have demonstrated that the depletion of E2F1 leads to reduced levels of homologous recombination (HR), resulting in interrupted DNA replication and the subsequent accumulation of DNA lesions. Our results demonstrate that the depletion of E2F1 also causes reduced RAD51-mediated DNA repair and diminished cell viability resulting from DNA damage. Furthermore, the extent of RAD51 and RPA colocalization is reduced in response to DNA damage; however, RPA single-stranded DNA (ssDNA) nucleofilament formation is not affected following the depletion of E2F1, implying that ssDNA gaps accumulate when RAD51-mediated DNA gap filling or repair is diminished. Surprisingly, we also demonstrate that E2F1 forms foci with RAD51 or RPA at DNA break sites on damaged DNA. These findings provide evidence of a molecular mechanism underlying the E2F1-mediated regulation of HR activity and predict a fundamental shift in the function of E2F1 from regulating cell division to accelerating tumor development.
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Affiliation(s)
- Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Keun Pil Kim
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea.
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54
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Pokorná P, Krepl M, Bártová E, Šponer J. Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network. J Chem Theory Comput 2019; 15:5659-5673. [DOI: 10.1021/acs.jctc.9b00434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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55
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Jibrim RLM, de Carvalho CV, Invitti AL, Schor E. Expression of the TFDP1 gene in the endometrium of women with deep infiltrating endometriosis. Gynecol Endocrinol 2019; 35:490-493. [PMID: 30638096 DOI: 10.1080/09513590.2018.1540569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The field of endometriosis etiopathogenesis aims to identify the origin of disease in endometrial disorders. Changes in gene and protein expression related to cell adhesion, collagenases, and, mainly, cell cycle regulators have been identified. We set out to analyze the expression of the transcription factor DP-1 (TFDP1) gene, which encodes a protein that controls the G1/S phase passage of the cell cycle, in the endometrium of women with deep infiltrating endometriosis (DIE). Samples of endometrium from both endometriosis-affected women and healthy women were collected, cultured and maintained at the Cell Bank of the Pelvic Pain and Endometriosis Unit of the Federal University of Sao Paulo. This study analyzed five samples from the endometrium cell culture of healthy patients (i.e. no pelvic disease, as determined by means of laparoscopic tubal ligation) and six samples from women diagnosed with DIE. Samples were evaluated for TFDP1 gene expression by real-time PCR. We observed a downregulation of TFDP1 in the endometrium cells of women with DIE when compared to the control (a fold-change of -2.05, p value=.011). The TFDP1 gene is part of the cell cycle pathway, but its function is not yet clear. Additional studies are necessary to clarify the function of TFDP1 in endometriosis etiopathogenesis.
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Affiliation(s)
- Rodrigo Lopes Meime Jibrim
- a Gynecology Department, Pelvic Pain and Endometriosis Unit , Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM) , Sao Paulo , Brazil
| | - Cristina Valletta de Carvalho
- a Gynecology Department, Pelvic Pain and Endometriosis Unit , Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM) , Sao Paulo , Brazil
| | - Adriana Luckow Invitti
- a Gynecology Department, Pelvic Pain and Endometriosis Unit , Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM) , Sao Paulo , Brazil
| | - Eduardo Schor
- a Gynecology Department, Pelvic Pain and Endometriosis Unit , Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM) , Sao Paulo , Brazil
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56
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Topacio BR, Zatulovskiy E, Cristea S, Xie S, Tambo CS, Rubin SM, Sage J, Kõivomägi M, Skotheim JM. Cyclin D-Cdk4,6 Drives Cell-Cycle Progression via the Retinoblastoma Protein's C-Terminal Helix. Mol Cell 2019; 74:758-770.e4. [PMID: 30982746 PMCID: PMC6800134 DOI: 10.1016/j.molcel.2019.03.020] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 02/01/2019] [Accepted: 03/19/2019] [Indexed: 01/10/2023]
Abstract
The cyclin-dependent kinases Cdk4 and Cdk6 form complexes with D-type cyclins to drive cell proliferation. A well-known target of cyclin D-Cdk4,6 is the retinoblastoma protein Rb, which inhibits cell-cycle progression until its inactivation by phosphorylation. However, the role of Rb phosphorylation by cyclin D-Cdk4,6 in cell-cycle progression is unclear because Rb can be phosphorylated by other cyclin-Cdks, and cyclin D-Cdk4,6 has other targets involved in cell division. Here, we show that cyclin D-Cdk4,6 docks one side of an alpha-helix in the Rb C terminus, which is not recognized by cyclins E, A, and B. This helix-based docking mechanism is shared by the p107 and p130 Rb-family members across metazoans. Mutation of the Rb C-terminal helix prevents its phosphorylation, promotes G1 arrest, and enhances Rb's tumor suppressive function. Our work conclusively demonstrates that the cyclin D-Rb interaction drives cell division and expands the diversity of known cyclin-based protein docking mechanisms.
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Affiliation(s)
| | | | - Sandra Cristea
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shicong Xie
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Carrie S Tambo
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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57
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Anbo H, Sato M, Okoshi A, Fukuchi S. Functional Segments on Intrinsically Disordered Regions in Disease-Related Proteins. Biomolecules 2019; 9:biom9030088. [PMID: 30841624 PMCID: PMC6468909 DOI: 10.3390/biom9030088] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 01/05/2023] Open
Abstract
One of the unique characteristics of intrinsically disordered proteins (IPDs) is the existence of functional segments in intrinsically disordered regions (IDRs). A typical function of these segments is binding to partner molecules, such as proteins and DNAs. These segments play important roles in signaling pathways and transcriptional regulation. We conducted bioinformatics analysis to search these functional segments based on IDR predictions and database annotations. We found more than a thousand potential functional IDR segments in disease-related proteins. Large fractions of proteins related to cancers, congenital disorders, digestive system diseases, and reproductive system diseases have these functional IDRs. Some proteins in nervous system diseases have long functional segments in IDRs. The detailed analysis of some of these regions showed that the functional segments are located on experimentally verified IDRs. The proteins with functional IDR segments generally tend to come and go between the cytoplasm and the nucleus. Proteins involved in multiple diseases tend to have more protein-protein interactors, suggesting that hub proteins in the protein-protein interaction networks can have multiple impacts on human diseases.
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Affiliation(s)
- Hiroto Anbo
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi, Gunma 371-0816, Japan.
| | - Masaya Sato
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi, Gunma 371-0816, Japan.
| | - Atsushi Okoshi
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi, Gunma 371-0816, Japan.
| | - Satoshi Fukuchi
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi, Gunma 371-0816, Japan.
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58
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Sanidas I, Morris R, Fella KA, Rumde PH, Boukhali M, Tai EC, Ting DT, Lawrence MS, Haas W, Dyson NJ. A Code of Mono-phosphorylation Modulates the Function of RB. Mol Cell 2019; 73:985-1000.e6. [PMID: 30711375 DOI: 10.1016/j.molcel.2019.01.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/26/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022]
Abstract
Hyper-phosphorylation of RB controls its interaction with E2F and inhibits its tumor suppressor properties. However, during G1 active RB can be mono-phosphorylated on any one of 14 CDK phosphorylation sites. Here, we used quantitative proteomics to profile protein complexes formed by each mono-phosphorylated RB isoform (mP-RB) and identified the associated transcriptional outputs. The results show that the 14 sites of mono-phosphorylation co-ordinate RB's interactions and confer functional specificity. All 14 mP-RBs interact with E2F/DP proteins, but they provide different shades of E2F regulation. RB mono-phosphorylation at S811, for example, alters RB transcriptional activity by promoting its association with NuRD complexes. The greatest functional differences between mP-RBs are evident beyond the cell cycle machinery. RB mono-phosphorylation at S811 or T826 stimulates the expression of oxidative phosphorylation genes, increasing cellular oxygen consumption. These results indicate that RB activation signals are integrated in a phosphorylation code that determines the diversity of RB activity.
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Affiliation(s)
- Ioannis Sanidas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Katerina A Fella
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Purva H Rumde
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Eric C Tai
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA.
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59
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Leviczky T, Molnár E, Papdi C, Őszi E, Horváth GV, Vizler C, Nagy V, Pauk J, Bögre L, Magyar Z. E2FA and E2FB transcription factors coordinate cell proliferation with seed maturation. Development 2019; 146:dev.179333. [PMID: 31666236 PMCID: PMC6899031 DOI: 10.1242/dev.179333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/21/2019] [Indexed: 01/31/2023]
Abstract
The E2F transcription factors and the RETINOBLASTOMA-RELATED repressor protein are principal regulators coordinating cell proliferation with differentiation, but their role during seed development is little understood. We show that in fully developed Arabidopsis thaliana embryos, cell number was not affected either in single or double mutants for the activator-type E2FA and E2FB. Accordingly, these E2Fs are only partially required for the expression of cell cycle genes. In contrast, the expression of key seed maturation genes LEAFY COTYLEDON 1/2 (LEC1/2), ABSCISIC ACID INSENSITIVE 3, FUSCA 3 and WRINKLED 1 is upregulated in the e2fab double mutant embryo. In accordance, E2FA directly regulates LEC2, and mutation at the consensus E2F-binding site in the LEC2 promoter de-represses its activity during the proliferative stage of seed development. In addition, the major seed storage reserve proteins, 12S globulin and 2S albumin, became prematurely accumulated at the proliferating phase of seed development in the e2fab double mutant. Our findings reveal a repressor function of the activator E2Fs to restrict the seed maturation programme until the cell proliferation phase is completed. Highlighted Article: During seed and embryo development the E2FA and E2FB transcription factors coordinate cell proliferation with differentiation and accumulation of seed reserves; however, they are not essential for sustaining cell proliferation.
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Affiliation(s)
- Tünde Leviczky
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Eszter Molnár
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Csaba Papdi
- Royal Holloway University of London, Department of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, UK
| | - Erika Őszi
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor V. Horváth
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Csaba Vizler
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Viktór Nagy
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - János Pauk
- Department of Biotechnology, Cereal Research Non-Profit Ltd. Co., Alsó kikötő sor 9, 6726 Szeged, Hungary
| | - László Bögre
- Royal Holloway University of London, Department of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, UK
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
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60
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Kim HR, Rahman FU, Kim KS, Kim EK, Cho SM, Lee K, Moon OS, Seo YW, Yoon WK, Won YS, Kang H, Kim HC, Nam KH. Critical Roles of E2F3 in Growth and Musculo-skeletal Phenotype in Mice. Int J Med Sci 2019; 16:1557-1563. [PMID: 31839743 PMCID: PMC6909802 DOI: 10.7150/ijms.39068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/11/2019] [Indexed: 12/24/2022] Open
Abstract
E2F3, a member of the E2F family, plays a critical role in cell cycle and proliferation by targeting downstream, retinoblastoma (RB) a tumor suppressor family protein. The purpose of this study, was to investigate the role and function of E2F3 in vivo. We examined phenotypic abnormalities, by deletion of the E2f3 gene in mice. Complete ablation of the E2F3 was fully penetrant, in the pure C57BL/6N background. The E2f3+/ - mouse embryo developed normally without fatal disorder. However, they exhibited reduced body weight, growth retardation, skeletal imperfection, and poor grip strength ability. Findings suggest that E2F3 has a pivotal role in muscle and bone development, and affect normal mouse growth.
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Affiliation(s)
- Hae-Rim Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Faiz Ur Rahman
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Kwang-Soo Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea.,Department of Animal Science and Technology, Chung-Ang University, Seodong-daero 4726, Gyeonggi 17546, Korea
| | - Eun-Kyeung Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Sang-Mi Cho
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Kihoon Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Ok-Sung Moon
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Young-Won Seo
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Won-Kee Yoon
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Young-Suk Won
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Hoyoung Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Hyoung-Chin Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
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Sun W, Lv J, Duan L, Lin R, Li Y, Li S, Fu C, Zhao L, Xin S. Long noncoding RNA H19 promotes vascular remodeling by sponging let-7a to upregulate the expression of cyclin D1. Biochem Biophys Res Commun 2018; 508:1038-1042. [PMID: 30551879 DOI: 10.1016/j.bbrc.2018.11.185] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022]
Abstract
Vascular remodeling is mainly caused by excessive proliferation of vascular smooth muscle cells (VSMCs). Noncoding RNAs (ncRNAs) have emerged as important regulators in diverse pathological processes. Previous work has shown the functions and mechanisms of long noncoding RNA H19 (LncRNA H19) on VSMCs. As long noncoding RNAs (lncRNAs) are complex in their mechanisms of action, the aim of the study is to identify if there are any other molecular mechanisms of LncRNA H19 on VSMCs. In vivo studies demonstrated that cyclin D1 was overexpressed in neointima of balloon-injured artery. In vitro studies identified that the overexpression of LncRNA H19 promoted VSMCs proliferation and cyclin D1 upregulation. On the contrary, cellular proliferation and expression of cyclin D1 were inhibited in VSMCs after infection with let-7a. Furthermore, luciferase reporter assays and RNA pull-down assays were used to explore the regulatory mechanism, we found that LncRNA H19 functioned as a competing endogenous RNA (ceRNA) by sponging let-7a to promote the expression of the target gene cyclin D1. In conclusion, LncRNA H19 positively regulated cyclin D1 expression through directly binding to let-7a in VSMCs. Our findings provide new insight into the mechanism of LncRNA H19 in VSMCs proliferation and vascular remodeling, and further indicate the implications of LncRNA H19 in the diagnosis and treatment of vascular proliferative diseases.
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Affiliation(s)
- Weifeng Sun
- Department of Vascular Surgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Junyuan Lv
- Department of Breast and Thyroid Surgery, The Affiliated Hospital of Zunyi Medical College, Zunyi, 563000, China
| | - Liren Duan
- Department of Vascular Surgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Ruoran Lin
- Department of Vascular Surgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yugang Li
- Department of Vascular Surgery, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Shanqiong Li
- Department of Pharmacology, School of Pharmacy, Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, China
| | - Chen Fu
- Department of Pharmacology, School of Pharmacy, Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, China
| | - Shijie Xin
- Department of Vascular Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.
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62
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Alizad-Rahvar AR, Sadeghi M. Ambiguity in logic-based models of gene regulatory networks: An integrative multi-perturbation analysis. PLoS One 2018; 13:e0206976. [PMID: 30458000 PMCID: PMC6245684 DOI: 10.1371/journal.pone.0206976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/23/2018] [Indexed: 01/13/2023] Open
Abstract
Most studies of gene regulatory network (GRN) inference have focused extensively on identifying the interaction map of the GRNs. However, in order to predict the cellular behavior, modeling the GRN in terms of logic circuits, i.e., Boolean networks, is necessary. The perturbation techniques, e.g., knock-down and over-expression, should be utilized for identifying the underlying logic behind the interactions. However, we will show that by using only transcriptomic data obtained by single-perturbation experiments, we cannot observe all regulatory interactions, and this invisibility causes ambiguity in our model. Consequently, we need to employ the data of multiple omics layers (genome, transcriptome, and proteome) as well as multiple perturbation experiments to reduce or eliminate ambiguity in our modeling. In this paper, we introduce a multi-step perturbation experiment to deal with ambiguity. Moreover, we perform a thorough analysis to investigate which types of perturbations and omics layers play the most important role in the unambiguous modeling of the GRNs and how much ambiguity will be eliminated by considering more perturbations and more omics layers. Our analysis shows that performing both knock-down and over-expression is necessary in order to achieve the least ambiguous model. Moreover, the more steps of the perturbation are taken, the more ambiguity is eliminated. In addition, we can even achieve an unambiguous model of the GRN by using multi-step perturbation and integrating transcriptomic, protein-protein interaction, and cis-element data. Finally, we demonstrate the effect of utilizing different types of perturbation experiment and integrating multi-omics data on identifying the logic behind the regulatory interactions in a synthetic GRN. In conclusion, relying on the results of only knock-down experiments and not including as many omics layers as possible in the GRN inference, makes the results ambiguous, unreliable, and less accurate.
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Affiliation(s)
- Amir Reza Alizad-Rahvar
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- * E-mail: (ARA); (MS)
| | - Mehdi Sadeghi
- National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
- * E-mail: (ARA); (MS)
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63
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Hu R, Wang MQ, Niu WB, Wang YJ, Liu YY, Liu LY, Wang M, Zhong J, You HY, Wu XH, Deng N, Lu L, Wei LB. SKA3 promotes cell proliferation and migration in cervical cancer by activating the PI3K/Akt signaling pathway. Cancer Cell Int 2018; 18:183. [PMID: 30459531 PMCID: PMC6236911 DOI: 10.1186/s12935-018-0670-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/30/2018] [Indexed: 01/03/2023] Open
Abstract
Background Cervical cancer (CC) is one of the most common cancers among females worldwide. Spindle and kinetochore-associated complex subunit 3 (SKA3), located on chromosome 13q, was identified as a novel gene involved in promoting malignant transformation in cancers. However, the function and underlying mechanisms of SKA3 in CC remain unknown. Using the Oncomine database, we found that expression of SKA3 mRNA is higher in CC tissues than in normal tissues and is linked with poor prognosis. Methods In our study, immunohistochemistry showed increased expression of SKA3 in CC tissues. The effect of SKA3 on cell proliferation and migration was evaluated by CCK8, clone formation, Transwell and wound-healing assays in HeLa and SiHa cells with stable SKA3 overexpression and knockdown. In addition, we established a xenograft tumor model in vivo. Results SKA3 overexpression promoted cell proliferation and migration and accelerated tumor growth. We further identified that SKA3 is involved in regulating cell cycle progression and the PI3K/Akt signaling pathway via RNA-sequencing (RNA-Seq) and gene set enrichment analyses. Western blotting results revealed that SKA3 overexpression increased levels of p-Akt, cyclin E2, CDK2, cyclin D1, CDK4, E2F1 and p-Rb in HeLa cells. Additionally, the use of an Akt inhibitor (GSK690693) significantly reversed the cell proliferation capacity induced by SKA3 overexpression in HeLa cells. Conclusions We suggest that SKA3 overexpression contributes to CC cell growth and migration by promoting cell cycle progression and activating the PI3K-Akt signaling pathway, which may provide potential novel therapeutic targets for CC treatment.
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Affiliation(s)
- Rong Hu
- 1Shenzhen Hospital, Southern Medical University, No. 1333, Xinhu Road, Bao'an District, Shenzhen, 518101 Guangdong China.,2School of Traditional Chinese Medicine, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
| | - Ming-Qing Wang
- 1Shenzhen Hospital, Southern Medical University, No. 1333, Xinhu Road, Bao'an District, Shenzhen, 518101 Guangdong China.,2School of Traditional Chinese Medicine, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
| | - Wen-Bo Niu
- 5Cancer Research Institute, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
| | - Yan-Jing Wang
- 3Zhujiang Hospital of Southern Medical University, No. 253, Industrial Avenue, Haizhu District, Guangzhou, 510280 Guangdong China
| | - Yang-Yang Liu
- Zhongshan Huangpu People's Hospital, No. 32, Long'an Street, Huangpu Town, Zhongshan, 528429 Guangdong China
| | - Ling-Yu Liu
- 1Shenzhen Hospital, Southern Medical University, No. 1333, Xinhu Road, Bao'an District, Shenzhen, 518101 Guangdong China.,2School of Traditional Chinese Medicine, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
| | - Ming Wang
- 3Zhujiang Hospital of Southern Medical University, No. 253, Industrial Avenue, Haizhu District, Guangzhou, 510280 Guangdong China
| | - Juan Zhong
- 1Shenzhen Hospital, Southern Medical University, No. 1333, Xinhu Road, Bao'an District, Shenzhen, 518101 Guangdong China.,2School of Traditional Chinese Medicine, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
| | - Hai-Yan You
- 1Shenzhen Hospital, Southern Medical University, No. 1333, Xinhu Road, Bao'an District, Shenzhen, 518101 Guangdong China.,2School of Traditional Chinese Medicine, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
| | - Xiao-Hui Wu
- 1Shenzhen Hospital, Southern Medical University, No. 1333, Xinhu Road, Bao'an District, Shenzhen, 518101 Guangdong China.,2School of Traditional Chinese Medicine, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
| | - Ning Deng
- 2School of Traditional Chinese Medicine, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
| | - Lu Lu
- 4The First Affiliated Hospital, Guangzhou University of Chinese Medicine, No.16 Baiyun Airport Road, Baiyun District, Guangzhou, 510405 Guangdong China
| | - Lian-Bo Wei
- 1Shenzhen Hospital, Southern Medical University, No. 1333, Xinhu Road, Bao'an District, Shenzhen, 518101 Guangdong China.,2School of Traditional Chinese Medicine, Southern Medical University, No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou, 510515 Guangdong China
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64
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E2F1 Mediates the Retinoic Acid-Induced Transcription of Tshz1 during Neuronal Differentiation in a Cell Division-Dependent Manner. Mol Cell Biol 2018; 38:MCB.00217-18. [PMID: 30104253 DOI: 10.1128/mcb.00217-18] [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: 05/03/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022] Open
Abstract
The involvement of cell division in cellular differentiation has long been accepted. Cell division may be required not only for the expansion of a differentiated cell population but also for the execution of differentiation processes. Nonetheless, knowledge regarding how specific differentiation processes are controlled in a cell division-dependent manner is far from complete. Here, we determined the involvement of cell division in neuronal differentiation. We initially confirmed that cell division is an essential event for the neuronal differentiation of P19 embryonic carcinoma cells. We investigated the induction mechanisms of Tshz1, whose expression is induced by retinoic acid (RA) in a cell division-dependent manner. Promoter analysis of Tshz1 revealed a specific region required for RA-dependent transcription. A series of experiments was used to identify E2F1 as the induction factor for the RA-dependent transcription of Tshz1 We propose that E2F1 mediates neuronal differentiation in a cell division-dependent manner.
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65
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The RASSF6 Tumor Suppressor Protein Regulates Apoptosis and Cell Cycle Progression via Retinoblastoma Protein. Mol Cell Biol 2018; 38:MCB.00046-18. [PMID: 29891515 DOI: 10.1128/mcb.00046-18] [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: 01/26/2018] [Accepted: 06/07/2018] [Indexed: 02/06/2023] Open
Abstract
RASSF6 is a member of the tumor suppressor Ras association domain family (RASSF) proteins. RASSF6 is frequently suppressed in human cancers, and its low expression level is associated with poor prognosis. RASSF6 regulates cell cycle arrest and apoptosis and plays a tumor suppressor role. Mechanistically, RASSF6 blocks MDM2-mediated p53 degradation and enhances p53 expression. However, RASSF6 also induces cell cycle arrest and apoptosis in a p53-negative background, which implies that the tumor suppressor function of RASSF6 does not depend solely on p53. In this study, we revealed that RASSF6 mediates cell cycle arrest and apoptosis via pRb. RASSF6 enhances the interaction between pRb and protein phosphatase. RASSF6 also enhances P16INK4A and P14ARF expression by suppressing BMI1. In this way, RASSF6 increases unphosphorylated pRb and augments the interaction between pRb and E2F1. Moreover, RASSF6 induces TP73 target genes via pRb and E2F1 in a p53-negative background. Finally, we confirmed that RASSF6 depletion induces polyploid cells in p53-negative HCT116 cells. In conclusion, RASSF6 behaves as a tumor suppressor in cancers with loss of function of p53, and pRb is implicated in this function of RASSF6.
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66
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Abstract
The canonical model of RB-mediated tumour suppression developed over the past 30 years is based on the regulation of E2F transcription factors to restrict cell cycle progression. Several additional functions have been proposed for RB, on the basis of which a non-canonical RB pathway can be described. Mechanistically, the non-canonical RB pathway promotes histone modification and regulates chromosome structure in a manner distinct from cell cycle regulation. These functions have implications for chemotherapy response and resistance to targeted anticancer agents. This Opinion offers a framework to guide future studies of RB in basic and clinical research.
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Affiliation(s)
- Frederick A Dick
- London Regional Cancer Program, Children's Health Research Institute, Western University, London, Ontario, Canada.
- London Regional Cancer Program, Department of Biochemistry, Western University, London, Ontario, Canada.
| | - David W Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Julien Sage
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Laboratory of Molecular Oncology, Harvard Medical School, Charlestown, MA, USA
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67
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Wang J, Zhang Y, Wei H, Zhang X, Wu Y, Gong A, Xia Y, Wang W, Xu M. The mir-675-5p regulates the progression and development of pancreatic cancer via the UBQLN1-ZEB1-mir200 axis. Oncotarget 2018; 8:24978-24987. [PMID: 28212565 PMCID: PMC5421903 DOI: 10.18632/oncotarget.15330] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 01/19/2017] [Indexed: 01/07/2023] Open
Abstract
Pancreatic cancer (PC) is a highly lethal disease due to extensive metastatic lesions. Accumulating evidence suggests that miR-675-5p plays different roles in metastasis through the regulation of epithelial to mesenchymal (EMT) and the mesenchymal to epithelial transitions (MET) in different cancers. ZEB1 promotes the EMT process by controlling the expression of E-cadherin and may have a reciprocal regulation with Ubiquilin1 (UBQLN1) and mir-200 family in cancer progression. In the present study, we showed that decreased expression of miR-675-5p is associated with the enhanced cell proliferation and survival of PC cells, while the increased expression of mir-675-5p shows the opposite one. The mir-675-5p could decrease the expression of mir-200 which is intermediated by ZEB1, and increase the expression of UBQLN1 gene. The mir-675-5p can increase the expression of ZEB1 mRNA, but the ZEB1 protein level was decreased. When mir-675-5p mimics and siUBQLN1 were co-transfected into the pancreatic cancer Patu8988 cells, the expression of ZEB1 protein was increased. It suggests that mir-675-5p may affect ZEB1 in a post-transcriptional level which was verified to be regulated by UBQLN1 protein. Hence, mir-675-5p regulates the progression of pancreatic cancer cells through the UBQLN1-ZEB1-mir200 pathway.
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Affiliation(s)
- Jue Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212000, China
| | - Youli Zhang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212000, China
| | - Hong Wei
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212000, China
| | - Xingxing Zhang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212000, China
| | - Yan Wu
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang 212000, China
| | - Aihua Gong
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang 212000, China
| | - Yu Xia
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212000, China
| | - Wenbing Wang
- Department of Public Health, School of Medicine, Jiangsu University, Zhenjiang 212000, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212000, China
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68
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Kim M, Tang JP, Moon NS. An alternatively spliced form affecting the Marked Box domain of Drosophila E2F1 is required for proper cell cycle regulation. PLoS Genet 2018; 14:e1007204. [PMID: 29420631 PMCID: PMC5821395 DOI: 10.1371/journal.pgen.1007204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/21/2018] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
Across metazoans, cell cycle progression is regulated by E2F family transcription factors that can function as either transcriptional activators or repressors. For decades, the Drosophila E2F family has been viewed as a streamlined RB/E2F network, consisting of one activator (dE2F1) and one repressor (dE2F2). Here, we report that an uncharacterized isoform of dE2F1, hereon called dE2F1b, plays an important function during development and is functionally distinct from the widely-studied dE2F1 isoform, dE2F1a. dE2F1b contains an additional exon that inserts 16 amino acids to the evolutionarily conserved Marked Box domain. Analysis of de2f1b-specific mutants generated via CRISPR/Cas9 indicates that dE2F1b is a critical regulator of the cell cycle during development. This is particularly evident in endocycling salivary glands in which a tight control of dE2F1 activity is required. Interestingly, close examination of mitotic tissues such as eye and wing imaginal discs suggests that dE2F1b plays a repressive function as cells exit from the cell cycle. We also provide evidence demonstrating that dE2F1b differentially interacts with RBF1 and alters the recruitment of RBF1 and dE2F1 to promoters. Collectively, our data suggest that dE2F1b is a novel member of the E2F family, revealing a previously unappreciated complexity in the Drosophila RB/E2F network.
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Affiliation(s)
- Minhee Kim
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
| | - Jack P. Tang
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
| | - Nam-Sung Moon
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
- * E-mail:
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69
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Schwarz C, Johnson A, Kõivomägi M, Zatulovskiy E, Kravitz CJ, Doncic A, Skotheim JM. A Precise Cdk Activity Threshold Determines Passage through the Restriction Point. Mol Cell 2018; 69:253-264.e5. [PMID: 29351845 PMCID: PMC5790185 DOI: 10.1016/j.molcel.2017.12.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/28/2017] [Accepted: 12/19/2017] [Indexed: 11/24/2022]
Abstract
At the restriction point (R), mammalian cells irreversibly commit to divide. R has been viewed as a point in G1 that is passed when growth factor signaling initiates a positive feedback loop of Cdk activity. However, recent studies have cast doubt on this model by claiming R occurs prior to positive feedback activation in G1 or even before completion of the previous cell cycle. Here we reconcile these results and show that whereas many commonly used cell lines do not exhibit a G1 R, primary fibroblasts have a G1 R that is defined by a precise Cdk activity threshold and the activation of cell-cycle-dependent transcription. A simple threshold model, based solely on Cdk activity, predicted with more than 95% accuracy whether individual cells had passed R. That a single measurement accurately predicted cell fate shows that the state of complex regulatory networks can be assessed using a few critical protein activities.
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Affiliation(s)
- Clayton Schwarz
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Amy Johnson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Andreas Doncic
- Department of Cell Biology & Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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70
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Abbas MN, Kausar S, Sun YX, Sun Y, Wang L, Qian C, Wei GQ, Zhu BJ, Liu CL. Molecular cloning, expression, and characterization of E2F transcription factor 4 from Antheraea pernyi. BULLETIN OF ENTOMOLOGICAL RESEARCH 2017; 107:839-846. [PMID: 28436337 DOI: 10.1017/s0007485317000426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The E2F transcription factor family is distributed widely in eukaryotes and has been well studied among mammals. In the present study, the E2F transcription factor 4 (E2F4) gene was isolated from fat bodies of Antheraea pernyi and sequenced. E2F4 comprised a 795 bp open reading frame encoding a deduced amino acid sequence of 264 amino acid residues. The recombinant protein was expressed in Escherichia coli (Transetta DE3), and anti-E2F4 antibodies were prepared. The deduced amino acid sequence displayed significant homology to an E2F4-like protein from Bombyx mori L. Quantitative real-time polymerase chain reaction analysis revealed that E2F4 expression was highest in the integument, followed by the fat body, silk glands, and haemocytes. The expression of E2F4 was upregulated in larvae challenged by bacterial (Escherichia coli, Micrococcus luteus), viral (nuclear polyhedrosis virus), and fungal (Beauveria bassiana) pathogens. These observations indicated that E2F4 is an inducible protein in the immune response of A. pernyi and probably in other insects.
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Affiliation(s)
- M N Abbas
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - S Kausar
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Y-X Sun
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Y Sun
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - L Wang
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - C Qian
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - G-Q Wei
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - B-J Zhu
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - C-L Liu
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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71
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Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals. J Hum Genet 2017; 63:213-230. [PMID: 29192238 DOI: 10.1038/s10038-017-0347-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 01/07/2023]
Abstract
Clarifying allele frequencies of disease-related genetic variants in a population is important in genomic medicine; however, such data is not yet available for the Japanese population. To estimate frequencies of actionable pathogenic variants in the Japanese population, we examined the reported pathological variants in genes recommended by the American College of Medical Genetics and Genomics (ACMG) in our reference panel of genomic variations, 2KJPN, which was created by whole-genome sequencing of 2049 individuals of the resident cohort of the Tohoku Medical Megabank Project. We searched for pathogenic variants in 2KJPN for 57 autosomal ACMG-recommended genes responsible for 26 diseases and then examined their frequencies. By referring to public databases of pathogenic variations, we identified 143 reported pathogenic variants in 2KJPN for the 57 ACMG recommended genes based on a classification system. At the individual level, 21% of the individuals were found to have at least one reported pathogenic allele. We then conducted a literature survey to review the variants and to check for evidence of pathogenicity. Our results suggest that a substantial number of people have reported pathogenic alleles for the ACMG genes, and reviewing variants is indispensable for constructing the information infrastructure of genomic medicine for the Japanese population.
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72
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Shang A, Lu WY, Yang M, Zhou C, Zhang H, Cai ZX, Wang WW, Wang WX, Wu GQ. miR-9 induces cell arrest and apoptosis of oral squamous cell carcinoma via CDK 4/6 pathway. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2017; 46:1754-1762. [PMID: 29073835 DOI: 10.1080/21691401.2017.1391825] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Oral cancer remains a major public concern with considerable socioeconomic impact in the world, especially in southeast Asia. Despite substantial advancements have been made in treating oral cancer, the five-year survival rate for OSCC remained undesirable, and 35-55% patients developed recurrence within two years even with multimodality therapeutic strategies. Hence, identification of novel biomarkers for diagnosis and evaluating clinical outcome is of vital importance. MicroRNAs are 22-24 nt non-coding RNAs that could bind to 3' UTR of target mRNAs, thereby inducing degradation of mRNA or inhibiting translation. Due to its implication in regulation of post-transcriptional processes, the role of miRNAs in malignancies has been extensively studied, among which the discovery of functional miR-9 in oral squamous cell carcinoma (OSCC) remained to be elucidated. We first demonstrated that miR-9 was down-regulated in 21 OSCC patients, and we further found that forced expression of miR-9 could result in deterred cell proliferation and decreased ability to migrate and form colonies. Flow cytometry displayed cell-cycle arrested at G0/G1 phase. We next used Targetscan to predict target genes of miR-9. CDK6, a protein highly implicated in cell cycle control, was chosen for verification. Down-regulation of CDK6 and Cyclin D1 in Tca8113 transfected with miR-9 mimics indicate that the complex formed by both proteins may be the effector of the antiproliferative function of miR-9 in OSCCs. Considering small molecules are developed to target CDK4/6, our finding may provide valuable scientific evidence for research and development of therapies and diagnostic methodology in OSCCs.
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Affiliation(s)
- Anquan Shang
- a Department of Laboratory Medicine, , Tongji Hospital of Tongji University , Shanghai , China.,b Department of Laboratory Medicine , The Sixth People's Hospital of Yancheng City , Yancheng , Jiangsu , China
| | - Wen-Ying Lu
- b Department of Laboratory Medicine , The Sixth People's Hospital of Yancheng City , Yancheng , Jiangsu , China
| | - Man Yang
- c Department of Laboratory Medicine , Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine , Yancheng , Jiangsu , China.,d School of Biology & Basic Medical Sciences , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Cheng Zhou
- b Department of Laboratory Medicine , The Sixth People's Hospital of Yancheng City , Yancheng , Jiangsu , China
| | - Hong Zhang
- b Department of Laboratory Medicine , The Sixth People's Hospital of Yancheng City , Yancheng , Jiangsu , China
| | - Zheng-Xin Cai
- b Department of Laboratory Medicine , The Sixth People's Hospital of Yancheng City , Yancheng , Jiangsu , China
| | - Wei-Wei Wang
- e Department of Pathology , The First People's Hospital of Yancheng City , Yancheng , Jiangsu , China.,f Department of Pathology , The Sixth People's Hospital of Yancheng City , Yancheng , Jiangsu , China
| | - Wan-Xiang Wang
- g Department of Laboratory Medicine , The First People's Hospital of Yancheng City , Yancheng , Jiangsu , China
| | - Gui-Qi Wu
- h Department of General Surgery , The Sixth People's Hospital of Yancheng City , Yancheng , Jiangsu , China
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73
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Yruela I, Oldfield CJ, Niklas KJ, Dunker AK. Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity. Genome Biol Evol 2017; 9:1248-1265. [PMID: 28430951 PMCID: PMC5434936 DOI: 10.1093/gbe/evx073] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2017] [Indexed: 12/11/2022] Open
Abstract
Studies of diverse phylogenetic lineages reveal that protein disorder increases in concert with organismic complexity but that differences nevertheless exist among lineages. To gain insight into this phenomenology, we analyzed all of the transcription factor (TF) families for which sequences are known for 17 species spanning bacteria, yeast, algae, land plants, and animals and for which the number of different cell types has been reported in the primary literature. Although the fraction of disordered residues in TF sequences is often moderately or poorly correlated with organismic complexity as gauged by cell-type number (r2 < 0.5), an unbiased and phylogenetically broad analysis shows that organismic complexity is positively and strongly correlated with the total number of TFs, the number of their spliced variants and their total disordered residues content (r2 > 0.8). Furthermore, the correlation between the fraction of disordered residues and cell-type number becomes stronger when confined to the TF families participating in cell cycle, cell size, cell division, cell differentiation, or cell proliferation, and other important developmental processes. The data also indicate that evolutionarily simpler organisms allow for the detection of subtle differences in the conserved IDRs of TFs as well as changes in variable IDRs, which can influence the DNA recognition and multifunctionality of TFs through direct or indirect mechanisms. Although strong correlations cannot be taken as evidence for cause-and-effect relationships, we interpret our data to indicate that increasing TF disorder likely was an important factor contributing to the evolution of organismic complexity and not merely a concurrent unrelated effect of increasing organismic complexity.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain.,Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Christopher J Oldfield
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN
| | - Karl J Niklas
- School of Integrative Plant Science, Cornell University, Ithaca, NY
| | - A Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN
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74
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Perumal N, Perumal M, Kannan A, Subramani K, Halagowder D, Sivasithamparam N. Morin impedes Yap nuclear translocation and fosters apoptosis through suppression of Wnt/β-catenin and NF-κB signaling in Mst1 overexpressed HepG2 cells. Exp Cell Res 2017; 355:124-141. [DOI: 10.1016/j.yexcr.2017.03.062] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 12/12/2022]
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75
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Liban TJ, Medina EM, Tripathi S, Sengupta S, Henry RW, Buchler NE, Rubin SM. Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family. Proc Natl Acad Sci U S A 2017; 114:4942-4947. [PMID: 28439018 PMCID: PMC5441720 DOI: 10.1073/pnas.1619170114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD-CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein-E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.
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Affiliation(s)
- Tyler J Liban
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Edgar M Medina
- Department of Biology, Duke University, Durham, NC 27708
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Satyaki Sengupta
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - R William Henry
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Nicolas E Buchler
- Department of Biology, Duke University, Durham, NC 27708
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064;
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76
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The human retinoblastoma susceptibility gene (RB1): an evolutionary story in primates. Mamm Genome 2017; 28:198-212. [PMID: 28401291 DOI: 10.1007/s00335-017-9689-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
Abstract
The tumor suppressor gene RB1 (Human Retinoblastoma Susceptibility Gene) plays a prominent role in normal development, gene transcription, DNA replication, repair, and mitosis. Its complete biallelic dysfunction in retinoblasts is the main cause of retinoblastoma in the human. Although this gene has been evolutionary conserved, comparisons between the reference and human RB1 coding region with its counterparts in 19 non-human primates showed 359 sites where nucleotide replacements took place during the radiation of these species. These resulted in missense substitutions in 97 codons, 91 of which by amino acids with radically different physicochemical properties. Several in frame deletions and two insertions were also observed in the N-terminal region of the pRB protein where the highest number of amino acid substitutions and radical amino changes were found. Fifty-six codons were inferred to be under negative selection and five under positive selection. Differences in codon usage showed evident phylogenetic signals, with hominids generally presenting higher indices of codon bias than other catarrhines. The lineage leading to platyrrhines and, within platyrrhines, the lineage leading to Saimiri boliviensis showed a high rate of nucleotide substitutions and amino acids. Finally, several RB1 alterations associated to retinoblastoma in the human were present in several non-human primates without an apparent pathological effect.
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77
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Audagnotto M, Dal Peraro M. Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput Struct Biotechnol J 2017; 15:307-319. [PMID: 28458782 PMCID: PMC5397102 DOI: 10.1016/j.csbj.2017.03.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 02/09/2023] Open
Abstract
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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78
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Abstract
The p53 tumor suppressor is highly regulated at the level of protein degradation and transcriptional activity. The key players of the pathway, p53, MDM2, and MDMX are present at multiple conformational states that are responsive to regulation by post-translational modifications and protein-protein interactions. The structures of major functional domains of these proteins have been determined, but the mechanisms of several intrinsically disordered regions remain unclear despite their critical roles in signaling and regulation. Recent studies suggest that these disordered regions function in part by dynamic intra molecular interactions with the structured domains to regulate p53 DNA binding, MDM2 ubiquitin E3 ligase activity, and MDMX-p53 binding. These findings provide new insight on how p53 is controlled by various stress signals, and suggest potential targets for the search of allosteric regulators of the p53 pathway.
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Affiliation(s)
- Jiandong Chen
- Molecular Oncology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
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79
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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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80
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Kulkarni A, Scully TJ, O'Donnell LA. The antiviral cytokine interferon-gamma restricts neural stem/progenitor cell proliferation through activation of STAT1 and modulation of retinoblastoma protein phosphorylation. J Neurosci Res 2016; 95:1582-1601. [PMID: 27862183 PMCID: PMC5432422 DOI: 10.1002/jnr.23987] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/18/2016] [Accepted: 10/14/2016] [Indexed: 12/20/2022]
Abstract
Neural stem/progenitor cells (NPSCs) express receptors for many inflammatory cytokines, with varying effects on differentiation and proliferation depending on the stage of development and the milieu of inflammatory mediators. In primary neurons and astrocytes, we recently showed that interferon gamma (IFNγ), a potent antiviral cytokine that is required for the control and clearance of many central nervous system (CNS) infections, could differentially affect cell survival and cell cycle progression depending upon the cell type and the profile of activated intracellular signaling molecules. Here, we show that IFNγ inhibits proliferation of primary NSPCs through dephosphorylation of the tumor suppressor Retinoblastoma protein (pRb), which is dependent on activation of signal transducers and activators of transcription‐1 (STAT1) signaling pathways. Our results show i) IFNγ inhibits neurosphere growth and proliferation rate in a dose‐dependent manner; ii) IFNγ blocks cell cycle progression through a late‐stage G1/S phase restriction; iii) IFNγ induces phosphorylation and expression of STAT1 and STAT3; iv) IFNγ decreases cyclin E/cdk2 expression and reduces phosphorylation of cyclin D1 and pRb on serine residue 795; and v) the effects of IFNγ on NSPC proliferation, cell cycle protein expression, and pRb phosphorylation are STAT1‐dependent. These data define a mechanism by which IFNγ could contribute to a reduction in NSPC proliferation in inflammatory conditions. Further delineation of the effects of inflammatory cytokines on NSPC growth could improve our understanding of how CNS infections and other inflammatory events disrupt brain development and NSPC function. © 2016 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Apurva Kulkarni
- Duquesne University, Mylan School of Pharmacy, 600 Forbes Avenue, Pittsburgh, PA, 15282
| | - Taylor J Scully
- Duquesne University, Mylan School of Pharmacy, 600 Forbes Avenue, Pittsburgh, PA, 15282
| | - Lauren A O'Donnell
- Duquesne University, Mylan School of Pharmacy, 600 Forbes Avenue, Pittsburgh, PA, 15282
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81
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Abstract
The E2F family of transcription factors is a key determinant of cell proliferation in response to extra- and intra-cellular signals. Within this family, E2F4 is a transcriptional repressor whose activity is critical to engage and maintain cell cycle arrest in G0/G1 in conjunction with members of the retinoblastoma (RB) family. However, recent observations challenge this paradigm and indicate that E2F4 has a multitude of functions in cells besides this cell cycle regulatory role, including in embryonic and adult stem cells, during regenerative processes, and in cancer. Some of these new functions are independent of the RB family and involve direct activation of target genes. Here we review the canonical functions of E2F4 and discuss recent evidence expanding the role of this transcription factor, with a focus on cell fate decisions in tissue homeostasis and regeneration.
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Affiliation(s)
- Jenny Hsu
- a Departments of Pediatrics and Genetics , Stanford University , Stanford , CA , USA
| | - Julien Sage
- a Departments of Pediatrics and Genetics , Stanford University , Stanford , CA , USA
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82
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Abstract
How and when eukaryotic cells make the irrevocable commitment to divide remain central questions in the cell-cycle field. Parallel studies in yeast and mammalian cells seemed to suggest analogous control mechanisms operating during the G1 phase—at Start or the restriction (R) point, respectively—to integrate nutritional and developmental signals and decide between distinct cell fates: cell-cycle arrest or exit versus irreversible commitment to a round of division. Recent work has revealed molecular mechanisms underlying this decision-making process in both yeast and mammalian cells but also cast doubt on the nature and timing of cell-cycle commitment in multicellular organisms. These studies suggest an expanded temporal window of mitogen sensing under certain growth conditions, illuminate unexpected obstacles and exit ramps on the path to full cell-cycle commitment, and raise new questions regarding the functions of cyclin-dependent kinases (CDKs) that drive G1 progression and S-phase entry.
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Affiliation(s)
- Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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83
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Gubern A, Joaquin M, Marquès M, Maseres P, Garcia-Garcia J, Amat R, González-Nuñez D, Oliva B, Real FX, de Nadal E, Posas F. The N-Terminal Phosphorylation of RB by p38 Bypasses Its Inactivation by CDKs and Prevents Proliferation in Cancer Cells. Mol Cell 2016; 64:25-36. [PMID: 27642049 DOI: 10.1016/j.molcel.2016.08.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/21/2016] [Accepted: 08/10/2016] [Indexed: 02/06/2023]
Abstract
Control of the G1/S phase transition by the Retinoblastoma (RB) tumor suppressor is critical for the proliferation of normal cells in tissues, and its inactivation is one of the most fundamental events leading to cancer. Cyclin-dependent kinase (CDK) phosphorylation inactivates RB to promote cell cycle-regulated gene expression. Here we show that, upon stress, the p38 stress-activated protein kinase (SAPK) maximizes cell survival by downregulating E2F gene expression through the targeting of RB. RB undergoes selective phosphorylation by p38 in its N terminus; these phosphorylations render RB insensitive to the inactivation by CDKs. p38 phosphorylation of RB increases its affinity toward the E2F transcription factor, represses gene expression, and delays cell-cycle progression. Remarkably, introduction of a RB phosphomimetic mutant in cancer cells reduces colony formation and decreases their proliferative and tumorigenic potential in mice.
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Affiliation(s)
- Albert Gubern
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Manel Joaquin
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Miriam Marquès
- Epithelial Carcinogenesis Group, Cancer Cell Biology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; Departament de Ciències Experimentals i de la Salut, UPF, 08003 Barcelona, Spain
| | - Pedro Maseres
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Javier Garcia-Garcia
- Structural Bioinformatics Group (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Ramon Amat
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Daniel González-Nuñez
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Baldo Oliva
- Structural Bioinformatics Group (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Cancer Cell Biology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; Departament de Ciències Experimentals i de la Salut, UPF, 08003 Barcelona, Spain
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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84
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Liban TJ, Thwaites MJ, Dick FA, Rubin SM. Structural Conservation and E2F Binding Specificity within the Retinoblastoma Pocket Protein Family. J Mol Biol 2016; 428:3960-3971. [PMID: 27567532 DOI: 10.1016/j.jmb.2016.08.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/24/2016] [Accepted: 08/17/2016] [Indexed: 11/24/2022]
Abstract
The human pocket proteins retinoblastoma (Rb), p107, and p130 are critical negative regulators of the cell cycle and contribute to tumor suppression. While strong structural conservation within the pocket protein family provides for some functional redundancy, important differences have been observed and may underlie the reason that Rb is a uniquely potent tumor suppressor. It has been proposed that distinct pocket protein activities are mediated by their different E2F transcription factor binding partners. In humans, Rb binds E2F1-E2F5, whereas p107 and p130 almost exclusively associate with E2F4 and E2F5. To identify the molecular determinants of this specificity, we compared the crystal structures of Rb and p107 pocket domains and identified several key residues that contribute to E2F selectivity in the pocket family. Mutation of these residues in p107 to match the analogous residue in Rb results in an increase in affinity for E2F1 and E2F2 and an increase in the ability of p107 to inhibit E2F2 transactivation. Additionally, we investigated how phosphorylation by Cyclin-dependent kinase on distinct residues regulates p107 affinity for the E2F4 transactivation domain. We found that phosphorylation of residues S650 and S975 weakens the E2F4 transactivation domain binding. Our data reveal molecular features of pocket proteins that are responsible for their similarities and differences in function and regulation.
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Affiliation(s)
- Tyler J Liban
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Michael J Thwaites
- Department of Biochemistry, Western University, London Regional Cancer Program and Children's Health Research Institute, London, Ontario, Canada
| | - Frederick A Dick
- Department of Biochemistry, Western University, London Regional Cancer Program and Children's Health Research Institute, London, Ontario, Canada
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.
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85
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Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters. Nat Commun 2016; 7:12301. [PMID: 27465258 PMCID: PMC4974476 DOI: 10.1038/ncomms12301] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 06/20/2016] [Indexed: 12/13/2022] Open
Abstract
The MuvB complex recruits transcription factors to activate or repress genes with cell cycle-dependent expression patterns. MuvB contains the DNA-binding protein LIN54, which directs the complex to promoter cell cycle genes homology region (CHR) elements. Here we characterize the DNA-binding properties of LIN54 and describe the structural basis for recognition of a CHR sequence. We biochemically define the CHR consensus as TTYRAA and determine that two tandem cysteine rich regions are required for high-affinity DNA association. A crystal structure of the LIN54 DNA-binding domain in complex with a CHR sequence reveals that sequence specificity is conferred by two tyrosine residues, which insert into the minor groove of the DNA duplex. We demonstrate that this unique tyrosine-mediated DNA binding is necessary for MuvB recruitment to target promoters. Our results suggest a model in which MuvB binds near transcription start sites and plays a role in positioning downstream nucleosomes.
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86
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Zhang J, Xu K, Liu P, Geng Y, Wang B, Gan W, Guo J, Wu F, Chin YR, Berrios C, Lien EC, Toker A, DeCaprio JA, Sicinski P, Wei W. Inhibition of Rb Phosphorylation Leads to mTORC2-Mediated Activation of Akt. Mol Cell 2016; 62:929-942. [PMID: 27237051 DOI: 10.1016/j.molcel.2016.04.023] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/07/2015] [Accepted: 04/21/2016] [Indexed: 12/23/2022]
Abstract
The retinoblastoma (Rb) protein exerts its tumor suppressor function primarily by inhibiting the E2F family of transcription factors that govern cell-cycle progression. However, it remains largely elusive whether the hyper-phosphorylated, non-E2F1-interacting form of Rb has any physiological role. Here we report that hyper-phosphorylated Rb directly binds to and suppresses the function of mTORC2 but not mTORC1. Mechanistically, Rb, but not p107 or p130, interacts with Sin1 and blocks the access of Akt to mTORC2, leading to attenuated Akt activation and increased sensitivity to chemotherapeutic drugs. As such, inhibition of Rb phosphorylation by depleting cyclin D or using CDK4/6 inhibitors releases Rb-mediated mTORC2 suppression. This, in turn, leads to elevated Akt activation to confer resistance to chemotherapeutic drugs in Rb-proficient cells, which can be attenuated with Akt inhibitors. Therefore, our work provides a molecular basis for the synergistic usage of CDK4/6 and Akt inhibitors in treating Rb-proficient cancer.
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Affiliation(s)
- Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kai Xu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China.,Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Pengda Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bin Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, 400042, P. R. China
| | - Wenjian Gan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Fei Wu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200040, P.R. China
| | - Y Rebecca Chin
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christian Berrios
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Evan C Lien
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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87
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The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nat Commun 2016; 7:11370. [PMID: 27102219 PMCID: PMC4844696 DOI: 10.1038/ncomms11370] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/18/2016] [Indexed: 12/30/2022] Open
Abstract
The transition to multicellularity has occurred numerous times in all domains of life, yet its initial steps are poorly understood. The volvocine green algae are a tractable system for understanding the genetic basis of multicellularity including the initial formation of cooperative cell groups. Here we report the genome sequence of the undifferentiated colonial alga, Gonium pectorale, where group formation evolved by co-option of the retinoblastoma cell cycle regulatory pathway. Significantly, expression of the Gonium retinoblastoma cell cycle regulator in unicellular Chlamydomonas causes it to become colonial. The presence of these changes in undifferentiated Gonium indicates extensive group-level adaptation during the initial step in the evolution of multicellularity. These results emphasize an early and formative step in the evolution of multicellularity, the evolution of cell cycle regulation, one that may shed light on the evolutionary history of other multicellular innovations and evolutionary transitions.
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88
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Huang PH, Cook R, Zoumpoulidou G, Luczynski MT, Mittnacht S. Retinoblastoma family proteins: New players in DNA repair by non-homologous end-joining. Mol Cell Oncol 2016; 3:e1053596. [PMID: 27308588 PMCID: PMC4905371 DOI: 10.1080/23723556.2015.1053596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 05/17/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
Loss of retinoblastoma protein (RB1) function is a major driver in cancer development. We have recently reported that, in addition to its well-documented functions in cell cycle and fate control, RB1 and its paralogs have a novel role in regulating DNA repair by non-homologous end joining (NHEJ). Here we summarize our findings and present mechanistic hypotheses on how RB1 may support the DNA repair process and the therapeutic implications for patients who harbor RB1-negative cancers.
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Affiliation(s)
- Paul H. Huang
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
| | - Rebecca Cook
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
- Cancer Cell Signalling, UCL Cancer Institute, University College London, London, UK
| | - Georgia Zoumpoulidou
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
| | - Maciej T. Luczynski
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
| | - Sibylle Mittnacht
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
- Cancer Cell Signalling, UCL Cancer Institute, University College London, London, UK
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89
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Abstract
Protein phosphatase 2A (PP2A) plays a critical multi-faceted role in the regulation of the cell cycle. It is known to dephosphorylate over 300 substrates involved in the cell cycle, regulating almost all major pathways and cell cycle checkpoints. PP2A is involved in such diverse processes by the formation of structurally distinct families of holoenzymes, which are regulated spatially and temporally by specific regulators. Here, we review the involvement of PP2A in the regulation of three cell signaling pathways: wnt, mTOR and MAP kinase, as well as the G1→S transition, DNA synthesis and mitotic initiation. These processes are all crucial for proper cell survival and proliferation and are often deregulated in cancer and other diseases.
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Affiliation(s)
- Nathan Wlodarchak
- a McArdle Laboratory for Cancer Research, University of Wisconsin-Madison , Madison , WI , USA
| | - Yongna Xing
- a McArdle Laboratory for Cancer Research, University of Wisconsin-Madison , Madison , WI , USA
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90
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Wei KY, Smolke CD. Engineering dynamic cell cycle control with synthetic small molecule-responsive RNA devices. J Biol Eng 2015; 9:21. [PMID: 26594238 PMCID: PMC4654890 DOI: 10.1186/s13036-015-0019-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/27/2015] [Indexed: 01/08/2023] Open
Abstract
Background The cell cycle plays a key role in human health and disease, including development and cancer. The ability to easily and reversibly control the mammalian cell cycle could mean improved cellular reprogramming, better tools for studying cancer, more efficient gene therapy, and improved heterologous protein production for medical or industrial applications. Results We engineered RNA-based control devices to provide specific and modular control of gene expression in response to exogenous inputs in living cells. Specifically, we identified key regulatory nodes that arrest U2-OS cells in the G0/1 or G2/M phases of the cycle. We then optimized the most promising key regulators and showed that, when these optimized regulators are placed under the control of a ribozyme switch, we can inducibly and reversibly arrest up to ~80 % of a cellular population in a chosen phase of the cell cycle. Characterization of the reliability of the final cell cycle controllers revealed that the G0/1 control device functions reproducibly over multiple experiments over several weeks. Conclusions To our knowledge, this is the first time synthetic RNA devices have been used to control the mammalian cell cycle. This RNA platform represents a general class of synthetic biology tools for modular, dynamic, and multi-output control over mammalian cells. Electronic supplementary material The online version of this article (doi:10.1186/s13036-015-0019-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathy Y Wei
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA 94305 USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA 94305 USA
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91
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Gibson TJ, Dinkel H, Van Roey K, Diella F. Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. Cell Commun Signal 2015; 13:42. [PMID: 26581338 PMCID: PMC4652402 DOI: 10.1186/s12964-015-0121-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/13/2015] [Indexed: 12/17/2022] Open
Abstract
It has become clear in outline though not yet in detail how cellular regulatory and signalling systems are constructed. The essential machines are protein complexes that effect regulatory decisions by undergoing internal changes of state. Subcomponents of these cellular complexes are assembled into molecular switches. Many of these switches employ one or more short peptide motifs as toggles that can move between one or more sites within the switch system, the simplest being on-off switches. Paradoxically, these motif modules (termed short linear motifs or SLiMs) are both hugely abundant but difficult to research. So despite the many successes in identifying short regulatory protein motifs, it is thought that only the “tip of the iceberg” has been exposed. Experimental and bioinformatic motif discovery remain challenging and error prone. The advice presented in this article is aimed at helping researchers to uncover genuine protein motifs, whilst avoiding the pitfalls that lead to reports of false discovery.
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Affiliation(s)
- Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
| | - Holger Dinkel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
| | - Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany. .,Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D69117, Heidelberg, Germany.
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92
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CDK6-a review of the past and a glimpse into the future: from cell-cycle control to transcriptional regulation. Oncogene 2015; 35:3083-91. [PMID: 26500059 DOI: 10.1038/onc.2015.407] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/22/2015] [Accepted: 09/22/2015] [Indexed: 12/19/2022]
Abstract
The G1 cell-cycle kinase CDK6 has long been thought of as a redundant homolog of CDK4. Although the two kinases have very similar roles in cell-cycle progression, it has recently become apparent that they differ in tissue-specific functions and contribute differently to tumor development. CDK6 is directly involved in transcription in tumor cells and in hematopoietic stem cells. These functions point to a role of CDK6 in tissue homeostasis and differentiation that is partially independent of CDK6's kinase activity and is not shared with CDK4. We review the literature on the contribution of CDK6 to transcription in an attempt to link the new findings on CDK6's transcriptional activity to cell-cycle progression. Finally, we note that anticancer therapies based on the inhibition of CDK6 kinase activity fail to take into account its kinase-independent role in tumor development.
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93
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Sengupta S, Henry RW. Regulation of the retinoblastoma–E2F pathway by the ubiquitin–proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1289-97. [DOI: 10.1016/j.bbagrm.2015.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 12/16/2022]
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94
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DAVELAAR AKUENIL, STRAUB DANIELLE, PARIKH KAUSHALB, LAU LIANA, FOCKENS PAUL, KRISHNADATH KAUSILIAK. Increased phosphorylation on residue S795 of the retinoblastoma protein in esophageal adenocarcinoma. Int J Oncol 2015; 47:583-91. [DOI: 10.3892/ijo.2015.3040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/05/2015] [Indexed: 12/20/2022] Open
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95
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Iwahori S, Hakki M, Chou S, Kalejta RF. Molecular Determinants for the Inactivation of the Retinoblastoma Tumor Suppressor by the Viral Cyclin-dependent Kinase UL97. J Biol Chem 2015; 290:19666-80. [PMID: 26100623 DOI: 10.1074/jbc.m115.660043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Indexed: 01/10/2023] Open
Abstract
The retinoblastoma (Rb) tumor suppressor restricts cell cycle progression by repressing E2F-responsive transcription. Cellular cyclin-dependent kinase (CDK)-mediated Rb inactivation through phosphorylation disrupts Rb-E2F complexes, stimulating transcription. The human cytomegalovirus (HCMV) UL97 protein is a viral CDK (v-CDK) that phosphorylates Rb. Here we show that UL97 phosphorylates 11 of the 16 consensus CDK sites in Rb. A cleft within Rb accommodates peptides with the amino acid sequence LXCXE. UL97 contains three such motifs. We determined that the first LXCXE motif (L1) of UL97 and the Rb cleft enhance UL97-mediated Rb phosphorylation. A UL97 mutant with a non-functional L1 motif (UL97-L1m) displayed significantly reduced Rb phosphorylation at multiple sites. Curiously, however, it efficiently disrupted Rb-E2F complexes but failed to relieve Rb-mediated repression of E2F reporter constructs. The HCMV immediate early 1 protein cooperated with UL97-L1m to inactivate Rb in transfection assays, likely indicating that cells infected with a UL97-L1m mutant virus show no defects in growth or E2F-responsive gene expression because of redundant viral mechanisms to inactivate Rb. Our data suggest that UL97 possesses a mechanism to elicit E2F-dependent gene expression distinct from disruption of Rb-E2F complexes and dependent upon both the L1 motif of UL97 and the cleft region of Rb.
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Affiliation(s)
- Satoko Iwahori
- From the Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
| | - Morgan Hakki
- the Division of Infectious Diseases, Oregon Health and Science University and
| | - Sunwen Chou
- the Division of Infectious Diseases, Oregon Health and Science University and Veterans Affairs Portland Health Care System, Portland, Oregon 97239
| | - Robert F Kalejta
- From the Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
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96
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Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis. G3-GENES GENOMES GENETICS 2015; 5:1503-15. [PMID: 25999584 PMCID: PMC4502384 DOI: 10.1534/g3.115.019166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RBf2 is a recently evolved retinoblastoma family member in Drosophila that differs from RBf1, especially in the C-terminus. To investigate whether the unique features of RBf2 contribute to diverse roles in gene regulation, we performed chromatin immunoprecipitation sequencing for both RBf2 and RBf1 in embryos. A previous model for RB−E2F interactions suggested that RBf1 binds dE2F1 or dE2F2, whereas RBf2 is restricted to binding to dE2F2; however, we found that RBf2 targets approximately twice as many genes as RBf1. Highly enriched among the RBf2 targets were ribosomal protein genes. We tested the functional significance of this finding by assessing RBf activity on ribosomal protein promoters and the endogenous genes. RBf1 and RBf2 significantly repressed expression of some ribosomal protein genes, although not all bound genes showed transcriptional effects. Interestingly, many ribosomal protein genes are similarly targeted in human cells, indicating that these interactions may be relevant for control of ribosome biosynthesis and growth. We carried out bioinformatic analysis to investigate the basis for differential targeting by these two proteins and found that RBf2-specific promoters have distinct sequence motifs, suggesting unique targeting mechanisms. Association of RBf2 with these promoters appears to be independent of dE2F2/dDP, although promoters bound by both RBf1 and RBf2 require dE2F2/dDP. The presence of unique RBf2 targets suggest that evolutionary appearance of this corepressor represents the acquisition of potentially novel roles in gene regulation for the RB family.
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97
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Guiley KZ, Liban TJ, Felthousen JG, Ramanan P, Litovchick L, Rubin SM. Structural mechanisms of DREAM complex assembly and regulation. Genes Dev 2015; 29:961-74. [PMID: 25917549 PMCID: PMC4421984 DOI: 10.1101/gad.257568.114] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 01/01/2023]
Abstract
To understand the biochemical mechanisms underpinning DREAM function and regulation, Guiley et al. investigated the structural basis for DREAM assembly. Together, the data inform a novel target interface for studying MuvB and p130 function and the design of inhibitors that prevent tumor escape in quiescence. The DREAM complex represses cell cycle genes during quiescence through scaffolding MuvB proteins with E2F4/5 and the Rb tumor suppressor paralog p107 or p130. Upon cell cycle entry, MuvB dissociates from p107/p130 and recruits B-Myb and FoxM1 for up-regulating mitotic gene expression. To understand the biochemical mechanisms underpinning DREAM function and regulation, we investigated the structural basis for DREAM assembly. We identified a sequence in the MuvB component LIN52 that binds directly to the pocket domains of p107 and p130 when phosphorylated on the DYRK1A kinase site S28. A crystal structure of the LIN52–p107 complex reveals that LIN52 uses a suboptimal LxSxExL sequence together with the phosphate at nearby S28 to bind the LxCxE cleft of the pocket domain with high affinity. The structure explains the specificity for p107/p130 over Rb in the DREAM complex and how the complex is disrupted by viral oncoproteins. Based on insights from the structure, we addressed how DREAM is disassembled upon cell cycle entry. We found that p130 and B-Myb can both bind the core MuvB complex simultaneously but that cyclin-dependent kinase phosphorylation of p130 weakens its association. Together, our data inform a novel target interface for studying MuvB and p130 function and the design of inhibitors that prevent tumor escape in quiescence.
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Affiliation(s)
- Keelan Z Guiley
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Tyler J Liban
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Jessica G Felthousen
- Division of Hematology, Oncology, and Palliative Care, Richmond, Virginia 23298, USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Parameshwaran Ramanan
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Larisa Litovchick
- Division of Hematology, Oncology, and Palliative Care, Richmond, Virginia 23298, USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA;
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98
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Sengupta S, Lingnurkar R, Carey TS, Pomaville M, Kar P, Feig M, Wilson CA, Knott JG, Arnosti DN, Henry RW. The Evolutionarily Conserved C-terminal Domains in the Mammalian Retinoblastoma Tumor Suppressor Family Serve as Dual Regulators of Protein Stability and Transcriptional Potency. J Biol Chem 2015; 290:14462-75. [PMID: 25903125 DOI: 10.1074/jbc.m114.599993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Indexed: 11/06/2022] Open
Abstract
The retinoblastoma (RB) tumor suppressor and related family of proteins play critical roles in development through their regulation of genes involved in cell fate. Multiple regulatory pathways impact RB function, including the ubiquitin-proteasome system with deregulated RB destruction frequently associated with pathogenesis. With the current study we explored the mechanisms connecting proteasome-mediated turnover of the RB family to the regulation of repressor activity. We find that steady state levels of all RB family members, RB, p107, and p130, were diminished during embryonic stem cell differentiation concomitant with their target gene acquisition. Proteasome-dependent turnover of the RB family is mediated by distinct and autonomously acting instability elements (IE) located in their C-terminal regulatory domains in a process that is sensitive to cyclin-dependent kinase (CDK4) perturbation. The IE regions include motifs that contribute to E2F-DP transcription factor interaction, and consistently, p107 and p130 repressor potency was reduced by IE deletion. The juxtaposition of degron sequences and E2F interaction motifs appears to be a conserved feature across the RB family, suggesting the potential for repressor ubiquitination and specific target gene regulation. These findings establish a mechanistic link between regulation of RB family repressor potency and the ubiquitin-proteasome system.
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Key Words
- retinoblastoma, RB, p107, p130, E2F-DP, cyclin, CDK, protein stability, proteasome, degron, transcriptional repression.
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Affiliation(s)
- Satyaki Sengupta
- From the Department of Biochemistry and Molecular Biology, Graduate Program in Physiology, and
| | - Raj Lingnurkar
- From the Department of Biochemistry and Molecular Biology
| | | | | | - Parimal Kar
- From the Department of Biochemistry and Molecular Biology
| | - Michael Feig
- From the Department of Biochemistry and Molecular Biology
| | - Catherine A Wilson
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824
| | - Jason G Knott
- From the Department of Biochemistry and Molecular Biology, Department of Animal Science, Michigan State University, East Lansing, Michigan 48824
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99
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Kang H, Kiess A, Chung CH. Emerging biomarkers in head and neck cancer in the era of genomics. Nat Rev Clin Oncol 2014; 12:11-26. [PMID: 25403939 DOI: 10.1038/nrclinonc.2014.192] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Head and neck cancer (HNC) broadly includes carcinomas arising from the mucosal epithelia of the head and neck region as well as various cell types of salivary glands and the thyroid. As reflected by the multiple sites and histologies of HNC, the molecular characteristics and clinical outcomes of this disease vary widely. In this Review, we focus on established and emerging biomarkers that are most relevant to nasopharyngeal carcinoma and head and neck squamous-cell carcinoma (HNSCC), which includes primary sites in the oral cavity, oropharynx, hypopharynx and larynx. Applications and limitations of currently established biomarkers are discussed along with examples of successful biomarker development. For emerging biomarkers, preclinical or retrospective data are also described in the context of recently completed comprehensive molecular analyses of HNSCC, which provide a broad genetic landscape and molecular classification beyond histology and clinical characteristics. We will highlight the ongoing effort that will see a shift from prognostic to predictive biomarker development in HNC with the goal of delivering individualized cancer therapy.
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Affiliation(s)
- Hyunseok Kang
- Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Medical Institutions, 1650 Orleans Street, CRB-1 Room 344, Baltimore, MD 21287-0013, USA
| | - Ana Kiess
- Department of Radiation Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Medical Institutions, 1650 Orleans Street, CRB-1 Room 344, Baltimore, MD 21287-0013, USA
| | - Christine H Chung
- 1] Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Medical Institutions, 1650 Orleans Street, CRB-1 Room 344, Baltimore, MD 21287-0013, USA. [2] Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Johns Hopkins Medical Institutions, 1650 Orleans Street, CRB-1 Room 344, Baltimore, MD 21287-0013, USA
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100
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Jansma AL, Martinez-Yamout MA, Liao R, Sun P, Dyson HJ, Wright PE. The high-risk HPV16 E7 oncoprotein mediates interaction between the transcriptional coactivator CBP and the retinoblastoma protein pRb. J Mol Biol 2014; 426:4030-4048. [PMID: 25451029 DOI: 10.1016/j.jmb.2014.10.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 10/25/2014] [Accepted: 10/29/2014] [Indexed: 11/24/2022]
Abstract
The oncoprotein E7 from human papillomavirus (HPV) strains that confer high cancer risk mediates cell transformation by deregulating host cellular processes and activating viral gene expression through recruitment of cellular proteins such as the retinoblastoma protein (pRb) and the cyclic-AMP response element binding binding protein (CBP) and its paralog p300. Here we show that the intrinsically disordered N-terminal region of E7 from high-risk HPV16 binds the TAZ2 domain of CBP with greater affinity than E7 from low-risk HPV6b. HPV E7 and the tumor suppressor p53 compete for binding to TAZ2. The TAZ2 binding site in E7 overlaps the LxCxE motif that is crucial for interaction with pRb. While TAZ2 and pRb compete for binding to a monomeric E7 polypeptide, the full-length E7 dimer mediates an interaction between TAZ2 and pRb by promoting formation of a ternary complex. Cell-based assays show that expression of full-length HPV16 E7 promotes increased pRb acetylation and that this response depends both on the presence of CBP/p300 and on the ability of E7 to form a dimer. These observations suggest a model for the oncogenic effect of high-risk HPV16 E7. The disordered region of one E7 molecule in the homodimer interacts with the pocket domain of pRb, while the same region of the other E7 molecule binds the TAZ2 domain of CBP/p300. Through its ability to dimerize, E7 recruits CBP/p300 and pRb into a ternary complex, bringing the histone acetyltransferase domain of CBP/p300 into proximity to pRb and promoting acetylation, leading to disruption of cell cycle control.
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Affiliation(s)
- Ariane L Jansma
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rong Liao
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peiqing Sun
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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