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Emanuele MJ, Enrico TP, Mouery RD, Wasserman D, Nachum S, Tzur A. Complex Cartography: Regulation of E2F Transcription Factors by Cyclin F and Ubiquitin. Trends Cell Biol 2020; 30:640-652. [PMID: 32513610 PMCID: PMC7859860 DOI: 10.1016/j.tcb.2020.05.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
The E2F family of transcriptional regulators sits at the center of cell cycle gene expression and plays vital roles in normal and cancer cell cycles. Whereas control of E2Fs by the retinoblastoma family of proteins is well established, much less is known about their regulation by ubiquitin pathways. Recent studies placed the Skp1-Cul1-F-box-protein (SCF) family of E3 ubiquitin ligases with the F-box protein Cyclin F at the center of E2F regulation, demonstrating temporal proteolysis of both activator and atypical repressor E2Fs. Importantly, these E2F members, in particular activator E2F1 and repressors E2F7 and E2F8, form a feedback circuit at the crossroads of cell cycle and cell death. Moreover, Cyclin F functions in a reciprocal circuit with the cell cycle E3 ligase anaphase-promoting complex/cyclosome (APC/C), which also controls E2F7 and E2F8. This review focuses on the complex contours of feedback within this circuit, highlighting the deep crosstalk between E2F, SCF-Cyclin F, and APC/C in regulating the oscillator underlying human cell cycles.
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Affiliation(s)
- Michael J Emanuele
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Taylor P Enrico
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D Mouery
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Genetics and Molecular Biology Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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152
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Lees A, McIntyre AJ, Crawford NT, Falcone F, McCann C, Holohan C, Quinn GP, Roberts JZ, Sessler T, Gallagher PF, Gregg GMA, McAllister K, McLaughlin KM, Allen WL, Egan LJ, Ryan AE, Labonte-Wilson MJ, Dunne PD, Wappett M, Coyle VM, Johnston PG, Kerr EM, Longley DB, McDade SS. The pseudo-caspase FLIP(L) regulates cell fate following p53 activation. Proc Natl Acad Sci U S A 2020; 117:17808-17819. [PMID: 32661168 PMCID: PMC7395556 DOI: 10.1073/pnas.2001520117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
p53 is the most frequently mutated, well-studied tumor-suppressor gene, yet the molecular basis of the switch from p53-induced cell-cycle arrest to apoptosis remains poorly understood. Using a combination of transcriptomics and functional genomics, we unexpectedly identified a nodal role for the caspase-8 paralog and only human pseudo-caspase, FLIP(L), in regulating this switch. Moreover, we identify FLIP(L) as a direct p53 transcriptional target gene that is rapidly up-regulated in response to Nutlin-3A, an MDM2 inhibitor that potently activates p53. Genetically or pharmacologically inhibiting expression of FLIP(L) using siRNA or entinostat (a clinically relevant class-I HDAC inhibitor) efficiently promoted apoptosis in colorectal cancer cells in response to Nutlin-3A, which otherwise predominantly induced cell-cycle arrest. Enhanced apoptosis was also observed when entinostat was combined with clinically relevant, p53-activating chemotherapy in vitro, and this translated into enhanced in vivo efficacy. Mechanistically, FLIP(L) inhibited p53-induced apoptosis by blocking activation of caspase-8 by the TRAIL-R2/DR5 death receptor; notably, this activation was not dependent on receptor engagement by its ligand, TRAIL. In the absence of caspase-8, another of its paralogs, caspase-10 (also transcriptionally up-regulated by p53), induced apoptosis in Nutlin-3A-treated, FLIP(L)-depleted cells, albeit to a lesser extent than in caspase-8-proficient cells. FLIP(L) depletion also modulated transcription of canonical p53 target genes, suppressing p53-induced expression of the cell-cycle regulator p21 and enhancing p53-induced up-regulation of proapoptotic PUMA. Thus, even in the absence of caspase-8/10, FLIP(L) silencing promoted p53-induced apoptosis by enhancing PUMA expression. Thus, we report unexpected, therapeutically relevant roles for FLIP(L) in determining cell fate following p53 activation.
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Affiliation(s)
- Andrea Lees
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Alexander J McIntyre
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Nyree T Crawford
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Fiammetta Falcone
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Christopher McCann
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Caitriona Holohan
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Gerard P Quinn
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Jamie Z Roberts
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Tamas Sessler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Peter F Gallagher
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Gemma M A Gregg
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Katherine McAllister
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Kirsty M McLaughlin
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Wendy L Allen
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Laurence J Egan
- Discipline of Pharmacology & Therapeutics, Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland
| | - Aideen E Ryan
- Discipline of Pharmacology & Therapeutics, Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland
- Regenerative Medicine Institute, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland
| | - Melissa J Labonte-Wilson
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Philip D Dunne
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Mark Wappett
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Vicky M Coyle
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Patrick G Johnston
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Emma M Kerr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom;
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom;
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153
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Greenwood EJD, Williamson JC, Sienkiewicz A, Naamati A, Matheson NJ, Lehner PJ. Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection. Cell Rep 2020; 27:1579-1596.e7. [PMID: 31042482 PMCID: PMC6506760 DOI: 10.1016/j.celrep.2019.04.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/19/2019] [Accepted: 04/02/2019] [Indexed: 12/26/2022] Open
Abstract
HIV-1 encodes four “accessory proteins” (Vif, Vpr, Vpu, and Nef), dispensable for viral replication in vitro but essential for viral pathogenesis in vivo. Well characterized cellular targets have been associated with Vif, Vpu, and Nef, which counteract host restriction and promote viral replication. Conversely, although several substrates of Vpr have been described, their biological significance remains unclear. Here, we use complementary unbiased mass spectrometry-based approaches to demonstrate that Vpr is both necessary and sufficient for the DCAF1/DDB1/CUL4 E3 ubiquitin ligase-mediated degradation of at least 38 cellular proteins, causing systems-level changes to the cellular proteome. We therefore propose that promiscuous targeting of multiple host factors underpins complex Vpr-dependent cellular phenotypes and validate this in the case of G2/M cell cycle arrest. Our model explains how Vpr modulates so many cell biological processes and why the functional consequences of previously described Vpr targets, identified and studied in isolation, have proved elusive. HIV-1 Vpr is responsible for almost all proteomic changes in HIV-1-infected cells Vpr directly targets multiple nuclear proteins for degradation Vpr cellular phenotypes (e.g., cell cycle arrest) stem from broad substrate targeting Targeting of a few proteins is conserved across diverse primate lentiviral species
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Affiliation(s)
- Edward J D Greenwood
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
| | - James C Williamson
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Agata Sienkiewicz
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Adi Naamati
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Nicholas J Matheson
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
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154
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Exploration of gene expression profiles and immune microenvironment between high and low tumor mutation burden groups in prostate cancer. Int Immunopharmacol 2020; 86:106709. [PMID: 32593155 DOI: 10.1016/j.intimp.2020.106709] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Tumor mutation burden (TMB) has been established as a biomarker for response to immune therapy and prognosis in various cancers. However, the association between TMB and prognosis of prostate cancer (PCa) remains unclear. This study aimed to investigate the impact of TMB in biochemical recurrence (BCR) and the immune microenvironment in high and low TMB groups. METHODS Mutation data, gene expression, clinicopathological information were downloaded from The Cancer Genome Atlas (TCGA). Mutation types and TMB values were identified. All samples were divided into high and low TMB groups with median TMB value as the cutoff point. The BCR-free survival rates, Differentially expressed genes (DEGs) and immune cells infiltrations in different TMB groups were identified. RESULTS The most common variant type and SNV were single nucleotide polymorphism and C > T. respectively. High TMB level was significantly associated with older age, positive lymph node, higher International Society of Urological Pathology (ISUP) grade, advanced stage and poor BCR-free survival. 132 DEGs were identified and involved in receptor ligand activity and hormone activity. High expression of six core genes UBE2C, PLK1, CDC20, BUB1, CDK1 and HJURP were associated with worse BCR-free survival. The analysis of immune cells infiltration revealed that the amount of activated CD4+ memory T cells was significantly different in high and low TMB groups. CONCLUSIONS The current study comprehensively described the summary of mutation and TMB related DEGs in PCa. TMB was associated with BCR-free survival and the infiltration of activated CD4+ memory T cells in the immune microenvironment.
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155
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Choudhary S, Burns SC, Mirsafian H, Li W, Vo DT, Qiao M, Lei X, Smith AD, Penalva LO. Genomic analyses of early responses to radiation inglioblastoma reveal new alterations at transcription,splicing, and translation levels. Sci Rep 2020; 10:8979. [PMID: 32488114 PMCID: PMC7265345 DOI: 10.1038/s41598-020-65638-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022] Open
Abstract
High-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. Changes at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio-resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy. Our integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.
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Affiliation(s)
- Saket Choudhary
- Computational Biology and Bioinformatics, University of Southern California, California, USA
| | - Suzanne C Burns
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Hoda Mirsafian
- Computational Biology and Bioinformatics, University of Southern California, California, USA
| | - Wenzheng Li
- Computational Biology and Bioinformatics, University of Southern California, California, USA
| | - Dat T Vo
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Texas, USA
| | - Mei Qiao
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Xiufen Lei
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Andrew D Smith
- Computational Biology and Bioinformatics, University of Southern California, California, USA
| | - Luiz O Penalva
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, Texas, USA.
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, Texas, USA.
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156
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Wong ZS, Sokol-Borrelli SL, Olias P, Dubey JP, Boyle JP. Head-to-head comparisons of Toxoplasma gondii and its near relative Hammondia hammondi reveal dramatic differences in the host response and effectors with species-specific functions. PLoS Pathog 2020; 16:e1008528. [PMID: 32574210 PMCID: PMC7360062 DOI: 10.1371/journal.ppat.1008528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/14/2020] [Accepted: 04/08/2020] [Indexed: 01/09/2023] Open
Abstract
Toxoplasma gondii and Hammondia hammondi are closely-related coccidian intracellular parasites that differ in their ability to cause disease in animal and (likely) humans. The role of the host response in these phenotypic differences is not known and to address this we performed a transcriptomic analysis of a monocyte cell line (THP-1) infected with these two parasite species. The pathways altered by infection were shared between species ~95% the time, but the magnitude of the host response to H. hammondi was significantly higher compared to T. gondii. Accompanying this divergent host response was an equally divergent impact on the cell cycle of the host cell. In contrast to T. gondii, H. hammondi infection induces cell cycle arrest via pathways linked to DNA-damage responses and cellular senescence and robust secretion of multiple chemokines that are known to be a part of the senescence associated secretory phenotype (SASP). Remarkably, prior T. gondii infection or treatment with T. gondii-conditioned media suppressed responses to H. hammondi infection, and promoted the replication of H. hammondi in recipient cells. Suppression of inflammatory responses to H. hammondi was found to be mediated by the T. gondii effector IST, and this finding was consistent with reduced functionality of the H. hammondi IST ortholog compared to its T. gondii counterpart. Taken together our data suggest that T. gondii manipulation of the host cell is capable of suppressing previously unknown stress and/or DNA-damage induced responses that occur during infection with H. hammondi, and that one important impact of this T. gondii mediated suppression is to promote parasite replication.
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Affiliation(s)
- Zhee Sheen Wong
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sarah L. Sokol-Borrelli
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - J. P. Dubey
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland, United States of America
| | - Jon P. Boyle
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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157
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Schade AE, Fischer M, DeCaprio JA. RB, p130 and p107 differentially repress G1/S and G2/M genes after p53 activation. Nucleic Acids Res 2020; 47:11197-11208. [PMID: 31667499 PMCID: PMC6868438 DOI: 10.1093/nar/gkz961] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/09/2019] [Accepted: 10/26/2019] [Indexed: 12/19/2022] Open
Abstract
Cell cycle gene expression occurs in two waves. The G1/S genes encode factors required for DNA synthesis and the G2/M genes contribute to mitosis. The Retinoblastoma protein (RB) and DREAM complex (DP, RB-like, E2F4 and MuvB) cooperate to repress all cell cycle genes during G1 and inhibit entry into the cell cycle. DNA damage activates p53 leading to increased levels of p21 and inhibition of cell cycle progression. Whether the G1/S and G2/M genes are differentially repressed by RB and the RB-like proteins p130 and p107 in response to DNA damage is not known. We performed gene expression profiling of primary human fibroblasts upon DNA damage and assessed the effects on G1/S and G2/M genes. Upon p53 activation, p130 and RB cooperated to repress the G1/S genes. In addition, in the absence of RB and p130, p107 contributed to repression of G1/S genes. In contrast, G2/M genes were repressed by p130 and p107 after p53 activation. Furthermore, repression of G2/M genes by p107 and p130 led to reduced entry into mitosis. Our data demonstrates specific roles for RB, p130-DREAM, and p107-DREAM in p53 and p21 mediated repression of cell cycle genes.
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Affiliation(s)
- Amy E Schade
- Program in Virology, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Boston, MA 02115, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Martin Fischer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany
| | - James A DeCaprio
- Program in Virology, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Boston, MA 02115, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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158
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Storey AJ, Naceanceno KS, Lan RS, Washam CL, Orr LM, Mackintosh SG, Tackett AJ, Edmondson RD, Wang Z, Li HY, Frett B, Kendrick S, Byrum SD. ProteoViz: a tool for the analysis and interactive visualization of phosphoproteomics data. Mol Omics 2020; 16:316-326. [PMID: 32347222 DOI: 10.1039/c9mo00149b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantitative proteomics generates large datasets with increasing depth and quantitative information. With the advance of mass spectrometry and increasingly larger data sets, streamlined methodologies and tools for analysis and visualization of phosphoproteomics are needed both at the protein and modified peptide levels. To assist in addressing this need, we developed ProteoViz, which includes a set of R scripts that perform normalization and differential expression analysis of both the proteins and enriched phosphorylated peptides, and identify sequence motifs, kinases, and gene set enrichment pathways. The tool generates interactive visualization plots that allow users to interact with the phosphoproteomics results and quickly identify proteins and phosphorylated peptides of interest for their biological study. The tool also links significant phosphosites with sequence motifs and pathways that will help explain the experimental conditions and guide future experiments. Here, we present the workflow and demonstrate its functionality by analyzing a phosphoproteomic data set from two lymphoma cell lines treated with kinase inhibitors. The scripts and data are freely available at and via the ProteomeXchange with identifier PXD015606.
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Affiliation(s)
- Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
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FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer. Cell Rep 2020; 26:3076-3086.e6. [PMID: 30865895 PMCID: PMC6425951 DOI: 10.1016/j.celrep.2019.02.054] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 12/23/2022] Open
Abstract
The transcription factor FOXM1 contributes to cell cycle progression and is significantly upregulated in basal-like breast cancer (BLBC). Despite its importance in normal and cancer cell cycles, we lack a complete understanding of mechanisms that regulate FOXM1. We identified USP21 in an RNAi-based screen for deubiquitinases that control FOXM1 abundance. USP21 increases the stability of FOXM1, and USP21 binds and deubiquitinates FOXM1 in vivo and in vitro, indicating a direct enzyme-substrate relationship. Depleting USP21 downregulates the FOXM1 transcriptional network and causes a signifi-cant delay in cell cycle progression. Significantly, USP21 depletion sensitized BLBC cell lines and mouse xenograft tumors to paclitaxel, an anti-mitotic, frontline therapy in BLBC treatment. USP21 is the most frequently amplified deubiquitinase in BLBC patient tumors, and its amplification co-occurs with the upregulation of FOXM1 protein. Altogether, these data suggest a role for USP21 in the proliferation and potentially treatment of FOXM1-high, USP21-high BLBC. The cell cycle transcription factor FOXM1 is activated in basal-like breast cancer (BLBC) and associated with therapeutic resistance and poor patient outcomes. Arceci et al. show USP21 antagonizes FOXM1 degradation, thereby promoting proliferation and paclitaxel resistance. USP21 is catalytically active and recurrently overexpressed in BLBC, representing a potential therapeutic target.
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160
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The circRNA circSEPT9 mediated by E2F1 and EIF4A3 facilitates the carcinogenesis and development of triple-negative breast cancer. Mol Cancer 2020; 19:73. [PMID: 32264877 PMCID: PMC7137343 DOI: 10.1186/s12943-020-01183-9] [Citation(s) in RCA: 248] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/12/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Increasing studies have shown that circRNA is closely related to the carcinogenesis and development of many cancers. However, biological functions and the underlying molecular mechanism of circRNAs in triple-negative breast cancer (TNBC) remain largely unclear so far. METHODS Here, we investigated the expression pattern of circRNAs in four pairs of TNBC tissues and paracancerous normal tissues using RNA-sequencing. The expression and prognostic significance of circSEPT9 were evaluated with qRT-PCR and in situ hybridization in two TNBC cohorts. The survival curves were drawn by the Kaplan-Meier method, and statistical significance was estimated with the log-rank test. A series of in vitro and in vivo functional experiments were executed to investigate the role of circSEPT9 in the carcinogenesis and development of TNBC. Mechanistically, we explored the potential regulatory effects of E2F1 and EIF4A3 on biogenesis of circSEPT9 with chromatin immunoprecipitation (ChIP), luciferase reporter and RNA immunoprecipitation (RIP) assays. Furthermore, fluorescent in situ hybridization (FISH), luciferase reporter and biotin-coupled RNA pull-down assays were implemented to verify the relationship between the circSEPT9 and miR-637 in TNBC. RESULTS Increased expression of circSEPT9 was found in TNBC tissues, which was positively correlated with advanced clinical stage and poor prognosis. Knockdown of circSEPT9 significantly suppressed the proliferation, migration and invasion of TNBC cells, induced apoptosis and autophagy in TNBC cells as well as inhibited tumor growth and metastasis in vivo. Whereas up-regulation of circSEPT9 exerted opposite effects. Further mechanism research demonstrated that circSEPT9 could regulate the expression of Leukemia Inhibitory Factor (LIF) via sponging miR-637 and activate LIF/Stat3 signaling pathway involved in progression of TNBC. More importantly, we discovered that E2F1 and EIF4A3 might promote the biogenesis of circSEPT9. CONCLUSIONS Our data reveal that the circSEPT9 mediated by E2F1 and EIF4A3 facilitates the carcinogenesis and development of triple-negative breast cancer through circSEPT9/miR-637/LIF axis. Therefore, circSEPT9 could be used as a potential prognostic marker and therapeutical target for TNBC.
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161
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Knudsen ES, Nambiar R, Rosario SR, Smiraglia DJ, Goodrich DW, Witkiewicz AK. Pan-cancer molecular analysis of the RB tumor suppressor pathway. Commun Biol 2020; 3:158. [PMID: 32242058 PMCID: PMC7118159 DOI: 10.1038/s42003-020-0873-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/26/2020] [Indexed: 12/21/2022] Open
Abstract
The retinoblastoma tumor suppressor gene (RB1) plays a critical role in coordinating multiple pathways that impact cancer initiation, disease progression, and therapeutic responses. Here we probed molecular features associated with the RB-pathway across 31 tumor-types. While the RB-pathway has been purported to exhibit multiple mutually exclusive genetic events, only RB1 alteration is mutually exclusive with deregulation of CDK4/6 activity. An ER+ breast cancer model with targeted RB1 deletion was used to identify signatures of CDK4/6 activity and RB-dependency (CDK4/6-RB integrated signature). This signature was prognostic in tumor-types with gene expression features indicative of slower growth. Single copy loss on chromosome 13q encompassing the RB1 locus is prevalent in many cancers, yielding reduced expression of multiple genes in cis, and is inversely related to the CDK4/6-RB integrated signature supporting a cause-effect relationship. Genes that are positively and inversely correlated with the CDK4/6-RB integrated signature define new tumor-specific pathways associated with RB-pathway activity.
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Affiliation(s)
- Erik S Knudsen
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA. .,Department of Molecular and Cellular Biology, Buffalo, USA. .,Center for Personalized Medicine, Buffalo, USA.
| | - Ram Nambiar
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Molecular and Cellular Biology, Buffalo, USA
| | - Spencer R Rosario
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Genetics and Genomics, Buffalo, USA
| | - Dominic J Smiraglia
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Genetics and Genomics, Buffalo, USA
| | - David W Goodrich
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Pharmacology and Therapeutics, Buffalo, USA
| | - Agnieszka K Witkiewicz
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA. .,Center for Personalized Medicine, Buffalo, USA. .,Department of Pathology, Buffalo, USA.
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162
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Erdős E, Bálint BL. NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells. Int J Mol Sci 2020; 21:E1910. [PMID: 32168782 PMCID: PMC7139668 DOI: 10.3390/ijms21061910] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 12/23/2022] Open
Abstract
Nuclear Receptor Subfamily 2 Group F Member 2 (NR2F2) is a member of the steroid/thyroid hormone receptor superfamily with a crucial role in organogenesis, angiogenesis, cardiovascular development and tumorigenesis. However, there is limited knowledge about the cistrome and transcriptome of NR2F2 in breast cancer. In this study, we mapped the regulatory mechanism by NR2F2 using functional genomic methods. To investigate the clinical significance of NR2F2 in breast cancer, The Cancer Genome Atlas (TCGA) data were used. These results show that a high NR2F2 is associated with better survival of a specific subset of patients, namely those with luminal A breast cancer. Therefore, genome-wide NR2F2 and estrogen receptor alpha (ERα) binding sites were mapped in luminal A breast cancer cells using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), revealing that most NR2F2 overlap with ERα that are co-occupied by forkhead box A1 (FOXA1) and GATA binding protein 3 (GATA3) in active enhancer regions. NR2F2 overlaps with highly frequent ERα chromatin interactions, which are essential for the formation of ERα-bound super-enhancers. In the process of the transcriptome profiling of NR2F2-depleted breast cancer cells such differentially expressed genes have been identified that are involved in endocrine therapy resistance and are also ERα target genes. Overall, these findings demonstrate that the NR2F2 nuclear receptor has a key role in ERα-mediated transcription and it can offer a potential therapeutic target in patients with luminal A breast cancer.
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Affiliation(s)
- Edina Erdős
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary;
- Doctoral School of Molecular Cell and Immune Biology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary
| | - Bálint László Bálint
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary;
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163
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Synergistic activation of p53 by actinomycin D and nutlin-3a is associated with the upregulation of crucial regulators and effectors of innate immunity. Cell Signal 2020; 69:109552. [PMID: 32032660 PMCID: PMC7126238 DOI: 10.1016/j.cellsig.2020.109552] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/31/2020] [Accepted: 01/31/2020] [Indexed: 02/02/2023]
Abstract
Actinomycin D and nutlin-3a (A + N) activate p53, partly through induction of phosphorylation on Ser392. The death of A549 cells induced by A + N morphologically resembles inflammation-inducing pyroptosis - cell destruction triggered by activated caspase-1. The treatment with A + N (or camptothecin) strongly upregulated caspase-1 and its two activators: IFI16 and NLRP1, however, caspase-1 activation was not detected. A549 cells may have been primed for pyroptosis, with the absence of a crucial trigger. The investigation of additional innate immunity elements revealed that A + N (or camptothecin) stimulated the expression of NLRX1, STING (stimulator of interferon genes) and two antiviral proteins, IFIT1 and IFIT3. IFI16 and caspase-1 are coded by p53-regulated genes which led us to investigate regulation of NLRP1, NLRX1, STING, IFIT1 and IFIT3 in p53-dependent mode. The upregulation of NLRP1, NLRX1 and STING was attenuated in p53 knockdown cells. The upsurge of the examined genes, and activation of p53, was inhibited by C16, an inhibitor of PKR kinase. PKR was tested due to its ability to phosphorylate p53 on Ser392. Surprisingly, C16 was active even in PKR knockdown cells. The ability of C16 to prevent activation of p53 and expression of innate immunity genes may be the source of its strong anti-inflammatory action. Moreover, cells exposed to A + N can influence neighboring cells in paracrine fashion, for instance, they shed ectodomain of COL17A1 protein and induce, in p53-dependent mode, the expression of gene for interleukin-7. Further, the activation of p53 also spurred the expression of SOCS1, an inhibitor of interferon triggered STAT1-dependent signaling. We conclude that, stimulation of p53 primes cells for the production of interferons (through upregulation of STING), and may activate negative-feedback within this signaling system by enhancing the production of SOCS1. Actinomycin D and nutlin-3a strongly and synergistically activate p53 protein Strongly activated p53 promotes expression of innate immunity genes Strong activation of innate immunity genes can be prevented by C16 compound By inducing SOCS1 protein p53 can prevent overactivation of interferon signaling Strongly activated p53 can send signal to nearby immune cells through interleukin-7
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164
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Manzione MG, Rombouts J, Steklov M, Pasquali L, Sablina A, Gelens L, Qian J, Bollen M. Co-regulation of the antagonistic RepoMan:Aurora-B pair in proliferating cells. Mol Biol Cell 2020; 31:419-438. [PMID: 31967936 PMCID: PMC7185888 DOI: 10.1091/mbc.e19-12-0698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromosome segregation during mitosis is antagonistically regulated by the Aurora-B kinase and RepoMan (recruits PP1 onto mitotic chromatin at anaphase)-associated phosphatases PP1/PP2A. Aurora B is overexpressed in many cancers but, surprisingly, this only rarely causes lethal aneuploidy. Here we show that RepoMan abundance is regulated by the same mechanisms that control Aurora B, including FOXM1-regulated expression and proteasomal degradation following ubiquitination by APC/C-CDH1 or SCFFBXW7. The deregulation of these mechanisms can account for the balanced co-overexpression of Aurora B and RepoMan in many cancers, which limits chromosome segregation errors. In addition, Aurora B and RepoMan independently promote cancer cell proliferation by reducing checkpoint-induced cell-cycle arrest during interphase. The co–up-regulation of RepoMan and Aurora B in tumors is inversely correlated with patient survival, underscoring its potential importance for tumor progression. Finally, we demonstrate that high RepoMan levels sensitize cancer cells to Aurora-B inhibitors. Hence, the co–up-regulation of RepoMan and Aurora B is associated with tumor aggressiveness but also exposes a vulnerable target for therapeutic intervention.
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Affiliation(s)
| | - Jan Rombouts
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Mikhail Steklov
- VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Lorenzo Pasquali
- Dermatology and Venereology Section, Department of Medicine Solna, Karolinska Institutet, SE-17176 Stockholm, Sweden
| | - Anna Sablina
- Department of Oncology, KU Leuven, B-3000 Leuven, Belgium.,VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Junbin Qian
- Laboratory of Biosignaling & Therapeutics, KU Leuven, B-3000 Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium.,VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, KU Leuven, B-3000 Leuven, Belgium
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165
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Genome-Wide Transcriptome Analysis of Human Papillomavirus 16-Infected Primary Keratinocytes Reveals Subtle Perturbations Mostly due to E7 Protein Expression. J Virol 2020; 94:JVI.01360-19. [PMID: 31748387 DOI: 10.1128/jvi.01360-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/10/2019] [Indexed: 01/03/2023] Open
Abstract
It is established that the host cell transcriptomes of natural lesions, organotypic rafts, and human papillomavirus (HPV)-immortalized keratinocytes are altered in the presence of HPV genomes. However, the establishment of HPV-harboring cell lines requires selection and immortalization, which makes it impossible to distinguish between alterations directly induced by HPV or indirectly by the need for immortalization or selection. To address direct effects of HPV infection on the host cell transcriptome, we have used our recently established infection model that allows efficient infection of primary keratinocytes with HPV16 virions. We observed only a small set of genes to be deregulated at the transcriptional level at 7 days postinfection (dpi), most of which fall into the category regulated by pocket proteins pRb, p107, and p130. Furthermore, cell cycle genes were not deregulated in cells infected with a virus lacking E7 despite the presence of episomal genome and viral transcripts. These findings imply that the majority of transcriptional changes are due to the E7 protein impairing pocket protein function. Additional pathways, such as the Fanconi anemia-BRCA pathway, became perturbed only after long-term culturing of infected cells. When grown as organotypic raft cultures, keratinocytes infected with wild-type but not E7 mutant virus had perturbed transcriptional regulation of pathways previously identified in natural lesions and in rafts derived from immortalized keratinocytes. We conclude that the HPV infection model provides a valuable tool to distinguish immediate transcriptional alterations from those induced by persistent infection and the need for selection and immortalization.IMPORTANCE To establish infection and complete the viral life cycle, human papillomavirus (HPV) needs to alter the transcriptional program of host cells. Until recently, studies were restricted to keratinocyte-derived cell lines immortalized by HPV due to the lack of experimental systems to efficiently infect primary keratinocytes. Need for selection and immortalization made it impossible to distinguish between alterations induced by HPV and secondary adaptation due to selection and immortalization. With our recent establishment of an extracellular matrix (ECM)-to-cell transfer system allowing efficient infection of primary keratinocytes, we were able to identify transcriptional changes attributable to HPV16 infection. Most perturbed genes fall into the class of S-phase genes, which are regulated by pocket proteins. Indeed, infection with viruses lacking E7 abrogated most transcriptional changes. It is important to note that many transcriptional alterations thought to be important for the HPV life cycle are actually late events that may reflect immortalization and, possibly, disease progression.
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166
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Uxa S, Bernhart SH, Mages CFS, Fischer M, Kohler R, Hoffmann S, Stadler PF, Engeland K, Müller GA. DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation. Nucleic Acids Res 2019; 47:9087-9103. [PMID: 31400114 PMCID: PMC6753476 DOI: 10.1093/nar/gkz635] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/07/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
Most human cancers acquire mutations causing defects in the p53 signaling pathway. The tumor suppressor p53 becomes activated in response to genotoxic stress and is essential for arresting the cell cycle to facilitate DNA repair or to initiate apoptosis. p53-induced cell cycle-arrest is mediated by expression of the CDK inhibitor p21WAF1/Cip1, which prevents phosphorylation and inactivation of the pocket proteins RB, p130, and p107. In a hypophosphorylated state, pocket proteins bind to E2F factors forming RB-E2F and DREAM transcriptional repressor complexes. Here, we analyze the influence of RB and DREAM on p53-induced gene repression and cell-cycle arrest. We show that abrogation of DREAM function by knockout of the DREAM component LIN37 results in a reduced repression of cell-cycle genes. We identify the genes repressed by the p53-DREAM pathway and describe a set of genes that is downregulated by p53 independent of LIN37/DREAM. Most strikingly, p53-dependent repression of cell-cycle genes is completely abrogated in LIN37-/-;RB-/- cells leading to a loss of the G1/S checkpoint. Taken together, we show that DREAM and RB are key factors in the p53 signaling pathway to downregulate a large number of cell-cycle genes and to arrest the cell cycle at the G1/S transition.
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Affiliation(s)
- Sigrid Uxa
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany
| | - Christina F S Mages
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Robin Kohler
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Peter F Stadler
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Research Center for Civilization Diseases; and Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Leipzig University, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, A-1090 Wien, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogota, Colombia.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Kurt Engeland
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Gerd A Müller
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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167
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Ahmed F. Integrated Network Analysis Reveals FOXM1 and MYBL2 as Key Regulators of Cell Proliferation in Non-small Cell Lung Cancer. Front Oncol 2019; 9:1011. [PMID: 31681566 PMCID: PMC6804573 DOI: 10.3389/fonc.2019.01011] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Loss of control on cell division is an important factor for the development of non-small cell lung cancer (NSCLC), however, its molecular mechanism and gene regulatory network are not clearly understood. This study utilized the systems bioinformatics approach to reveal the “driver-network” involve in tumorigenic processes in NSCLC. Methods: A meta-analysis of gene expression data of NSCLC was integrated with protein-protein interaction (PPI) data to construct an NSCLC network. MCODE and iRegulone were used to identify the local clusters and its upstream transcription regulators involve in NSCLC. Pair-wise gene expression correlation was performed using GEPIA. The survival analysis was performed by the Kaplan-Meier plot. Results: This study identified a local “driver-network” with highest MCODE score having 26 up-regulated genes involved in the process of cell proliferation in NSCLC. Interestingly, the “driver-network” is under the regulation of TFs FOXM1 and MYBL2 as well as miRNAs. Furthermore, the overexpression of member genes in “driver-network” and the TFs are associated with poor overall survival (OS) in NSCLC patients. Conclusion: This study identified a local “driver-network” and its upstream regulators responsible for the cell proliferation in NSCLC, which could be promising biomarkers and therapeutic targets for NSCLC treatment.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, University of Jeddah, Jeddah, Saudi Arabia.,University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
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168
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Rotelli MD, Bolling AM, Killion AW, Weinberg AJ, Dixon MJ, Calvi BR. An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue. G3 (BETHESDA, MD.) 2019; 9:3087-3100. [PMID: 31387856 PMCID: PMC6778782 DOI: 10.1534/g3.119.400581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/31/2019] [Indexed: 12/23/2022]
Abstract
Cell division and tissue growth must be coordinated with development. Defects in these processes are the basis for a number of diseases, including developmental malformations and cancer. We have conducted an unbiased RNAi screen for genes that are required for growth in the Drosophila wing, using GAL4-inducible short hairpin RNA (shRNA) fly strains made by the Drosophila RNAi Screening Center. shRNA expression down the center of the larval wing disc using dpp-GAL4, and the central region of the adult wing was then scored for tissue growth and wing hair morphology. Out of 4,753 shRNA crosses that survived to adulthood, 18 had impaired wing growth. FlyBase and the new Alliance of Genome Resources knowledgebases were used to determine the known or predicted functions of these genes and the association of their human orthologs with disease. The function of eight of the genes identified has not been previously defined in Drosophila The genes identified included those with known or predicted functions in cell cycle, chromosome segregation, morphogenesis, metabolism, steroid processing, transcription, and translation. All but one of the genes are similar to those in humans, and many are associated with disease. Knockdown of lin-52, a subunit of the Myb-MuvB transcription factor, or βNACtes6, a gene involved in protein folding and trafficking, resulted in a switch from cell proliferation to an endoreplication growth program through which wing tissue grew by an increase in cell size (hypertrophy). It is anticipated that further analysis of the genes that we have identified will reveal new mechanisms that regulate tissue growth during development.
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Affiliation(s)
- Michael D Rotelli
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Anna M Bolling
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Andrew W Killion
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | | | - Michael J Dixon
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405 and
- Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202
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169
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Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors. Proc Natl Acad Sci U S A 2019; 116:21715-21726. [PMID: 31591222 DOI: 10.1073/pnas.1912858116] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Meningiomas account for one-third of all primary brain tumors. Although typically benign, about 20% of meningiomas are aggressive, and despite the rigor of the current histopathological classification system there remains considerable uncertainty in predicting tumor behavior. Here, we analyzed 160 tumors from all 3 World Health Organization (WHO) grades (I through III) using clinical, gene expression, and sequencing data. Unsupervised clustering analysis identified 3 molecular types (A, B, and C) that reliably predicted recurrence. These groups did not directly correlate with the WHO grading system, which classifies more than half of the tumors in the most aggressive molecular type as benign. Transcriptional and biochemical analyses revealed that aggressive meningiomas involve loss of the repressor function of the DREAM complex, which results in cell-cycle activation; only tumors in this category tend to recur after full resection. These findings should improve our ability to predict recurrence and develop targeted treatments for these clinically challenging tumors.
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170
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Nudelman KNH, McDonald BC, Lahiri DK, Saykin AJ. Biological Hallmarks of Cancer in Alzheimer's Disease. Mol Neurobiol 2019; 56:7173-7187. [PMID: 30993533 PMCID: PMC6728183 DOI: 10.1007/s12035-019-1591-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/01/2019] [Indexed: 11/26/2022]
Abstract
Although Alzheimer's disease (AD) is an international health research priority for our aging population, little therapeutic progress has been made. This lack of progress may be partially attributable to disease heterogeneity. Previous studies have identified an inverse association of cancer and AD, suggesting that cancer history may be one source of AD heterogeneity. These findings are particularly interesting in light of the number of common risk factors and two-hit models hypothesized to commonly drive both diseases. We reviewed the ten hallmark biological alterations of cancer cells to investigate overlap with the AD literature and identified overlap of all ten hallmarks in AD, including (1) potentially common underlying risk factors, such as increased inflammation, deregulated cellular energetics, and genome instability; (2) inversely regulated mechanisms, including cell death and evading growth suppressors; and (3) functions with more complex, pleiotropic mechanisms, some of which may be stage-dependent in AD, such as cell adhesion/contact inhibition and angiogenesis. Additionally, we discuss the recent observation of a biological link between cancer and AD neuropathology. Finally, we address the therapeutic implications of this topic. The significant overlap of functional pathways and molecules between these diseases, some similarly and some oppositely regulated or functioning in each disease, supports the need for more research to elucidate cancer-related AD genetic and functional heterogeneity, with the aims of better understanding AD risk mediators, as well as further exploring the potential for some types of drug repurposing towards AD therapeutic development.
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Affiliation(s)
- Kelly N. H. Nudelman
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, IN, USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, IN, USA
| | - Brenna C. McDonald
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, IN, USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, IN, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, IN, USA
- Department of Psychiatry, Indiana University School of Medicine, IN, USA
| | - Debomoy K. Lahiri
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, IN, USA
- Department of Psychiatry, Indiana University School of Medicine, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, IN, USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, IN, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
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171
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Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hartmann W, Dirksen U, Gymrek M, Anderson ND, Shlien A, Rotblat B, Kirchner T, Delattre O, Grünewald TGP. Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes. Nat Commun 2019; 10:4128. [PMID: 31511524 PMCID: PMC6739408 DOI: 10.1038/s41467-019-12071-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/16/2019] [Indexed: 12/02/2022] Open
Abstract
Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.
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Affiliation(s)
- Julian Musa
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Florencia Cidre-Aranaz
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marie-Ming Aynaud
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Maximilian M L Knott
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Olivier Mirabeau
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Gal Mazor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mor Varon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tilman L B Hölting
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Moritz Gartlgruber
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Shunya Ohmura
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marlene Dallmayer
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Michaela C Baldauf
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Stefanie Stein
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Giuseppina Sannino
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jing Li
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Frank Westermann
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk Institute of Pathology, University Hospital of Münster, Münster, Germany
| | - Uta Dirksen
- Department of Pediatric Hematology and Oncology, University Hospital of Essen, Essen, Germany
| | - Melissa Gymrek
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathaniel D Anderson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Barak Rotblat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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172
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Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment. Neurobiol Dis 2019; 132:104583. [PMID: 31445158 DOI: 10.1016/j.nbd.2019.104583] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023] Open
Abstract
Dravet syndrome (DS) is an early onset refractory epilepsy typically caused by de novo heterozygous variants in SCN1A encoding the α-subunit of the neuronal sodium channel Nav1.1. The syndrome is characterized by age-related progression of seizures, cognitive decline and movement disorders. We hypothesized that the distinct neurodevelopmental features in DS are caused by the disruption of molecular pathways in Nav1.1 haploinsufficient cells resulting in perturbed neural differentiation and maturation. Here, we established DS-patient and control induced pluripotent stem cell derived neural progenitor cells (iPSC NPC) and GABAergic inter-neuronal (iPSC GABA) cells. The DS-patient iPSC GABA cells showed a shift in sodium current activation and a perturbed response to induced oxidative stress. Transcriptome analysis revealed specific dysregulations of genes for chromatin structure, mitotic progression, neural plasticity and excitability in DS-patient iPSC NPCs and DS-patient iPSC GABA cells versus controls. The transcription factors FOXM1 and E2F1, positive regulators of the disrupted pathways for histone modification and cell cycle regulation, were markedly up-regulated in DS-iPSC GABA lines. Our study highlights transcriptional changes and disrupted pathways of chromatin remodeling in Nav1.1 haploinsufficient GABAergic cells, providing a molecular framework that overlaps with that of neurodevelopmental disorders and other epilepsies.
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173
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Laaniste L, Srivastava PK, Stylianou J, Syed N, Cases-Cunillera S, Shkura K, Zeng Q, Rackham OJL, Langley SR, Delahaye-Duriez A, O'Neill K, Williams M, Becker A, Roncaroli F, Petretto E, Johnson MR. Integrated systems-genetic analyses reveal a network target for delaying glioma progression. Ann Clin Transl Neurol 2019; 6:1616-1638. [PMID: 31420939 PMCID: PMC6764637 DOI: 10.1002/acn3.50850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022] Open
Abstract
Objective To identify a convergent, multitarget proliferation characteristic for astrocytoma transformation that could be targeted for therapy discovery. Methods Using an integrated functional genomics approach, we prioritized networks associated with astrocytoma progression using the following criteria: differential co‐expression between grade II and grade III IDH1‐mutated and 1p/19q euploid astrocytomas, preferential enrichment for genetic risk to cancer, association with patient survival and sample‐level genomic features. Drugs targeting the identified multitarget network characteristic for astrocytoma transformation were computationally predicted using drug transcriptional perturbation data and validated using primary human astrocytoma cells. Results A single network, M2, consisting of 177 genes, was associated with glioma progression on the basis of the above criteria. Functionally, M2 encoded physically interacting proteins regulating cell cycle processes and analysis of genome‐wide gene‐regulatory interactions using mutual information and DNA–protein interactions revealed the known regulators of cell cycle processes FoxM1, B‐Myb, and E2F2 as key regulators of M2. These results suggest functional disruption of M2 via gene mutation or altered expression as a convergent pathway regulating astrocytoma transformation. By considering M2 as a multitarget drug target regulating astrocytoma transformation, we identified several drugs that are predicted to restore M2 expression in anaplastic astrocytoma toward its low‐grade profile and of these, we validated the known antiproliferative drug resveratrol as down‐regulating multiple nodes of M2 including at nanomolar concentrations achievable in human cerebrospinal fluid by oral dosing. Interpretation Our results identify M2 as a multitarget network characteristic for astrocytoma progression and encourage M2‐based drug screening to identify new compounds for preventing glioma transformation.
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Affiliation(s)
- Liisi Laaniste
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Julianna Stylianou
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Nelofer Syed
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Qingyu Zeng
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Sarah R Langley
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.,Duke-NUS Medical School, Singapore
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.,PROTECT, INSERM, Université Paris Diderot, Sorbonne Paris Cité, France
| | - Kevin O'Neill
- Department of Neurosurgery, Imperial College Healthcare NHS Trust, London, UK
| | - Matthew Williams
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Albert Becker
- Department of Neuropathology, University of Bonn Medical Centre, Bonn, Germany
| | - Federico Roncaroli
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Enrico Petretto
- Duke-NUS Medical School, Singapore.,MRC London Institute of Medical Sciences (LMS), Imperial College London, London, UK
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
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174
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Dabydeen SA, Desai A, Sahoo D. Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. Mol Biol Cell 2019; 30:1770-1779. [PMID: 31091168 PMCID: PMC6727750 DOI: 10.1091/mbc.e19-01-0013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/04/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022] Open
Abstract
Cell proliferation is essential for the development and maintenance of all organisms and is dysregulated in cancer. Using synchronized cells progressing through the cell cycle, pioneering microarray studies defined cell cycle genes based on cyclic variation in their expression. However, the concordance of the small number of synchronized cell studies has been limited, leading to discrepancies in definition of the transcriptionally regulated set of cell cycle genes within and between species. Here we present an informatics approach based on Boolean logic to identify cell cycle genes. This approach used the vast array of publicly available gene expression data sets to query similarity to CCNB1, which encodes the cyclin subunit of the Cdk1-cyclin B complex that triggers the G2-to-M transition. In addition to highlighting conservation of cell cycle genes across large evolutionary distances, this approach identified contexts where well-studied genes known to act during the cell cycle are expressed and potentially acting in nondivision contexts. An accessible web platform enables a detailed exploration of the cell cycle gene lists generated using the Boolean logic approach. The methods employed are straightforward to extend to processes other than the cell cycle.
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Affiliation(s)
- Sarah A. Dabydeen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
| | - Arshad Desai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093
| | - Debashis Sahoo
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
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175
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Rotelli MD, Policastro RA, Bolling AM, Killion AW, Weinberg AJ, Dixon MJ, Zentner GE, Walczak CE, Lilly MA, Calvi BR. A Cyclin A-Myb-MuvB-Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles. PLoS Genet 2019; 15:e1008253. [PMID: 31291240 PMCID: PMC6645565 DOI: 10.1371/journal.pgen.1008253] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/22/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022] Open
Abstract
Endoreplication is a cell cycle variant that entails cell growth and periodic genome duplication without cell division, and results in large, polyploid cells. Cells switch from mitotic cycles to endoreplication cycles during development, and also in response to conditional stimuli during wound healing, regeneration, aging, and cancer. In this study, we use integrated approaches in Drosophila to determine how mitotic cycles are remodeled into endoreplication cycles, and how similar this remodeling is between induced and developmental endoreplicating cells (iECs and devECs). Our evidence suggests that Cyclin A / CDK directly activates the Myb-MuvB (MMB) complex to induce transcription of a battery of genes required for mitosis, and that repression of CDK activity dampens this MMB mitotic transcriptome to promote endoreplication in both iECs and devECs. iECs and devECs differed, however, in that devECs had reduced expression of E2F1-dependent genes that function in S phase, whereas repression of the MMB transcriptome in iECs was sufficient to induce endoreplication without a reduction in S phase gene expression. Among the MMB regulated genes, knockdown of AurB protein and other subunits of the chromosomal passenger complex (CPC) induced endoreplication, as did knockdown of CPC-regulated cytokinetic, but not kinetochore, proteins. Together, our results indicate that the status of a CycA-Myb-MuvB-AurB network determines the decision to commit to mitosis or switch to endoreplication in both iECs and devECs, and suggest that regulation of different steps of this network may explain the known diversity of polyploid cycle types in development and disease.
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Affiliation(s)
- Michael D. Rotelli
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Robert A. Policastro
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Anna M. Bolling
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Andrew W. Killion
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Abraham J. Weinberg
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Michael J. Dixon
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Gabriel E. Zentner
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Claire E. Walczak
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Mary A. Lilly
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian R. Calvi
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- Indiana University School of Medicine, Bloomington, Indiana, United States of America
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176
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NOL12 Repression Induces Nucleolar Stress-Driven Cellular Senescence and Is Associated with Normative Aging. Mol Cell Biol 2019; 39:MCB.00099-19. [PMID: 30988155 DOI: 10.1128/mcb.00099-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/06/2019] [Indexed: 02/07/2023] Open
Abstract
The nucleolus is a subnuclear compartment with key roles in rRNA synthesis and ribosome biogenesis, complex processes that require hundreds of proteins and factors. Alterations in nucleolar morphology and protein content have been linked to the control of cell proliferation and stress responses and, recently, further implicated in cell senescence and ageing. In this study, we report the functional role of NOL12 in the nucleolar homeostasis of human primary fibroblasts. NOL12 repression induces specific changes in nucleolar morphology, with increased nucleolar area but reduced nucleolar number, along with nucleolar accumulation and increased levels of fibrillarin and nucleolin. Moreover, NOL12 repression leads to stabilization and activation of p53 in an RPL11-dependent manner, which arrests cells at G2 phase and ultimately leads to senescence. Importantly, we found NOL12 repression in association with nucleolar stress-like responses in human fibroblasts from elderly donors, disclosing it as a biomarker in human chronological aging.
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177
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Chromosomal instability and pro-inflammatory response in aging. Mech Ageing Dev 2019; 182:111118. [PMID: 31102604 DOI: 10.1016/j.mad.2019.111118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/25/2019] [Accepted: 05/14/2019] [Indexed: 01/10/2023]
Abstract
Aging refers to the progressive deterioration of tissue and organ function over time. Increasing evidence points to the accumulation of highly damaged cell cycle-arrested cells with age (cellular senescence) as major reason for the development of certain aging-associated diseases. Recent studies have independently shown that aneuploidy, an abnormal chromosome set, occurs in senescent cells, and that the accumulation of cytoplasmic DNA driven by faulty chromosome segregation during mitosis aids in the establishment of senescence and its associated secretory phenotype known as SASP. Here we review the emerging link between chromosomal instability (CIN) and senescence in the context of aging, with emphasis on the cGAS-STING pathway activation and its role in the development of the SASP. Based on current evidence, we propose that age-associated CIN in mitotically active cells contributes to aging and its associated diseases, and we discuss the inhibition of CIN as a potential strategy to prevent the generation of aneuploid senescent cells and thereby to delay aging.
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178
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Knudsen ES, Pruitt SC, Hershberger PA, Witkiewicz AK, Goodrich DW. Cell Cycle and Beyond: Exploiting New RB1 Controlled Mechanisms for Cancer Therapy. Trends Cancer 2019; 5:308-324. [PMID: 31174843 DOI: 10.1016/j.trecan.2019.03.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 12/14/2022]
Abstract
Recent studies highlight the importance of the RB1 tumor suppressor as a target for cancer therapy. Canonically, RB1 regulates cell cycle progression and represents the downstream target for cyclin-dependent kinase (CDK) 4/6 inhibitors that are in clinical use. However, newly discovered features of the RB1 pathway suggest new therapeutic strategies to counter resistance and improve precision medicine. These therapeutic strategies include deepening cell cycle exit with CDK4/6 inhibitor combinations, selectively targeting tumors that have lost RB1, and expanding therapeutic index by mitigating therapy-associated adverse effects. In addition, RB1 impacts immunological features of tumors and the microenvironment that can enhance sensitivity to immunotherapy. Lastly, RB1 specifies epigenetically determined cell lineage states that are disrupted during therapy resistance and could be re-installed through the direct use of epigenetic therapies. Thus, new opportunities are emerging to improve cancer therapy by exploiting the RB1 pathway.
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Affiliation(s)
- Erik S Knudsen
- Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA.
| | - Steven C Pruitt
- Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Pamela A Hershberger
- Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA; Department of Oral Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Agnieszka K Witkiewicz
- Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA; Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - David W Goodrich
- Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
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179
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Braun L, Brenier-Pinchart MP, Hammoudi PM, Cannella D, Kieffer-Jaquinod S, Vollaire J, Josserand V, Touquet B, Couté Y, Tardieux I, Bougdour A, Hakimi MA. The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH2. Nat Microbiol 2019; 4:1208-1220. [PMID: 31036909 PMCID: PMC6591128 DOI: 10.1038/s41564-019-0431-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022]
Abstract
The protozoan parasite Toxoplasma gondii has co-evolved with its homeothermic hosts (humans included) strategies that drive its quasi-asymptomatic persistence in hosts, hence optimizing the chance of transmission to new hosts. Persistence, which starts with a small subset of parasites that escape host immune killing and colonize the so-called immune privileged tissues where they differentiate into a low replicating stage, is driven by the interleukin 12 (IL-12)-interferon-γ (IFN-γ) axis. Recent characterization of a family of Toxoplasma effectors that are delivered into the host cell, in which they rewire the host cell gene expression, has allowed the identification of regulators of the IL-12-IFN-γ axis, including repressors. We now report on the dense granule-resident effector, called TEEGR (Toxoplasma E2F4-associated EZH2-inducing gene regulator) that counteracts the nuclear factor-κB (NF-κB) signalling pathway. Once exported into the host cell, TEEGR ends up in the nucleus where it not only complexes with the E2F3 and E2F4 host transcription factors to induce gene expression, but also promotes shaping of a non-permissive chromatin through its capacity to switch on EZH2. Remarkably, EZH2 fosters the epigenetic silencing of a subset of NF-κB-regulated cytokines, thereby strongly contributing to the host immune equilibrium that influences the host immune response and promotes parasite persistence in mice.
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Affiliation(s)
- Laurence Braun
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Marie-Pierre Brenier-Pinchart
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Pierre-Mehdi Hammoudi
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Dominique Cannella
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | | | - Julien Vollaire
- OPTIMAL Small Animal Imaging Facility, Institute for Advanced Biosciences, Grenoble, France
| | - Véronique Josserand
- OPTIMAL Small Animal Imaging Facility, Institute for Advanced Biosciences, Grenoble, France
| | - Bastien Touquet
- Team Membrane and Cell Dynamics of Host Parasite Interactions, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, Grenoble, France
| | - Isabelle Tardieux
- Team Membrane and Cell Dynamics of Host Parasite Interactions, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Alexandre Bougdour
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France.
| | - Mohamed-Ali Hakimi
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France.
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180
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Wu XL, Wang LK, Xue J, Dai YJ, Yang DD, Qu M, Guo F, Han L, Sun GY. A study of the impact of inhibitors of DNA binding-1 on proliferation and migration in human colon carcinoma cells. Kaohsiung J Med Sci 2019; 35:209-213. [PMID: 30887652 DOI: 10.1002/kjm2.12037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/09/2019] [Indexed: 11/09/2022] Open
Abstract
This study aims to explore the effect of an inhibitor of DNA binding-1 (Id-1) on the proliferation and migration of human colon carcinoma cell line SW480 and HT-29. SW480 and HT-29 cells transfected with Id-1-interference sequence were assigned to the experimental groups (inhibition groups 1 and 2), and SW480 and HT-29 cells with blank interference sequence (blank groups) and blank load transfection (blank load groups) were assigned as the control groups. The expression of Id-1 in six groups was detected by reverse transcription-polymerase chain reaction (RT-PCR) and Western blot. Cell proliferation in vitro was assessed by MTT assay. RT-PCR and Western blot results demonstrated that the mRNA and protein expressions of Id-1 in the inhibition group 1 were lower than those in the blank group 1 and blank load group 1. RT-PCR and Western blot results revealed that the mRNA and protein expressions of Id-1 were lower in the inhibition group 2 than in the blank group 2 and blank load group 2. The results of the growth curve revealed that proliferation ability was significantly weaker from the third day in the inhibition groups 1 and 2 than in the blank group and blank load group. Transwell chamber experiment and Matrigel invasion assay revealed that the number of Transwell cells significantly decreased in the inhibition groups 1 and 2 than in the blank groups and blank load groups (P < 0.01). Id-1 significantly promotes the proliferation and migration of human colon carcinoma cell lines SW480 and HT-29.
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Affiliation(s)
- Xue-Liang Wu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Li-Kun Wang
- Department of Ultrasound, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Jun Xue
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Yong-Jun Dai
- Department of Gastrointestinal Surgery, The first Affiliated Hospital of Hebei Medical University, Shijiazhuang City, China
| | - Dong-Dong Yang
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Ming Qu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Fei Guo
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Lei Han
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Guang-Yuan Sun
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
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181
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Min M, Spencer SL. Spontaneously slow-cycling subpopulations of human cells originate from activation of stress-response pathways. PLoS Biol 2019; 17:e3000178. [PMID: 30865623 PMCID: PMC6433297 DOI: 10.1371/journal.pbio.3000178] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 03/25/2019] [Accepted: 02/20/2019] [Indexed: 01/16/2023] Open
Abstract
Slow-cycling subpopulations exist in bacteria, yeast, and mammalian systems. In the case of cancer, slow-cycling subpopulations have been proposed to give rise to drug resistance. However, the origin of slow-cycling human cells is poorly studied, in large part due to lack of markers to identify these rare cells. Slow-cycling cells pass through a noncycling period marked by low CDK2 activity and high p21 levels. Here, we use this knowledge to isolate these naturally slow-cycling cells from a heterogeneous population and perform RNA sequencing to delineate the transcriptome underlying the slow-cycling state. We show that cellular stress responses—the p53 transcriptional response and the integrated stress response (ISR)—are the most salient causes of spontaneous entry into the slow-cycling state. Finally, we show that cells’ ability to enter the slow-cycling state enhances their survival in stressful conditions. Thus, the slow-cycling state is hardwired to stress responses to promote cellular survival in unpredictable environments. Single-cell time-lapse imaging and transcriptomic analysis reveal why some human cells proliferate more slowly than the majority of the population, with cellular stress responses triggering entry into a slow-cycling state to promote cellular survival in unpredictable environments. Even within a genetically identical population, some cells proliferate more slowly than others. Slow-cycling cells have been implicated in resistance to antibiotics, antifungals, and cancer therapies, yet the origin of the slow-cycling state remains poorly understood. Here, we isolate a naturally slow-cycling subpopulation of human cells and find that the slow-cycling state is induced by moderate activation of stress responses. We further show that the ability to enter this slow-cycling state protects cells from further stress, consistent with its association with drug resistance. We propose that the existence of the slow-cycling state thereby promotes long-term survival of populations that occasionally experience mildly stressful environments.
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Affiliation(s)
- Mingwei Min
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, Colorado, United States of America
| | - Sabrina L. Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, Boulder, Colorado, United States of America
- * E-mail:
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182
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Chibon F, Lesluyes T, Valentin T, Le Guellec S. CINSARC signature as a prognostic marker for clinical outcome in sarcomas and beyond. Genes Chromosomes Cancer 2019; 58:124-129. [PMID: 30387235 DOI: 10.1002/gcc.22703] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022] Open
Abstract
Prognostication is a key issue for sarcoma patients' care as it triggers the therapeutic approach including chemotherapy, which is still not standard for localized patients. Current prognostic evaluation, based on the FNCLCC grading system, has recently been improved by the CINSARC signature outperforming histology-based grading system by identifying high-risk patients in every grade, even in those considered as low. CINSARC is an expression-based signature related to mitosis and chromosome integrity with prognostic value in a wide range of cancers additional to sarcoma. First developed with frozen material, CINSARC is now coupled with NanoString technology allowing evaluation from FFPE blocks used in clinical practice. Consequently, CINSARC is currently evaluated in clinical trials with a dual objective of demonstrating the benefit of chemotherapy in sarcoma patients and testing its response prediction. Considering its overarching value in oncology, its development is welcome in any cancers where the prognostication needs to be improved.
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Affiliation(s)
- Frederic Chibon
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,Department of Pathology, Institut Claudius Regaud, Toulouse, France
| | - Tom Lesluyes
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,University of Bordeaux, Bordeaux, France.,Institut Claudius Regaud, Toulouse, France
| | - Thibaud Valentin
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,Department of Medical Oncology, Institut Claudius Regaud, Toulouse, France
| | - Sophie Le Guellec
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,Department of Pathology, Institut Claudius Regaud, Toulouse, France
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183
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Schade AE, Oser MG, Nicholson HE, DeCaprio JA. Cyclin D-CDK4 relieves cooperative repression of proliferation and cell cycle gene expression by DREAM and RB. Oncogene 2019; 38:4962-4976. [PMID: 30833638 PMCID: PMC6586519 DOI: 10.1038/s41388-019-0767-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/24/2019] [Accepted: 02/19/2019] [Indexed: 12/19/2022]
Abstract
The Retinoblastoma protein (RB) restricts cell cycle gene expression and entry into the cell cycle. The RB-related protein p130 forms the DREAM (DP, RB-like, E2F and MuvB) complex and contributes to repression of cell cycle dependent genes during quiescence. Although both RB and DREAM bind and repress an overlapping set of E2F dependent gene promoters, it remains unclear if they cooperate to restrict cell cycle entry. To test the specific contributions of RB and DREAM, we generated RB and p130 knockout cells in primary human fibroblasts. Knockout of both p130 and RB yielded higher levels of cell cycle gene expression in G0 and G1 cells compared to cells with knockout of RB alone, indicating a role for DREAM and RB in repression of cell cycle genes. We observed that RB played a dominant role in E2F dependent gene repression during mid to late G1 while DREAM activity was more prominant during G0 and early G1. Cyclin D - Cyclin Dependent Kinase 4 (CDK4) dependent phosphorylation of p130 occurred during early G1 and led to the release of p130 and MuvB from E2F4 and decreased p130 and MuvB binding to cell cycle promoters. Specific inhibition of CDK4 activity by palbociclib blocked DREAM complex disassembly during cell cycle entry. In addition, sensitivity to CDK4 inhibition was dependent on RB and an intact DREAM complex in both normal cells as well as in palbociclib-sensitive cancer cell lines. Although RB knockout cells were partially resistant to CDK4 inhibition, RB and p130 double knockout cells were significantly more resistant to palbociclib treatment. These results indicate that DREAM cooperates with RB in repressing E2F dependent gene expression and cell cycle entry and supports a role for DREAM as a therapeutic target in cancer.
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Affiliation(s)
- Amy E Schade
- Program in Virology, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Boston, MA, 02115, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Hilary E Nicholson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - James A DeCaprio
- Program in Virology, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Boston, MA, 02115, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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184
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Hafner A, Bulyk ML, Jambhekar A, Lahav G. The multiple mechanisms that regulate p53 activity and cell fate. Nat Rev Mol Cell Biol 2019; 20:199-210. [DOI: 10.1038/s41580-019-0110-x] [Citation(s) in RCA: 452] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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185
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Ng JCF, Quist J, Grigoriadis A, Malim MH, Fraternali F. Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases. Nucleic Acids Res 2019; 47:1178-1194. [PMID: 30624727 PMCID: PMC6379723 DOI: 10.1093/nar/gky1316] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/19/2018] [Accepted: 01/04/2019] [Indexed: 12/25/2022] Open
Abstract
APOBEC3 cytidine deaminases are largely known for their innate immune protection from viral infections. Recently, members of the family have been associated with a distinct mutational activity in some cancer types. We report a pan-tissue, pan-cancer analysis of RNA-seq data specific to the APOBEC3 genes in 8,951 tumours, 786 cancer cell lines and 6,119 normal tissues. By deconvolution of levels of different cell types in tumour admixtures, we demonstrate that APOBEC3B (A3B), the primary candidate as a cancer mutagen, shows little association with immune cell types compared to its paralogues. We present a pipeline called RESPECTEx (REconstituting SPecific Cell-Type Expression) and use it to deconvolute cell-type specific expression levels in a given cohort of tumour samples. We functionally annotate APOBEC3 co-expressing genes, and create an interactive visualization tool which 'barcodes' the functional enrichment (http://fraternalilab.kcl.ac.uk/apobec-barcodes/). These analyses reveal that A3B expression correlates with cell cycle and DNA repair genes, whereas the other APOBEC3 members display specificity for immune processes and immune cell populations. We offer molecular insights into the functions of individual APOBEC3 proteins in antiviral and proliferative contexts, and demonstrate the diversification this family of enzymes displays at the transcriptomic level, despite their high similarity in protein sequences and structures.
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Affiliation(s)
- Joseph C F Ng
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Jelmar Quist
- Cancer Bioinformatics, School of Cancer and Pharmaceutical Sciences, CRUK King's Health Partners Centre, Breast Cancer Now Research Unit, King's College London, London, UK
| | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer and Pharmaceutical Sciences, CRUK King's Health Partners Centre, Breast Cancer Now Research Unit, King's College London, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
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186
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Polyomavirus T Antigen Induces APOBEC3B Expression Using an LXCXE-Dependent and TP53-Independent Mechanism. mBio 2019; 10:mBio.02690-18. [PMID: 30723127 PMCID: PMC6428753 DOI: 10.1128/mbio.02690-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
APOBEC3B is a single-stranded DNA cytosine deaminase with beneficial innate antiviral functions. However, misregulated APOBEC3B can also be detrimental by inflicting APOBEC signature C-to-T and C-to-G mutations in genomic DNA of multiple cancer types. Polyomavirus and papillomavirus oncoproteins induce APOBEC3B overexpression, perhaps to their own benefit, but little is known about the cellular mechanisms hijacked by these viruses to do so. Here we investigate the molecular mechanism of APOBEC3B upregulation by the polyomavirus large T antigen. First, we demonstrate that the upregulated APOBEC3B enzyme is strongly nuclear and partially localized to virus replication centers. Second, truncated T antigen (truncT) is sufficient for APOBEC3B upregulation, and the RB-interacting motif (LXCXE), but not the p53-binding domain, is required. Third, genetic knockdown of RB1 alone or in combination with RBL1 and/or RBL2 is insufficient to suppress truncT-mediated induction of APOBEC3B Fourth, CDK4/6 inhibition by palbociclib is also insufficient to suppress truncT-mediated induction of APOBEC3B Last, global gene expression analyses in a wide range of human cancers show significant associations between expression of APOBEC3B and other genes known to be regulated by the RB/E2F axis. These experiments combine to implicate the RB/E2F axis in promoting APOBEC3B transcription, yet they also suggest that the polyomavirus RB-binding motif has at least one additional function in addition to RB inactivation for triggering APOBEC3B upregulation in virus-infected cells.IMPORTANCE The APOBEC3B DNA cytosine deaminase is overexpressed in many different cancers and correlates with elevated frequencies of C-to-T and C-to-G mutations in 5'-TC motifs, oncogene activation, acquired drug resistance, and poor clinical outcomes. The mechanisms responsible for APOBEC3B overexpression are not fully understood. Here, we show that the polyomavirus truncated T antigen (truncT) triggers APOBEC3B overexpression through its RB-interacting motif, LXCXE, which in turn likely modulates the binding of E2F family transcription factors to promote APOBEC3B expression. This work strengthens the mechanistic linkage between active cell cycling, APOBEC3B overexpression, and cancer mutagenesis. Although this mutational mechanism damages cellular genomes, viruses may leverage it to promote evolution, immune escape, and pathogenesis. The cellular portion of the mechanism may also be relevant to nonviral cancers, where genetic mechanisms often activate the RB/E2F axis and APOBEC3B mutagenesis contributes to tumor evolution.
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187
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Fischer M. Conservation and divergence of the p53 gene regulatory network between mice and humans. Oncogene 2019; 38:4095-4109. [PMID: 30710145 PMCID: PMC6755996 DOI: 10.1038/s41388-019-0706-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 12/29/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022]
Abstract
Understanding the p53 tumor suppressor pathway remains crucial for the design of anticancer strategies. Studies in human tumors and mouse models help to unravel the molecular mechanisms that underlie the p53 signaling pathway. Yet, the p53 gene regulatory network (GRN) is not the same in mice and humans. The comparison of the regulatory networks of p53 in mice and humans reveals that gene up- and down-regulation by p53 are distinctly affected during evolution. Importantly, gene up-regulation by p53 underwent more rapid evolution and gene down-regulation has been evolutionarily constrained. This difference stems from the two major mechanisms employed by p53 to regulate gene expression: up-regulation through direct p53 target gene binding and indirect down-regulation through the p53-p21-DREAM pathway. More than 1000 genes have been identified to differ in their p53-dependent expression between mice and humans. Analysis of p53 gene expression profiles and p53 binding data reveal that turnover of p53 binding sites is the major mechanism underlying extensive variation in p53-dependent gene up-regulation. Only a core set of high-confidence genes appears to be directly regulated by p53 in both species. In contrast to up-regulation, p53-induced down-regulation is well conserved between mice and humans and controls cell cycle genes. Here a curated data set is provided that extends the previously established web-atlas at www.targetgenereg.org to assess the p53 response of any human gene of interest and its mouse ortholog. Taken together, the analysis reveals a limited translation potential from mouse models to humans for the p53 GRN.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany. .,Molecular Oncology Group, Medical School, University of Leipzig, 04103, Leipzig, Germany.
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188
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Werwein E, Cibis H, Hess D, Klempnauer KH. Activation of the oncogenic transcription factor B-Myb via multisite phosphorylation and prolyl cis/trans isomerization. Nucleic Acids Res 2019; 47:103-121. [PMID: 30321399 PMCID: PMC6326806 DOI: 10.1093/nar/gky935] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/01/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022] Open
Abstract
The oncogenic transcription factor B-Myb is an essential regulator of late cell cycle genes whose activation by phosphorylation is still poorly understood. We describe a stepwise phosphorylation mechanism of B-Myb, which involves sequential phosphorylations mediated by cyclin-dependent kinase (Cdk) and Polo-like kinase 1 (Plk1) and Pin1-facilitated peptidyl-prolyl cis/trans isomerization. Our data suggest a model in which initial Cdk-dependent phosphorylation of B-Myb enables subsequent Pin1 binding and Pin1-induced conformational changes of B-Myb. This, in turn, initiates further phosphorylation of Cdk-phosphosites, enabling Plk1 docking and subsequent Plk1-mediated phosphorylation of B-Myb to finally allow B-Myb to stimulate transcription of late cell cycle genes. Our observations reveal novel mechanistic hierarchies of B-Myb phosphorylation and activation and uncover regulatory principles that might also apply to other Myb family members. Strikingly, overexpression of B-Myb and of factors mediating its activation strongly correlates with adverse prognoses for tumor patients, emphasizing B-Myb's role in tumorigenesis.
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Affiliation(s)
- Eugen Werwein
- Institute for Biochemistry Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Hannah Cibis
- Institute for Biochemistry Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstr. 66, CH-4058 Basel, Switzerland
| | - Karl-Heinz Klempnauer
- Institute for Biochemistry Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
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189
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Bainor AJ, Saini S, Calderon A, Casado-Polanco R, Giner-Ramirez B, Moncada C, Cantor DJ, Ernlund A, Litovchick L, David G. The HDAC-Associated Sin3B Protein Represses DREAM Complex Targets and Cooperates with APC/C to Promote Quiescence. Cell Rep 2018; 25:2797-2807.e8. [PMID: 30517867 PMCID: PMC6324198 DOI: 10.1016/j.celrep.2018.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/12/2018] [Accepted: 11/02/2018] [Indexed: 12/17/2022] Open
Abstract
The mammalian DREAM complex is responsible for the transcriptional repression of hundreds of cell-cycle-related genes in quiescence. How the DREAM complex recruits chromatin-modifying entities to aid in its repression remains unknown. Using unbiased proteomics analysis, we have uncovered a robust association between the chromatin-associated Sin3B protein and the DREAM complex. We have determined that genetic inactivation of Sin3B results in the de-repression of DREAM target genes during quiescence but is insufficient to allow quiescent cells to resume proliferation. However, inactivation of APC/CCDH1 was sufficient for Sin3B-/- cells, but not parental cells, to re-enter the cell cycle. These studies identify Sin3B as a transcriptional corepressor associated with the DREAM complex in quiescence and reveals a functional cooperation between E2F target repression and APC/CCDH1 in the negative regulation of cell-cycle progression.
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Affiliation(s)
- Anthony J Bainor
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Siddharth Saini
- Department of Internal Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Alexander Calderon
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Raquel Casado-Polanco
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Belén Giner-Ramirez
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Claudia Moncada
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - David J Cantor
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Amanda Ernlund
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Larisa Litovchick
- Department of Internal Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Gregory David
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA; Department of Urology, NYU Langone Medical Center, New York, NY 10016, USA; NYU Cancer Institute, NYU Langone Medical Center, New York, NY 10016, USA.
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190
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Marzec K, Burgess A. The Oncogenic Functions of MASTL Kinase. Front Cell Dev Biol 2018; 6:162. [PMID: 30555827 PMCID: PMC6282046 DOI: 10.3389/fcell.2018.00162] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/08/2018] [Indexed: 01/14/2023] Open
Abstract
MASTL kinase is a master regulator of mitosis, essential for ensuring that mitotic substrate phosphorylation is correctly maintained. It achieves this through the phosphorylation of alpha-endosulfine and subsequent inhibition of the tumor suppressor PP2A-B55 phosphatase. In recent years MASTL has also emerged as a novel oncogenic kinase that is upregulated in a number of cancer types, correlating with chromosome instability and poor patient survival. While the chromosome instability is likely directly linked to MASTL's control of mitotic phosphorylation, several new studies indicated that MASTL has additional effects outside of mitosis and beyond regulation of PP2A-B55. These include control of normal DNA replication timing, and regulation of AKT/mTOR and Wnt/β-catenin oncogenic kinase signaling. In this review, we will examine the phenotypes and mechanisms for how MASTL, ENSA, and PP2A-B55 deregulation drives tumor progression and metastasis. Finally, we will explore the rationale for the future development of MASTL inhibitors as new cancer therapeutics.
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Affiliation(s)
- Kamila Marzec
- ANZAC Research Institute, University of Sydney, Sydney, NSW, Australia
| | - Andrew Burgess
- ANZAC Research Institute, University of Sydney, Sydney, NSW, Australia.,Faculty of Medicine and Health, Concord Clinical School, University of Sydney, Sydney, NSW, Australia
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191
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TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets. Nat Commun 2018; 9:4866. [PMID: 30451831 PMCID: PMC6242972 DOI: 10.1038/s41467-018-06699-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on 17q marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that TBX2 is a constituent of the recently established core regulatory circuitry in neuroblastoma with features of a cell identity transcription factor, driving proliferation through activation of p21-DREAM repressed FOXM1 target genes. Combined MYCN/TBX2 knockdown enforces cell growth arrest suggesting that TBX2 enhances MYCN sustained activation of FOXM1 targets. Targeting transcriptional addiction by combined CDK7 and BET bromodomain inhibition shows synergistic effects on cell viability with strong repressive effects on CRC gene expression and p53 pathway response as well as several genes implicated in transcriptional regulation. In conclusion, we provide insight into the role of the TBX2 CRC gene in transcriptional dependency of neuroblastoma cells warranting clinical trials using BET and CDK7 inhibitors. In high-risk neuroblastoma cases, gains in chromosome 17q are common. Here, the authors investigate the epigenomics and transcriptomics of neuroblastoma, identifying TBX2 as a core regulatory circuitry component enhancing the reactivation of DREAM targets by MYCN/FOXM1.
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192
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Kernan J, Bonacci T, Emanuele MJ. Who guards the guardian? Mechanisms that restrain APC/C during the cell cycle. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1924-1933. [PMID: 30290241 DOI: 10.1016/j.bbamcr.2018.09.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/04/2018] [Accepted: 09/23/2018] [Indexed: 11/25/2022]
Abstract
The cell cycle is principally controlled by Cyclin Dependent Kinases (CDKs), whose oscillating activities are determined by binding to Cyclin coactivators. Cyclins exhibit dynamic changes in abundance as cells pass through the cell cycle. The sequential, timed accumulation and degradation of Cyclins, as well as many other proteins, imposes order on the cell cycle and contributes to genome maintenance. The destruction of many cell cycle regulated proteins, including Cyclins A and B, is controlled by a large, multi-subunit E3 ubiquitin ligase termed the Anaphase Promoting Complex/Cyclosome (APC/C). APC/C activity is tightly regulated during the cell cycle. Its activation state increases dramatically in mid-mitosis and it remains active until the end of G1 phase. Following its mandatory inactivation at the G1/S boundary, APC/C activity remains low until the subsequent mitosis. Due to its role in guarding against the inappropriate or untimely accumulation of Cyclins, the APC/C is a core component of the cell cycle oscillator. In addition to the regulation of Cyclins, APC/C controls the degradation of many other substrates. Therefore, it is vital that the activity of APC/C itself be tightly guarded. The APC/C is most well studied for its role and regulation during mitosis. However, the APC/C also plays a similarly important and conserved role in the maintenance of G1 phase. Here we review the diverse mechanisms counteracting APC/C activity throughout the cell cycle and the importance of their coordinated actions on cell growth, proliferation, and disease.
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Affiliation(s)
- Jennifer Kernan
- Lineberger Comprehensive Cancer Center, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America
| | - Thomas Bonacci
- Lineberger Comprehensive Cancer Center, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America.
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193
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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194
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Qin S, Huang X, Wang D, Hu X, Yuan Y, Sun X, Tan Z, Gu Y, Cheng X, He C, Su Z. Identification of characteristic genes distinguishing neural stem cells from astrocytes. Gene 2018; 681:26-35. [PMID: 30266499 DOI: 10.1016/j.gene.2018.09.044] [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: 05/03/2018] [Revised: 09/07/2018] [Accepted: 09/24/2018] [Indexed: 01/11/2023]
Abstract
BACKGROUND Neural stem cells (NSCs) have unique biological characteristics such as continuous proliferation and multipotential differentiation, providing a possible method for restoration of central nervous system (CNS) function after injury or disease. NSCs and astrocytes share many similar biological properties including cell morphology and molecular expression and can trans-differentiate into each other under certain conditions. However, characteristic genes specifically expressed by NSCs have not been well described. METHODS To provide insights into the characteristic expression of NSCs, bioinformatics analysis of two microarrays of mouse NSCs and astrocytes was performed. Compared to astrocytes, the differentially expressed genes (DEGs) in NSCs were identified and annotated by GO, KEGG and GSEA analysis, respectively. Then key genes were screened by protein-protein interaction (PPI) network and modules analysis, and were verified using multiple high-throughput sequencing resources. Finally, the expression difference between the two cell types was confirmed by Real-time Quantitative PCR (qPCR), western blotting and immunochemical analysis. RESULTS In the present study, 282 and 250 NSC-enriched genes from two microarrays were identified and annotated respectively, and the 77 overlapping DEGs were then selected. From the PPI network 24 key genes in three modules were screened out. Importantly, sequencing data of tissues showed that these 24 key genes tended to be highly expressed in NSCs compared with astrocytes. Furthermore, qPCR and western blot analysis of cultured NSCs and astrocytes showed two genes (KIF2C and TOP2A) were not only differentially expressed in RNA level but also at the protein level. Importantly, the NSC-specific genes KIF2C and TOP2A were validated by immunohistochemistry in vivo. CONCLUSION In present study, we identified 2 hub genes (KIF2C and TOP2A) that might serve as potential biomarkers for distinguishing NSCs from astrocytes, contributing to our comprehensive understanding of the biological properties and functions of NSCs.
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Affiliation(s)
- Shangyao Qin
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China
| | - Xiao Huang
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China
| | - Dan Wang
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China
| | - Xin Hu
- Department of Neurological Surgery, Xixi Hospital of Hangzhou, Hangzhou, China
| | - Yimin Yuan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China
| | - Xiu Sun
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China
| | - Zijian Tan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China
| | - Yakun Gu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China
| | - Xueyan Cheng
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China
| | - Cheng He
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China.
| | - Zhida Su
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai, China.
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195
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The cell cycle regulatory DREAM complex is disrupted by high expression of oncogenic B-Myb. Oncogene 2018; 38:1080-1092. [PMID: 30206359 PMCID: PMC6377300 DOI: 10.1038/s41388-018-0490-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022]
Abstract
Overexpression of the oncogene MYBL2 (B-Myb) is associated with increased cell proliferation and serves as marker of poor prognosis in cancer. However, the mechanism by which B-Myb alters the cell cycle is not fully understood. In proliferating cells, B-Myb interacts with the MuvB core complex including LIN9, LIN37, LIN52, RBBP4, and LIN54, forming the MMB (Myb-MuvB) complex, and promotes transcription of genes required for mitosis. Alternatively, the MuvB core interacts with Rb-like protein p130 and E2F4-DP1 to form the DREAM complex that mediates global repression of cell cycle genes in G0/G1, including a subset of MMB target genes. Here, we show that overexpression of B-Myb disrupts the DREAM complex in human cells, and this activity depends on the intact MuvB-binding domain in B-Myb. Furthermore, we found that B-Myb regulates the protein expression levels of the MuvB core subunit LIN52, a key adaptor for assembly of both the DREAM and MMB complexes, by a mechanism that requires S28 phosphorylation site in LIN52. Given that high expression of B-Myb correlates with global loss of repression of DREAM target genes in breast and ovarian cancer, our findings offer mechanistic insights for aggressiveness of cancers with MYBL2 amplification, and establish the rationale for targeting B-Myb to restore cell cycle control.
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196
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Kim S, Ma L, Shokhirev MN, Quigley I, Kintner C. Multicilin and activated E2f4 induce multiciliated cell differentiation in primary fibroblasts. Sci Rep 2018; 8:12369. [PMID: 30120325 PMCID: PMC6098136 DOI: 10.1038/s41598-018-30791-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/02/2018] [Indexed: 12/18/2022] Open
Abstract
Multiciliated cells (MCCs) are specialized epithelial cells that project hundreds of motile cilia. To form these cilia, MCCs differentiate by dramatically expanding centriole number, using assembly factors required for centriole duplication during the cell cycle and multiple, novel assembly sites, called the deuterosome. The small coiled-coil protein, Multicilin, acting in a complex with the E2F proteins can initiate multiciliated cell differentiation, but reportedly only in a limited range of epithelial progenitors. To examine the nature of this restricted activity, we analyzed Multicilin activity in primary mouse embryonic fibroblasts (MEFs), a cell type distant from the epithelial lineages where MCCs normally arise. We show that Multicilin transcriptional activity is markedly attenuated in MEFs, where it induces only limited centriole expansion in a small fraction of cells. We further show that this transcriptional block is largely bypassed by expressing Multicilin along with a form of E2f4 where a generic activation domain from HSV1 VP16 (E2f4VP16) is fused to the carboxy terminus. MEFs respond to Multicilin and E2f4VP16 by undergoing massive centriole expansion via the deuterosome pathway, recapitulating a temporal sequence of organelle biogenesis that occurs in epithelial progenitors during MCC differentiation. These results suggest that the pattern of organelle biogenesis occurring in differentiating MCCs is largely determined by the transcriptional changes induced by Multicilin.
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Affiliation(s)
- Seongjae Kim
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Lina Ma
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Ian Quigley
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Chris Kintner
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
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197
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Bonacci T, Suzuki A, Grant GD, Stanley N, Cook JG, Brown NG, Emanuele MJ. Cezanne/OTUD7B is a cell cycle-regulated deubiquitinase that antagonizes the degradation of APC/C substrates. EMBO J 2018; 37:e98701. [PMID: 29973362 PMCID: PMC6092620 DOI: 10.15252/embj.201798701] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 11/09/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase and key regulator of cell cycle progression. Since APC/C promotes the degradation of mitotic cyclins, it controls cell cycle-dependent oscillations in cyclin-dependent kinase (CDK) activity. Both CDKs and APC/C control a large number of substrates and are regulated by analogous mechanisms, including cofactor-dependent activation. However, whereas substrate dephosphorylation is known to counteract CDK, it remains largely unknown whether deubiquitinating enzymes (DUBs) antagonize APC/C substrate ubiquitination during mitosis. Here, we demonstrate that Cezanne/OTUD7B is a cell cycle-regulated DUB that opposes the ubiquitination of APC/C targets. Cezanne is remarkably specific for K11-linked ubiquitin chains, which are formed by APC/C in mitosis. Accordingly, Cezanne binds established APC/C substrates and reverses their APC/C-mediated ubiquitination. Cezanne depletion accelerates APC/C substrate degradation and causes errors in mitotic progression and formation of micronuclei. These data highlight the importance of tempered APC/C substrate destruction in maintaining chromosome stability. Furthermore, Cezanne is recurrently amplified and overexpressed in numerous malignancies, suggesting a potential role in genome maintenance and cancer cell proliferation.
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Affiliation(s)
- Thomas Bonacci
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aussie Suzuki
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gavin D Grant
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Stanley
- Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeanette G Cook
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas G Brown
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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198
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Miller I, Min M, Yang C, Tian C, Gookin S, Carter D, Spencer SL. Ki67 is a Graded Rather than a Binary Marker of Proliferation versus Quiescence. Cell Rep 2018; 24:1105-1112.e5. [PMID: 30067968 PMCID: PMC6108547 DOI: 10.1016/j.celrep.2018.06.110] [Citation(s) in RCA: 355] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 05/11/2018] [Accepted: 06/28/2018] [Indexed: 02/07/2023] Open
Abstract
Ki67 staining is widely used as a proliferation indicator in the clinic, despite poor understanding of this protein's function or dynamics. Here, we track Ki67 levels under endogenous control in single cells over time and find that Ki67 accumulation occurs only during S, G2, and M phases. Ki67 is degraded continuously in G1 and G0 phases, regardless of the cause of entry into G0/quiescence. Consequently, the level of Ki67 during G0 and G1 in individual cells is highly heterogeneous and depends on how long an individual cell has spent in G0. Thus, Ki67 is a graded rather than a binary marker both for cell-cycle progression and time since entry into quiescence.
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Affiliation(s)
- Iain Miller
- Department of Biochemistry, University of Colorado-Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Mingwei Min
- Department of Biochemistry, University of Colorado-Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Chen Yang
- Department of Biochemistry, University of Colorado-Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA; Department of Molecular, Cellular, and Developmental Biology, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Chengzhe Tian
- Department of Biochemistry, University of Colorado-Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Sara Gookin
- Department of Biochemistry, University of Colorado-Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Dylan Carter
- Department of Biochemistry, University of Colorado-Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado-Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado-Boulder, Boulder, CO 80303, USA.
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199
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Macedo JC, Vaz S, Bakker B, Ribeiro R, Bakker PL, Escandell JM, Ferreira MG, Medema R, Foijer F, Logarinho E. FoxM1 repression during human aging leads to mitotic decline and aneuploidy-driven full senescence. Nat Commun 2018; 9:2834. [PMID: 30026603 PMCID: PMC6053425 DOI: 10.1038/s41467-018-05258-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 06/22/2018] [Indexed: 12/20/2022] Open
Abstract
Aneuploidy, an abnormal chromosome number, has been linked to aging and age-associated diseases, but the underlying molecular mechanisms remain unknown. Here we show, through direct live-cell imaging of young, middle-aged, and old-aged primary human dermal fibroblasts, that aneuploidy increases with aging due to general dysfunction of the mitotic machinery. Increased chromosome mis-segregation in elderly mitotic cells correlates with an early senescence-associated secretory phenotype (SASP) and repression of Forkhead box M1 (FoxM1), the transcription factor that drives G2/M gene expression. FoxM1 induction in elderly and Hutchison–Gilford progeria syndrome fibroblasts prevents aneuploidy and, importantly, ameliorates cellular aging phenotypes. Moreover, we show that senescent fibroblasts isolated from elderly donors’ cultures are often aneuploid, and that aneuploidy is a key trigger into full senescence phenotypes. Based on this feedback loop between cellular aging and aneuploidy, we propose modulation of mitotic efficiency through FoxM1 as a potential strategy against aging and progeria syndromes. Evidence for mitotic decline in aged cells and for aneuploidy-driven progression into full senescence is limited. Here, the authors find that in aged cells, mitotic gene repression leads to increased chromosome mis-segregation and aneuploidy that triggers permanent cell cycle arrest and full senescence.
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Affiliation(s)
- Joana Catarina Macedo
- Aging and Aneuploidy Laboratory, IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal.,i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Sara Vaz
- Aging and Aneuploidy Laboratory, IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal.,i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Bjorn Bakker
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen, NL-9713 AV, Groningen, The Netherlands
| | - Rui Ribeiro
- Aging and Aneuploidy Laboratory, IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal.,i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Petra Lammigje Bakker
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen, NL-9713 AV, Groningen, The Netherlands
| | - Jose Miguel Escandell
- Telomere and Genome Stability Laboratory, Instituto Gulbenkian de Ciência, 2781-901, Oeiras, Portugal
| | - Miguel Godinho Ferreira
- Telomere and Genome Stability Laboratory, Instituto Gulbenkian de Ciência, 2781-901, Oeiras, Portugal.,Telomere Shortening and Cancer Laboratory, Institute for Research on Cancer and Aging (IRCAN), UMR7284, U1081, UNS, 06107, Nice, France
| | - René Medema
- Division of Cell Biology and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen, NL-9713 AV, Groningen, The Netherlands
| | - Elsa Logarinho
- Aging and Aneuploidy Laboratory, IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal. .,i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal. .,Cell Division Unit, Faculty of Medicine, Department of Experimental Biology, Universidade do Porto, 4200-319, Porto, Portugal.
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200
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Iness AN, Litovchick L. MuvB: A Key to Cell Cycle Control in Ovarian Cancer. Front Oncol 2018; 8:223. [PMID: 29942794 PMCID: PMC6004728 DOI: 10.3389/fonc.2018.00223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/30/2018] [Indexed: 02/05/2023] Open
Abstract
Cancer cells are characterized by uncontrolled proliferation, whereas the ability to enter quiescence or dormancy is important for cancer cell survival and disease recurrence. Therefore, understanding the mechanisms regulating cell cycle progression and exit is essential for improving patient outcomes. The MuvB complex of five proteins (LIN9, LIN37, LIN52, RBBP4, and LIN54), also known as LINC (LIN complex), is important for coordinated cell cycle gene expression. By participating in the formation of three distinct transcriptional regulatory complexes, including DREAM (DP, RB-like, E2F, and MuvB), MMB (Myb-MuvB), and FoxM1–MuvB, MuvB represents a unique regulator mediating either transcriptional activation (during S–G2 phases) or repression (during quiescence). With no known enzymatic activities in any of the MuvB-associated complexes, studies have focused on the therapeutic potential of protein kinases responsible for initiating DREAM assembly or downstream enzymatic targets of MMB. Furthermore, the mechanisms governing the formation and activity of each complex (DREAM, MMB, or FoxM1–MuvB) may have important consequences for therapeutic response. The MMB complex is associated with prognostic markers of aggressiveness in several cancers, whereas the DREAM complex is tied to disease recurrence through its role in maintaining quiescence. Here, we review recent developments in our understanding of MuvB function in the context of cancer. We specifically highlight the rationale for additional investigation of MuvB in high-grade serous ovarian cancer and the need for further translational research.
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Affiliation(s)
- Audra N Iness
- Division of Hematology, Oncology and Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Larisa Litovchick
- Division of Hematology, Oncology and Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
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