101
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Rizzotto D, Englmaier L, Villunger A. At a Crossroads to Cancer: How p53-Induced Cell Fate Decisions Secure Genome Integrity. Int J Mol Sci 2021; 22:ijms221910883. [PMID: 34639222 PMCID: PMC8509445 DOI: 10.3390/ijms221910883] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022] Open
Abstract
P53 is known as the most critical tumor suppressor and is often referred to as the guardian of our genome. More than 40 years after its discovery, we are still struggling to understand all molecular details on how this transcription factor prevents oncogenesis or how to leverage current knowledge about its function to improve cancer treatment. Multiple cues, including DNA-damage or mitotic errors, can lead to the stabilization and nuclear translocation of p53, initiating the expression of multiple target genes. These transcriptional programs may be cell-type- and stimulus-specific, as is their outcome that ultimately imposes a barrier to cellular transformation. Cell cycle arrest and cell death are two well-studied consequences of p53 activation, but, while being considered critical, they do not fully explain the consequences of p53 loss-of-function phenotypes in cancer. Here, we discuss how mitotic errors alert the p53 network and give an overview of multiple ways that p53 can trigger cell death. We argue that a comparative analysis of different types of p53 responses, elicited by different triggers in a time-resolved manner in well-defined model systems, is critical to understand the cell-type-specific cell fate induced by p53 upon its activation in order to resolve the remaining mystery of its tumor-suppressive function.
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Affiliation(s)
- Dario Rizzotto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; (D.R.); (L.E.)
| | - Lukas Englmaier
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; (D.R.); (L.E.)
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria
| | - Andreas Villunger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; (D.R.); (L.E.)
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Correspondence:
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102
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Lewis R, Maurer HC, Singh N, Gonzalez-Menendez I, Wirth M, Schick M, Zhang L, Isaakidis K, Scherger AK, Schulze V, Lu J, Zenz T, Steiger K, Rad R, Quintanilla-Martinez L, Espeli M, Balabanian K, Keller U, Habringer S. CXCR4 hyperactivation cooperates with TCL1 in CLL development and aggressiveness. Leukemia 2021; 35:2895-2905. [PMID: 34363012 PMCID: PMC8478649 DOI: 10.1038/s41375-021-01376-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 02/06/2023]
Abstract
Aberrant CXCR4 activity has been implicated in lymphoma pathogenesis, disease progression, and resistance to therapies. Using a mouse model with a gain-of-function CXCR4 mutation (CXCR4C1013G) that hyperactivates CXCR4 signaling, we identified CXCR4 as a crucial activator of multiple key oncogenic pathways. CXCR4 hyperactivation resulted in an expansion of transitional B1 lymphocytes, which represent the precursors of chronic lymphocytic leukemia (CLL). Indeed, CXCR4 hyperactivation led to a significant acceleration of disease onset and a more aggressive phenotype in the murine Eµ-TCL1 CLL model. Hyperactivated CXCR4 signaling cooperated with TCL1 to cause a distinct oncogenic transcriptional program in B cells, characterized by PLK1/FOXM1-associated pathways. In accordance, Eµ-TCL1;CXCR4C1013G B cells enriched a transcriptional signature from patients with Richter's syndrome, an aggressive transformation of CLL. Notably, MYC activation in aggressive lymphoma was associated with increased CXCR4 expression. In line with this finding, additional hyperactive CXCR4 signaling in the Eµ-Myc mouse, a model of aggressive B-cell cancer, did not impact survival. In summary, we here identify CXCR4 hyperactivation as a co-driver of an aggressive lymphoma phenotype.
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MESH Headings
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Disease Progression
- Female
- Forkhead Box Protein M1/genetics
- Forkhead Box Protein M1/metabolism
- Gene Expression Regulation, Leukemic
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mutation
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Proto-Oncogene Proteins/physiology
- Receptors, CXCR4/genetics
- Receptors, CXCR4/metabolism
- Polo-Like Kinase 1
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Affiliation(s)
- Richard Lewis
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- School of Medicine, Technische Universität München, Munich, Germany
| | - H Carlo Maurer
- Internal Medicine II, School of Medicine, Technische Universität München, Munich, Germany
| | - Nikita Singh
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Irene Gonzalez-Menendez
- Institute of Pathology and Neuropathology and Comprehensive Cancer Center Tübingen, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus Schick
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Le Zhang
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Konstandina Isaakidis
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Veronika Schulze
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Junyan Lu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, Universitätsspital and Universität Zürich, Zurich, Switzerland
| | - Katja Steiger
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Roland Rad
- TranslaTUM, Center for Translational Cancer Research, Technische Universität München, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology and Comprehensive Cancer Center Tübingen, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Marion Espeli
- Université de Paris, Institut de Recherche Saint-Louis, EMiLy, INSERM U1160, Paris, France
- CNRS, GDR3697 "Microenvironment of Tumor Niches", Micronit, France
- OPALE Carnot Institute, The Organization for Partnerships in Leukemia, Hôpital Saint-Louis, Paris, France
| | - Karl Balabanian
- Université de Paris, Institut de Recherche Saint-Louis, EMiLy, INSERM U1160, Paris, France
- CNRS, GDR3697 "Microenvironment of Tumor Niches", Micronit, France
- OPALE Carnot Institute, The Organization for Partnerships in Leukemia, Hôpital Saint-Louis, Paris, France
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
| | - Stefan Habringer
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Berlin Institute of Health at Charité (BIH), Berlin, Germany.
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103
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Abstract
Perfectly orchestrated periodic gene expression during cell cycle progression is essential for maintaining genome integrity and ensuring that cell proliferation can be stopped by environmental signals. Genetic and proteomic studies during the past two decades revealed remarkable evolutionary conservation of the key mechanisms that control cell cycle-regulated gene expression, including multisubunit DNA-binding DREAM complexes. DREAM complexes containing a retinoblastoma family member, an E2F transcription factor and its dimerization partner, and five proteins related to products of Caenorhabditis elegans multivulva (Muv) class B genes lin-9, lin-37, lin-52, lin-53, and lin-54 (comprising the MuvB core) have been described in diverse organisms, from worms to humans. This review summarizes the current knowledge of the structure, function, and regulation of DREAM complexes in different organisms, as well as the role of DREAM in human disease. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Hayley Walston
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298, USA;
| | - Audra N Iness
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Larisa Litovchick
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298, USA; .,Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA.,Massey Cancer Center, Richmond, Virginia 23298, USA
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104
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Garwain O, Sun X, Iyer DR, Li R, Zhu LJ, Kaufman PD. The chromatin-binding domain of Ki-67 together with p53 protects human chromosomes from mitotic damage. Proc Natl Acad Sci U S A 2021; 118:e2021998118. [PMID: 34353903 PMCID: PMC8364191 DOI: 10.1073/pnas.2021998118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Vertebrate mammals express a protein called Ki-67 which is most widely known as a clinically useful marker of highly proliferative cells. Previous studies of human cells indicated that acute depletion of Ki-67 can elicit a delay at the G1/S boundary of the cell cycle, dependent on induction of the checkpoint protein p21. Consistent with those observations, we show here that acute Ki-67 depletion causes hallmarks of DNA damage, and the damage occurs even in the absence of checkpoint signaling. This damage is not observed in cells traversing S phase but is instead robustly detected in mitotic cells. The C-terminal chromatin-binding domain of Ki-67 is necessary and sufficient to protect cells from this damage. We also observe synergistic effects when Ki-67 and p53 are simultaneously depleted, resulting in increased levels of chromosome bridges at anaphase, followed by the appearance of micronuclei. Therefore, these studies identify the C terminus of Ki-67 as an important module for genome stability.
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Affiliation(s)
- Osama Garwain
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xiaoming Sun
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Divya Ramalingam Iyer
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
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105
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Coronel L, Riege K, Schwab K, Förste S, Häckes D, Semerau L, Bernhart SH, Siebert R, Hoffmann S, Fischer M. Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress. Nucleic Acids Res 2021; 49:7437-7456. [PMID: 34197623 PMCID: PMC8287911 DOI: 10.1093/nar/gkab575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/25/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Despite its prominence, the mechanisms through which the tumor suppressor p53 regulates most genes remain unclear. Recently, the regulatory factor X 7 (RFX7) emerged as a suppressor of lymphoid neoplasms, but its regulation and target genes mediating tumor suppression remain unknown. Here, we identify a novel p53-RFX7 signaling axis. Integrative analysis of the RFX7 DNA binding landscape and the RFX7-regulated transcriptome in three distinct cell systems reveals that RFX7 directly controls multiple established tumor suppressors, including PDCD4, PIK3IP1, MXD4, and PNRC1, across cell types and is the missing link for their activation in response to p53 and stress. RFX7 target gene expression correlates with cell differentiation and better prognosis in numerous cancer types. Interestingly, we find that RFX7 sensitizes cells to Doxorubicin by promoting apoptosis. Together, our work establishes RFX7’s role as a ubiquitous regulator of cell growth and fate determination and a key node in the p53 transcriptional program.
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Affiliation(s)
- Luis Coronel
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Katjana Schwab
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Silke Förste
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - David Häckes
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Lena Semerau
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
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106
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Hernández Borrero LJ, El-Deiry WS. Tumor suppressor p53: Biology, signaling pathways, and therapeutic targeting. Biochim Biophys Acta Rev Cancer 2021; 1876:188556. [PMID: 33932560 PMCID: PMC8730328 DOI: 10.1016/j.bbcan.2021.188556] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022]
Abstract
TP53 is the most commonly mutated gene in human cancer with over 100,000 literature citations in PubMed. This is a heavily studied pathway in cancer biology and oncology with a history that dates back to 1979 when p53 was discovered. The p53 pathway is a complex cellular stress response network with multiple diverse inputs and downstream outputs relevant to its role as a tumor suppressor pathway. While inroads have been made in understanding the biology and signaling in the p53 pathway, the p53 family, transcriptional readouts, and effects of an array of mutants, the pathway remains challenging in the realm of clinical translation. While the role of mutant p53 as a prognostic factor is recognized, the therapeutic modulation of its wild-type or mutant activities remain a work-in-progress. This review covers current knowledge about the biology, signaling mechanisms in the p53 pathway and summarizes advances in therapeutic development.
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Affiliation(s)
- Liz J Hernández Borrero
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, United States of America; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, United States of America; The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI 02912, United States of America; Cancer Center at Brown University, Warren Alpert Medical School, Brown University, Providence, RI 02912, United States of America
| | - Wafik S El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, United States of America; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, United States of America; The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI 02912, United States of America; Cancer Center at Brown University, Warren Alpert Medical School, Brown University, Providence, RI 02912, United States of America.
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107
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KBoost: a new method to infer gene regulatory networks from gene expression data. Sci Rep 2021; 11:15461. [PMID: 34326402 PMCID: PMC8322418 DOI: 10.1038/s41598-021-94919-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/06/2021] [Indexed: 01/11/2023] Open
Abstract
Reconstructing gene regulatory networks is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-the-art algorithms are often not able to process large amounts of data within reasonable time. Furthermore, many of the existing methods predict numerous false positives and have limited capabilities to integrate other sources of information, such as previously known interactions. Here we introduce KBoost, an algorithm that uses kernel PCA regression, boosting and Bayesian model averaging for fast and accurate reconstruction of gene regulatory networks. We have benchmarked KBoost against other high performing algorithms using three different datasets. The results show that our method compares favorably to other methods across datasets. We have also applied KBoost to a large cohort of close to 2000 breast cancer patients and 24,000 genes in less than 2 h on standard hardware. Our results show that molecularly defined breast cancer subtypes also feature differences in their GRNs. An implementation of KBoost in the form of an R package is available at: https://github.com/Luisiglm/KBoost and as a Bioconductor software package.
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108
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Hernandez Borrero L, Dicker DT, Santiago J, Sanders J, Tian X, Ahsan N, Lev A, Zhou L, El-Deiry WS. A subset of CB002 xanthine analogs bypass p53-signaling to restore a p53 transcriptome and target an S-phase cell cycle checkpoint in tumors with mutated-p53. eLife 2021; 10:70429. [PMID: 34324416 PMCID: PMC8321552 DOI: 10.7554/elife.70429] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022] Open
Abstract
Mutations in TP53 occur commonly in the majority of human tumors and confer aggressive tumor phenotypes, including metastasis and therapy resistance. CB002 and structural-analogs restore p53 signaling in tumors with mutant-p53 but we find that unlike other xanthines such as caffeine, pentoxifylline, and theophylline, they do not deregulate the G2 checkpoint. Novel CB002-analogs induce pro-apoptotic Noxa protein in an ATF3/4-dependent manner, whereas caffeine, pentoxifylline, and theophylline do not. By contrast to caffeine, CB002-analogs target an S-phase checkpoint associated with increased p-RPA/RPA2, p-ATR, decreased Cyclin A, p-histone H3 expression, and downregulation of essential proteins in DNA-synthesis and DNA-repair. CB002-analog #4 enhances cell death, and decreases Ki-67 in patient-derived tumor-organoids without toxicity to normal human cells. Preliminary in vivo studies demonstrate anti-tumor efficacy in mice. Thus, a novel class of anti-cancer drugs shows the activation of p53 pathway signaling in tumors with mutated p53, and targets an S-phase checkpoint.
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Affiliation(s)
- Liz Hernandez Borrero
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - David T Dicker
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - John Santiago
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Jennifer Sanders
- The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States.,Department of Pediatrics, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Xiaobing Tian
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, United States
| | - Avital Lev
- The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States
| | - Lanlan Zhou
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Wafik S El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States.,Hematology-Oncology Division, Department of Medicine, Rhode Island Hospital and Brown University, Providence, United States
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109
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Abstract
The current model of replication-dependent (RD) histone biosynthesis posits that RD histone gene expression is coupled to DNA replication, occurring only in S phase of the cell cycle once DNA synthesis has begun. However, several key factors in the RD histone biosynthesis pathway are up-regulated by E2F or phosphorylated by CDK2, suggesting these processes may instead begin much earlier, at the point of cell-cycle commitment. In this study, we use both fixed- and live-cell imaging of human cells to address this question, revealing a hybrid model in which RD histone biosynthesis is first initiated in G1, followed by a strong increase in histone production in S phase of the cell cycle. This suggests a mechanism by which cells that have committed to the cell cycle build up an initial small pool of RD histones to be available for the start of DNA replication, before producing most of the necessary histones required in S phase. Thus, a clear distinction exists at completion of mitosis between cells that are born with the intention of proceeding through the cell cycle and replicating their DNA and cells that have chosen to exit the cell cycle and have no immediate need for histone synthesis.
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110
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Hernandez Borrero L, Dicker DT, Santiago J, Sanders J, Tian X, Ahsan N, Lev A, Zhou L, El-Deiry WS. A subset of CB002 xanthine analogs bypass p53-signaling to restore a p53 transcriptome and target an S-phase cell cycle checkpoint in tumors with mutated-p53. eLife 2021. [PMID: 34324416 DOI: 10.10.7554/elife.70429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutations in TP53 occur commonly in the majority of human tumors and confer aggressive tumor phenotypes, including metastasis and therapy resistance. CB002 and structural-analogs restore p53 signaling in tumors with mutant-p53 but we find that unlike other xanthines such as caffeine, pentoxifylline, and theophylline, they do not deregulate the G2 checkpoint. Novel CB002-analogs induce pro-apoptotic Noxa protein in an ATF3/4-dependent manner, whereas caffeine, pentoxifylline, and theophylline do not. By contrast to caffeine, CB002-analogs target an S-phase checkpoint associated with increased p-RPA/RPA2, p-ATR, decreased Cyclin A, p-histone H3 expression, and downregulation of essential proteins in DNA-synthesis and DNA-repair. CB002-analog #4 enhances cell death, and decreases Ki-67 in patient-derived tumor-organoids without toxicity to normal human cells. Preliminary in vivo studies demonstrate anti-tumor efficacy in mice. Thus, a novel class of anti-cancer drugs shows the activation of p53 pathway signaling in tumors with mutated p53, and targets an S-phase checkpoint.
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Affiliation(s)
- Liz Hernandez Borrero
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - David T Dicker
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - John Santiago
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Jennifer Sanders
- The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States.,Department of Pediatrics, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Xiaobing Tian
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, United States
| | - Avital Lev
- The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States
| | - Lanlan Zhou
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Wafik S El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States.,Hematology-Oncology Division, Department of Medicine, Rhode Island Hospital and Brown University, Providence, United States
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111
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Fujihara KM, Corrales Benitez M, Cabalag CS, Zhang BZ, Ko HS, Liu DS, Simpson KJ, Haupt Y, Lipton L, Haupt S, Phillips WA, Clemons NJ. SLC7A11 Is a Superior Determinant of APR-246 (Eprenetapopt) Response than TP53 Mutation Status. Mol Cancer Ther 2021; 20:1858-1867. [PMID: 34315763 DOI: 10.1158/1535-7163.mct-21-0067] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/24/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
APR-246 (eprenetapopt) is in clinical development with a focus on hematologic malignancies and is promoted as a mutant-p53 reactivation therapy. Currently, the detection of at least one TP53 mutation is an inclusion criterion for patient selection into most APR-246 clinical trials. Preliminary results from our phase Ib/II clinical trial investigating APR-246 combined with doublet chemotherapy [cisplatin and 5-fluorouracil (5-FU)] in metastatic esophageal cancer, together with previous preclinical studies, indicate that TP53 mutation status alone may not be a sufficient biomarker for APR-246 response. This study aims to identify a robust biomarker for response to APR-246. Correlation analysis of the PRIMA-1 activity (lead compound to APR-246) with mutational status, gene expression, protein expression, and metabolite abundance across over 700 cancer cell lines (CCL) was performed. Functional validation and a boutique siRNA screen of over 850 redox-related genes were also conducted. TP53 mutation status was not consistently predictive of response to APR-246. The expression of SLC7A11, the cystine/glutamate transporter, was identified as a superior determinant of response to APR-246. Genetic regulators of SLC7A11, including ATF4, MDM2, wild-type p53, and c-Myc, were confirmed to also regulate cancer-cell sensitivity to APR-246. In conclusion, SLC7A11 expression is a broadly applicable determinant of sensitivity to APR-246 across cancer and should be utilized as the key predictive biomarker to stratify patients for future clinical investigation of APR-246.
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Affiliation(s)
- Kenji M Fujihara
- Gastrointestinal Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Carlos S Cabalag
- Gastrointestinal Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Bonnie Z Zhang
- Gastrointestinal Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Hyun S Ko
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David S Liu
- Gastrointestinal Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,HPB Surgery, Austin Health, Heidelberg, Victoria, Australia
| | - Kaylene J Simpson
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ygal Haupt
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Cancer Therapeutics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Lara Lipton
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sue Haupt
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Cancer Therapeutics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Parkville, Victoria, Australia
| | - Wayne A Phillips
- Gastrointestinal Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Surgery at St. Vincent's Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas J Clemons
- Gastrointestinal Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
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112
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Chappaz S, McArthur K, Kealy L, Law CW, Tailler M, Lane RM, Lieschke A, Ritchie ME, Good-Jacobson KL, Strasser A, Kile BT. Homeostatic apoptosis prevents competition-induced atrophy in follicular B cells. Cell Rep 2021; 36:109430. [PMID: 34289356 DOI: 10.1016/j.celrep.2021.109430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/13/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022] Open
Abstract
While the intrinsic apoptosis pathway is thought to play a central role in shaping the B cell lineage, its precise role in mature B cell homeostasis remains elusive. Using mice in which mature B cells are unable to undergo apoptotic cell death, we show that apoptosis constrains follicular B (FoB) cell lifespan but plays no role in marginal zone B (MZB) cell homeostasis. In these mice, FoB cells accumulate abnormally. This intensifies intercellular competition for BAFF, resulting in a contraction of the MZB cell compartment, and reducing the growth, trafficking, and fitness of FoB cells. Diminished BAFF signaling dampens the non-canonical NF-κB pathway, undermining FoB cell growth despite the concurrent triggering of a protective p53 response. Thus, MZB and FoB cells exhibit a differential requirement for the intrinsic apoptosis pathway. Homeostatic apoptosis constrains the size of the FoB cell compartment, thereby preventing competition-induced FoB cell atrophy.
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Affiliation(s)
- Stéphane Chappaz
- Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia; ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia.
| | - Kate McArthur
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Liam Kealy
- Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia; Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
| | - Charity W Law
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Maximilien Tailler
- Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
| | - Rachael M Lane
- Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
| | | | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Kim L Good-Jacobson
- Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia; Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
| | - Andreas Strasser
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia; Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia
| | - Benjamin T Kile
- Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia; ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010 VIC, Australia; Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, 5005 SA, Australia.
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113
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Woodstock DL, Sammons MA, Fischer M. p63 and p53: Collaborative Partners or Dueling Rivals? Front Cell Dev Biol 2021; 9:701986. [PMID: 34291055 PMCID: PMC8287303 DOI: 10.3389/fcell.2021.701986] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022] Open
Abstract
The tumor suppressor p53 and its oncogenic sibling p63 (ΔNp63) direct opposing fates in tumor development. These paralog proteins are transcription factors that elicit their tumor suppressive and oncogenic capacity through the regulation of both shared and unique target genes. Both proteins predominantly function as activators of transcription, leading to a paradigm shift away from ΔNp63 as a dominant negative to p53 activity. The discovery of p53 and p63 as pioneer transcription factors regulating chromatin structure revealed new insights into how these paralogs can both positively and negatively influence each other to direct cell fate. The previous view of a strict rivalry between the siblings needs to be revisited, as p53 and p63 can also work together toward a common goal.
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Affiliation(s)
- Dana L Woodstock
- Department of Biological Sciences, The State University of New York at Albany, Albany, NY, United States
| | - Morgan A Sammons
- Department of Biological Sciences, The State University of New York at Albany, Albany, NY, United States
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
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114
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DeSalvo J, Ban Y, Li L, Sun X, Jiang Z, Kerr DA, Khanlari M, Boulina M, Capecchi MR, Partanen JM, Chen L, Kondo T, Ornitz DM, Trent JC, Eid JE. ETV4 and ETV5 drive synovial sarcoma through cell cycle and DUX4 embryonic pathway control. J Clin Invest 2021; 131:141908. [PMID: 33983905 DOI: 10.1172/jci141908] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Synovial sarcoma is an aggressive malignancy with no effective treatments for patients with metastasis. The synovial sarcoma fusion SS18-SSX, which recruits the SWI/SNF-BAF chromatin remodeling and polycomb repressive complexes, results in epigenetic activation of FGF receptor (FGFR) signaling. In genetic FGFR-knockout models, culture, and xenograft synovial sarcoma models treated with the FGFR inhibitor BGJ398, we show that FGFR1, FGFR2, and FGFR3 were crucial for tumor growth. Transcriptome analyses of BGJ398-treated cells and histological and expression analyses of mouse and human synovial sarcoma tumors revealed prevalent expression of two ETS factors and FGFR targets, ETV4 and ETV5. We further demonstrate that ETV4 and ETV5 acted as drivers of synovial sarcoma growth, most likely through control of the cell cycle. Upon ETV4 and ETV5 knockdown, we observed a striking upregulation of DUX4 and its transcriptional targets that activate the zygotic genome and drive the atrophy program in facioscapulohumeral dystrophy patients. In addition to demonstrating the importance of inhibiting all three FGFRs, the current findings reveal potential nodes of attack for the cancer with the discovery of ETV4 and ETV5 as appropriate biomarkers and molecular targets, and activation of the embryonic DUX4 pathway as a promising approach to block synovial sarcoma tumors.
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Affiliation(s)
- Joanna DeSalvo
- Department of Medicine, Division of Medical Oncology.,Sylvester Comprehensive Cancer Center, and
| | - Yuguang Ban
- Sylvester Comprehensive Cancer Center, and.,Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Luyuan Li
- Department of Medicine, Division of Medical Oncology.,Sylvester Comprehensive Cancer Center, and
| | | | - Zhijie Jiang
- University of Miami Center for Computational Science, Coral Gables, Florida, USA
| | | | | | - Maria Boulina
- Analytical Imaging Core Facility, Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Mario R Capecchi
- Department of Human Genetics, Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah, USA
| | - Juha M Partanen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lin Chen
- Center of Bone Metabolism and Repair, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jonathan C Trent
- Department of Medicine, Division of Medical Oncology.,Sylvester Comprehensive Cancer Center, and
| | - Josiane E Eid
- Department of Medicine, Division of Medical Oncology.,Sylvester Comprehensive Cancer Center, and
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115
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Lees A, Sessler T, McDade S. Dying to Survive-The p53 Paradox. Cancers (Basel) 2021; 13:3257. [PMID: 34209840 PMCID: PMC8268032 DOI: 10.3390/cancers13133257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
The p53 tumour suppressor is best known for its canonical role as "guardian of the genome", activating cell cycle arrest and DNA repair in response to DNA damage which, if irreparable or sustained, triggers activation of cell death. However, despite an enormous amount of work identifying the breadth of the gene regulatory networks activated directly and indirectly in response to p53 activation, how p53 activation results in different cell fates in response to different stress signals in homeostasis and in response to p53 activating anti-cancer treatments remains relatively poorly understood. This is likely due to the complex interaction between cell death mechanisms in which p53 has been activated, their neighbouring stressed or unstressed cells and the local stromal and immune microenvironment in which they reside. In this review, we evaluate our understanding of the burgeoning number of cell death pathways affected by p53 activation and how these may paradoxically suppress cell death to ensure tissue integrity and organismal survival. We also discuss how these functions may be advantageous to tumours that maintain wild-type p53, the understanding of which may provide novel opportunity to enhance treatment efficacy.
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Affiliation(s)
- Andrea Lees
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK;
| | | | - Simon McDade
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK;
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116
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Mauro LJ, Seibel MI, Diep CH, Spartz A, Perez Kerkvliet C, Singhal H, Swisher EM, Schwartz LE, Drapkin R, Saini S, Sesay F, Litovchick L, Lange CA. Progesterone Receptors Promote Quiescence and Ovarian Cancer Cell Phenotypes via DREAM in p53-Mutant Fallopian Tube Models. J Clin Endocrinol Metab 2021; 106:1929-1955. [PMID: 33755733 PMCID: PMC8499172 DOI: 10.1210/clinem/dgab195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Indexed: 02/08/2023]
Abstract
CONTEXT The ability of ovarian steroids to modify ovarian cancer (OC) risk remains controversial. Progesterone is considered to be protective; recent studies indicate no effect or enhanced OC risk. Knowledge of progesterone receptor (PR) signaling during altered physiology that typifies OC development is limited. OBJECTIVE This study defines PR-driven oncogenic signaling mechanisms in p53-mutant human fallopian tube epithelia (hFTE), a precursor of the most aggressive OC subtype. METHODS PR expression in clinical samples of serous tubal intraepithelial carcinoma (STIC) lesions and high-grade serous OC (HGSC) tumors was analyzed. Novel PR-A and PR-B isoform-expressing hFTE models were characterized for gene expression and cell cycle progression, emboli formation, and invasion. PR regulation of the DREAM quiescence complex and DYRK1 kinases was established. RESULTS STICs and HGSC express abundant activated phospho-PR. Progestin promoted reversible hFTE cell cycle arrest, spheroid formation, and invasion. RNAseq/biochemical studies revealed potent ligand-independent/-dependent PR actions, progestin-induced regulation of the DREAM quiescence complex, and cell cycle target genes through enhanced complex formation and chromatin recruitment. Disruption of DREAM/DYRK1s by pharmacological inhibition, HPV E6/E7 expression, or DYRK1A/B depletion blocked progestin-induced cell arrest and attenuated PR-driven gene expression and associated OC phenotypes. CONCLUSION Activated PRs support quiescence and pro-survival/pro-dissemination cell behaviors that may contribute to early HGSC progression. Our data support an alternative perspective on the tenet that progesterone always confers protection against OC. STICs can reside undetected for decades prior to invasive disease; our studies reveal clinical opportunities to prevent the ultimate development of HGSC by targeting PRs, DREAM, and/or DYRKs.
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Affiliation(s)
- Laura J Mauro
- University of Minnesota, Masonic Cancer Center, Minneapolis, MN 55455, USA
- University of Minnesota, Department of Animal Science, St. Paul, MN 55108, USA
| | - Megan I Seibel
- University of Minnesota, Masonic Cancer Center, Minneapolis, MN 55455, USA
| | - Caroline H Diep
- University of Minnesota, Masonic Cancer Center, Minneapolis, MN 55455, USA
| | - Angela Spartz
- University of Minnesota, Masonic Cancer Center, Minneapolis, MN 55455, USA
| | | | - Hari Singhal
- Northwestern University, Department of Surgery, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Elizabeth M Swisher
- University of Washington Seattle, Dept Obstetrics & Gynecology, Division of Gynecologic Oncology, Seattle, WA 98109, USA
| | - Lauren E Schwartz
- University of Pennsylvania, Dept of Pathology and Laboratory Medicine, Philadelphia, PA 19104, USA
| | - Ronny Drapkin
- University of Pennsylvania, Penn Ovarian Cancer Research Center, Dept Obstetrics & Gynecology, Philadelphia, PA 19104, USA
| | - Siddharth Saini
- Virginia Commonwealth University, Massey Cancer Center, Dept. Internal Medicine, Division of Hematology, Oncology & Palliative Care, Richmond, VA 23298, USA
| | - Fatmata Sesay
- Virginia Commonwealth University, Massey Cancer Center, Dept. Internal Medicine, Division of Hematology, Oncology & Palliative Care, Richmond, VA 23298, USA
| | - Larisa Litovchick
- Virginia Commonwealth University, Massey Cancer Center, Dept. Internal Medicine, Division of Hematology, Oncology & Palliative Care, Richmond, VA 23298, USA
| | - Carol A Lange
- University of Minnesota, Masonic Cancer Center, Minneapolis, MN 55455, USA
- University of Minnesota, Dept Medicine, Division of Hematology, Oncology & Transplantation, Minneapolis, MN 55455, USA
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117
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Tong DR, Zhou W, Katz C, Regunath K, Venkatesh D, Ihuegbu C, Manfredi JJ, Laptenko O, Prives C. p53 Frameshift Mutations Couple Loss-of-Function with Unique Neomorphic Activities. Mol Cancer Res 2021; 19:1522-1533. [PMID: 34045312 DOI: 10.1158/1541-7786.mcr-20-0691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022]
Abstract
p53 mutations that result in loss of transcriptional activity are commonly found in numerous types of cancer. While the majority of these are missense mutations that map within the central DNA-binding domain, truncations and/or frameshift mutations can also occur due to various nucleotide substitutions, insertions, or deletions. These changes result in mRNAs containing premature stop codons that are translated into a diverse group of C-terminally truncated proteins. Here we characterized three p53 frameshift mutant proteins expressed from the endogenous TP53 locus in U2OS osteosarcoma and HCT116 colorectal cancer cell lines. These mutants retain intact DNA-binding domains but display altered oligomerization properties. Despite their abnormally high expression levels, they are mostly transcriptionally inactive and unable to initiate a stimuli-induced transcriptional program characteristic of wild-type p53. However, one of these variant p53 proteins, I332fs*14, which resembles naturally expressed TAp53 isoforms β and γ, retains some residual antiproliferative activity and can induce cellular senescence in HCT116 cells. Cells expressing this mutant also display decreased motility in migration assays. Hence, this p53 variant exhibits a combination of loss-of-gain and gain-of-function characteristics, distinguishing it from both wild type p53 and p53 loss. IMPLICATIONS: p53 frameshift mutants display a mixture of residual antiproliferative and neomorphic functions that may be differentially exploited for targeted therapy.
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Affiliation(s)
- David R Tong
- Department of Biological Sciences, Columbia University, New York, New York
| | - Wen Zhou
- Department of Biological Sciences, Columbia University, New York, New York
| | - Chen Katz
- Department of Biological Sciences, Columbia University, New York, New York
| | - Kausik Regunath
- Department of Biological Sciences, Columbia University, New York, New York
| | - Divya Venkatesh
- Department of Biological Sciences, Columbia University, New York, New York
| | - Chinyere Ihuegbu
- Department of Biological Sciences, Columbia University, New York, New York
| | - James J Manfredi
- Department of Oncological Sciences, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, New York.
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York.
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118
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Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, Golbazi A, Maenpaa E, Stricker K, Guha Thakurta S, Zhang T, Rad R, Pan J, Nusinow DP, Paulo JA, Schweppe DK, Vaites LP, Harper JW, Gygi SP. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 2021; 184:3022-3040.e28. [PMID: 33961781 PMCID: PMC8165030 DOI: 10.1016/j.cell.2021.04.011] [Citation(s) in RCA: 398] [Impact Index Per Article: 132.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/05/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022]
Abstract
Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. The first, BioPlex 3.0, results from affinity purification of 10,128 human proteins-half the proteome-in 293T cells and includes 118,162 interactions among 14,586 proteins. The second results from 5,522 immunoprecipitations in HCT116 cells. These networks model the interactome whose structure encodes protein function, localization, and complex membership. Comparison across cell lines validates thousands of interactions and reveals extensive customization. Whereas shared interactions reside in core complexes and involve essential proteins, cell-specific interactions link these complexes, "rewiring" subnetworks within each cell's interactome. Interactions covary among proteins of shared function as the proteome remodels to produce each cell's phenotype. Viewable interactively online through BioPlexExplorer, these networks define principles of proteome organization and enable unknown protein characterization.
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Affiliation(s)
- Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Raphael J Bruckner
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Joe R Cannon
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kurt Baltier
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Fana Gebreab
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Melanie P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Thornock
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriela Zarraga
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley Tam
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brandon M Gassaway
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Panov
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Parzen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sipei Fu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Arvene Golbazi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Eila Maenpaa
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Keegan Stricker
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ramin Rad
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua Pan
- Broad Institute, Cambridge, MA 02142, USA
| | - David P Nusinow
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Devin K Schweppe
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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119
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Aquino Perez C, Burocziova M, Jenikova G, Macurek L. CK1-mediated phosphorylation of FAM110A promotes its interaction with mitotic spindle and controls chromosomal alignment. EMBO Rep 2021; 22:e51847. [PMID: 34080749 DOI: 10.15252/embr.202051847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 01/10/2023] Open
Abstract
Progression through the cell cycle is driven by cyclin-dependent kinases that control gene expression, orchestration of mitotic spindle, and cell division. To identify new regulators of the cell cycle, we performed transcriptomic analysis of human non-transformed cells expressing a fluorescent ubiquitination-based cell cycle indicator and identified 701 transcripts differentially expressed in G1 and G2 cells. Family with sequence similarity 110 member A (FAM110A) protein is highly expressed in G2 cells and localized at mitotic spindle and spindle poles during mitosis. Depletion of FAM110A impairs chromosomal alignment, delays metaphase-to-anaphase transition, and affects spindle positioning. Using mass spectrometry and immunoprecipitation, we identified casein kinase I (CK1) in complex with FAM110A during mitosis. CK1 phosphorylates the C-terminal domain of FAM110A in vitro, and inhibition of CK1 reduces phosphorylation of mitotic FAM110A. Wild-type FAM110A, but not the FAM110A-S252-S255A mutant deficient in CK1 phosphorylation, rescues the chromosomal alignment, duration of mitosis, and orientation of the mitotic spindle after depletion of endogenous FAM110A. We propose that CK1 regulates chromosomal alignment by phosphorylating FAM110A and promoting its interaction with mitotic spindle.
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Affiliation(s)
- Cecilia Aquino Perez
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Monika Burocziova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Gabriela Jenikova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Libor Macurek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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Hoppe MM, Jaynes P, Wardyn JD, Upadhyayula SS, Tan TZ, Lie S, Lim DGZ, Pang BNK, Lim S, P S Yeong J, Karnezis A, Chiu DS, Leung S, Huntsman DG, Sedukhina AS, Sato K, Topp MD, Scott CL, Choi H, Patel NR, Brown R, Kaye SB, Pitt JJ, Tan DSP, Jeyasekharan AD. Quantitative imaging of RAD51 expression as a marker of platinum resistance in ovarian cancer. EMBO Mol Med 2021; 13:e13366. [PMID: 33709473 PMCID: PMC8103098 DOI: 10.15252/emmm.202013366] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/23/2022] Open
Abstract
Early relapse after platinum chemotherapy in epithelial ovarian cancer (EOC) portends poor survival. A-priori identification of platinum resistance is therefore crucial to improve on standard first-line carboplatin-paclitaxel treatment. The DNA repair pathway homologous recombination (HR) repairs platinum-induced damage, and the HR recombinase RAD51 is overexpressed in cancer. We therefore designed a REMARK-compliant study of pre-treatment RAD51 expression in EOC, using fluorescent quantitative immunohistochemistry (qIHC) to overcome challenges in quantitation of protein expression in situ. In a discovery cohort (n = 284), RAD51-High tumours had shorter progression-free and overall survival compared to RAD51-Low cases in univariate and multivariate analyses. The association of RAD51 with relapse/survival was validated in a carboplatin monotherapy SCOTROC4 clinical trial cohort (n = 264) and was predominantly noted in HR-proficient cancers (Myriad HRDscore < 42). Interestingly, overexpression of RAD51 modified expression of immune-regulatory pathways in vitro, while RAD51-High tumours showed exclusion of cytotoxic T cells in situ. Our findings highlight RAD51 expression as a determinant of platinum resistance and suggest possible roles for therapy to overcome immune exclusion in RAD51-High EOC. The qIHC approach is generalizable to other proteins with a continuum instead of discrete/bimodal expression.
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Affiliation(s)
- Michal M Hoppe
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Patrick Jaynes
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Joanna D Wardyn
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | | | - Tuan Zea Tan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Stefanus Lie
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Diana G Z Lim
- Department of PathologyNational University HospitalSingapore
| | - Brendan N K Pang
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of PathologyNational University HospitalSingapore
| | - Sherlly Lim
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Joe P S Yeong
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Anthony Karnezis
- British Columbia Cancer AgencyVancouverBCCanada
- Present address:
Pathology and Lab medicineUC Davis Medical CentreSacramentoCAUSA
| | | | | | | | - Anna S Sedukhina
- Department of PharmacogenomicsSt. Marianna UniversityKawasakiJapan
| | - Ko Sato
- Department of PharmacogenomicsSt. Marianna UniversityKawasakiJapan
| | - Monique D Topp
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical ResearchParkvilleVic.Australia
| | - Hyungwon Choi
- Saw Swee Hock School of Public HealthNational University of SingaporeSingapore
| | | | - Robert Brown
- Division of CancerImperial College LondonLondonUK
| | - Stan B Kaye
- Department of Haematology‐OncologyNational University HospitalSingapore
| | - Jason J Pitt
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - David S P Tan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of Haematology‐OncologyNational University HospitalSingapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- Department of Haematology‐OncologyNational University HospitalSingapore
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121
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Doffe F, Carbonnier V, Tissier M, Leroy B, Martins I, Mattsson JSM, Micke P, Pavlova S, Pospisilova S, Smardova J, Joerger AC, Wiman KG, Kroemer G, Soussi T. Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene. Cell Death Differ 2021; 28:1477-1492. [PMID: 33257846 PMCID: PMC8166836 DOI: 10.1038/s41418-020-00672-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
Infrequent and rare genetic variants in the human population vastly outnumber common ones. Although they may contribute significantly to the genetic basis of a disease, these seldom-encountered variants may also be miss-identified as pathogenic if no correct references are available. Somatic and germline TP53 variants are associated with multiple neoplastic diseases, and thus have come to serve as a paradigm for genetic analyses in this setting. We searched 14 independent, globally distributed datasets and recovered TP53 SNPs from 202,767 cancer-free individuals. In our analyses, 19 new missense TP53 SNPs, including five novel variants specific to the Asian population, were recurrently identified in multiple datasets. Using a combination of in silico, functional, structural, and genetic approaches, we showed that none of these variants displayed loss of function compared to the normal TP53 gene. In addition, classification using ACMG criteria suggested that they are all benign. Considered together, our data reveal that the TP53 coding region shows far more polymorphism than previously thought and present high ethnic diversity. They furthermore underline the importance of correctly assessing novel variants in all variant-calling pipelines associated with genetic diagnoses for cancer.
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Affiliation(s)
- Flora Doffe
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden
| | - Vincent Carbonnier
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Manon Tissier
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Bernard Leroy
- Department of Life Science, Sorbonne Université, Paris, France
| | - Isabelle Martins
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Johanna S M Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarka Pavlova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jana Smardova
- Faculty of Science, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Klas G Wiman
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden
| | - Guido Kroemer
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Thierry Soussi
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France.
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden.
- Department of Life Science, Sorbonne Université, Paris, France.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
- Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France.
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E2F1 Maintains Gastric Cancer Stemness Properties by Regulating Stemness-Associated Genes. JOURNAL OF ONCOLOGY 2021; 2021:6611327. [PMID: 33986804 PMCID: PMC8093057 DOI: 10.1155/2021/6611327] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/06/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022]
Abstract
Purpose To determine the regulatory role of E2F1 in maintaining gastric cancer stemness properties and the clinical significance of E2F1 in gastric cancer. Materials and Methods We conducted a tumor spheroid formation assay to enrich gastric cancer stem-like cells. The protein and mRNA expression levels of genes were measured using Western Blot and qRT-PCR. Lentivirus-mediated overexpression and downregulation of E2F1 were performed to evaluate the effect of E2F1 on the stemness properties of gastric cancer cells. The effect of E2F1 on gastric cancer cell sensitivity of 5-Fu was evaluated using cell viability assay and TdT-mediated dUTP Nick-End Labeling staining. We also analyzed the association between E2F1 expression and clinical characteristics in gastric cancer patients. The KM plotter database was used to analyze the relationship between E2F1 and overall survival in GC patients. Results We found that E2F1 expression was significantly higher in gastric cancer tissues than in the paired adjacent normal tissues (p < 0.05) and was positively correlated with tumor size (p < 0.05), T stage (p < 0.05), and differentiation degree (p < 0.05). KM plotter database demonstrated a close association between higher E2F1 expression level and worse overall survival of gastric cancer patients (p < 0.05). In vitro assay illustrated that E2F1 could regulate the expression of stemness-associated genes, such as BMI1, OCT4, Nanog, and CD44, and maintain the tumor spheroid formation ability of gastric cancer cells. E2F1 enhanced 5-Fu resistance in gastric cancer cells, and the E2F1 expression level was correlated with the prognosis of gastric cancer patients receiving 5-Fu therapy. The expression levels of stemness-associated genes were also significantly higher in gastric cancer tissues than the paired adjacent normal tissues (p < 0.05). A positive correlation was observed between E2F1 and BMI1 (r = 0.422, p < 0.05), CD44 (r = 0.634, p < 0.05), OCT4 (r = 0.456, p < 0.05), and Nanog (r = 0.337, p < 0.05) in gastric cancer tissues. The co-overexpression of E2F1 and stemness-associated genes was associated with worse overall survival. Conclusion E2F1 plays a significant role in gastric cancer progression by maintaining gastric cancer stemness properties through the regulation of stemness-associated genes. The close association between E2F1 and poor prognosis of patients suggests that E2F1 could serve as a prognostic biomarker and a therapeutic target in gastric cancer patients.
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Exploration of immune-related genes in high and low tumor mutation burden groups of chromophobe renal cell carcinoma. Biosci Rep 2021; 40:225779. [PMID: 32662515 PMCID: PMC7378265 DOI: 10.1042/bsr20201491] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/05/2020] [Accepted: 07/13/2020] [Indexed: 02/05/2023] Open
Abstract
Renal cell carcinoma (RCC) is one of most common cancers with gradually increasing incidence and high mortality. Chromogenic RCC (chRCC) is the third most common histological subtype of RCC, accounting for approximately 5–7% of RCC. In our study, the transcriptome expression profile data (n=89) of chRCC, corresponding clinical data (n=113) and the somatic mutation data (n=66) were obtained from the TCGA database. We first analyzed the mutation data of chRCC patients and divided chRCC patients into high and low tumor mutation burden (TMB) groups based on the median TMB. We found that high TMB was significantly associated with worse prognosis and could promote tumor metastasis and development. Moreover, four different immune-related genes (BIRC5, PDGFRL, INHBE, IL20RB) were also identified. We found that BIRC5 was significantly overexpressed in the high TMB group and correlated with worse prognosis. The results of univariate and multivariate COX analyses demonstrated that BIRC5 (hazard ratio (HR) = 2.094) may serve as a prognostic indicator for patients with chRCC with high TMB. In addition, we identified the possible functional pathways of BIRC5 through gene set enrichment analysis (GSEA) enrichment. A positive correlation was obtained between BIRC5 and the abundance of CD4+ T cells. The results of our study revealed their correlation between the immune-related genes and clinicopathologic features as well as potential functional pathways as well as immune infiltrating cells, which may provide more data about the development of chRCC immunotherapy.
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124
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Mining TCGA database for tumor mutation burden and their clinical significance in bladder cancer. Biosci Rep 2021; 40:222532. [PMID: 32239176 PMCID: PMC7178217 DOI: 10.1042/bsr20194337] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Bladder cancer is the ninth most-common cancer worldwide and it is associated with high morbidity and mortality. Tumor mutational burden (TMB) is an emerging biomarker in cancer characterized by microsatellite instability. TMB has been described as a powerful predictor of tumor behavior and response to immunotherapy. METHODS A total of 443 bladder cancer samples obtained from The Cancer Genome Atlas (TCGA) were analyzed for mutation types, TMB values, and prognostic value of TMB. Differentially expressed genes (DEGs) were identified from the TMB groupings. Functional analysis was performed to assess the prognostic value of the first 30 core genes. CIBERSORT algorithm was used to determine the correlation between the immune cells and TMB subtypes. RESULTS Single nucleotide polymorphism (SNP) and C>T were reported as the most common missense mutations and we also identified a high rate of mutations in TP53, TTN, KMT2D. Bladder cancer patients with high TMB showed a better prognosis. Enrichment analysis of the DEGs revealed that they were involved in the regulation of the P13K-Akt signaling pathway, cytokine-cytokine receptor interaction, and Ras signaling pathway. The high expression of hub genes ADRA2A, CXCL12, S1PR1, ADAMTS9, F13A1, and SPON1 was correlated with poor overall survival. Besides, significant differences in the composition of the immune cells of T cells CD8, T cells CD4 memory activated, NK cells resting and Mast cells resting were observed. CONCLUSIONS The present study provides a comprehensive and systematic analysis of the prediction of TMB in bladder cancer and its clinical significance. Also, the study provides additional prognostic information and opportunities for immunotherapy in bladder cancer.
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125
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Kumari R, Jat P. Mechanisms of Cellular Senescence: Cell Cycle Arrest and Senescence Associated Secretory Phenotype. Front Cell Dev Biol 2021; 9:645593. [PMID: 33855023 PMCID: PMC8039141 DOI: 10.3389/fcell.2021.645593] [Citation(s) in RCA: 645] [Impact Index Per Article: 215.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a stable cell cycle arrest that can be triggered in normal cells in response to various intrinsic and extrinsic stimuli, as well as developmental signals. Senescence is considered to be a highly dynamic, multi-step process, during which the properties of senescent cells continuously evolve and diversify in a context dependent manner. It is associated with multiple cellular and molecular changes and distinct phenotypic alterations, including a stable proliferation arrest unresponsive to mitogenic stimuli. Senescent cells remain viable, have alterations in metabolic activity and undergo dramatic changes in gene expression and develop a complex senescence-associated secretory phenotype. Cellular senescence can compromise tissue repair and regeneration, thereby contributing toward aging. Removal of senescent cells can attenuate age-related tissue dysfunction and extend health span. Senescence can also act as a potent anti-tumor mechanism, by preventing proliferation of potentially cancerous cells. It is a cellular program which acts as a double-edged sword, with both beneficial and detrimental effects on the health of the organism, and considered to be an example of evolutionary antagonistic pleiotropy. Activation of the p53/p21WAF1/CIP1 and p16INK4A/pRB tumor suppressor pathways play a central role in regulating senescence. Several other pathways have recently been implicated in mediating senescence and the senescent phenotype. Herein we review the molecular mechanisms that underlie cellular senescence and the senescence associated growth arrest with a particular focus on why cells stop dividing, the stability of the growth arrest, the hypersecretory phenotype and how the different pathways are all integrated.
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Affiliation(s)
- Ruchi Kumari
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, United Kingdom
| | - Parmjit Jat
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, United Kingdom
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126
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Zhao C, Zhang N, Cui X, Zhang X, Ren Y, Su C, He J, Zhang W, Sun X, Yang J, Gao X. Integrative analysis regarding the correlation between GAS2 family genes and human glioma prognosis. Cancer Med 2021; 10:2826-2839. [PMID: 33713047 PMCID: PMC8026934 DOI: 10.1002/cam4.3829] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Background Emerging oncogenes were reportedly linked to the complicated subtypes and pathogenesis of clinical gliomas. Herein, we first comprehensively explored the potential correlation between growth‐arrest‐specific two family genes (GAS2, GAS2L1, GAS2L2, GAS2L3) and gliomas by bioinformatics analysis and cellular experiments. Methods Based on the available datasets of TCGA (The Cancer Genome Atlas), CGGA (Chinese Glioma Genome Atlas), and Oncomine databases, we performed a series of analyses, such as gene expression, survival prognosis, DNA methylation, immune infiltration, and partner enrichment. We also utilized two glioma cell lines to conduct the colony formation and wound‐healing assay. Results GAS2L3 gene was highly expressed in glioma tissues compared to normal brain tissues (p < 0.05). We further observed the relationship between the high expressed GAS2L3 and poor clinical prognosis of brain low‐grade glioma (LGG) cases in our Cox proportional hazard model (hazard ratio [HR] = 0.1715, p < 0.001). Moreover, DNA hypomethylation status of GAS2L3 was correlated with the high expression of GAS2L3 in LGG tissues and the poor clinical prognosis of primary glioma cases (p < 0.05). We also found that the high expression of GAS2L3 was associated with the infiltration level of immune cells, especially the T cells (p < 0.0001). Functional enrichment analysis of GAS2L3‐correlated genes and interaction partners further indicated that GAS2L3 might take part in the occurrence of glioma by influencing a series of biological behaviors, such as cell division, cytoskeleton binding, and cell adhesion. Additionally, our cellular experiment data suggested that a highly expressed GAS2L3 gene contributes to the enhanced proliferation and migration of glioma cells. Conclusion This study first analyzed the potential role of GAS2 family genes, especially GAS2L3, in the clinical prognosis and possible functional mechanisms of glioma, which gives a novel insight into the relationship between GAS2L3 and LGG.
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Affiliation(s)
- Chunyan Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Nan Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xiaoteng Cui
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin, China
| | - Xinxin Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Yuanyuan Ren
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Chao Su
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Jinyan He
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Wei Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xiaoming Sun
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
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Zimmermann MT, Mathison AJ, Stodola T, Evans DB, Abrudan JL, Demos W, Tschannen M, Aldakkak M, Geurts J, Lomberk G, Tsai S, Urrutia R. Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level. Front Oncol 2021; 11:606820. [PMID: 33747920 PMCID: PMC7973372 DOI: 10.3389/fonc.2021.606820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
We investigated germline variation in pancreatic ductal adenocarcinoma (PDAC) predisposition genes in 535 patients, using a custom-built panel and a new complementary bioinformatic approach. Our panel assessed genes belonging to DNA repair, cell cycle checkpoints, migration, and preneoplastic pancreatic conditions. Our bioinformatics approach integrated annotations of variants by using data derived from both germline and somatic references. This integrated approach with expanded evidence enabled us to consider patterns even among private mutations, supporting a functional role for certain alleles, which we believe enhances individualized medicine beyond classic gene-centric approaches. Concurrent evaluation of three levels of evidence, at the gene, sample, and cohort level, has not been previously done. Overall, we identified in PDAC patient germline samples, 12% with mutations previously observed in pancreatic cancers, 23% with mutations previously discovered by sequencing other human tumors, and 46% with mutations with germline associations to cancer. Non-polymorphic protein-coding pathogenic variants were found in 18.4% of patient samples. Moreover, among patients with metastatic PDAC, 16% carried at least one pathogenic variant, and this subgroup was found to have an improved overall survival (22.0 months versus 9.8; p=0.008) despite a higher pre-treatment CA19-9 level (p=0.02). Genetic alterations in DNA damage repair genes were associated with longer overall survival among patients who underwent resection surgery (92 months vs. 46; p=0.06). ATM alterations were associated with more frequent metastatic stage (p = 0.04) while patients with BRCA1 or BRCA2 alterations had improved overall survival (79 months vs. 39; p=0.05). We found that mutations in genes associated with chronic pancreatitis were more common in non-white patients (p<0.001) and associated with longer overall survival (52 months vs. 26; p=0.004), indicating the need for greater study of the relationship among these factors. More than 90% of patients were found to have variants of uncertain significance, which is higher than previously reported. Furthermore, we generated 3D models for selected mutant proteins, which suggested distinct mechanisms underlying their dysfunction, likely caused by genetic alterations. Notably, this type of information is not predictable from sequence alone, underscoring the value of structural bioinformatics to improve genomic interpretation. In conclusion, the variation in PDAC predisposition genes appears to be more extensive than anticipated. This information adds to the growing body of literature on the genomic landscape of PDAC and brings us closer to a more widespread use of precision medicine for this challenging disease.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Angela J Mathison
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tim Stodola
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Douglas B Evans
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jenica L Abrudan
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Wendy Demos
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Michael Tschannen
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Mohammed Aldakkak
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jennifer Geurts
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Genetic Counseling Program, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Gwen Lomberk
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Susan Tsai
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Raul Urrutia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States
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Iness AN, Rubinsak L, Meas SJ, Chaoul J, Sayeed S, Pillappa R, Temkin SM, Dozmorov MG, Litovchick L. Oncogenic B-Myb Is Associated With Deregulation of the DREAM-Mediated Cell Cycle Gene Expression Program in High Grade Serous Ovarian Carcinoma Clinical Tumor Samples. Front Oncol 2021; 11:637193. [PMID: 33747961 PMCID: PMC7969987 DOI: 10.3389/fonc.2021.637193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/08/2021] [Indexed: 12/21/2022] Open
Abstract
Cell cycle control drives cancer progression and treatment response in high grade serous ovarian carcinoma (HGSOC). MYBL2 (encoding B-Myb), an oncogene with prognostic significance in several cancers, is highly expressed in most HGSOC cases; however, the clinical significance of B-Myb in this disease has not been well-characterized. B-Myb is associated with cell proliferation through formation of the MMB (Myb and MuvB core) protein complex required for transcription of mitotic genes. High B-Myb expression disrupts the formation of another transcriptional cell cycle regulatory complex involving the MuvB core, DREAM (DP, RB-like, E2F, and MuvB), in human cell lines. DREAM coordinates cell cycle dependent gene expression by repressing over 800 cell cycle genes in G0/G1. Here, we take a bioinformatics approach to further evaluate the effect of B-Myb expression on DREAM target genes in HGSOC and validate our cellular model with clinical specimens. We show that MYBL2 is highly expressed in HGSOC and correlates with expression of DREAM and MMB target genes in both The Cancer Genome Atlas (TCGA) as well as independent analyses of HGSOC primary tumors (N = 52). High B-Myb expression was also associated with poor overall survival in the TCGA cohort and analysis by a DREAM target gene expression signature yielded a negative impact on survival. Together, our data support the conclusion that high expression of MYBL2 is associated with deregulation of DREAM/MMB-mediated cell cycle gene expression programs in HGSOC and may serve as a prognostic factor independent of its cell cycle role. This provides rationale for further, larger scale studies aimed to determine the clinical predictive value of the B-Myb gene expression signature for treatment response as well as patient outcomes.
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Affiliation(s)
- Audra N Iness
- Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Lisa Rubinsak
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, United States
| | - Steven J Meas
- School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Jessica Chaoul
- School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Sadia Sayeed
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Raghavendra Pillappa
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States
| | - Sarah M Temkin
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, United States
| | - Mikhail G Dozmorov
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States.,Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States.,Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States
| | - Larisa Litovchick
- Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
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129
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Ho NTT, Rahane CS, Pramanik S, Kim PS, Kutzner A, Heese K. FAM72, Glioblastoma Multiforme (GBM) and Beyond. Cancers (Basel) 2021; 13:cancers13051025. [PMID: 33804473 PMCID: PMC7957592 DOI: 10.3390/cancers13051025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Glioblastoma multiforme (GBM) is a serious and aggressive cancer disease that has not allowed scientists to rest for decades. In this review, we consider the new gene pair |-SRGAP2–FAM72-| and discuss its role in the cell cycle and the possibility of defining new therapeutic approaches for the treatment of GBM and other cancers via this gene pair |-SRGAP2–FAM72-|. Abstract Neural stem cells (NSCs) offer great potential for regenerative medicine due to their excellent ability to differentiate into various specialized cell types of the brain. In the central nervous system (CNS), NSC renewal and differentiation are under strict control by the regulation of the pivotal SLIT-ROBO Rho GTPase activating protein 2 (SRGAP2)—Family with sequence similarity 72 (FAM72) master gene (i.e., |-SRGAP2–FAM72-|) via a divergent gene transcription activation mechanism. If the gene transcription control unit (i.e., the intergenic region of the two sub-gene units, SRGAP2 and FAM72) gets out of control, NSCs may transform into cancer stem cells and generate brain tumor cells responsible for brain cancer such as glioblastoma multiforme (GBM). Here, we discuss the surveillance of this |-SRGAP2–FAM72-| master gene and its role in GBM, and also in light of FAM72 for diagnosing various types of cancers outside of the CNS.
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Affiliation(s)
- Nguyen Thi Thanh Ho
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
| | - Chinmay Satish Rahane
- Maharashtra Institute of Medical Education and Research, Talegaon Dabhade, Maharashtra 410507, India;
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany;
| | - Pok-Son Kim
- Department of Mathematics, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 136-702, Korea;
| | - Arne Kutzner
- Department of Information Systems, College of Computer Science, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
- Correspondence:
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Branigan TB, Kozono D, Schade AE, Deraska P, Rivas HG, Sambel L, Reavis HD, Shapiro GI, D'Andrea AD, DeCaprio JA. MMB-FOXM1-driven premature mitosis is required for CHK1 inhibitor sensitivity. Cell Rep 2021; 34:108808. [PMID: 33657372 PMCID: PMC7970065 DOI: 10.1016/j.celrep.2021.108808] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/24/2020] [Accepted: 02/09/2021] [Indexed: 12/25/2022] Open
Abstract
To identify genes whose loss confers resistance to CHK1 inhibitors, we perform genome-wide CRISPR-Cas9 screens in non-small-cell lung cancer (NSCLC) cell lines treated with the CHK1 inhibitor prexasertib (CHK1i). Five of the top six hits of the screens, MYBL2 (B-MYB), LIN54, FOXM1, cyclin A2 (CCNA2), and CDC25B, are cell-cycle-regulated genes that contribute to entry into mitosis. Knockout of MMB-FOXM1 complex components LIN54 and FOXM1 reduce CHK1i-induced DNA replication stress markers and premature mitosis during Late S phase. Activation of a feedback loop between the MMB-FOXM1 complex and CDK1 is required for CHK1i-induced premature mitosis in Late S phase and subsequent replication catastrophe, indicating that dysregulation of the S to M transition is necessary for CHK1 inhibitor sensitivity. These findings provide mechanistic insights into small molecule inhibitors currently studied in clinical trials and provide rationale for combination therapies. Branigan et al., by using genome-wide CRISPR screens, identify the MMB-FOXM1 complex as being required for CHK1 inhibitor (CHK1i) sensitivity. Their study shows that CHK1i-induced premature activation of the G2/M transcriptional program by this complex triggers a breakdown in the separation of DNA synthesis and mitosis, leading to replication catastrophe.
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Affiliation(s)
- Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - David Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amy E Schade
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Peter Deraska
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hembly G Rivas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Larissa Sambel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hunter D Reavis
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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131
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Kim MJ, Cervantes C, Jung YS, Zhang X, Zhang J, Lee SH, Jun S, Litovchick L, Wang W, Chen J, Fang B, Park JI. PAF remodels the DREAM complex to bypass cell quiescence and promote lung tumorigenesis. Mol Cell 2021; 81:1698-1714.e6. [PMID: 33626321 PMCID: PMC8052288 DOI: 10.1016/j.molcel.2021.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/15/2020] [Accepted: 01/29/2021] [Indexed: 01/01/2023]
Abstract
The DREAM complex orchestrates cell quiescence and the cell cycle. However, how the DREAM complex is deregulated in cancer remains elusive. Here, we report that PAF (PCLAF/KIAA0101) drives cell quiescence exit to promote lung tumorigenesis by remodeling the DREAM complex. PAF is highly expressed in lung adenocarcinoma (LUAD) and is associated with poor prognosis. Importantly, Paf knockout markedly suppressed LUAD development in mouse models. PAF depletion induced LUAD cell quiescence and growth arrest. PAF is required for the global expression of cell-cycle genes controlled by the repressive DREAM complex. Mechanistically, PAF inhibits DREAM complex formation by binding to RBBP4, a core DREAM subunit, leading to transactivation of DREAM target genes. Furthermore, pharmacological mimicking of PAF-depleted transcriptomes inhibited LUAD tumor growth. Our results unveil how the PAF-remodeled DREAM complex bypasses cell quiescence to promote lung tumorigenesis and suggest that the PAF-DREAM axis may be a therapeutic vulnerability in lung cancer.
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Affiliation(s)
- Moon Jong Kim
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher Cervantes
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Youn-Sang Jung
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Xiaoshan Zhang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Ho Lee
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sohee Jun
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Larisa Litovchick
- Department of Internal Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bingliang Fang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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132
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Yang S, Lin S, Liu K, Liu Y, Xu P, Zheng Y, Deng Y, Zhang D, Zhai Z, Li N, Ren X, Dai Z, Kang H. Identification of an immune-related RNA-binding protein signature to predict survival and targeted therapy responses in liver cancer. Genomics 2021; 113:795-804. [PMID: 33524497 DOI: 10.1016/j.ygeno.2021.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/25/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022]
Abstract
RNA-binding proteins (RBPs) play crucial roles in multiple cancers. However, very few RBPs and their association with immune genes have been systematically studied in liver cancer (LC). We aimed to identify an immune-related RBP signature to predict the survival of LC patients. Bioinformatics methods were used to identify differentially expressed, immune-related, and prognostic RBPs and to develop an immune-related RBP signature based on data from the Cancer Genome Atlas (TCGA) cohort. We obtained eight differentially expressed, immune-related, and prognostic RBPs to construct a risk signature. The signature could effectively distinguish between high- and low-risk patients, and its predictive capacity was validated in the International Cancer Genomics Consortium (ICGC) cohort. We speculated that the high-risk group was more sensitive to targeted therapy. The immune-related RBP signature is an independent prognostic biomarker for LC patients and can expand the application of targeted therapy through patient stratification.
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Affiliation(s)
- Si Yang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Kang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yuanxing Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Peng Xu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zheng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yujiao Deng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Dai Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xueting Ren
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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James CD, Saini S, Sesay F, Ko K, Felthousen-Rusbasan J, Iness AN, Nulton T, Windle B, Dozmorov MG, Morgan IM, Litovchick L. Restoring the DREAM Complex Inhibits the Proliferation of High-Risk HPV Positive Human Cells. Cancers (Basel) 2021; 13:489. [PMID: 33513914 PMCID: PMC7866234 DOI: 10.3390/cancers13030489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 11/28/2022] Open
Abstract
High-risk (HR) human papillomaviruses are known causative agents in 5% of human cancers including cervical, ano-genital and head and neck carcinomas. In part, HR-HPV causes cancer by targeting host-cell tumor suppressors including retinoblastoma protein (pRb) and RB-like proteins p107 and p130. HR-HPV E7 uses a LxCxE motif to bind RB proteins, impairing their ability to control cell-cycle dependent transcription. E7 disrupts DREAM (Dimerization partner, RB-like, E2F and MuvB), a transcriptional repressor complex that can include p130 or p107, but not pRb, which regulates genes required for cell cycle progression. However, it is not known whether disruption of DREAM plays a significant role in HPV-driven tumorigenesis. In the DREAM complex, LIN52 is an adaptor that binds directly to p130 via an E7-like LxSxE motif. Replacement of the LxSxE sequence in LIN52 with LxCxE (LIN52-S20C) increases p130 binding and partially restores DREAM assembly in HPV-positive keratinocytes and human cervical cancer cells, inhibiting proliferation. Our findings demonstrate that disruption of the DREAM complex by E7 is an important process promoting cellular proliferation by HR-HPV. Restoration of the DREAM complex in HR-HPV positive cells may therefore have therapeutic benefits in HR-HPV positive cancers.
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Affiliation(s)
- Claire D. James
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
| | - Siddharth Saini
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
| | - Fatmata Sesay
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
| | - Kevin Ko
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
| | - Jessica Felthousen-Rusbasan
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
| | - Audra N. Iness
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
| | - Tara Nulton
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
| | - Brad Windle
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
- Massey Cancer Center, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA;
- Department of Pathology, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
| | - Iain M. Morgan
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
- Massey Cancer Center, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
| | - Larisa Litovchick
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
- Massey Cancer Center, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
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Sirtuin 5 Is Regulated by the SCF Cyclin F Ubiquitin Ligase and Is Involved in Cell Cycle Control. Mol Cell Biol 2021; 41:MCB.00269-20. [PMID: 33168699 DOI: 10.1128/mcb.00269-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/03/2020] [Indexed: 12/31/2022] Open
Abstract
The ubiquitin-proteasome system is essential for cell cycle progression. Cyclin F is a cell cycle-regulated substrate adapter F-box protein for the Skp1, CUL1, and F-box protein (SCF) family of E3 ubiquitin ligases. Despite its importance in cell cycle progression, identifying cyclin F-bound SCF complex (SCFCyclin F) substrates has remained challenging. Since cyclin F overexpression rescues a yeast mutant in the cdc4 gene, we considered the possibility that other genes that genetically modify cdc4 mutant lethality could also encode cyclin F substrates. We identified the mitochondrial and cytosolic deacylating enzyme sirtuin 5 (SIRT5) as a novel cyclin F substrate. SIRT5 has been implicated in metabolic processes, but its connection to the cell cycle is not known. We show that cyclin F interacts with and controls the ubiquitination, abundance, and stability of SIRT5. We show SIRT5 knockout results in a diminished G1 population and a subsequent increase in both S and G2/M. Global proteomic analyses reveal cyclin-dependent kinase (CDK) signaling changes congruent with the cell cycle changes in SIRT5 knockout cells. Together, these data demonstrate that SIRT5 is regulated by cyclin F and suggest a connection between SIRT5, cell cycle regulation, and metabolism.
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135
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Morris BB, Wages NA, Grant PA, Stukenberg PT, Gentzler RD, Hall RD, Akerley WL, Varghese TK, Arnold SM, Williams TM, Coppola V, Jones DR, Auble DT, Mayo MW. MYBL2-Driven Transcriptional Programs Link Replication Stress and Error-prone DNA Repair With Genomic Instability in Lung Adenocarcinoma. Front Oncol 2021; 10:585551. [PMID: 33489883 PMCID: PMC7821388 DOI: 10.3389/fonc.2020.585551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/16/2020] [Indexed: 12/21/2022] Open
Abstract
It has long been recognized that defects in cell cycle checkpoint and DNA repair pathways give rise to genomic instability, tumor heterogeneity, and metastasis. Despite this knowledge, the transcription factor-mediated gene expression programs that enable survival and proliferation in the face of enormous replication stress and DNA damage have remained elusive. Using robust omics data from two independent studies, we provide evidence that a large cohort of lung adenocarcinomas exhibit significant genome instability and overexpress the DNA damage responsive transcription factor MYB proto-oncogene like 2 (MYBL2). Across two studies, elevated MYBL2 expression was a robust marker of poor overall survival and disease-free survival outcomes, regardless of disease stage. Clinically, elevated MYBL2 expression identified patients with aggressive early onset disease, increased lymph node involvement, and increased incidence of distant metastases. Analysis of genomic sequencing data demonstrated that MYBL2 High lung adenocarcinomas had elevated somatic mutation burden, widespread chromosomal alterations, and alterations in single-strand DNA break repair pathways. In this study, we provide evidence that impaired single-strand break repair, combined with a loss of cell cycle regulators TP53 and RB1, give rise to MYBL2-mediated transcriptional programs. Omics data supports a model wherein tumors with significant genomic instability upregulate MYBL2 to drive genes that control replication stress responses, promote error-prone DNA repair, and antagonize faithful homologous recombination repair. Our study supports the use of checkpoint kinase 1 (CHK1) pharmacological inhibitors, in targeted MYBL2 High patient cohorts, as a future therapy to improve lung adenocarcinoma patient outcomes.
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Affiliation(s)
- Benjamin B. Morris
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Department of Pathology, University of Virginia, Charlottesville, VA, United States
| | - Nolan A. Wages
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Patrick A. Grant
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL, United States
| | - P. Todd Stukenberg
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Ryan D. Gentzler
- Division of Medical Oncology, Department of Internal Medicine, Hematology/Oncology, University of Virginia Health System, Charlottesville, VA, United States
| | - Richard D. Hall
- Division of Medical Oncology, Department of Internal Medicine, Hematology/Oncology, University of Virginia Health System, Charlottesville, VA, United States
| | - Wallace L. Akerley
- Department of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, Salt Lake City, UT, United States
| | - Thomas K. Varghese
- Division of Thoracic Surgery, Department of Surgery, University of Utah, Salt Lake City, UT, United States
| | - Susanne M. Arnold
- Department of Internal Medicine, Division of Medical Oncology, Markey Cancer Center, Lexington, KY, United States
| | - Terence M. Williams
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - David R. Jones
- Department of Thoracic Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, United States
| | - David T. Auble
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Marty W. Mayo
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
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136
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Jiang AM, Ren MD, Liu N, Gao H, Wang JJ, Zheng XQ, Fu X, Liang X, Ruan ZP, Tian T, Yao Y. Tumor Mutation Burden, Immune Cell Infiltration, and Construction of Immune-Related Genes Prognostic Model in Head and Neck Cancer. Int J Med Sci 2021; 18:226-238. [PMID: 33390791 PMCID: PMC7738958 DOI: 10.7150/ijms.51064] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide, and the prognosis of HNSCC remains bleak. Numerous studies revealed that the tumor mutation burden (TMB) could predict the survival outcomes of a variety of tumors. Objectives: This study aimed to investigate the TMB and immune cell infiltration in these patients and construct an immune-related genes (IRGs) prognostic model. Methods: The expression data of 546 HNSCC patients were obtained from The Cancer Genome Atlas (TCGA) database. All patients were divided into high- and low- TMB groups, and the relationship between TMB and clinical relevance was further analyzed. The differentially expressed genes (DEGs) were identified using the R software package, limma. Functional enrichment analyses were conducted to identify the significantly enriched pathways between two groups. CIBERSORT algorithm was adopted to calculate the abundance of 22 leukocyte subtypes. The IRGs prognostic model was constructed via the multivariate Cox regression analysis. Results: Missense mutation and single nucleotide variants (SNV) were the most predominant mutation types in HNSCC. TP53, TTN, and FAT1 were the most frequently mutated genes. Patients with high TMB were observed with worse survival outcomes. The functional analysis of TMB associated DEGs showed that the identified DEGs mainly involved in spliceosome, RNA degradation, proteasome, and RNA polymerase pathways. We observed that macrophages, T cells CD8, and T cells CD4 memory were the most commonly infiltrated subtypes of immune cells in HNSCC. Finally, an IRGs prognostic model was constructed, and the AUC of the ROC curve was 0.635. Conclusions: Our results suggest that high TMB is associated with poor prognosis in HNSCC patients. The constructed model has potential prognostic value for the prognosis of these individuals, and it needs to be further validated in large-scale and prospective studies.
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Affiliation(s)
- Ai-Min Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Meng-Di Ren
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Na Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Jing-Jing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xiao-Qiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xuan Liang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Zhi-Ping Ruan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Tao Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
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Allmann S, Mayer L, Olma J, Kaina B, Hofmann TG, Tomicic MT, Christmann M. Benzo[a]pyrene represses DNA repair through altered E2F1/E2F4 function marking an early event in DNA damage-induced cellular senescence. Nucleic Acids Res 2020; 48:12085-12101. [PMID: 33166399 PMCID: PMC7708059 DOI: 10.1093/nar/gkaa965] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/25/2020] [Accepted: 10/16/2020] [Indexed: 01/08/2023] Open
Abstract
Transcriptional regulation of DNA repair is of outmost importance for the restoration of DNA integrity upon genotoxic stress. Here we report that the potent environmental carcinogen benzo[a]pyrene (B[a]P) activates a cellular DNA damage response resulting in transcriptional repression of mismatch repair (MMR) genes (MSH2, MSH6, EXO1) and of RAD51, the central homologous recombination repair (HR) component, ultimately leading to downregulation of MMR and HR. B[a]P-induced gene repression is caused by abrogated E2F1 signalling. This occurs through proteasomal degradation of E2F1 in G2-arrested cells and downregulation of E2F1 mRNA expression in G1-arrested cells. Repression of E2F1-mediated transcription and silencing of repair genes is further mediated by the p21-dependent E2F4/DREAM complex. Notably, repression of DNA repair is also observed following exposure to the active B[a]P metabolite BPDE and upon ionizing radiation and occurs in response to a p53/p21-triggered, irreversible cell cycle arrest marking the onset of cellular senescence. Overall, our results suggest that repression of MMR and HR is an early event during genotoxic-stress induced senescence. We propose that persistent downregulation of DNA repair might play a role in the maintenance of the senescence phenotype, which is associated with an accumulation of unrepairable DNA lesions.
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Affiliation(s)
- Sebastian Allmann
- Institute of Toxicology, University Medical Center, Johannes Gutenberg University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Laura Mayer
- Institute of Toxicology, University Medical Center, Johannes Gutenberg University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Jessika Olma
- Institute of Toxicology, University Medical Center, Johannes Gutenberg University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Johannes Gutenberg University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center, Johannes Gutenberg University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Maja T Tomicic
- Institute of Toxicology, University Medical Center, Johannes Gutenberg University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Markus Christmann
- Institute of Toxicology, University Medical Center, Johannes Gutenberg University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
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138
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High Risk α-HPV E6 Impairs Translesion Synthesis by Blocking POLη Induction. Cancers (Basel) 2020; 13:cancers13010028. [PMID: 33374731 PMCID: PMC7793514 DOI: 10.3390/cancers13010028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 01/22/2023] Open
Abstract
Simple Summary Cervical cancers (CaCx) are caused by the expression of human papillomavirus oncogenes (HPV E6 and E7). Here, in vitro assays, computational approaches and immunohistochemical analysis of cervical biopsies show that HPV oncogenes impair translesion synthesis (TLS). This limits the pathway’s ability to prevent replication stress from causing fork collapse and DNA damage. As a result, HPV oncogenes make cells more sensitive to replication stressing agents, such as Cisplatin. Mechanistically, HPV E6 prevents replication stress from triggering the accumulation of a TLS-specific polymerase (POLη). Supplying exogenous POLη to CaCx cells rescues TLS and lowers Cisplatin toxicity. Abstract High risk genus α human papillomaviruses (α-HPVs) express two versatile oncogenes (α-HPV E6 and E7) that cause cervical cancer (CaCx) by degrading tumor suppressor proteins (p53 and RB). α-HPV E7 also promotes replication stress and alters DNA damage responses (DDR). The translesion synthesis pathway (TLS) mitigates DNA damage by preventing replication stress from causing replication fork collapse. Computational analysis of gene expression in CaCx transcriptomic datasets identified a frequent increased expression of TLS genes. However, the essential TLS polymerases did not follow this pattern. These data were confirmed with in vitro and ex vivo systems. Further interrogation of TLS, using POLη as a representative TLS polymerase, demonstrated that α-HPV16 E6 blocks TLS polymerase induction by degrading p53. This doomed the pathway, leading to increased replication fork collapse and sensitivity to treatments that cause replication stress (e.g., UV and Cisplatin). This sensitivity could be overcome by the addition of exogenous POLη.
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139
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Riege K, Kretzmer H, Sahm A, McDade SS, Hoffmann S, Fischer M. Dissecting the DNA binding landscape and gene regulatory network of p63 and p53. eLife 2020; 9:e63266. [PMID: 33263276 PMCID: PMC7735755 DOI: 10.7554/elife.63266] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
The transcription factor p53 is the best-known tumor suppressor, but its sibling p63 is a master regulator of epidermis development and a key oncogenic driver in squamous cell carcinomas (SCC). Despite multiple gene expression studies becoming available, the limited overlap of reported p63-dependent genes has made it difficult to decipher the p63 gene regulatory network. Particularly, analyses of p63 response elements differed substantially among the studies. To address this intricate data situation, we provide an integrated resource that enables assessing the p63-dependent regulation of any human gene of interest. We use a novel iterative de novo motif search approach in conjunction with extensive ChIP-seq data to achieve a precise global distinction between p53-and p63-binding sites, recognition motifs, and potential co-factors. We integrate these data with enhancer:gene associations to predict p63 target genes and identify those that are commonly de-regulated in SCC representing candidates for prognosis and therapeutic interventions.
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Affiliation(s)
- Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University BelfastBelfastUnited Kingdom
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
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140
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Abstract
Head and neck squamous cell carcinoma (HNSCC) associated with high-risk human papilloma virus (HPV) infection is a growing clinical problem. The WEE1 kinase inhibitor AZD1775 (WEE1i) overrides cell cycle checkpoints and is being studied in HNSCC regimens. We show that the HPV16 E6/E7 oncoproteins sensitize HNSCC cells to single-agent WEE1i treatment through activation of a FOXM1-CDK1 circuit that drives mitotic gene expression and DNA damage. An isogenic cell system indicated that E6 largely accounts for these phenotypes in ways that extend beyond p53 inactivation. A targeted genomic analysis implicated FOXM1 signaling downstream of E6/E7 expression and analyses of primary tumors and The Cancer Genome Atlas (TCGA) data revealed an activated FOXM1-directed promitotic transcriptional signature in HPV+ versus HPV- HNSCCs. Finally, we demonstrate the causality of FOXM1 in driving WEE1i sensitivity. These data suggest that elevated basal FOXM1 activity predisposes HPV+ HNSCC to WEE1i-induced toxicity and provide mechanistic insights into WEE1i and HPV+ HNSCC therapies.
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141
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P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development. Biosci Rep 2020; 39:221381. [PMID: 31789342 PMCID: PMC6914664 DOI: 10.1042/bsr20192114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/15/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022] Open
Abstract
TP63 is a member of the TP53 gene family, sharing a common gene structure that produces two groups of mRNAs' encoding proteins with different N-terminal regions (ΔN and TA isoforms); both transcripts are also subjected to alternative splicing mechanisms at C-terminus, generating a variety of isoforms. p63 is a master regulator of epidermal development and homoeostasis as well as an important player in tumorigenesis and cancer progression with both oncogenic and tumour suppressive roles. A number of studies have aimed at the identification of p63 target genes, allowing the dissection of the molecular pathways orchestrated by the different isoforms. In the present study we investigated in more detail the p63 responsiveness of the WDFY2 (WD repeat and FYVE domain containing 2) gene, encoding for an endosomal protein identified as a binding partner of the PI-3K/AKT signalling pathway. We showed that overexpression of different p63 isoforms was able to induce WDFY2 expression in TP53-null cells. The p63-dependent transcriptional activation was associated with specific response elements (REs) that have been identified by a bioinformatics tool and validated by yeast- and mammal-based assays. Interestingly, to confirm that WDFY2 belongs to the p63 network of cancer regulation, we analysed the impact of WDFY2 alterations, by showing its frequent deletion in different types of tumours and suggesting its expression level as a prognostic biomarker. Lastly, we identified a chromosomal translocation involving the WDFY2 locus in a patient affected by a rare congenital limb anomaly, indicating WDFY2 as a possible susceptibility gene placed downstream p63 in the network of limb development.
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142
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Sammons MA, Nguyen TAT, McDade SS, Fischer M. Tumor suppressor p53: from engaging DNA to target gene regulation. Nucleic Acids Res 2020; 48:8848-8869. [PMID: 32797160 PMCID: PMC7498329 DOI: 10.1093/nar/gkaa666] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/24/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
The p53 transcription factor confers its potent tumor suppressor functions primarily through the regulation of a large network of target genes. The recent explosion of next generation sequencing protocols has enabled the study of the p53 gene regulatory network (GRN) and underlying mechanisms at an unprecedented depth and scale, helping us to understand precisely how p53 controls gene regulation. Here, we discuss our current understanding of where and how p53 binds to DNA and chromatin, its pioneer-like role, and how this affects gene regulation. We provide an overview of the p53 GRN and the direct and indirect mechanisms through which p53 affects gene regulation. In particular, we focus on delineating the ubiquitous and cell type-specific network of regulatory elements that p53 engages; reviewing our understanding of how, where, and when p53 binds to DNA and the mechanisms through which these events regulate transcription. Finally, we discuss the evolution of the p53 GRN and how recent work has revealed remarkable differences between vertebrates, which are of particular importance to cancer researchers using mouse models.
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Affiliation(s)
- Morgan A Sammons
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Thuy-Ai T Nguyen
- Genome Integrity & Structural Biology Laboratory and Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
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143
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Sun JH, Hou JP, Kang YZ. Clinical significance of expression of PPP1R105 in hepatocellular carcinoma. Shijie Huaren Xiaohua Zazhi 2020; 28:765-776. [DOI: 10.11569/wcjd.v28.i16.765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common malignant tumor with a poor prognosis. In this study, we evaluated the expression of the PPP1R105 gene in HCC and its relationship with prognosis through bioinformatics analysis. Then, we used immunohistochemistry to verify the expression of PPP1R105 protein.
AIM To investigate the expression of PPP1R105 (Ki-67 or MKI67) in HCC and its clinical significance.
METHODS The relative expression data of the PPP1R105 gene in various tumor tissues were retrieved from the tumor protein database and TCGA database and compared between cancer and paired normal tissues. The protein-protein interaction network (PPI) of PPP1R105 was constructed by using the STRING database. The progression free survival (DFS) and overall survival (OS) between the high and low PPP1R105 expression groups were compared. Eighty-one HCC patients who underwent surgery were retrospectively included in the study, and PPP1R105 protein expression was detected by immunohistochemistry. The relationship between PPP1R105 protein expression and patients' features was evaluated.
RESULTS The expression levels of PPP1R105 mRNA in different tumors were not significantly different. In HCC, the expression level of PPP1R105 mRNA was significantly higher than that of normal liver tissue, and the expression level was related with clinical stage. The aggregation index of PPI was 0.99, and the enrichment of protein interaction network was significant (P < 0.01). PPP1R105 was mainly enriched in cell cycle, cell aging, virus carcinogenesis, and p53 signaling pathway. The positive correlation between KIF18B and PPP1R105 was the most significant (rperson = 0.91, P < 0.05), while the negative correlation between MCELL and PPP1R105 was the most significant (rperson = -0.59, P < 0.05). DFS (HR = 1.90, P < 0.01) and OS (HR = 1.90, P < 0.01) in the high PPP1R105 expression group were significantly shorter than those in the low expression group. PPP1R105 protein was mainly expressed in the cytoplasm and nucleolus of the cells. Of the included 81 patients, 30 (37.0%) showed high expression of PPP1R105 protein. The proportion of patients with high expression of PPP1R105 protein was higher than that of patients with low expression of MIK67 protein (P < 0.05).
CONCLUSION PPP1R105 is highly expressed in patients with HCC, which is related to a poor DFS and OS. PPP1R105 can be used as a poor prognostic molecular marker in HCC.
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Affiliation(s)
- Jian-He Sun
- Department of Hepatobiliary Surgery, People's Hospital of Baodi District, Tianjin 301800, China
| | - Ji-Ping Hou
- Department of Hepatobiliary Surgery, People's Hospital of Baodi District, Tianjin 301800, China
| | - Yong-Zhen Kang
- Department of Hepatobiliary Surgery, People's Hospital of Baodi District, Tianjin 301800, China
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144
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Pan Z, Li L, Qian Y, Ge X, Hu X, Zhang Y, Ge M, Huang P. The differences of regulatory networks between papillary and anaplastic thyroid carcinoma: an integrative transcriptomics study. Cancer Biol Ther 2020; 21:853-862. [PMID: 32887540 DOI: 10.1080/15384047.2020.1803009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Unlike papillary thyroid cancer (PTC), anaplastic thyroid carcinoma (ATC) is extremely aggressive and rapidly lethal without effective therapies. However, the differences of master regulators and regulatory networks between PTC and ATC remain unclear. Methods: Three representative datasets comprising 32 ATC, 69 PTC, and 78 normal thyroid tissue samples were combined to form a large dataset. Differentially expressed genes (DEGs) were identified and enriched by limma package and gene set enrichment analysis, respectively. Subsequently, protein-protein interaction network and transcription factors (TFs) regulatory network were constructed to identify gene modules and master regulators. Further, master regulators were validated by RT-PCR and western blot. Finally, Kaplan-Meier plotter was applied to evaluate their prognostic values. Results: A total of 560 DEGs were identified as ATC-specific malignant signature. The regulatory network analysis showed that nine master regulators were significantly correlated with three gene modules and potentially regulated the expression of DEGs in three gene modules, respectively. Furthermore, CREB3L1, FOSL2, E2F1 and CAT were significantly associated with overall survival of thyroid cancer patients. FOXM1, FOSL2, MYBL2, AVEN and E2F1 were unfavorable factors of recurrence-free survival (RFS), while CAT was a favorable factor of RFS. RT-PCR and western blot confirmed that six TFs were obviously up-regulated in ATC tissues/cell line as compared with PTC and normal thyroid tissues/cell lines, respectively. In addition, 19 ATC-specific kinases were identified to illustrate the potential post-translational modification. Conclusions: Our findings provide a comprehensive insight into malignant mechanism of ATC, which may indicate their value in the future investigation of ATC.
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Affiliation(s)
- Zongfu Pan
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College , Hangzhou, China
| | - Lu Li
- Department of Pharmacy, The First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, China
| | - Yangyang Qian
- Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College , Hangzhou, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital , Hangzhou, China
| | - Xinyang Ge
- Student Council Blood Drive Committee, Heartland Christian School , Columbiana, OH, USA
| | - Xiaoping Hu
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College , Hangzhou, China
| | - Yiwen Zhang
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College , Hangzhou, China
| | - Minghua Ge
- Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College , Hangzhou, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital , Hangzhou, China
| | - Ping Huang
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College , Hangzhou, China
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145
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Pattschull G, Walz S, Gründl M, Schwab M, Rühl E, Baluapuri A, Cindric-Vranesic A, Kneitz S, Wolf E, Ade CP, Rosenwald A, von Eyss B, Gaubatz S. The Myb-MuvB Complex Is Required for YAP-Dependent Transcription of Mitotic Genes. Cell Rep 2020; 27:3533-3546.e7. [PMID: 31216474 DOI: 10.1016/j.celrep.2019.05.071] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/18/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
YAP and TAZ, downstream effectors of the Hippo pathway, are important regulators of proliferation. Here, we show that the ability of YAP to activate mitotic gene expression is dependent on the Myb-MuvB (MMB) complex, a master regulator of genes expressed in the G2/M phase of the cell cycle. By carrying out genome-wide expression and binding analyses, we found that YAP promotes binding of the MMB subunit B-MYB to the promoters of mitotic target genes. YAP binds to B-MYB and stimulates B-MYB chromatin association through distal enhancer elements that interact with MMB-regulated promoters through chromatin looping. The cooperation between YAP and B-MYB is critical for YAP-mediated entry into mitosis. Furthermore, the expression of genes coactivated by YAP and B-MYB is associated with poor survival of cancer patients. Our findings provide a molecular mechanism by which YAP and MMB regulate mitotic gene expression and suggest a link between two cancer-relevant signaling pathways.
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Affiliation(s)
- Grit Pattschull
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Susanne Walz
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Marco Gründl
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Melissa Schwab
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Eva Rühl
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Wuerzburg, Wuerzburg 97074, Germany
| | | | - Susanne Kneitz
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Carsten P Ade
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Andreas Rosenwald
- Institute of Pathology and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg 97080, Germany
| | - Björn von Eyss
- Leibniz Institute on Aging, Fritz Lipmann Institute e.V., Jena 07745, Germany
| | - Stefan Gaubatz
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany.
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146
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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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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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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: 59] [Impact Index Per Article: 14.8] [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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149
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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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150
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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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