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Nuclear Dynamics and Chromatin Structure: Implications for Pancreatic Cancer. Cells 2021; 10:cells10102624. [PMID: 34685604 PMCID: PMC8534098 DOI: 10.3390/cells10102624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
Changes in nuclear shape have been extensively associated with the dynamics and functionality of cancer cells. In most normal cells, nuclei have a regular ellipsoid shape and minimal variation in nuclear size; however, an irregular nuclear contour and abnormal nuclear size is often observed in cancer, including pancreatic cancer. Furthermore, alterations in nuclear morphology have become the 'gold standard' for tumor staging and grading. Beyond the utility of altered nuclear morphology as a diagnostic tool in cancer, the implications of altered nuclear structure for the biology and behavior of cancer cells are profound as changes in nuclear morphology could impact cellular responses to physical strain, adaptation during migration, chromatin organization, and gene expression. Here, we aim to highlight and discuss the factors that regulate nuclear dynamics and their implications for pancreatic cancer biology.
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Azoulay D, Sonkin V, Akria L, Rozano Gorelick A, Trakhtenbrot L, Hershkovitz D, Shaoul E, Rozen S, Dementiev E, Cohen HI, Suriu C, Braester A. Hairy cell leukemia-variant without typical morphology and with near-tetraploid DNA content. CYTOMETRY PART B-CLINICAL CYTOMETRY 2017; 94:169-171. [DOI: 10.1002/cyto.b.21503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/04/2016] [Accepted: 12/12/2016] [Indexed: 11/08/2022]
Affiliation(s)
- David Azoulay
- Department of Hematology; Galilee Medical Center; Nahariya Israel
| | - Vadim Sonkin
- Department of Pathology; Galilee Medical Center; Nahariya Israel
| | - Luiza Akria
- Department of Hematology; Galilee Medical Center; Nahariya Israel
| | | | | | - Dov Hershkovitz
- Department of Pathology; Rambam Health Care Campus; Haifa Israel
| | - Ety Shaoul
- Department of Hematology; Galilee Medical Center; Nahariya Israel
| | - Simona Rozen
- Department of Hematology; Galilee Medical Center; Nahariya Israel
| | - Eugene Dementiev
- Department of Pathology; Galilee Medical Center; Nahariya Israel
| | - Hector I Cohen
- Department of Pathology; Galilee Medical Center; Nahariya Israel
| | - Celia Suriu
- Department of Hematology; Galilee Medical Center; Nahariya Israel
| | - Andrei Braester
- Department of Hematology; Galilee Medical Center; Nahariya Israel
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Lyons SM, Achorn C, Kedersha NL, Anderson PJ, Ivanov P. YB-1 regulates tiRNA-induced Stress Granule formation but not translational repression. Nucleic Acids Res 2016; 44:6949-60. [PMID: 27174937 PMCID: PMC5001593 DOI: 10.1093/nar/gkw418] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/30/2016] [Indexed: 12/16/2022] Open
Abstract
Stress-induced angiogenin (ANG)-mediated tRNA cleavage promotes a cascade of cellular events that starts with production of tRNA-derived stress-induced RNAs (tiRNAs) and culminates with enhanced cell survival. This stress response program relies on a subset tiRNAs that inhibit translation initiation and induce the assembly of stress granules (SGs), cytoplasmic ribonucleoprotein complexes with cytoprotective and pro-survival properties. SG-promoting tiRNAs bear oligoguanine motifs at their 5'-ends, assemble G-quadruplex-like structures and interact with the translational silencer YB-1. We used CRISPR/Cas9-based genetic manipulations and biochemical approaches to examine the role of YB-1 in tiRNA-mediated translational repression and SG assembly. We found that YB-1 directly binds to tiRNAs via its cold shock domain. This interaction is required for packaging of tiRNA-repressed mRNAs into SGs but is dispensable for tiRNA-mediated translational repression. Our studies reveal the functional role of YB-1 in the ANG-mediated stress response program.
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Affiliation(s)
- Shawn M Lyons
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Chris Achorn
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Nancy L Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA Department of Medicine, Harvard Medical School, Boston, MA 02115, USA The Broad Institute of Harvard and M.I.T., Cambridge, MA 02142, USA
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Lorenzin F, Benary U, Baluapuri A, Walz S, Jung LA, von Eyss B, Kisker C, Wolf J, Eilers M, Wolf E. Different promoter affinities account for specificity in MYC-dependent gene regulation. eLife 2016; 5. [PMID: 27460974 PMCID: PMC4963202 DOI: 10.7554/elife.15161] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells. DOI:http://dx.doi.org/10.7554/eLife.15161.001 Genes with the potential to cause tumors and cancer are commonly called oncogenes. One example of an oncogene encodes for a protein called MYC and many tumors contain high levels of this protein. MYC is a transcription factor and studies of aggressive tumors suggested that, like most other transcription factors, MYC binds to and regulates the activity of a small number of genes in tumors. However, other studies went on to show that MYC actually binds to thousands of genes and somehow only regulates a subset of them during tumor development. Lorenzin et al. set out to understand how this process works by generating human cells in which the concentration of MYC protein could be altered. In the experiments, the concentration was varied from normal healthy levels to the high levels found in aggressive tumors. The amount of MYC bound to genes and the extent to which it activated the genes inside these cells was also measured. Lorenzin et al. found that increasing MYC levels from normal to tumor-specific levels did not affect MYC binding at genes where the transcription factor was already strongly bound in normal cells. Rather, MYC binding increased only at genes that were weakly bound in normal cells. Consistent with this observation, only genes at which MYC was weakly bound in normal cells were activated by increasing MYC levels. This observation suggests that increasing the concentration of MYC protein from normal to tumor-specific levels “fills up” previously empty binding sites around these genes with the transcription factor. Lorenzin et al. also used mathematical modeling to understand how the concentrations of MYC in normal and tumor cells might explain how MYC behaves in cells. Together, the results imply that the MYC transcription factor regulates distinct sets of genes in normal and tumor cells according to how much MYC is present. Further studies may show that the altered regulation of a tumor-specific set of genes is important for tumor development and could use this new information to identify new targets for treating MYC-driven tumors. DOI:http://dx.doi.org/10.7554/eLife.15161.002
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Affiliation(s)
- Francesca Lorenzin
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Uwe Benary
- Group Mathematical Modeling of Cellular Processes, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Apoorva Baluapuri
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Susanne Walz
- Core Unit Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Lisa Anna Jung
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany.,Rudolf-Virchow-Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Björn von Eyss
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caroline Kisker
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Jana Wolf
- Group Mathematical Modeling of Cellular Processes, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Elmar Wolf
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
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Pinder J, Salsman J, Dellaire G. Nuclear domain 'knock-in' screen for the evaluation and identification of small molecule enhancers of CRISPR-based genome editing. Nucleic Acids Res 2015; 43:9379-92. [PMID: 26429972 PMCID: PMC4627099 DOI: 10.1093/nar/gkv993] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 09/21/2015] [Indexed: 12/31/2022] Open
Abstract
CRISPR is a genome-editing platform that makes use of the bacterially-derived endonuclease Cas9 to introduce DNA double-strand breaks at precise locations in the genome using complementary guide RNAs. We developed a nuclear domain knock-in screen, whereby the insertion of a gene encoding the green fluorescent protein variant Clover is inserted by Cas9-mediated homology directed repair (HDR) within the first exon of genes that are required for the structural integrity of subnuclear domains such as the nuclear lamina and promyelocytic leukemia nuclear bodies (PML NBs). Using this approach, we compared strategies for enhancing CRISPR-mediated HDR, focusing on known genes and small molecules that impact non-homologous end joining (NHEJ) and homologous recombination (HR). Ultimately, we identified the small molecule RS-1 as a potent enhancer of CRISPR-based genome editing, enhancing HDR 3- to 6-fold depending on the locus and transfection method. We also characterized U2OS human osteosarcoma cells expressing Clover-tagged PML and demonstrate that this strategy generates cell lines with PML NBs that are structurally and functionally similar to bodies in the parental cell line. Thus, the nuclear domain knock-in screen that we describe provides a simple means of rapidly evaluating methods and small molecules that have the potential to enhance Cas9-mediated HDR.
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Affiliation(s)
- Jordan Pinder
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, B3H 4R2, Canada
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Zhang G, He LS, Wong YH, Yu L, Qian PY. siRNA transfection in the barnacle Amphibalanus amphitrite larvae. J Exp Biol 2015; 218:2505-9. [DOI: 10.1242/jeb.120113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/15/2015] [Indexed: 01/20/2023]
Abstract
RNA interference (RNAi) provides an efficient and specific technique for functional genomic studies. Yet, no successful application of RNAi has been reported in barnacles. In this study, siRNA against p38 MAPK was synthesized and then transfected into A. amphitrite larvae at either nauplius or cyprid stage, or both. Effects of siRNA transfection on p38 MAPK level were hardly detectable in the cyprids that their corresponding nauplii were transfected. In contrast, larvae that were transfected at cyprid stage showed lower level of p38 MAPK than the blank and reagent controls. However, significantly decreased level of phosphorylated p38 MAPK (pp38 MAPK) and reduced settlement rate were observed only in the “Double Transfection”, in which larvae were exposed to siRNA solution at both the nauplius and cyprid stages. Relatively longer transfection time and more cells of the larvae exposed to siRNA directly might explain the higher efficiency in the “Double Transfection”.
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Affiliation(s)
- Gen Zhang
- Environmental Science Programs, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Li-sheng He
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Science, No. 62, Fenghuang Road, Sanya City, Hainan Province, China, 572000
| | - Yue Him Wong
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Li Yu
- Environmental Science Programs, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Pei-yuan Qian
- Environmental Science Programs, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- KAUST Global Collaborative Research Program, Division of Life Science, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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