1
|
Rex EA, Seo D, Chappidi S, Pinkham C, Brito Oliveira S, Embry A, Heisler D, Liu Y, Munir M, Luger K, Alto NM, da Fonseca FG, Orchard R, Hancks DC, Gammon DB. FEAR antiviral response pathway is independent of interferons and countered by poxvirus proteins. Nat Microbiol 2024; 9:988-1006. [PMID: 38538832 DOI: 10.1038/s41564-024-01646-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
The human facilitates chromatin transcription (FACT) complex is a chromatin remodeller composed of human suppressor of Ty 16 homologue (hSpt16) and structure-specific recognition protein-1 subunits that regulates cellular gene expression. Whether FACT regulates host responses to infection remained unclear. We identify a FACT-mediated, interferon-independent, antiviral pathway that restricts poxvirus replication. Cell culture and bioinformatics approaches suggest that early viral gene expression triggers nuclear accumulation of SUMOylated hSpt16 subunits required for the expression of E26 transformation-specific sequence-1 (ETS-1)-a transcription factor that activates virus restriction programs. However, biochemical studies show that poxvirus-encoded A51R proteins block ETS-1 expression by outcompeting structure-specific recognition protein-1 binding to SUMOylated hSpt16 and by tethering SUMOylated hSpt16 to microtubules. Furthermore, A51R antagonism of FACT enhances poxvirus replication in human cells and virulence in mice. Finally, we show that FACT also restricts rhabdoviruses, flaviviruses and orthomyxoviruses, suggesting broad roles for FACT in antiviral immunity. Our study reveals the FACT-ETS-1 antiviral response (FEAR) pathway to be critical for eukaryotic antiviral immunity and describes a unique mechanism of viral immune evasion.
Collapse
Affiliation(s)
- Emily A Rex
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dahee Seo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sruthi Chappidi
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chelsea Pinkham
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sabrynna Brito Oliveira
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aaron Embry
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David Heisler
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Liu
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Moiz Munir
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Neal M Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Robert Orchard
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Don B Gammon
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
2
|
Wang P, Fan N, Yang W, Cao P, Liu G, Zhao Q, Guo P, Li X, Lin X, Jiang N, Nashun B. Transcriptional regulation of FACT involves Coordination of chromatin accessibility and CTCF binding. J Biol Chem 2024; 300:105538. [PMID: 38072046 PMCID: PMC10808957 DOI: 10.1016/j.jbc.2023.105538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Histone chaperone FACT (facilitates chromatin transcription) is well known to promote chromatin recovery during transcription. However, the mechanism how FACT regulates genome-wide chromatin accessibility and transcription factor binding has not been fully elucidated. Through loss-of-function studies, we show here that FACT component Ssrp1 is required for DNA replication and DNA damage repair and is also essential for progression of cell phase transition and cell proliferation in mouse embryonic fibroblast cells. On the molecular level, absence of the Ssrp1 leads to increased chromatin accessibility, enhanced CTCF binding, and a remarkable change in dynamic range of gene expression. Our study thus unequivocally uncovers a unique mechanism by which FACT complex regulates transcription by coordinating genome-wide chromatin accessibility and CTCF binding.
Collapse
Affiliation(s)
- Peijun Wang
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Na Fan
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wanting Yang
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China
| | - Pengbo Cao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China
| | - Guojun Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Qi Zhao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Pengfei Guo
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xihe Li
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animals, Hohhot, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
| | - Buhe Nashun
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| |
Collapse
|
3
|
Klein DC, Lardo SM, McCannell KN, Hainer SJ. FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells. BMC Biol 2023; 21:167. [PMID: 37542287 PMCID: PMC10403911 DOI: 10.1186/s12915-023-01669-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND The FACT complex is a conserved histone chaperone with critical roles in transcription and histone deposition. FACT is essential in pluripotent and cancer cells, but otherwise dispensable for most mammalian cell types. FACT deletion or inhibition can block induction of pluripotent stem cells, yet the mechanism through which FACT regulates cell fate decisions remains unclear. RESULTS To explore the mechanism for FACT function, we generated AID-tagged murine embryonic cell lines for FACT subunit SPT16 and paired depletion with nascent transcription and chromatin accessibility analyses. We also analyzed SPT16 occupancy using CUT&RUN and found that SPT16 localizes to both promoter and enhancer elements, with a strong overlap in binding with OCT4, SOX2, and NANOG. Over a timecourse of SPT16 depletion, nucleosomes invade new loci, including promoters, regions bound by SPT16, OCT4, SOX2, and NANOG, and TSS-distal DNaseI hypersensitive sites. Simultaneously, transcription of Pou5f1 (encoding OCT4), Sox2, Nanog, and enhancer RNAs produced from these genes' associated enhancers are downregulated. CONCLUSIONS We propose that FACT maintains cellular pluripotency through a precise nucleosome-based regulatory mechanism for appropriate expression of both coding and non-coding transcripts associated with pluripotency.
Collapse
Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Santana M Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Kurtis N McCannell
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
4
|
Chen X, Li M, Wang D, Wang Q, Wei X, Liu X, Yang J, Kalvakolanu DV, Guo B, Zhang L. Histone chaperone SSRP1 is required for apoptosis inhibition and mitochondrial function in HCC via transcriptional promotion of TRAP1. Biochem Cell Biol 2023; 101:361-376. [PMID: 37084412 DOI: 10.1139/bcb-2023-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Epigenetic regulation contributes to human health and disease, especially cancer, but the mechanisms of many epigenetic regulators remain obscure. Most research is focused on gene regulatory processes, such as mRNA translation and DNA damage repair, rather than the effects on biological functions like mitochondrial activity and oxidative phosphorylation. Here, we identified an essential role for the histone chaperone structure-specific recognition protein 1 (SSRP1) in mitochondrial oxidative respiration in hepatocellular carcinoma, and found that SSRP1 suppression led to mitochondrial damage and decreased oxidative respiration. Further, we focused on TNF receptor-associated protein 1 (TRAP1), the only member of the heat shock protein 90 (HSP90) family, which directly interacts with selected respiratory complexes and affects their stability and activity. We confirmed that SSRP1 downregulation caused a decrease in TRAP1 expression at both the mRNA and protein levels. A chromatin immunoprecipitation assay also showed that SSRP1 could deposit in the TRAP1 promoter region, indicating that SSRP1 maintains mitochondrial function and reactive oxygen species levels through TRAP1. Additionally, rescue experiments and animal experiments confirmed the mechanism of SSRP1 and TRAP1 interaction. In summary, we identified a new mechanism that connects mitochondrial respiration and apoptosis, via SSRP1.
Collapse
Affiliation(s)
- Xuyang Chen
- Key Laboratory of Pathobiology, Ministry of Education, and Department of pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Mengxin Li
- Key Laboratory of Pathobiology, Ministry of Education, and Department of pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Ding Wang
- Key Laboratory of Pathobiology, Ministry of Education, and Department of pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Qian Wang
- Key Laboratory of Pathobiology, Ministry of Education, and Department of pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Xiaodong Wei
- Key Laboratory of Pathobiology, Ministry of Education, and Department of pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Xiaorui Liu
- Key Laboratory of Pathobiology, Ministry of Education, and Department of pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Jiaying Yang
- Key Laboratory of Pathobiology, Ministry of Education, and Department of pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Dhan V Kalvakolanu
- Greenebaum NCI Comprehensive Cancer Center, Department of Microbiology and Immunology University of Maryland School Medicine, Baltimore, MD, USA
| | - Baofeng Guo
- Department of Plastic Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, China
| | - Ling Zhang
- Key Laboratory of Pathobiology, Ministry of Education, and Department of pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| |
Collapse
|
5
|
Djakovic L, Hennig T, Reinisch K, Milić A, Whisnant AW, Wolf K, Weiß E, Haas T, Grothey A, Jürges CS, Kluge M, Wolf E, Erhard F, Friedel CC, Dölken L. The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes. Nat Commun 2023; 14:4591. [PMID: 37524699 PMCID: PMC10390501 DOI: 10.1038/s41467-023-40217-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/19/2023] [Indexed: 08/02/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) infection and stress responses disrupt transcription termination by RNA Polymerase II (Pol II). In HSV-1 infection, but not upon salt or heat stress, this is accompanied by a dramatic increase in chromatin accessibility downstream of genes. Here, we show that the HSV-1 immediate-early protein ICP22 is both necessary and sufficient to induce downstream open chromatin regions (dOCRs) when transcription termination is disrupted by the viral ICP27 protein. This is accompanied by a marked ICP22-dependent loss of histones downstream of affected genes consistent with impaired histone repositioning in the wake of Pol II. Efficient knock-down of the ICP22-interacting histone chaperone FACT is not sufficient to induce dOCRs in ΔICP22 infection but increases dOCR induction in wild-type HSV-1 infection. Interestingly, this is accompanied by a marked increase in chromatin accessibility within gene bodies. We propose a model in which allosteric changes in Pol II composition downstream of genes and ICP22-mediated interference with FACT activity explain the differential impairment of histone repositioning downstream of genes in the wake of Pol II in HSV-1 infection.
Collapse
Affiliation(s)
- Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Katharina Reinisch
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Andrea Milić
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Adam W Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Katharina Wolf
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Elena Weiß
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Tobias Haas
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Arnhild Grothey
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Christopher S Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Mildred Scheel Early Career Center, University of Würzburg, Beethovenstraße 1A, 97080, Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany.
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), 97080, Würzburg, Germany.
| |
Collapse
|
6
|
Rex EA, Seo D, Chappidi S, Pinkham C, Oliveira SB, Embry A, Heisler D, Liu Y, Luger K, Alto NM, da Fonseca FG, Orchard R, Hancks D, Gammon DB. A FACT-ETS-1 Antiviral Response Pathway Restricts Viral Replication and is Countered by Poxvirus A51R Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527673. [PMID: 36798356 PMCID: PMC9934636 DOI: 10.1101/2023.02.08.527673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The FACT complex is an ancient chromatin remodeling factor comprised of Spt16 and SSRP1 subunits that regulates specific eukaryotic gene expression programs. However, whether FACT regulates host immune responses to infection was unclear. Here, we identify an antiviral pathway mediated by FACT, distinct from the interferon response, that restricts poxvirus replication. We show that early viral gene expression triggers nuclear accumulation of specialized, SUMOylated Spt16 subunits of FACT required for expression of ETS-1, a downstream transcription factor that activates a virus restriction program. However, poxvirus-encoded A51R proteins block ETS-1 expression by outcompeting SSRP1 for binding to SUMOylated Spt16 in the cytosol and by tethering SUMOylated Spt16 to microtubules. Moreover, we show that A51R antagonism of FACT enhances both poxvirus replication in human cells and viral virulence in mice. Finally, we demonstrate that FACT also restricts unrelated RNA viruses, suggesting a broad role for FACT in antiviral immunity. Our study reveals the F ACT- E TS-1 A ntiviral R esponse (FEAR) pathway to be critical for eukaryotic antiviral immunity and describes a unique mechanism of viral immune evasion.
Collapse
|
7
|
McCauley MJ, Morse M, Becker N, Hu Q, Botuyan MV, Navarrete E, Huo R, Muthurajan UM, Rouzina I, Luger K, Mer G, Maher LJ, Williams MC. Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes. Cell Rep 2022; 41:111858. [PMID: 36577379 PMCID: PMC9807050 DOI: 10.1016/j.celrep.2022.111858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/06/2022] [Accepted: 11/30/2022] [Indexed: 12/28/2022] Open
Abstract
The histone chaperone FACT (facilitates chromatin transcription) enhances transcription in eukaryotic cells, targeting DNA-protein interactions. FACT, a heterodimer in humans, comprises SPT16 and SSRP1 subunits. We measure nucleosome stability and dynamics in the presence of FACT and critical component domains. Optical tweezers quantify FACT/subdomain binding to nucleosomes, displacing the outer wrap of DNA, disrupting direct DNA-histone (core site) interactions, altering the energy landscape of unwrapping, and increasing the kinetics of DNA-histone disruption. Atomic force microscopy reveals nucleosome remodeling, while single-molecule fluorescence quantifies kinetics of histone loss for disrupted nucleosomes, a process accelerated by FACT. Furthermore, two isolated domains exhibit contradictory functions; while the SSRP1 HMGB domain displaces DNA, SPT16 MD/CTD stabilizes DNA-H2A/H2B dimer interactions. However, only intact FACT tethers disrupted DNA to the histones and supports rapid nucleosome reformation over several cycles of force disruption/release. These results demonstrate that key FACT domains combine to catalyze both nucleosome disassembly and reassembly.
Collapse
Affiliation(s)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Nicole Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Emily Navarrete
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Ran Huo
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Uma M. Muthurajan
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado, Boulder, CO, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA, USA,Lead contact,Correspondence:
| |
Collapse
|
8
|
Lu X, He Y, Johnston RL, Nanayakarra D, Sankarasubramanian S, Lopez JA, Friedlander M, Kalimutho M, Hooper JD, Raninga PV, Khanna KK. CBL0137 impairs homologous recombination repair and sensitizes high-grade serous ovarian carcinoma to PARP inhibitors. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:355. [PMID: 36539830 PMCID: PMC9769062 DOI: 10.1186/s13046-022-02570-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND High-grade serous ovarian carcinomas (HGSCs) are a heterogeneous subtype of epithelial ovarian cancers and include serous cancers arising in the fallopian tube and peritoneum. These cancers are now subdivided into homologous recombination repair (HR)-deficient and proficient subgroups as this classification impacts on management and prognosis. PARP inhibitors (PARPi) have shown significant clinical efficacy, particularly as maintenance therapy following response to platinum-based chemotherapy in BRCA-mutant or homologous recombination (HR)-deficient HGSCs in both the 1st and 2nd line settings. However, PARPi have limited clinical benefit in HR-proficient HGSCs which make up almost 50% of HGSC and improving outcomes in these patients is now a high priority due to the poor prognosis with ineffectiveness of the current standard of care. There are a number of potential lines of investigation including efforts in sensitizing HR-proficient tumors to PARPi. Herein, we aimed to develop a novel combination therapy by targeting SSRP1 using a small molecule inhibitor CBL0137 with PARPi in HR-proficient HGSCs. EXPERIMENTAL DESIGN We tested anti-cancer activity of CBL0137 monotherapy using a panel of HGSC cell lines and patient-derived tumor cells in vitro. RNA sequencing was used to map global transcriptomic changes in CBL0137-treated patient-derived HR-proficient HGSC cells. We tested efficacy of CBL0137 in combination with PARPi using HGSC cell lines and patient-derived tumor cells in vitro and in vivo. RESULTS We show that SSRP1 inhibition using a small molecule, CBL0137, that traps SSRP1 onto chromatin, exerts a significant anti-growth activity in vitro against HGSC cell lines and patient-derived tumor cells, and also reduces tumor burden in vivo. CBL0137 induced DNA repair deficiency via inhibition of the HR repair pathway and sensitized SSRP1-high HR-proficient HGSC cell lines and patient-derived tumor cells/xenografts to the PARPi, Olaparib in vitro and in vivo. CBL0137 also enhanced the efficacy of DNA damaging platinum-based chemotherapy in HGSC patient-derived xenografts. CONCLUSION Our findings strongly suggest that combination of CBL0137 and PARP inhibition represents a novel therapeutic strategy for HR-proficient HGSCs that express high levels of SSRP1 and should be investigated in the clinic.
Collapse
Affiliation(s)
- Xue Lu
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia ,grid.1022.10000 0004 0437 5432School of Environment and Sciences, Griffith University, Nathan, QLD 4111 Australia
| | - Yaowu He
- grid.489335.00000000406180938Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102 Australia
| | - Rebecca L. Johnston
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Devathri Nanayakarra
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Sivanandhini Sankarasubramanian
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - J. Alejandro Lopez
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia ,grid.1022.10000 0004 0437 5432School of Environment and Sciences, Griffith University, Nathan, QLD 4111 Australia
| | - Michael Friedlander
- grid.415193.bUniversity of New South Wales Clinical School, Prince of Wales Hospital, Randwick, NSW 2031 Australia
| | - Murugan Kalimutho
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - John D. Hooper
- grid.489335.00000000406180938Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102 Australia
| | - Prahlad V. Raninga
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| | - Kum Kum Khanna
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006 Australia
| |
Collapse
|
9
|
Jeronimo C, Robert F. The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 2022; 13:16-38. [PMID: 35485711 PMCID: PMC9467567 DOI: 10.1080/21541264.2022.2069995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
Collapse
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| |
Collapse
|
10
|
The Current Status of SSRP1 in Cancer: Tribulation and Road Ahead. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:3528786. [PMID: 35463672 PMCID: PMC9020922 DOI: 10.1155/2022/3528786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/21/2022] [Indexed: 12/03/2022]
Abstract
Methods We search PubMed and Web of Sciences with keywords “SSRP1” and “Cancer.” Only English literature was included, and conference papers and abstract were all excluded. Results Transcription factors are classified into three groups based on their DNA binding motifs: simple helix-loop-helix (bHLH), classical zinc fingers (ZF-TFs), and homeodomains. The tumor-suppressive miR-497 (microRNA-497) acted as an undesirable regulator of SSRP1 upregulation, which led to tumor growth. The siRNA (small interfering RNA) knockdown of SSRP1 hindered cell proliferation along with incursion and glioma cell migration. Through the AKT (also known as protein kinase B) signaling pathway, SSRP1 silencing affected cancer apoptosis and cell proliferation. Conclusion The MAPK (mitogen-activated protein kinase) signaling pathway's phosphorylation was suppressed when SSRP1 was depleted. The effect of curaxins on p53 and NF-B (nuclear factor-κB), and their toxicity to cancer cells, is attributable to the FACT (facilitates chromatin transcription) complex's chromatin trapping.
Collapse
|
11
|
Robust co-immunoprecipitation with mass spectrometry for Caenorhabditis elegans using solid-phase enhanced sample preparation. Biotechniques 2022; 72:175-184. [PMID: 35297663 DOI: 10.2144/btn-2021-0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Studying protein interactions in vivo can reveal key molecular mechanisms of biological processes. Co-immunoprecipitation with mass spectrometry detects protein-protein interactions with high throughput. The nematode Caenorhabditis elegans is a powerful genetic model organism for in vivo studies. Yet its rigid and complex tissues require optimization for biochemistry applications to ensure reproducibility. The authors optimized co-immunoprecipitation with mass spectrometry by combining a native co-immunoprecipitation procedure with single-pot, solid-phase enhanced sample preparation. The authors' results for the highly conserved chromatin regulator FACT subunits HMG-3 and HMG-4 demonstrated that single-pot, solid-phase enhanced sample preparation-integrated co-immunoprecipitation with mass spectrometry procedures for C. elegans samples are highly robust. Moreover, in an accompanying study about the chromodomain factor MRG-1 (MRG15 in humans), the authors demonstrated remarkably high reproducibility for ten replicate experiments.
Collapse
|
12
|
Goswami I, Sandlesh P, Stablewski A, Toshkov I, Safina AF, Magnitov M, Wang J, Gurova K. FACT maintains nucleosomes during transcription and stem cell viability in adult mice. EMBO Rep 2022; 23:e53684. [PMID: 35179289 PMCID: PMC8982582 DOI: 10.15252/embr.202153684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 12/14/2022] Open
Abstract
Preservation of nucleosomes during replication has been extensively studied, while the maintenance of nucleosomes during transcription has gotten less attention. The histone chaperone FACT has a role in transcription elongation, although whether it disassembles or assembles nucleosomes during this process is unclear. To elucidate the function of FACT in mammals, we deleted the Ssrp1 subunit of FACT in adult mice. FACT loss is lethal, possibly due to the loss of the earliest progenitors in bone marrow and intestine, while more differentiated cells are not affected. Using cells isolated from several tissues, we show that FACT loss reduces the viability of stem cells but not of cells differentiated in vitro. FACT depletion increases chromatin accessibility in a transcription-dependent manner in adipose mesenchymal stem cells, indicating that nucleosomes are lost in these cells during transcription in the absence of FACT. We also observe activation of interferon (IFN) signaling and the accumulation of immunocytes in organs sensitive to FACT loss. Our data indicate that FACT maintains chromatin integrity during transcription in mammalian adult stem cells, suggesting that chromatin transcription in stem cells and differentiated cells is different.
Collapse
Affiliation(s)
- Imon Goswami
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Poorva Sandlesh
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA,Present address:
Department of Neurological SurgeryUniversity of PittsburghPittsburghPAUSA,Present address:
Department of NeurosurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Aimee Stablewski
- Transgenic Shared FacilityRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | | | - Alfiya F Safina
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Mikhail Magnitov
- Institute of Gene BiologyRussian Academy of SciencesMoscowRussia
| | - Jianmin Wang
- Department of Biostatistics and BioinformaticsRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Katerina Gurova
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| |
Collapse
|
13
|
Bhakat KK, Ray S. The FAcilitates Chromatin Transcription (FACT) complex: Its roles in DNA repair and implications for cancer therapy. DNA Repair (Amst) 2021; 109:103246. [PMID: 34847380 DOI: 10.1016/j.dnarep.2021.103246] [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] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/07/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022]
Abstract
Genomic DNA in the nucleus is wrapped around nucleosomes, a repeating unit of chromatin. The nucleosome, consisting of octamer of core histones, is a barrier for several cellular processes that require access to the naked DNA. The FAcilitates Chromatin Transcription (FACT), a histone chaperone complex, is involved in nucleosome remodeling via eviction or assembly of histones during transcription, replication, and DNA repair. Increasing evidence suggests that FACT plays an important role in multiple DNA repair pathways including transcription-coupled nucleotide excision repair (TC-NER) of UV-induced damage, DNA single- and double-strand breaks (DSBs) repair, and base excision repair (BER) of oxidized or alkylated damaged bases. Further, studies have shown overexpression of FACT in multiple types of cancer and its association with drug resistance and patients' poor prognosis. In this review, we discuss how FACT is accumulated at the damage site and what functions it performs. We describe the known mechanisms by which FACT facilitates repair of different types of DNA damage. Further, we highlight the recent advances in a class of FACT inhibitors, called curaxins, which show promise as a new adjuvant therapy to sensitize multiple types of cancer to chemotherapy and radiation.
Collapse
Affiliation(s)
- Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198.
| | - Sutapa Ray
- Department of Pediatric, Division of Hematology/oncology, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198
| |
Collapse
|
14
|
Ohsawa I, Kawano F. Chronic exercise training activates histone turnover in mouse skeletal muscle fibers. FASEB J 2021; 35:e21453. [PMID: 33749947 DOI: 10.1096/fj.202002027rr] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 11/11/2022]
Abstract
Epigenetic regulation of skeletal muscle adaptation to exercise is a recent topic for which there is limited information. This study investigated whether exercise training activates histone turnover in the skeletal muscle fibers of mice. Experiments using a tetracycline-inducible H2B-GFP expression model demonstrated that 4 weeks of running training, but not 2 weeks of training, significantly promoted the incorporation of H2B-GFP into nucleosomes and the dissociation of histone H3.3 at both transcriptionally upregulated and nonresponsive loci. Muscle-specific PGC-1α-b-overexpressing mice crossed with H2B-GFP mice showed a slight increase in H2B-GFP incorporation at transcriptionally active loci, but not in the dissociation of H3.3 from nucleosomes. Gene expression responses to a single bout of running were significantly enhanced in 4-week trained mice when compared with those in 2-week trained mice. The most drastic increase in the gene response was found in the expression of Hspa1a and Hspa1b, in which the magnitude of upregulation in response to running was significantly enhanced from 8-fold in 2 week trained mice to 97- and 121-fold in 4 week trained mice, respectively. It was also found that the HSP70 level increased during the training period. In a myonuclear immunohistochemical analysis of chromatin remodelers, we further found that the level of SPT16, an H2A-H2B-specific chaperone, was upregulated after running training. These results revealed that 4 weeks of running training activated histone turnover in skeletal muscle fibers. They also suggested that histone turnover led to loosening of the nucleosomes and enhanced gene responses to exercise.
Collapse
Affiliation(s)
- Ikumi Ohsawa
- Graduate School of Health Sciences, Matsumoto University, Matsumoto City, Nagano, Japan
| | - Fuminori Kawano
- Graduate School of Health Sciences, Matsumoto University, Matsumoto City, Nagano, Japan
| |
Collapse
|
15
|
Histone chaperone FACT complex inhibitor CBL0137 interferes with DNA damage repair and enhances sensitivity of medulloblastoma to chemotherapy and radiation. Cancer Lett 2021; 520:201-212. [PMID: 34271103 DOI: 10.1016/j.canlet.2021.07.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 11/21/2022]
Abstract
Medulloblastoma (MB) is a malignant pediatric brain tumor with a poor prognosis. Post-surgical radiation and cisplatin-based chemotherapy have been a mainstay of treatment, which often leads to substantial neurocognitive impairments and morbidity, highlighting the need for a novel therapeutic target to enhance the sensitivity of MB tumors to cytotoxic therapies. We performed a comprehensive study using a cohort of 71 MB patients' samples and pediatric MB cell lines and found that MB tumors have elevated levels of nucleosome remodeling FACT (FAcilitates Chromatin Transcription) complex and DNA repair enzyme AP-endonuclease1 (APE1). FACT interacts with APE1 and facilitates recruitment and acetylation of APE1 to promote repair of radiation and cisplatin-induced DNA damage. Further, levels of FACT and acetylated APE1 both are correlate strongly with MB patients' survival. Targeting FACT complex with CBL0137 inhibits DNA repair and alters expression of a subset of genes, and significantly improves the potency of cisplatin and radiation in vitro and in MB xenograft. Notably, combination of CBL0137 and cisplatin significantly suppressed MB tumor growth in an intracranial orthotopic xenograft model. We conclude that FACT complex promotes chemo-radiation resistance in MB, and FACT inhibitor CBL0137 can be used as a chemo-radiation sensitizer to augment treatment efficacy and reduce therapy-related toxicity in high-risk pediatric patients.
Collapse
|
16
|
Proteasomal Regulation of Mammalian SPT16 in Controlling Transcription. Mol Cell Biol 2021; 41:MCB.00452-20. [PMID: 33526453 DOI: 10.1128/mcb.00452-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
FACT (facilitates chromatin transcription), an essential and evolutionarily conserved heterodimer from yeast to humans, controls transcription and is found to be upregulated in various cancers. However, the basis for such upregulation is not clearly understood. Our recent results deciphering a new ubiquitin-proteasome system regulation of the FACT subunit SPT16 in orchestrating transcription in yeast hint at the involvement of the proteasome in controlling FACT in humans, with a link to cancer. To test this, we carried out experiments in human embryonic kidney (HEK293) cells, which revealed that human SPT16 undergoes ubiquitylation and that its abundance is increased following inhibition of the proteolytic activity of the proteasome, thus implying proteasomal regulation of human SPT16. Furthermore, we find that the increased abundance/expression of SPT16 in HEK293 cells alters the transcription of genes, including ones associated with cancer, and that the proteasomal degradation of SPT16 is impaired in kidney cancer (Caki-2) cells to upregulate SPT16. Like human SPT16, murine SPT16 in C2C12 cells also undergoes ubiquitylation and proteasomal degradation to regulate transcription. Collectively, our results reveal a proteasomal regulation of mammalian SPT16, with physiological relevance in controlling transcription, and implicate such proteasomal control in the upregulation of SPT16 in cancer.
Collapse
|
17
|
Wang P, Yang W, Zhao S, Nashun B. Regulation of chromatin structure and function: insights into the histone chaperone FACT. Cell Cycle 2021; 20:465-479. [PMID: 33590780 DOI: 10.1080/15384101.2021.1881726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In eukaryotic cells, changes in chromatin accessibility are necessary for chromatin to maintain its highly dynamic nature at different times during the cell cycle. Histone chaperones interact with histones and regulate chromatin dynamics. Facilitates chromatin transcription (FACT) is an important histone chaperone that plays crucial roles during various cellular processes. Here, we analyze the structural characteristics of FACT, discuss how FACT regulates nucleosome/chromatin reorganization and summarize possible functions of FACT in transcription, replication, and DNA repair. The possible involvement of FACT in cell fate determination is also discussed.Abbreviations: FACT: facilitates chromatin transcription, Spt16: suppressor of Ty16, SSRP1: structure-specific recognition protein-1, NTD: N-terminal domain, DD: dimerization domain, MD: middle domain, CTD: C-terminus domain, IDD: internal intrinsically disordered domain, HMG: high mobility group, CID: C-terminal intrinsically disordered domain, Nhp6: non-histone chromosomal protein 6, RNAPII: RNA polymerase II, CK2: casein kinase 2, AID: acidic inner disorder, PIC: pre-initiation complex, IR: ionizing radiation, DDSB: DNA double-strand break, PARlation: poly ADP-ribosylation, BER: base-excision repair, UVSSA: UV-stimulated scaffold protein A, HR: homologous recombination, CAF-1: chromatin assembly factor 1, Asf1: anti-silencing factor 1, Rtt106: regulator of Ty1 transposition protein 106, H3K56ac: H3K56 acetylation, KD: knock down, SETD2: SET domain containing 2, H3K36me3: trimethylation of lysine36 in histone H3, H2Bub: H2B ubiquitination, iPSCs: induced pluripotent stem cells, ESC: embryonic stem cell, H3K4me3: trimethylation of lysine 4 on histone H3 protein subunit, CHD1: chromodomain protein.
Collapse
Affiliation(s)
- Peijun Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wanting Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Shuxin Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Buhe Nashun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| |
Collapse
|
18
|
Tallman MM, Zalenski AA, Deighen AM, Schrock MS, Mortach S, Grubb TM, Kastury PS, Huntoon K, Summers MK, Venere M. The small molecule drug CBL0137 increases the level of DNA damage and the efficacy of radiotherapy for glioblastoma. Cancer Lett 2020; 499:232-242. [PMID: 33253788 DOI: 10.1016/j.canlet.2020.11.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/05/2020] [Accepted: 11/23/2020] [Indexed: 11/17/2022]
Abstract
Glioblastoma (GBM) is an incurable brain tumor with inevitable recurrence. This is in part due to a highly malignant cancer stem cell (CSC) subpopulation of tumor cells that is particularly resistant to conventional treatments, including radiotherapy. Here we show that CBL0137, a small molecule anti-cancer agent, sensitizes GBM CSCs to radiotherapy. CBL0137 sequesters the FACT (facilitates chromatin transcription) complex to chromatin, resulting in cytotoxicity preferentially within tumor cells. We show that when combined with radiotherapy, CBL0137 inhibited GBM CSC growth and resulted in more DNA damage in the CSCs compared to irradiation or drug alone. Using an in vivo subcutaneous model, we showed that the frequency of GBM CSCs was reduced when tumors were pretreated with CBL0137 and then exposed to irradiation. Survival studies with orthotopic GBM models resulted in significantly extended survival for mice treated with combinatorial therapy. As GBM CSCs contribute to the inevitable recurrence in patients, targeting them is imperative. This work establishes a new treatment paradigm for GBM that sensitizes CSCs to irradiation and may ultimately reduce tumor recurrence.
Collapse
Affiliation(s)
- Miranda M Tallman
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA; Biomedical Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Abigail A Zalenski
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA; Neuroscience Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Amanda M Deighen
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Morgan S Schrock
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Sherry Mortach
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Treg M Grubb
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Preetham S Kastury
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Kristin Huntoon
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Matthew K Summers
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Monica Venere
- Department of Radiation Oncology, James Cancer Hospital and Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA.
| |
Collapse
|
19
|
Chen F, Zhang W, Xie D, Gao T, Dong Z, Lu X. Histone chaperone FACT represses retrotransposon MERVL and MERVL-derived cryptic promoters. Nucleic Acids Res 2020; 48:10211-10225. [PMID: 32894293 PMCID: PMC7544220 DOI: 10.1093/nar/gkaa732] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Endogenous retroviruses (ERVs) were usually silenced by various histone modifications on histone H3 variants and respective histone chaperones in embryonic stem cells (ESCs). However, it is still unknown whether chaperones of other histones could repress ERVs. Here, we show that H2A/H2B histone chaperone FACT plays a critical role in silencing ERVs and ERV-derived cryptic promoters in ESCs. Loss of FACT component Ssrp1 activated MERVL whereas the re-introduction of Ssrp1 rescued the phenotype. Additionally, Ssrp1 interacted with MERVL and suppressed cryptic transcription of MERVL-fused genes. Remarkably, Ssrp1 interacted with and recruited H2B deubiquitinase Usp7 to Ssrp1 target genes. Suppression of Usp7 caused similar phenotypes as loss of Ssrp1. Furthermore, Usp7 acted by deubiquitinating H2Bub and thereby repressed the expression of MERVL-fused genes. Taken together, our study uncovers a unique mechanism by which FACT complex silences ERVs and ERV-derived cryptic promoters in ESCs.
Collapse
Affiliation(s)
- Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Dan Xie
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Tingting Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Zhiqiang Dong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Life Sciences, Nankai University, Tianjin 300307, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| |
Collapse
|
20
|
Tettey TT, Gao X, Shao W, Li H, Story BA, Chitsazan AD, Glaser RL, Goode ZH, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Rep 2020; 27:3770-3779.e7. [PMID: 31242411 DOI: 10.1016/j.celrep.2019.05.099] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/22/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
FACT (facilitates chromatin transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II (Pol II) transcription through nucleosomes in vitro. In this report, we describe a global analysis of FACT function in Pol II transcription in Drosophila. We present evidence that loss of FACT has a dramatic impact on Pol II elongation-coupled processes including histone H3 lysine 4 (H3K4) and H3K36 methylation, consistent with a role for FACT in coordinating histone modification and chromatin architecture during Pol II transcription. Importantly, we identify a role for FACT in the maintenance of promoter-proximal Pol II pausing, a key step in transcription activation in higher eukaryotes. These findings bring to light a broader role for FACT in the regulation of Pol II transcription.
Collapse
Affiliation(s)
- Theophilus T Tettey
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; The Open University, Walton Hall, Milton Keynes, Buckinghamshire MK7 6AA, UK
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Wanqing Shao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Benjamin A Story
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Alex D Chitsazan
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Robert L Glaser
- Wadsworth Center, New York State Department of Health, PO Box 509, Albany, NY 12201, USA
| | - Zach H Goode
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Christopher W Seidel
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Marco Blanchette
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| |
Collapse
|
21
|
Wang AS, Chen LC, Wu RA, Hao Y, McSwiggen DT, Heckert AB, Richardson CD, Gowen BG, Kazane KR, Vu JT, Wyman SK, Shin JJ, Darzacq X, Walter JC, Corn JE. The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells. Mol Cell 2020; 79:221-233.e5. [PMID: 32603710 PMCID: PMC7398558 DOI: 10.1016/j.molcel.2020.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 02/26/2020] [Accepted: 06/05/2020] [Indexed: 12/23/2022]
Abstract
Cas9 is a prokaryotic RNA-guided DNA endonuclease that binds substrates tightly in vitro but turns over rapidly when used to manipulate genomes in eukaryotic cells. Little is known about the factors responsible for dislodging Cas9 or how they influence genome engineering. Unbiased detection through proximity labeling of transient protein interactions in cell-free Xenopus laevis egg extract identified the dimeric histone chaperone facilitates chromatin transcription (FACT) as an interactor of substrate-bound Cas9. FACT is both necessary and sufficient to displace dCas9, and FACT immunodepletion converts Cas9's activity from multi-turnover to single turnover. In human cells, FACT depletion extends dCas9 residence times, delays genome editing, and alters the balance between indel formation and homology-directed repair. FACT knockdown also increases epigenetic marking by dCas9-based transcriptional effectors with a concomitant enhancement of transcriptional modulation. FACT thus shapes the intrinsic cellular response to Cas9-based genome manipulation most likely by determining Cas9 residence times.
Collapse
Affiliation(s)
- Alan S Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Leo C Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yvonne Hao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David T McSwiggen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alec B Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher D Richardson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan T Vu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stacia K Wyman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jiyung J Shin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
| |
Collapse
|
22
|
Histone chaperone FACT is essential to overcome replication stress in mammalian cells. Oncogene 2020; 39:5124-5137. [PMID: 32533099 PMCID: PMC7343669 DOI: 10.1038/s41388-020-1346-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 05/11/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022]
Abstract
The histone chaperone FACT is upregulated during mammary tumorigenesis and necessary for the viability and growth of breast tumor cells. We established that only proliferating tumor cells are sensitive to FACT knockdown, suggesting that FACT functions during DNA replication in tumor cells but not in normal cells. We hypothesized that the basal level of replication stress defines the FACT dependence of cells. Using genetic and chemical tools, we demonstrated that FACT is needed to overcome replication stress. In the absence of FACT during replication stress, the MCM2-7 helicase dissociates from chromatin, resulting in the absence of ssDNA accumulation, RPA binding, and activation of the ATR/CHK1 checkpoint response. Without this response, stalled replication forks are not stabilized, and new origin firing cannot be prevented, leading to the accumulation of DNA damage and cell death. Thus, we propose a novel role for FACT as a factor preventing helicase dissociation from chromatin during replication stress.
Collapse
|
23
|
Sandlesh P, Safina A, Goswami I, Prendergast L, Rosario S, Gomez EC, Wang J, Gurova KV. Prevention of Chromatin Destabilization by FACT Is Crucial for Malignant Transformation. iScience 2020; 23:101177. [PMID: 32498018 PMCID: PMC7267732 DOI: 10.1016/j.isci.2020.101177] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 03/23/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
Histone chaperone FACT is commonly expressed and essential for the viability of transformed but not normal cells, and its expression levels correlate with poor prognosis in patients with cancer. FACT binds several components of nucleosomes and has been viewed as a factor destabilizing nucleosomes to facilitate RNA polymerase passage. To connect FACT's role in transcription with the viability of tumor cells, we analyzed genome-wide FACT binding to chromatin in conjunction with transcription in mouse and human cells with different degrees of FACT dependence. Genomic distribution and density of FACT correlated with the intensity of transcription. However, FACT knockout or knockdown was unexpectedly accompanied by the elevation, rather than suppression, of transcription and with the destabilization of chromatin in transformed, but not normal cells. These data suggest that FACT stabilizes and reassembles nucleosomes disturbed by transcription. This function is vital for tumor cells because malignant transformation is accompanied by chromatin destabilization. FACT is essential for viability of the tumor, but not for normal cells FACT level depends on transcription, but transcription does not depend on FACT FACT preserves nucleosomes during transcription to maintain chromatin integrity FACT maintains chromatin in destabilized state during malignant transformation
Collapse
Affiliation(s)
- Poorva Sandlesh
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Imon Goswami
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Laura Prendergast
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Spenser Rosario
- Department of Cancer Genetics, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Eduardo C Gomez
- Department of Bioinformatics, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Jianmin Wang
- Department of Bioinformatics, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Carlton and Elm Streets, Buffalo, NY 14127, USA.
| |
Collapse
|
24
|
Chang HW, Nizovtseva EV, Razin SV, Formosa T, Gurova KV, Studitsky VM. Histone Chaperone FACT and Curaxins: Effects on Genome Structure and Function. ACTA ACUST UNITED AC 2019; 5. [PMID: 31853507 DOI: 10.20517/2394-4722.2019.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The histone chaperone FACT plays important roles in essentially every chromatin-associated process and is an important indirect target of the curaxin class of anti-cancer drugs. Curaxins are aromatiс compounds that intercalate into DNA and can trap FACT in bulk chromatin, thus interfering with its distribution and its functions in cancer cells. Recent studies have provided mechanistic insight into how FACT and curaxins cooperate to promote unfolding of nucleosomes and chromatin fibers, resulting in genome-wide disruption of contact chromatin domain boundaries, perturbation of higher order chromatin organization, and global disregulation of gene expression. Here, we discuss the implications of these insights for cancer biology.
Collapse
Affiliation(s)
- Han-Wen Chang
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Sergey V Razin
- Institute of Gene Biology RAS, 34/5 Vavilov Str., 119334 Moscow, Russia.,Biology Faculty, Lomonosov Moscow State University, 1 Leninskie Gory, 119992 Moscow, Russia
| | - Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, NY14263, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Lomonosov Moscow State University, 1 Leninskie Gory, 119992 Moscow, Russia
| |
Collapse
|
25
|
Bi L, Xie C, Yao M, Thae Hnit SS, Vignarajan S, Wang Y, Wang Q, Xi Z, Xu H, Li Z, de Souza P, Tee A, Wong M, Liu T, Zhao X, Zhou J, Xu L, Dong Q. The histone chaperone complex FACT promotes proliferative switch of G 0 cancer cells. Int J Cancer 2018; 145:164-178. [PMID: 30548853 DOI: 10.1002/ijc.32065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/05/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022]
Abstract
Cancer cell repopulation through cell cycle re-entry by quiescent (G0 ) cell is thought to be an important mechanism behind treatment failure and cancer recurrence. Facilitates Chromatin Transcription (FACT) is involved in DNA repair, replication and transcription by eviction of histones or loosening their contact with DNA. While FACT expression is known to be high in a range of cancers, the biological significance of the aberrant increase is not clear. We found that in prostate and lung cancer cells FACT mRNA and protein levels were low at G0 compared to the proliferating state but replenished upon cell cycle re-entry. Silencing of FACT with Dox-inducible shRNA hindered cell cycle re-entry by G0 cancer cells, which could be rescued by ectopic expression of FACT. An increase in SKP2, c-MYC and PIRH2 and a decrease in p27 protein levels seen upon cell cycle re-entry were prevented or diminished when FACT was silenced. Further, using mVenus-p27K- infected cancer cells to measure p27 degradation capacity, we confirm that inhibition of FACT at release from quiescence suppressed the p27 degradation capacity resulting in an increased mVenus-p27K- signal. In conclusion, FACT plays an important role in promoting the transition from G0 to the proliferative state and can be a potential therapeutic target to prevent prostate and lung cancer from progression and recurrence.
Collapse
Affiliation(s)
- Ling Bi
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chanlu Xie
- School of Science and Health, Western Sydney University, Sydney, NSW, Australia.,Central Clinical School and Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Mu Yao
- Central Clinical School and Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Su Su Thae Hnit
- School of Science and Health, Western Sydney University, Sydney, NSW, Australia
| | - Soma Vignarajan
- Central Clinical School and Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Yilun Wang
- Central Clinical School and Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Qian Wang
- Origins of Cancer Laboratory, Centenary Institute, Camperdown, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Zhichao Xi
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai, China
| | - Hongxi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai, China
| | - Zhong Li
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Paul de Souza
- School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Andrew Tee
- Children's Cancer Institute Australia for Medical Research, Sydney, NSW, Australia.,Center for Childhood Cancer Research, UNSW Medicine, Sydney, NSW, Australia
| | - Matthew Wong
- Children's Cancer Institute Australia for Medical Research, Sydney, NSW, Australia.,Center for Childhood Cancer Research, UNSW Medicine, Sydney, NSW, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, Sydney, NSW, Australia.,Center for Childhood Cancer Research, UNSW Medicine, Sydney, NSW, Australia
| | - Xiaodong Zhao
- Shanghai Center for Systems Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jia Zhou
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ling Xu
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qihan Dong
- School of Science and Health, Western Sydney University, Sydney, NSW, Australia.,Central Clinical School and Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| |
Collapse
|
26
|
Chang HW, Valieva ME, Safina A, Chereji RV, Wang J, Kulaeva OI, Morozov AV, Kirpichnikov MP, Feofanov AV, Gurova KV, Studitsky VM. Mechanism of FACT removal from transcribed genes by anticancer drugs curaxins. SCIENCE ADVANCES 2018; 4:eaav2131. [PMID: 30417101 PMCID: PMC6221510 DOI: 10.1126/sciadv.aav2131] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/10/2018] [Indexed: 05/21/2023]
Abstract
Human FACT (facilitates chromatin transcription) is a multifunctional protein complex that has histone chaperone activity and facilitates nucleosome survival and transcription through chromatin. Anticancer drugs curaxins induce FACT trapping on chromatin of cancer cells (c-trapping), but the mechanism of c-trapping is not fully understood. Here, we show that in cancer cells, FACT is highly enriched within the bodies of actively transcribed genes. Curaxin-dependent c-trapping results in redistribution of FACT from the transcribed chromatin regions to other genomic loci. Using a combination of biochemical and biophysical approaches, we have demonstrated that FACT is bound to and unfolds nucleosomes in the presence of curaxins. This tight binding to the nucleosome results in inhibition of FACT-dependent transcription in vitro in the presence of both curaxins and competitor chromatin, suggesting a mechanism of FACT trapping on bulk nucleosomes (n-trapping).
Collapse
Affiliation(s)
- Han-Wen Chang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Maria E. Valieva
- Biology Faculty, Lomonosov Moscow State University, 119992 Moscow, Russia
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Răzvan V. Chereji
- Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jianmin Wang
- Department of Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | | | - Alexandre V. Morozov
- Department of Physics and Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Mikhail P. Kirpichnikov
- Biology Faculty, Lomonosov Moscow State University, 119992 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Alexey V. Feofanov
- Biology Faculty, Lomonosov Moscow State University, 119992 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Katerina V. Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Vasily M. Studitsky
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Biology Faculty, Lomonosov Moscow State University, 119992 Moscow, Russia
| |
Collapse
|
27
|
Transcription-associated histone pruning demarcates macroH2A chromatin domains. Nat Struct Mol Biol 2018; 25:958-970. [PMID: 30291361 PMCID: PMC6178985 DOI: 10.1038/s41594-018-0134-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 08/17/2018] [Indexed: 02/01/2023]
Abstract
The histone variant macroH2A occupies large repressive domains throughout the genome, however mechanisms underlying its precise deposition remain poorly understood. Here, we characterized de novo chromatin deposition of macroH2A2 using temporal genomic profiling in murine-derived fibroblasts devoid of all macroH2A isoforms. We find that macroH2A2 is first pervasively deposited genome-wide at both steady state domains and adjacent transcribed regions, the latter of which are subsequently pruned, establishing mature macroH2A2 domains. Pruning of macroH2A2 can be counteracted by chemical inhibition of transcription. Further, CRISPR/Cas9-based locus-specific transcriptional manipulation reveals that gene activation depletes pre-existing macroH2A2, while silencing triggers ectopic macroH2A2 accumulation. We demonstrate that the FACT (facilitates chromatin transcription) complex is required for macroH2A2 pruning within transcribed chromatin. Taken together, we have identified active chromatin as a boundary for macroH2A domains through a transcription-associated ‘pruning’ mechanism that establishes and maintains the faithful genomic localization of macroH2A variants.
Collapse
|
28
|
Gurova K, Chang HW, Valieva ME, Sandlesh P, Studitsky VM. Structure and function of the histone chaperone FACT - Resolving FACTual issues. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30159-7. [PMID: 30055319 PMCID: PMC6349528 DOI: 10.1016/j.bbagrm.2018.07.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/12/2022]
Abstract
FAcilitates Chromatin Transcription (FACT) has been considered essential for transcription through chromatin mostly based on cell-free experiments. However, FACT inactivation in cells does not cause a significant reduction in transcription. Moreover, not all mammalian cells require FACT for viability. Here we synthesize information from different organisms to reveal the core function(s) of FACT and propose a model that reconciles the cell-free and cell-based observations. We describe FACT structure and nucleosomal interactions, and their roles in FACT-dependent transcription, replication and repair. The variable requirements for FACT among different tumor and non-tumor cells suggest that various FACT-dependent processes have significantly different levels of relative importance in different eukaryotic cells. We propose that the stability of chromatin, which might vary among different cell types, dictates these diverse requirements for FACT to support cell viability. Since tumor cells are among the most sensitive to FACT inhibition, this vulnerability could be exploited for cancer treatment.
Collapse
Affiliation(s)
- Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
| | - Han-Wen Chang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Maria E Valieva
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Poorva Sandlesh
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Vasily M Studitsky
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Biology Faculty, Lomonosov Moscow State University, Moscow, Russia.
| |
Collapse
|
29
|
Sandlesh P, Juang T, Safina A, Higgins MJ, Gurova KV. Uncovering the fine print of the CreERT2-LoxP system while generating a conditional knockout mouse model of Ssrp1 gene. PLoS One 2018; 13:e0199785. [PMID: 29953487 PMCID: PMC6023160 DOI: 10.1371/journal.pone.0199785] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/13/2018] [Indexed: 01/26/2023] Open
Abstract
FAcilitates Chromatin Transcription (FACT) is a complex of SSRP1 and SPT16 that is involved in chromatin remodeling during transcription, replication, and DNA repair. FACT has been mostly studied in cell-free or single cell model systems because general FACT knockout (KO) is embryonically lethal (E3.5). FACT levels are limited to the early stages of development and stem cell niches of adult tissues. FACT is upregulated in poorly differentiated aggressive tumors. Importantly, FACT inhibition (RNAi) is lethal for tumors but not normal cells, making FACT a lucrative target for anticancer therapy. To develop a better understanding of FACT function in the context of the mammalian organism under normal physiological conditions and in disease, we aimed to generate a conditional FACT KO mouse model. Because SPT16 stability is dependent on the SSRP1-SPT16 association and the presence of SSRP1 mRNA, we targeted the Ssrp1 gene using a CreERT2- LoxP approach to generate the FACT KO model. Here, we highlight the limitations of the CreERT2-LoxP (Rosa26) system that we encountered during the generation of this model. In vitro studies showed an inefficient excision rate of ectopically expressed CreERT2 (retroviral CreERT2) in fibroblasts with homozygous floxed Ssrp1. In vitro and in vivo studies showed that the excision efficiency could only be increased with germline expression of two alleles of Rosa26CreERT2. The expression of one germline Rosa26CreERT2 allele led to the incomplete excision of Ssrp1. The limited efficiency of the CreERT2-LoxP system may be sufficient for studies involving the deletion of genes that interfere with cell growth or viability due to the positive selection of the phenotype. However, it may not be sufficient for studies that involve the deletion of genes supporting growth, or those crucial for development. Although CreERT2-LoxP is broadly used, it has limitations that have not been widely discussed. This paper aims to encourage such discussions.
Collapse
Affiliation(s)
- Poorva Sandlesh
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Thierry Juang
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Michael J. Higgins
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Katerina V. Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- * E-mail:
| |
Collapse
|
30
|
Nesher E, Safina A, Aljahdali I, Portwood S, Wang ES, Koman I, Wang J, Gurova KV. Role of Chromatin Damage and Chromatin Trapping of FACT in Mediating the Anticancer Cytotoxicity of DNA-Binding Small-Molecule Drugs. Cancer Res 2018; 78:1431-1443. [PMID: 29339544 DOI: 10.1158/0008-5472.can-17-2690] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/30/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022]
Abstract
Precisely how DNA-targeting chemotherapeutic drugs trigger cancer cell death remains unclear, as it is difficult to separate direct DNA damage from other effects in cells. Recent work on curaxins, a class of small-molecule drugs with broad anticancer activity, shows that they interfere with histone-DNA interactions and destabilize nucleosomes without causing detectable DNA damage. Chromatin damage caused by curaxins is sensed by the histone chaperone FACT, which binds unfolded nucleosomes becoming trapped in chromatin. In this study, we investigated whether classical DNA-targeting chemotherapeutic drugs also similarly disturbed chromatin to cause chromatin trapping of FACT (c-trapping). Drugs that directly bound DNA induced both chromatin damage and c-trapping. However, chromatin damage occurred irrespective of direct DNA damage and was dependent on how a drug bound DNA, specifically, in the way it bound chromatinized DNA in cells. FACT was sensitive to a plethora of nucleosome perturbations induced by DNA-binding small molecules, including displacement of the linker histone, eviction of core histones, and accumulation of negative supercoiling. Strikingly, we found that the cytotoxicity of DNA-binding small molecules correlated with their ability to cause chromatin damage, not DNA damage. Our results suggest implications for the development of chromatin-damaging agents as selective anticancer drugs.Significance: These provocative results suggest that the anticancer efficacy of traditional DNA-targeting chemotherapeutic drugs may be based in large part on chromatin damage rather than direct DNA damage. Cancer Res; 78(6); 1431-43. ©2018 AACR.
Collapse
Affiliation(s)
- Elimelech Nesher
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, New York.,Institute for Translational Research, Ariel University, Ariel, Israel
| | - Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, New York
| | - Ieman Aljahdali
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, New York
| | - Scott Portwood
- Department of Medicine, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, New York
| | - Eunice S Wang
- Department of Medicine, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, New York
| | - Igor Koman
- Institute for Translational Research, Ariel University, Ariel, Israel
| | - Jianmin Wang
- Department of Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, New York.
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, New York.
| |
Collapse
|
31
|
Safina A, Cheney P, Pal M, Brodsky L, Ivanov A, Kirsanov K, Lesovaya E, Naberezhnov D, Nesher E, Koman I, Wang D, Wang J, Yakubovskaya M, Winkler D, Gurova K. FACT is a sensor of DNA torsional stress in eukaryotic cells. Nucleic Acids Res 2017; 45:1925-1945. [PMID: 28082391 PMCID: PMC5389579 DOI: 10.1093/nar/gkw1366] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/29/2016] [Indexed: 02/01/2023] Open
Abstract
Transitions of B-DNA to alternative DNA structures (ADS) can be triggered by negative torsional strain, which occurs during replication and transcription, and may lead to genomic instability. However, how ADS are recognized in cells is unclear. We found that the binding of candidate anticancer drug, curaxin, to cellular DNA results in uncoiling of nucleosomal DNA, accumulation of negative supercoiling and conversion of multiple regions of genomic DNA into left-handed Z-form. Histone chaperone FACT binds rapidly to the same regions via the SSRP1 subunit in curaxin-treated cells. In vitro binding of purified SSRP1 or its isolated CID domain to a methylated DNA fragment containing alternating purine/pyrimidines, which is prone to Z-DNA transition, is much stronger than to other types of DNA. We propose that FACT can recognize and bind Z-DNA or DNA in transition from a B to Z form. Binding of FACT to these genomic regions triggers a p53 response. Furthermore, FACT has been shown to bind to other types of ADS through a different structural domain, which also leads to p53 activation. Thus, we propose that FACT acts as a sensor of ADS formation in cells. Recognition of ADS by FACT followed by a p53 response may explain the role of FACT in DNA damage prevention.
Collapse
Affiliation(s)
- Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Peter Cheney
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Mahadeb Pal
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Leonid Brodsky
- Department of Evolutionary & Environmental Biology, Tauber Bioinformatics Research Center, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Alexander Ivanov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Kirill Kirsanov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Ekaterina Lesovaya
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia.,I.P. Pavlov Ryazan State Medical University, Ryazan, Russia
| | - Denis Naberezhnov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Elimelech Nesher
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA.,Department of Molecular Biology, Ariel University, Ariel 40700, Israel
| | - Igor Koman
- Department of Molecular Biology, Ariel University, Ariel 40700, Israel
| | - Dan Wang
- Department of Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Jianming Wang
- Department of Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Marianna Yakubovskaya
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Duane Winkler
- Department of Molecular and Cell Biology, University of Texas at Dallas, 800 W. Campbell Rd., Richardson, TX 75080, USA
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| |
Collapse
|
32
|
Cornella N, Tebaldi T, Gasperini L, Singh J, Padgett RA, Rossi A, Macchi P. The hnRNP RALY regulates transcription and cell proliferation by modulating the expression of specific factors including the proliferation marker E2F1. J Biol Chem 2017; 292:19674-19692. [PMID: 28972179 DOI: 10.1074/jbc.m117.795591] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/18/2017] [Indexed: 12/31/2022] Open
Abstract
The heterogeneous nuclear ribonucleoproteins (hnRNP) form a large family of RNA-binding proteins that exert numerous functions in RNA metabolism. RALY is a member of the hnRNP family that binds poly-U-rich elements within several RNAs and regulates the expression of specific transcripts. RALY is up-regulated in different types of cancer, and its down-regulation impairs cell cycle progression. However, the RALY's role in regulating RNA levels remains elusive. Here, we show that numerous genes coding for factors involved in transcription and cell cycle regulation exhibit an altered expression in RALY-down-regulated HeLa cells, consequently causing impairments in transcription, cell proliferation, and cell cycle progression. Interestingly, by comparing the list of RALY targets with the list of genes affected by RALY down-regulation, we found an enrichment of RALY mRNA targets in the down-regulated genes upon RALY silencing. The affected genes include the E2F transcription factor family. Given its role as proliferation-promoting transcription factor, we focused on E2F1. We demonstrate that E2F1 mRNA stability and E2F1 protein levels are reduced in cells lacking RALY expression. Finally, we also show that RALY interacts with transcriptionally active chromatin in both an RNA-dependent and -independent manner and that this association is abolished in the absence of active transcription. Taken together, our results highlight the importance of RALY as an indirect regulator of transcription and cell cycle progression through the regulation of specific mRNA targets, thus strengthening the possibility of a direct gene expression regulation exerted by RALY.
Collapse
Affiliation(s)
- Nicola Cornella
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Toma Tebaldi
- the Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Lisa Gasperini
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | | | | | - Annalisa Rossi
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy,
| | - Paolo Macchi
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy,
| |
Collapse
|
33
|
Fleyshman D, Prendergast L, Safina A, Paszkiewicz G, Commane M, Morgan K, Attwood K, Gurova K. Level of FACT defines the transcriptional landscape and aggressive phenotype of breast cancer cells. Oncotarget 2017; 8:20525-20542. [PMID: 28423528 PMCID: PMC5400524 DOI: 10.18632/oncotarget.15656] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 01/11/2017] [Indexed: 02/07/2023] Open
Abstract
Although breast cancer (BrCa) may be detected at an early stage, there is a shortage of markers that predict tumor aggressiveness and a lack of targeted therapies. Histone chaperone FACT, expressed in a limited number of normal cells, is overexpressed in different types of cancer, including BrCa. Recently, we found that FACT expression in BrCa correlates with markers of aggressive BrCa, which prompted us to explore the consequences of FACT inhibition in BrCa cells with varying levels of FACT. FACT inhibition using a small molecule or shRNA caused reduced growth and viability of all BrCa cells tested. Phenotypic changes were more severe in high- FACT cells (death or growth arrest) than in low-FACT cells (decreased proliferation). Though inhibition had no effect on the rate of general transcription, expression of individual genes was changed in a cell-specific manner. Initially distinct transcriptional profiles of BrCa cells became similar upon equalizing FACT expression. In high-FACT cells, FACT supports expression of genes involved in the regulation of cell cycle, DNA replication, maintenance of an undifferentiated cell state and regulated by the activity of several proto-oncogenes. In low-FACT cells, the presence of FACT reduces expression of genes encoding enzymes of steroid metabolism that are characteristic of differentiated mammary epithelia. Thus, we propose that FACT is both a marker and a target of aggressive BrCa cells, whose inhibition results in the death of BrCa or convertion of them to a less aggressive subtype.
Collapse
Affiliation(s)
- Daria Fleyshman
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Laura Prendergast
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | - Mairead Commane
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kelsey Morgan
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kristopher Attwood
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA.,Department of Biostatistics, University of Buffalo, SUNY, Buffalo, NY, USA
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| |
Collapse
|
34
|
Attwood K, Fleyshman D, Prendergast L, Paszkiewicz G, Omilian AR, Bshara W, Gurova K. Prognostic value of histone chaperone FACT subunits expression in breast cancer. BREAST CANCER-TARGETS AND THERAPY 2017; 9:301-311. [PMID: 28496363 PMCID: PMC5422336 DOI: 10.2147/bctt.s126390] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding the underlying reasons for tumor aggressiveness, such as why some tumors grow slowly and locally, while others rapidly progress to a lethal metastatic disease, is still limited. This is especially critical in breast cancer (BrCa) due to its high prevalence and also due to the possibility that it can be detected early. Several oncogenes and tumor suppressors have been identified and are used in the prognosis and treatment of BrCa. However, even with these markers, the outcome within BrCa subtypes is highly variable. Chromatin organization has long been acknowledged as a factor that plays an important role in tumor progression, but molecular mechanisms defining chromatin dynamics are largely missing. We have recently found that histone chaperone FACT (facilitates chromatin transcription) is overexpressed in ~18–20% of BrCa cases. FACT is elevated upon transformation of mammary epithelial cells and is essential for viability of tumor cells. BrCa cells with high FACT have a more aggressive transcriptional program than those with low FACT cells. Based on this we propose that FACT may be a marker of aggressive BrCa. In this study, we aimed to comprehensively characterize the pattern of FACT expression in BrCa in relation to other molecular and clinical prognostic markers. We developed and tested an assay for the detection and quantitation of protein levels of both FACT subunits, SSRP1, and SPT16, in clinical samples. We compared the value of mRNA and protein as potential markers of disease aggressiveness using a large cohort of patients (n=1092). We demonstrated that only SSRP1 immunohistochemical staining is a reliable indicator of FACT levels in tumor samples. High SSRP1 correlated with known markers of poor prognosis, such as negative hormone receptor status, presence of Her2, high-grade tumors, and tumors of later clinical stage. At the same time, no strong correlation between SSRP1 expression and survival was detected when all samples were analyzed together. Clear trend toward longer survival of patients with low or no SSRP1 expression in tumor samples was seen in several subgroups of patients, and most importantly significant association of high SSRP1 expression with shorter disease-free survival was detected in patients with early-stage and low-grade BrCa, the category of patients with the highest demand in predictive marker of disease progression.
Collapse
Affiliation(s)
| | | | | | | | - Angela R Omilian
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Wiam Bshara
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | |
Collapse
|
35
|
The FACT Complex Promotes Avian Leukosis Virus DNA Integration. J Virol 2017; 91:JVI.00082-17. [PMID: 28122976 DOI: 10.1128/jvi.00082-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/17/2017] [Indexed: 12/25/2022] Open
Abstract
All retroviruses need to integrate a DNA copy of their genome into the host chromatin. Cellular proteins regulating and targeting lentiviral and gammaretroviral integration in infected cells have been discovered, but the factors that mediate alpharetroviral avian leukosis virus (ALV) integration are unknown. In this study, we have identified the FACT protein complex, which consists of SSRP1 and Spt16, as a principal cellular binding partner of ALV integrase (IN). Biochemical experiments with purified recombinant proteins show that SSRP1 and Spt16 are able to individually bind ALV IN, but only the FACT complex effectively stimulates ALV integration activity in vitro Likewise, in infected cells, the FACT complex promotes ALV integration activity, with proviral integration frequency varying directly with cellular expression levels of the FACT complex. An increase in 2-long-terminal-repeat (2-LTR) circles in the depleted FACT complex cell line indicates that this complex regulates the ALV life cycle at the level of integration. This regulation is shown to be specific to ALV, as disruption of the FACT complex did not inhibit either lentiviral or gammaretroviral integration in infected cells.IMPORTANCE The majority of human gene therapy approaches utilize HIV-1- or murine leukemia virus (MLV)-based vectors, which preferentially integrate near genes and regulatory regions; thus, insertional mutagenesis is a substantial risk. In contrast, ALV integrates more randomly throughout the genome, which decreases the risks of deleterious integration. Understanding how ALV integration is regulated could facilitate the development of ALV-based vectors for use in human gene therapy. Here we show that the FACT complex directly binds and regulates ALV integration efficiency in vitro and in infected cells.
Collapse
|
36
|
Carter DR, Murray J, Cheung BB, Gamble L, Koach J, Tsang J, Sutton S, Kalla H, Syed S, Gifford AJ, Issaeva N, Biktasova A, Atmadibrata B, Sun Y, Sokolowski N, Ling D, Kim PY, Webber H, Clark A, Ruhle M, Liu B, Oberthuer A, Fischer M, Byrne J, Saletta F, Thwe LM, Purmal A, Haderski G, Burkhart C, Speleman F, De Preter K, Beckers A, Ziegler DS, Liu T, Gurova KV, Gudkov AV, Norris MD, Haber M, Marshall GM. Therapeutic targeting of the MYC signal by inhibition of histone chaperone FACT in neuroblastoma. Sci Transl Med 2016; 7:312ra176. [PMID: 26537256 DOI: 10.1126/scitranslmed.aab1803] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amplification of the MYCN oncogene predicts treatment resistance in childhood neuroblastoma. We used a MYC target gene signature that predicts poor neuroblastoma prognosis to identify the histone chaperone FACT (facilitates chromatin transcription) as a crucial mediator of the MYC signal and a therapeutic target in the disease. FACT and MYCN expression created a forward feedback loop in neuroblastoma cells that was essential for maintaining mutual high expression. FACT inhibition by the small-molecule curaxin compound CBL0137 markedly reduced tumor initiation and progression in vivo. CBL0137 exhibited strong synergy with standard chemotherapy by blocking repair of DNA damage caused by genotoxic drugs, thus creating a synthetic lethal environment in MYCN-amplified neuroblastoma cells and suggesting a treatment strategy for MYCN-driven neuroblastoma.
Collapse
Affiliation(s)
- Daniel R Carter
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia. School of Women's and Children's Health, UNSW Australia, Randwick, New South Wales 2031, Australia
| | - Jayne Murray
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Belamy B Cheung
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia. School of Women's and Children's Health, UNSW Australia, Randwick, New South Wales 2031, Australia
| | - Laura Gamble
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Jessica Koach
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Joanna Tsang
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Selina Sutton
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Heyam Kalla
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Sarah Syed
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Andrew J Gifford
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia. Department of Anatomical Pathology (SEALS), Prince of Wales Hospital, Randwick, New South Wales 2031, Australia
| | - Natalia Issaeva
- Department of Surgery, Otolaryngology, and Yale Cancer Center, Yale University, New Haven, CT 06511, USA
| | - Asel Biktasova
- Department of Surgery, Otolaryngology, and Yale Cancer Center, Yale University, New Haven, CT 06511, USA
| | - Bernard Atmadibrata
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Yuting Sun
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Nicolas Sokolowski
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Dora Ling
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Patrick Y Kim
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Hannah Webber
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Ashleigh Clark
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Michelle Ruhle
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Bing Liu
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - André Oberthuer
- Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, 50931 Cologne, Germany. Department of Neonatology and Pediatric Intensive Care Medicine, Children's Hospital, University of Cologne, 50931 Cologne, Germany
| | - Matthias Fischer
- Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, 50931 Cologne, Germany. Max Planck Institute for Metabolism Research, 50931 Cologne, Germany
| | - Jennifer Byrne
- Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, New South Wales 2145, Australia. University of Sydney Discipline of Paediatrics and Child Health, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, New South Wales 2145, Australia
| | - Federica Saletta
- Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, New South Wales 2145, Australia
| | - Le Myo Thwe
- Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, New South Wales 2145, Australia. University of Sydney Discipline of Paediatrics and Child Health, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, New South Wales 2145, Australia
| | | | | | | | - Frank Speleman
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), De Pintelaan 185, 9000 Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), De Pintelaan 185, 9000 Ghent, Belgium
| | - Anneleen Beckers
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), De Pintelaan 185, 9000 Ghent, Belgium
| | - David S Ziegler
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia. School of Women's and Children's Health, UNSW Australia, Randwick, New South Wales 2031, Australia. Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales 2031, Australia
| | - Tao Liu
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), De Pintelaan 185, 9000 Ghent, Belgium
| | - Katerina V Gurova
- Incuron, LLC, Buffalo, NY 14203, USA. Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Andrei V Gudkov
- Incuron, LLC, Buffalo, NY 14203, USA. Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Murray D Norris
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia. University of New South Wales Centre for Childhood Cancer Research, Randwick, New South Wales 2031, Australia
| | - Michelle Haber
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia.
| | - Glenn M Marshall
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales 2031, Australia. Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales 2031, Australia.
| |
Collapse
|
37
|
Chromatin remodeller SMARCA4 recruits topoisomerase 1 and suppresses transcription-associated genomic instability. Nat Commun 2016; 7:10549. [PMID: 26842758 PMCID: PMC4742980 DOI: 10.1038/ncomms10549] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/25/2015] [Indexed: 02/07/2023] Open
Abstract
Topoisomerase 1, an enzyme that relieves superhelical tension, is implicated in transcription-associated mutagenesis and genome instability-associated with neurodegenerative diseases as well as activation-induced cytidine deaminase. From proteomic analysis of TOP1-associated proteins, we identify SMARCA4, an ATP-dependent chromatin remodeller; FACT, a histone chaperone; and H3K4me3, a transcriptionally active chromatin marker. Here we show that SMARCA4 knockdown in a B-cell line decreases TOP1 recruitment to chromatin, and leads to increases in Igh/c-Myc chromosomal translocations, variable and switch region mutations and negative superhelicity, all of which are also observed in response to TOP1 knockdown. In contrast, FACT knockdown inhibits association of TOP1 with H3K4me3, and severely reduces DNA cleavage and Igh/c-Myc translocations, without significant effect on TOP1 recruitment to chromatin. We thus propose that SMARCA4 is involved in the TOP1 recruitment to general chromatin, whereas FACT is required for TOP1 binding to H3K4me3 at non-B DNA containing chromatin for the site-specific cleavage. Topoisomerase 1 (TOP1) relieves superhelical tension when DNA strands are unwound during transcription. Here, Husain et al. report that SMARCA4, an ATP-dependent chromatin remodeller, is associated with TOP1 and suppresses transcription-associated genomic instability.
Collapse
|
38
|
Bondarenko MT, Maluchenko NV, Valieva ME, Gerasimova NS, Kulaeva OI, Georgiev PG, Studitsky VM. Structure and function of histone chaperone FACT. Mol Biol 2015. [DOI: 10.1134/s0026893315060023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
39
|
Zhou W, Zhu Y, Dong A, Shen WH. Histone H2A/H2B chaperones: from molecules to chromatin-based functions in plant growth and development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:78-95. [PMID: 25781491 DOI: 10.1111/tpj.12830] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 05/06/2023]
Abstract
Nucleosomal core histones (H2A, H2B, H3 and H4) must be assembled, replaced or exchanged to preserve or modify chromatin organization and function according to cellular needs. Histone chaperones escort histones, and play key functions during nucleosome assembly/disassembly and in nucleosome structure configuration. Because of their location at the periphery of nucleosome, histone H2A-H2B dimers are remarkably dynamic. Here we focus on plant histone H2A/H2B chaperones, particularly members of the NUCLEOSOME ASSEMBLY PROTEIN-1 (NAP1) and FACILITATES CHROMATIN TRANSCRIPTION (FACT) families, discussing their molecular features, properties, regulation and function. Covalent histone modifications (e.g. ubiquitination, phosphorylation, methylation, acetylation) and H2A variants (H2A.Z, H2A.X and H2A.W) are also discussed in view of their crucial importance in modulating nucleosome organization and function. We further discuss roles of NAP1 and FACT in chromatin-based processes, such as transcription, DNA replication and repair. Specific functions of NAP1 and FACT are evident when their roles are considered with respect to regulation of plant growth and development and in plant responses to environmental stresses. Future major challenges remain in order to define in more detail the overlapping and specific roles of various members of the NAP1 family as well as differences and similarities between NAP1 and FACT family members, and to identify and characterize their partners as well as new families of chaperones to understand histone variant incorporation and chromatin target specificity.
Collapse
Affiliation(s)
- Wangbin Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
| |
Collapse
|
40
|
Komar AA. "Naked" FACT is unstable. Cell Cycle 2013; 12:2347. [PMID: 23856583 PMCID: PMC3841312 DOI: 10.4161/cc.25661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease; Department of Biological, Geological and Environmental Sciences; Cleveland State University; Cleveland, OH USA
| |
Collapse
|
41
|
Garcia H, Miecznikowski JC, Safina A, Commane M, Ruusulehto A, Kilpinen S, Leach RW, Attwood K, Li Y, Degan S, Omilian AR, Guryanova O, Papantonopoulou O, Wang J, Buck M, Liu S, Morrison C, Gurova KV. Facilitates chromatin transcription complex is an "accelerator" of tumor transformation and potential marker and target of aggressive cancers. Cell Rep 2013; 4:159-73. [PMID: 23831030 DOI: 10.1016/j.celrep.2013.06.013] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/31/2013] [Accepted: 06/07/2013] [Indexed: 11/27/2022] Open
Abstract
The facilitates chromatin transcription (FACT) complex is involved in chromatin remodeling during transcription, replication, and DNA repair. FACT was previously considered to be ubiquitously expressed and not associated with any disease. However, we discovered that FACT is the target of a class of anticancer compounds and is not expressed in normal cells of adult mammalian tissues, except for undifferentiated and stem-like cells. Here, we show that FACT expression is strongly associated with poorly differentiated aggressive cancers with low overall survival. In addition, FACT was found to be upregulated during in vitro transformation and to be necessary, but not sufficient, for driving transformation. FACT also promoted survival and growth of established tumor cells. Genome-wide mapping of chromatin-bound FACT indicated that FACT's role in cancer most likely involves selective chromatin remodeling of genes that stimulate proliferation, inhibit cell death and differentiation, and regulate cellular stress responses.
Collapse
Affiliation(s)
- Henry Garcia
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|