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Lin HY, Mohammadhosseini M, McClatchy J, Villamor-Payà M, Jeng S, Bottomly D, Tsai CF, Posso C, Jacobson J, Adey A, Gosline S, Liu T, McWeeney S, Stracker TH, Agarwal A. The TLK-ASF1 histone chaperone pathway plays a critical role in IL-1β-mediated AML progression. Blood 2024; 143:2749-2762. [PMID: 38498025 DOI: 10.1182/blood.2023022079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/19/2024] Open
Abstract
ABSTRACT Identifying and targeting microenvironment-driven pathways that are active across acute myeloid leukemia (AML) genetic subtypes should allow the development of more broadly effective therapies. The proinflammatory cytokine interleukin-1β (IL-1β) is abundant in the AML microenvironment and promotes leukemic growth. Through RNA-sequencing analysis, we identify that IL-1β-upregulated ASF1B (antisilencing function-1B), a histone chaperone, in AML progenitors compared with healthy progenitors. ASF1B, along with its paralogous protein ASF1A, recruits H3-H4 histones onto the replication fork during S-phase, a process regulated by Tousled-like kinase 1 and 2 (TLKs). Although ASF1s and TLKs are known to be overexpressed in multiple solid tumors and associated with poor prognosis, their functional roles in hematopoiesis and inflammation-driven leukemia remain unexplored. In this study, we identify that ASF1s and TLKs are overexpressed in multiple genetic subtypes of AML. We demonstrate that depletion of ASF1s significantly reduces leukemic cell growth in both in vitro and in vivo models using human cells. Using a murine model, we show that overexpression of ASF1B accelerates leukemia progression. Moreover, Asf1b or Tlk2 deletion delayed leukemia progression, whereas these proteins are dispensable for normal hematopoiesis. Through proteomics and phosphoproteomics analyses, we uncover that the TLK-ASF1 pathway promotes leukemogenesis by affecting the cell cycle and DNA damage pathways. Collectively, our findings identify the TLK1-ASF1 pathway as a novel mediator of inflammatory signaling and a promising therapeutic target for AML treatment across diverse genetic subtypes. Selective inhibition of this pathway offers potential opportunities to intervene effectively, address intratumoral heterogeneity, and ultimately improve clinical outcomes in AML.
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Affiliation(s)
- Hsin-Yun Lin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Division of Hematology and Oncology, Oregon Health & Science University, Portland, OR
- Department of Oncogenic Science, Oregon Health & Science University, Portland, OR
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR
| | - Mona Mohammadhosseini
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Division of Hematology and Oncology, Oregon Health & Science University, Portland, OR
- Department of Oncogenic Science, Oregon Health & Science University, Portland, OR
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR
| | - John McClatchy
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Division of Hematology and Oncology, Oregon Health & Science University, Portland, OR
- Department of Oncogenic Science, Oregon Health & Science University, Portland, OR
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR
| | - Marina Villamor-Payà
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Sophia Jeng
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR
| | - Daniel Bottomly
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR
| | - Chia-Feng Tsai
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA
| | - Camilo Posso
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA
| | - Jeremy Jacobson
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA
| | - Andrew Adey
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR
| | - Sara Gosline
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR
| | - Tao Liu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA
| | - Shannon McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR
| | - Travis H Stracker
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Division of Hematology and Oncology, Oregon Health & Science University, Portland, OR
- Department of Oncogenic Science, Oregon Health & Science University, Portland, OR
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR
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2
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Villamor-Payà M, Sanchiz-Calvo M, Smak J, Pais L, Sud M, Shankavaram U, Lovgren AK, Austin-Tse C, Ganesh VS, Gay M, Vilaseca M, Arauz-Garofalo G, Palenzuela L, VanNoy G, O’Donnell-Luria A, Stracker TH. De novo TLK1 and MDM1 mutations in a patient with a neurodevelopmental disorder and immunodeficiency. iScience 2024; 27:109984. [PMID: 38868186 PMCID: PMC11166698 DOI: 10.1016/j.isci.2024.109984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
The Tousled-like kinases 1 and 2 (TLK1/TLK2) regulate DNA replication, repair and chromatin maintenance. TLK2 variants underlie the neurodevelopmental disorder (NDD) 'Intellectual Disability, Autosomal Dominant 57' (MRD57), characterized by intellectual disability and microcephaly. Several TLK1 variants have been reported in NDDs but their functional significance is unknown. A male patient presenting with ID, seizures, global developmental delay, hypothyroidism, and primary immunodeficiency was determined to have a heterozygous TLK1 variant (c.1435C>G, p.Q479E), as well as a mutation in MDM1 (c.1197dupT, p.K400∗). Cells expressing TLK1 p.Q479E exhibited reduced cytokine responses and elevated DNA damage, but not increased radiation sensitivity or DNA repair defects. The TLK1 p.Q479E variant impaired kinase activity but not proximal protein interactions. Our study provides the first functional characterization of NDD-associated TLK1 variants and suggests that, such as TLK2, TLK1 variants may impact development in multiple tissues and should be considered in the diagnosis of rare NDDs.
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Affiliation(s)
- Marina Villamor-Payà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - María Sanchiz-Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Jordann Smak
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - Lynn Pais
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Malika Sud
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Uma Shankavaram
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - Alysia Kern Lovgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay S. Ganesh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Gianluca Arauz-Garofalo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Lluís Palenzuela
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Grace VanNoy
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne O’Donnell-Luria
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Travis H. Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
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3
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Shrestha B, Nieminen AI, Matilainen O. Loss of the histone chaperone UNC-85/ASF1 inhibits the epigenome-mediated longevity and modulates the activity of one-carbon metabolism. Cell Stress Chaperones 2024; 29:392-403. [PMID: 38608859 PMCID: PMC11039323 DOI: 10.1016/j.cstres.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Histone H3/H4 chaperone anti-silencing function 1 (ASF1) is a conserved factor mediating nucleosomal assembly and disassembly, playing crucial roles in processes such as replication, transcription, and DNA repair. Nevertheless, its involvement in aging has remained unclear. Here, we utilized the model organism Caenorhabditis elegans to demonstrate that the loss of UNC-85, the homolog of ASF1, leads to a shortened lifespan in a multicellular organism. Furthermore, we show that UNC-85 is required for epigenome-mediated longevity, as knockdown of the histone H3 lysine K4 methyltransferase ash-2 does not extend the lifespan of unc-85 mutants. In this context, we found that the longevity-promoting ash-2 RNA interference enhances UNC-85 activity by increasing its nuclear localization. Finally, our data indicate that the loss of UNC-85 increases the activity of one-carbon metabolism, and that downregulation of the one-carbon metabolism component dao-3/MTHFD2 partially rescues the short lifespan of unc-85 mutants. Together, these findings reveal UNC-85/ASF1 as a modulator of the central metabolic pathway and a factor regulating a pro-longevity response, thus shedding light on a mechanism of how nucleosomal maintenance associates with aging.
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Affiliation(s)
- Bideep Shrestha
- The Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Anni I Nieminen
- FIMM Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Olli Matilainen
- The Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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4
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Asquith CRM, East MP, Laitinen T, Alamillo-Ferrer C, Hartikainen E, Wells CI, Axtman AD, Drewry DH, Tizzard GJ, Poso A, Willson TM, Johnson GL. Discovery and optimization of narrow spectrum inhibitors of Tousled like kinase 2 (TLK2) using quantitative structure activity relationships. Eur J Med Chem 2024; 271:116357. [PMID: 38636130 DOI: 10.1016/j.ejmech.2024.116357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/24/2024] [Accepted: 03/24/2024] [Indexed: 04/20/2024]
Abstract
The oxindole scaffold has been the center of several kinase drug discovery programs, some of which have led to approved medicines. A series of two oxindole matched pairs from the literature were identified where TLK2 was potently inhibited as an off-target kinase. The oxindole has long been considered a promiscuous kinase inhibitor template, but across these four specific literature oxindoles TLK2 activity was consistent, while the kinome profile was radically different ranging from narrow to broad spectrum kinome coverage. We synthesized a large series of analogues, utilizing quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites, kinome profiling, and small-molecule x-ray structural analysis to optimize TLK2 inhibition and kinome selectivity. This resulted in the identification of several narrow spectrum, sub-family selective, chemical tool compounds including 128 (UNC-CA2-103) that could enable elucidation of TLK2 biology.
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Affiliation(s)
- Christopher R M Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland; Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carla Alamillo-Ferrer
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Erkka Hartikainen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carrow I Wells
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Timothy M Willson
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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5
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West KL, Kreiling N, Raney KD, Ghosal G, Leung JW. Autophosphorylation of the Tousled-like kinases TLK1 and TLK2 regulates recruitment to damaged chromatin via PCNA interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590659. [PMID: 38712247 PMCID: PMC11071368 DOI: 10.1101/2024.04.22.590659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tousled-like kinases 1 and 2 (TLK1 and 2) are cell cycle-regulated serine/threonine kinases that are involved in multiple biological processes. Mutation of TLK1 and 2 confer neurodegenerative diseases. Recent studies demonstrate that TLK1 and 2 are involved in DNA repair. However, there is no direct evidence that TLK1 and 2 function at DNA damage sites. Here, we show that both TLK1 and TLK2 are hyper-autophosphorylated at their N-termini, at least in part, mediated by their homo- or hetero-dimerization. We found that TLK1 and 2 hyper-autophosphorylation suppresses their recruitment to damaged chromatin. Furthermore, both TLK1 and 2 associate with PCNA specifically through their evolutionarily conserved non-canonical PCNA-interacting protein (PIP) box at the N-terminus, and mutation of the PIP-box abolishes their recruitment to DNA damage sites. Mechanistically, the TLK1 and 2 hyper-autophosphorylation masks the PIP-box and negatively regulates their recruitment to the DNA damage site. Overall, our study dissects the detailed genetic regulation of TLK1 and 2 at damaged chromatin, which provides important insights into their emerging roles in DNA repair.
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Affiliation(s)
- Kirk L. West
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Natasha Kreiling
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Kevin D. Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Justin W Leung
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
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6
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Gao E, Brown JAR, Jung S, Howe LJ. A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae reveals novel insights into factors that stabilize chromatin structure on newly replicated DNA. Genetics 2024; 226:iyae016. [PMID: 38407959 PMCID: PMC10990430 DOI: 10.1093/genetics/iyae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024] Open
Abstract
The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which employs a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. In this study, we tested the hypothesis that, in the absence of chromatin-stabilizing factors, DNA replication can promote cryptic transcription in Saccharomyces cerevisiae. Using a novel fluorescent reporter assay, we show that multiple factors, including Asf1, CAF-1, Rtt106, Spt6, and FACT, block transcription from a cryptic promoter, but are entirely or partially dispensable in G1-arrested cells, suggesting a requirement for DNA replication in chromatin disruption. Collectively, these results demonstrate that transcription fidelity is dependent on numerous factors that function to assemble chromatin on nascent DNA.
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Affiliation(s)
- Ellia Gao
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Joshua A R Brown
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Stephanie Jung
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - LeAnn J Howe
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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7
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Shrivastava A, Magani SKJ, Lokhande KB, Chintakhindi M, Singh A. Exploring the role of TLK2 mutation in tropical calcific pancreatitis: an in silico and molecular dynamics simulation study. J Biomol Struct Dyn 2024:1-20. [PMID: 38500246 DOI: 10.1080/07391102.2024.2329797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Tropical calcific pancreatitis (TCP) is a juvenile form of non-alcoholic chronic pancreatitis seen exclusively in tropical countries. The disease poses a high risk of complications, including pancreatic diabetes and cancer, leading to significant mortality due to poor diagnosis and ineffective treatments. This study employed whole exome sequencing (WES) of 5 TCP patient samples to identify genetic variants associated with TCP. Advanced computational techniques were used to gain atomic-level insights into disease progression, including microsecond-scale long MD simulations and essential dynamics. In silico virtual screening was performed to identify potential therapeutic compounds targeting the mutant protein using the Asinex and DrugBank compound library. WES analysis predicted several single nucleotide variants (SNVs) associated with TCP, including a novel missense variant (c.T1802A or p.V601E) in the TLK2 gene. Computational analysis revealed that the p.V601E mutation significantly affected the structure of the TLK2 kinase domain and its conformational dynamics, altering the interaction profile between ATP and the binding pocket. These changes could impact TLK2's kinase activity and functions, potentially correlating with TCP progression. Promising lead compounds that selectively bind to the TLK2 mutant protein were identified, offering potential for therapeutic interventions in TCP. These findings hold great potential for future research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Sri Krishna Jayadev Magani
- Cancer Biology Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Kiran Bharat Lokhande
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | | | - Ashutosh Singh
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
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8
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Asquith CRM, East MP, Laitinen T, Alamillo-Ferrer C, Hartikainen E, Wells CI, Axtman AD, Drewry DH, Tizzard GJ, Poso A, Willson TM, Johnson GL. Discovery and Optimization of Narrow Spectrum Inhibitors of Tousled Like Kinase 2 (TLK2) Using Quantitative Structure Activity Relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.28.573261. [PMID: 38234837 PMCID: PMC10793458 DOI: 10.1101/2023.12.28.573261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The oxindole scaffold has been the center of several kinase drug discovery programs, some of which have led to approved medicines. A series of two oxindole matched pairs from the literature were identified where TLK2 was a potent off-target kinase. The oxindole has long been considered a promiscuous inhibitor template, but across these 4 specific literature oxindoles TLK2 activity was consistent, while the kinome profile was radically different from narrow to broad spectrum coverage. We synthesized a large series of analogues and through quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites, small-molecule x-ray structural analysis and kinome profiling, narrow spectrum, sub-family selective, chemical tool compounds were identified to enable elucidation of TLK2 biology.
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Affiliation(s)
- Christopher R M Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carla Alamillo-Ferrer
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erkka Hartikainen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carrow I Wells
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Timothy M Willson
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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9
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Zhang Z, Liu S. The interaction between ASF1B and TLK1 promotes the malignant progression of low-grade glioma. Ann Med 2023; 55:1111-1122. [PMID: 36947060 PMCID: PMC10035952 DOI: 10.1080/07853890.2023.2169751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
AIM Low-grade glioma (LGG), which is the second most frequent adult brain malignancy, severely threatens patients' health and has a high recurrence rate. Histone H3/H4 chaperone anti-silencing function 1 B (ASF1B) has a tight association with the initiation and development of tumours. The expression and regulation mechanism of ASF1B in LGG were discussed. METHODS ASF1B expression in LGG patients as well as the association of ASF1B with overall survival and disease-free survival of LGG patients were predicted by GEPIA database. The independent prognostic value of ASF1B in LGG patients was investigated by TCGA database. RT-qPCR, together with western blot was applied for the assessment of ASF1B in LGG cell lines. After ASF1B expression was inhibited, CCK8 and colony formation assays judged cell proliferation. Flow cytometry analysis and TUNEL assay appraised cell cycle as well as apoptosis. Cell migratory and invasive capacities were measured by wound healing as well as Transwell assays. Western blot tested the expression of proliferation-, cycle-, apoptosis-, and metastasis-associated proteins. STRING and GeneMANIA database predicted the relationship between ASF1B and tousled-like kinase 1 (TLK1). ChIP assay testified the affinity of ASF1B with TLK1. Subsequently, TLK1 was overexpressed and ASF1B expression interfered, and the functional assays were executed. RESULTS ASF1B was discovered to be increased in LGG tissues and cells and indicates an unfavourable prognosis for LGG patients. ASF1B was not an independent prognostic factor for LGG. ASF1B deficiency obstructed the proliferation, cell cycle as well as metastasis of LGG cells, and induced cell death, which might be realized through the interaction with TLK1. CONCLUSION The interaction between ASF1B and TLK1 promoted the malignant progression of LGG.Key messagesTLK1 interacts with ASF1B.Interference with ASF1B inhibits the proliferative, invasive and migratory capabilities and induces the cycle arrest, along with the apoptosis of LGG cells.The interaction between ASF1B and TLK1 promotes the malignant progression of LGG.
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Affiliation(s)
- Zifa Zhang
- Neurosurgery Department, Shanxi Bethune Hospital, Taiyuan, Shanxi, P. R. China
- Shanxi Academy of Medical Sciences, Taiyuan, Shanxi, P. R. China
| | - Shuming Liu
- Emergency Department, Taiyuan People's Hospital, Taiyuan, Shanxi, P. R. China
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10
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Ghosh I, De Benedetti A. Untousling the Role of Tousled-like Kinase 1 in DNA Damage Repair. Int J Mol Sci 2023; 24:13369. [PMID: 37686173 PMCID: PMC10487508 DOI: 10.3390/ijms241713369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
DNA damage repair lies at the core of all cells' survival strategy, including the survival strategy of cancerous cells. Therefore, targeting such repair mechanisms forms the major goal of cancer therapeutics. The mechanism of DNA repair has been tousled with the discovery of multiple kinases. Recent studies on tousled-like kinases have brought significant clarity on the effectors of these kinases which stand to regulate DSB repair. In addition to their well-established role in DDR and cell cycle checkpoint mediation after DNA damage or inhibitors of replication, evidence of their suspected involvement in the actual DSB repair process has more recently been strengthened by the important finding that TLK1 phosphorylates RAD54 and regulates some of its activities in HRR and localization in the cell. Earlier findings of its regulation of RAD9 during checkpoint deactivation, as well as defined steps during NHEJ end processing, were earlier hints of its broadly important involvement in DSB repair. All this has opened up new avenues to target cancer cells in combination therapy with genotoxins and TLK inhibitors.
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Affiliation(s)
| | - Arrigo De Benedetti
- Department of Medicine, Department of Biochemistry, Louisiana Health Science Center-Shreveport, Shreveport, LA 71103, USA;
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11
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Villamor-Payà M, Sanchiz-Calvo M, Smak J, Pais L, Sud M, Shankavaram U, Lovgren AK, Austin-Tse C, Ganesh VS, Gay M, Vilaseca M, Arauz-Garofalo G, Palenzuela L, VanNoy G, O'Donnell-Luria A, Stracker TH. Identification of a de novo mutation in TLK1 associated with a neurodevelopmental disorder and immunodeficiency. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.22.23294267. [PMID: 37662408 PMCID: PMC10473813 DOI: 10.1101/2023.08.22.23294267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background The Tousled-like kinases 1 and 2 (TLK1/TLK2) regulate DNA replication, repair and chromatin maintenance. TLK2 variants are associated with 'Intellectual Disability, Autosomal Dominant 57' (MRD57), a neurodevelopmental disorder (NDD) characterized by intellectual disability (ID), autism spectrum disorder (ASD) and microcephaly. Several TLK1 variants have been reported in NDDs but their functional significance is unknown. Methods A male patient presenting with ID, seizures, global developmental delay, hypothyroidism, and primary immunodeficiency was determined to have a novel, heterozygous variant in TLK1 (c.1435C>G, p.Q479E) by genome sequencing (GS). Single cell gel electrophoresis, western blot, flow cytometry and RNA-seq were performed in patient-derived lymphoblast cell lines. In silico, biochemical and proteomic analysis were used to determine the functional impact of the p.Q479E variant and previously reported NDD-associated TLK1 variant, p.M566T. Results Transcriptome sequencing in patient-derived cells confirmed expression of TLK1 transcripts carrying the p.Q479E variant and revealed alterations in genes involved in class switch recombination and cytokine signaling. Cells expressing the p.Q479E variant exhibited reduced cytokine responses and higher levels of spontaneous DNA damage but not increased sensitivity to radiation or DNA repair defects. The p.Q479E and p.M566T variants impaired kinase activity but did not strongly alter localization or proximal protein interactions. Conclusion Our study provides the first functional characterization of TLK1 variants associated with NDDs and suggests potential involvement in central nervous system and immune system development. Our results indicate that, like TLK2 variants, TLK1 variants may impact development in multiple tissues and should be considered in the diagnosis of rare NDDs.
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Affiliation(s)
- Marina Villamor-Payà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - María Sanchiz-Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Jordann Smak
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - Lynn Pais
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Malika Sud
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Uma Shankavaram
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - Alysia Kern Lovgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay S Ganesh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Gianluca Arauz-Garofalo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Lluís Palenzuela
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Grace VanNoy
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne O'Donnell-Luria
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
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12
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Bhoir S, De Benedetti A. Targeting Prostate Cancer, the 'Tousled Way'. Int J Mol Sci 2023; 24:11100. [PMID: 37446279 DOI: 10.3390/ijms241311100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Androgen deprivation therapy (ADT) has been the mainstay of prostate cancer (PCa) treatment, with success in developing more effective inhibitors of androgen synthesis and antiandrogens in clinical practice. However, hormone deprivation and AR ablation have caused an increase in ADT-insensitive PCas associated with a poor prognosis. Resistance to ADT arises through various mechanisms, and most castration-resistant PCas still rely on the androgen axis, while others become truly androgen receptor (AR)-independent. Our research identified the human tousled-like kinase 1 (TLK1) as a crucial early mediator of PCa cell adaptation to ADT, promoting androgen-independent growth, inhibiting apoptosis, and facilitating cell motility and metastasis. Although explicit, the growing role of TLK1 biology in PCa has remained underrepresented and elusive. In this review, we aim to highlight the diverse functions of TLK1 in PCa, shed light on the molecular mechanisms underlying the transition from androgen-sensitive (AS) to an androgen-insensitive (AI) disease mediated by TLK1, and explore potential strategies to counteract this process. Targeting TLK1 and its associated signaling could prevent PCa progression to the incurable metastatic castration-resistant PCa (mCRPC) stage and provide a promising approach to treating PCa.
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Affiliation(s)
- Siddhant Bhoir
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA 71103, USA
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA 71103, USA
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13
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Zhong Z, Wang Y, Wang M, Yang F, Thomas QA, Xue Y, Zhang Y, Liu W, Jami-Alahmadi Y, Xu L, Feng S, Marquardt S, Wohlschlegel JA, Ausin I, Jacobsen SE. Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis. Nat Commun 2022; 13:6970. [PMID: 36379930 PMCID: PMC9666630 DOI: 10.1038/s41467-022-34648-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.
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Affiliation(s)
- Zhenhui Zhong
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yafei Wang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ming Wang
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Fan Yang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Quentin Angelo Thomas
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yan Xue
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yaxin Zhang
- grid.256111.00000 0004 1760 2876Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wanlu Liu
- grid.512487.dZhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400 Zhejiang China
| | - Yasaman Jami-Alahmadi
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Linhao Xu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, 06466 Germany
| | - Suhua Feng
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, CA 90095 USA
| | - Sebastian Marquardt
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - James A. Wohlschlegel
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Israel Ausin
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Steven E. Jacobsen
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 USA
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14
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López-Jiménez E, González-Aguilera C. Role of Chromatin Replication in Transcriptional Plasticity, Cell Differentiation and Disease. Genes (Basel) 2022; 13:genes13061002. [PMID: 35741764 PMCID: PMC9222293 DOI: 10.3390/genes13061002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chromatin organization is essential to maintain a correct regulation of gene expression and establish cell identity. However, during cell division, the replication of the genetic material produces a global disorganization of chromatin structure. In this paper, we describe the new scientific breakthroughs that have revealed the nature of the post-replicative chromatin and the mechanisms that facilitate its restoration. Moreover, we highlight the implications of these chromatin alterations in gene expression control and their impact on key biological processes, such as cell differentiation, cell reprogramming or human diseases linked to cell proliferation, such as cancer.
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Affiliation(s)
- Elena López-Jiménez
- Faculty of Medicine, National Heart and Lung Institute, Margaret Turner Warwick Centre for Fibrosing Lung Disease, Royal Brompton Campus, Imperial College London, London SW3 6LY, UK;
| | - Cristina González-Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
- Correspondence:
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15
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Khalil MI, De Benedetti A. Tousled-like kinase 1: a novel factor with multifaceted role in mCRPC progression and development of therapy resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:93-101. [PMID: 35582542 PMCID: PMC8992593 DOI: 10.20517/cdr.2021.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/14/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022]
Abstract
Standard treatment for advanced Prostate Cancer (PCa) consists of androgen deprivation therapy (ADT), but ultimately fails, resulting in the incurable phase of the disease: metastatic castration-resistant prostate cancer (mCRPC). Targeting PCa cells before their progression to mCRPC would greatly improve the outcome, if strategies could be devised selectively targeting androgen receptor (AR)-dependent and/or independent compensatory pathways which promote mCRPC development. Combination therapy by targeting the DNA damage response (DDR) along with ADT has been limited by general toxicity, and a goal of clinical trials is how to target the DDR more specifically. In recent years, our lab has identified a key role for the DDR kinase, TLK1, in mediating key aspects of adaptation to ADT, first by promoting a cell cycle arrest (through the TLK1>NEK1>ATR>Chk1 kinase cascade) under the unfavorable growth conditions (androgen deprivation), and then by reprogramming the PCa cells to adapt to androgen-independent growth via the NEK1>YAP/AR>CRPC conversion. In addition, TLK1 plays a key anti-apoptotic role via the NEK1>VDAC1 regulation on the intrinsic mitochondrial apoptotic pathway when the DDR is activated. Finally, TLK1 was recently identified as having an important role in motility and metastasis via regulation of the kinases MK5/PRAK and AKT (indirectly via AKTIP).
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Affiliation(s)
- Md Imtiaz Khalil
- Department of Biochemistry and Molecular Biology, LSU Health Sciences Center, Shreveport, LA 71103, USA
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology, LSU Health Sciences Center, Shreveport, LA 71103, USA
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16
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Ding N, Shao Z, Yuan F, Qu P, Li P, Lu D, Wang J, Zhu Q. Chk1 Inhibition Hinders the Restoration of H3.1K56 and H3.3K56 Acetylation and Reprograms Gene Transcription After DNA Damage Repair. Front Oncol 2022; 12:862592. [PMID: 35494003 PMCID: PMC9046994 DOI: 10.3389/fonc.2022.862592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022] Open
Abstract
H3K56 acetylation (H3K56Ac) was reported to play a critical role in chromatin assembly; thus, H3K56ac participates in the regulation of DNA replication, cell cycle progression, DNA repair, and transcriptional activation. To investigate the influence of DNA damage regulators on the acetylation of histone H3 and gene transcription, U2OS cells expressing SNAP-labeled H3.1 or SNAP-labeled H3.3 were treated with ATM, ATR, or a Chk1 inhibitor after ultraviolet (UV) radiation. The levels of H3.1K56ac, H3.3K56ac, and other H3 site-specific acetylation were checked at different time points until 24 h after UV radiation. The difference in gene transcription levels was also examined by mRNA sequencing. The results identified Chk1 as an important regulator of histone H3K56 acetylation in the restoration of both H3.1K56ac and H3.3K56ac. Moreover, compromising Chk1 activity via chemical inhibitors suppresses gene transcription after UV radiation. The study suggests a previously unknown role of Chk1 in regulating H3K56 and some other site-specific H3 acetylation and in reprograming gene transcription during DNA damage repair.
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Affiliation(s)
- Nan Ding
- Key Laboratory of Space Radiobiology of Gansu Province and Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Radiology and Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH, United States
- James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, United States
- *Correspondence: Nan Ding, ; Jufang Wang, ; Qianzheng Zhu,
| | - Zhiang Shao
- Key Laboratory of Space Radiobiology of Gansu Province and Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fangyun Yuan
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Pei Qu
- Key Laboratory of Space Radiobiology of Gansu Province and Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ping Li
- Key Laboratory of Space Radiobiology of Gansu Province and Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Radiology and Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH, United States
- James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, United States
| | - Dong Lu
- Key Laboratory of Space Radiobiology of Gansu Province and Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jufang Wang
- Key Laboratory of Space Radiobiology of Gansu Province and Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Nan Ding, ; Jufang Wang, ; Qianzheng Zhu,
| | - Qianzheng Zhu
- Department of Radiology and Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH, United States
- James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, United States
- *Correspondence: Nan Ding, ; Jufang Wang, ; Qianzheng Zhu,
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17
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Simon B, Lou HJ, Huet-Calderwood C, Shi G, Boggon TJ, Turk BE, Calderwood DA. Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. Nat Commun 2022; 13:749. [PMID: 35136069 PMCID: PMC8826447 DOI: 10.1038/s41467-022-28427-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 01/25/2022] [Indexed: 12/26/2022] Open
Abstract
Tousled-like kinases (TLKs) are nuclear serine-threonine kinases essential for genome maintenance and proper cell division in animals and plants. A major function of TLKs is to phosphorylate the histone chaperone proteins ASF1a and ASF1b to facilitate DNA replication-coupled nucleosome assembly, but how TLKs selectively target these critical substrates is unknown. Here, we show that TLK2 selectivity towards ASF1 substrates is achieved in two ways. First, the TLK2 catalytic domain recognizes consensus phosphorylation site motifs in the ASF1 C-terminal tail. Second, a short sequence at the TLK2 N-terminus docks onto the ASF1a globular N-terminal domain in a manner that mimics its histone H3 client. Disrupting either catalytic or non-catalytic interactions through mutagenesis hampers ASF1 phosphorylation by TLK2 and cell growth. Our results suggest that the stringent selectivity of TLKs for ASF1 is enforced by an unusual interaction mode involving mutual recognition of a short sequence motifs by both kinase and substrate. Tousled-like kinase 2 (TLK2) phosphorylates ASF1 histone chaperones to promote nucleosome assembly in S phase. Here, the authors show that TLK2 targets ASF1 by simulating its client protein histone H3, exploiting a primordial protein interaction surface for regulatory control.
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Affiliation(s)
- Bertrand Simon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | | | - Guangda Shi
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - David A Calderwood
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA. .,Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
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18
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Pavinato L, Villamor-Payà M, Sanchiz-Calvo M, Andreoli C, Gay M, Vilaseca M, Arauz-Garofalo G, Ciolfi A, Bruselles A, Pippucci T, Prota V, Carli D, Giorgio E, Radio FC, Antona V, Giuffrè M, Ranguin K, Colson C, De Rubeis S, Dimartino P, Buxbaum JD, Ferrero GB, Tartaglia M, Martinelli S, Stracker TH, Brusco A. Functional analysis of TLK2 variants and their proximal interactomes implicates impaired kinase activity and chromatin maintenance defects in their pathogenesis. J Med Genet 2022; 59:170-179. [PMID: 33323470 PMCID: PMC10631451 DOI: 10.1136/jmedgenet-2020-107281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/19/2020] [Accepted: 11/14/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The Tousled-like kinases 1 and 2 (TLK1 and TLK2) are involved in many fundamental processes, including DNA replication, cell cycle checkpoint recovery and chromatin remodelling. Mutations in TLK2 were recently associated with 'Mental Retardation Autosomal Dominant 57' (MRD57, MIM# 618050), a neurodevelopmental disorder characterised by a highly variable phenotype, including mild-to-moderate intellectual disability, behavioural abnormalities, facial dysmorphisms, microcephaly, epilepsy and skeletal anomalies. METHODS We re-evaluate whole exome sequencing and array-CGH data from a large cohort of patients affected by neurodevelopmental disorders. Using spatial proteomics (BioID) and single-cell gel electrophoresis, we investigated the proximity interaction landscape of TLK2 and analysed the effects of p.(Asp551Gly) and a previously reported missense variant (c.1850C>T; p.(Ser617Leu)) on TLK2 interactions, localisation and activity. RESULTS We identified three new unrelated MRD57 families. Two were sporadic and caused by a missense change (c.1652A>G; p.(Asp551Gly)) or a 39 kb deletion encompassing TLK2, and one was familial with three affected siblings who inherited a nonsense change from an affected mother (c.1423G>T; p.(Glu475Ter)). The clinical phenotypes were consistent with those of previously reported cases. The tested mutations strongly impaired TLK2 kinase activity. Proximal interactions between TLK2 and other factors implicated in neurological disorders, including CHD7, CHD8, BRD4 and NACC1, were identified. Finally, we demonstrated a more relaxed chromatin state in lymphoblastoid cells harbouring the p.(Asp551Gly) variant compared with control cells, conferring susceptibility to DNA damage. CONCLUSION Our study identified novel TLK2 pathogenic variants, confirming and further expanding the MRD57-related phenotype. The molecular characterisation of missense variants increases our knowledge about TLK2 function and provides new insights into its role in neurodevelopmental disorders.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, Torino, Italy
- Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marina Villamor-Payà
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Maria Sanchiz-Calvo
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Cristina Andreoli
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Marina Gay
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Marta Vilaseca
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Gianluca Arauz-Garofalo
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Tommaso Pippucci
- Medical Genetics Unity, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Valentina Prota
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Diana Carli
- Department of Pediatrics and Public Health and Pediatric Sciences, University of Turin, Torino, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Turin, Torino, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Vincenzo Antona
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Mario Giuffrè
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Kara Ranguin
- Department of Genetics, Reference center for Rare Diseases and Developmental Anomalies, Caen, France
| | - Cindy Colson
- Department of Genetics, Reference center for Rare Diseases and Developmental Anomalies, Caen, France
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Giovanni Battista Ferrero
- Department of Pediatrics and Public Health and Pediatric Sciences, University of Turin, Torino, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Roma, Italy
| | - Travis H Stracker
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
- Radiation Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Torino, Italy
- Unit of Medical Genetics, "Città della Salute e della Scienza" University Hospital, Torino, Italy
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19
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Lee SB, Chang TY, Lee NZ, Yu ZY, Liu CY, Lee HY. Design, synthesis and biological evaluation of bisindole derivatives as anticancer agents against Tousled-like kinases. Eur J Med Chem 2022; 227:113904. [PMID: 34662748 DOI: 10.1016/j.ejmech.2021.113904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 11/03/2022]
Abstract
This study presents the design, synthesis, and characterization of bisindole molecules as anti-cancer agents against Tousled-like kinases (TLKs). We show that compound 2 composed of an indirubin-3'-oxime group linked with a (N-methylpiperidin-2-yl)ethyl moiety possessed inhibitory activity toward both TLK1 and TLK2 in vitro and diminished the phosphorylation level of the downstream substrate anti-silencing function 1 (ASF1) in replicating cells. The treatment of compound 2 impaired DNA replication, slowed S-phase progression, and triggered DNA damage response in replicating cells. Structure optimization further discovered six derivatives exhibiting potent TLK inhibitory activity and revealed the importance of the tertiary amine-containing moiety of the side chain. Moreover, the derivatives 6, 17, 19, and 20 strongly suppressed the growth of triple-negative breast cancer MDA-MB-231 cells, non-small cell lung cancer A549 cells, and colorectal cancer HCT-116 cells, while normal lung fibroblast MRC5 and IMR90 cells showed a lower response to these compounds. Taken together, this study identifies tertiary amine-linked indirubin-3'-oximes as potent anticancer agents that inhibit TLK activity.
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Affiliation(s)
- Sung-Bau Lee
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Ting-Yu Chang
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Nian-Zhe Lee
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Zih-Yao Yu
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Chi-Yuan Liu
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Hsueh-Yun Lee
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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20
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Piette BL, Alerasool N, Lin ZY, Lacoste J, Lam MHY, Qian WW, Tran S, Larsen B, Campos E, Peng J, Gingras AC, Taipale M. Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains. Mol Cell 2021; 81:2549-2565.e8. [PMID: 33957083 DOI: 10.1016/j.molcel.2021.04.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022]
Abstract
Hsp70s comprise a deeply conserved chaperone family that has a central role in maintaining protein homeostasis. In humans, Hsp70 client specificity is provided by 49 different co-factors known as J domain proteins (JDPs). However, the cellular function and client specificity of JDPs have largely remained elusive. We have combined affinity purification-mass spectrometry (AP-MS) and proximity-dependent biotinylation (BioID) to characterize the interactome of all human JDPs and Hsp70s. The resulting network suggests specific functions for many uncharacterized JDPs, and we establish a role of conserved JDPs DNAJC9 and DNAJC27 in histone chaperoning and ciliogenesis, respectively. Unexpectedly, we find that the J domain of DNAJC27 but not of other JDPs can fully replace the function of endogenous DNAJC27, suggesting a previously unappreciated role for J domains themselves in JDP specificity. More broadly, our work expands the role of the Hsp70-regulated proteostasis network and provides a platform for further discovery of JDP-dependent functions.
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Affiliation(s)
- Benjamin L Piette
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Nader Alerasool
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Jessica Lacoste
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mandy Hiu Yi Lam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephanie Tran
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Eric Campos
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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21
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Structural insights into histone chaperone Asf1 and its characterization from Plasmodium falciparum. Biochem J 2021; 478:1117-1136. [PMID: 33501928 DOI: 10.1042/bcj20200891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Asf1 is a highly conserved histone chaperone that regulates tightly coupled nucleosome assembly/disassembly process. We observed that Plasmodium falciparum Asf1 (PfAsf1) is ubiquitously expressed in different stages of the life cycle of the parasite. To gain further insight into its biological activity, we solved the structure of N-terminal histone chaperone domain of PfAsf1 (1-159 amino acids) by X-ray crystallography to a resolution of 2.4 Å. The structure is composed of two beta-sheet to form a beta-sandwich, which resembles an immunoglobulin-like fold. The surface-charge distribution of PfAsf1 is distinct from yAsf1 and hAsf1 although the core-structure shows significant similarity. The crystal-structure indicated that PfAsf1 may exist in a dimeric-state which was further confirmed by solution cross-linking experiment. PfAsf1 was found to specifically interact with Plasmodium histone H3 and H4 and was able to deposit H3/H4 dimer onto DNA-template to form disomes, showing its characteristic histone chaperone activity. We mapped the critical residues of PfAsf1 involved in histone H3/H4 interaction and confirmed by site-directed mutagenesis. Further analysis indicates that histone interacting surface of Asf1 is highly conserved while the dimerization interface is variable. Our results identify the role of PfAsf1 as a mediator of chromatin assembly in Plasmodium falciparum, which is the causative agent of malignant malaria in humans.
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22
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Ni C, Zheng K, Gao Y, Chen Y, Shi K, Ni C, Jin G, Yu G. ACOT4 accumulation via AKT-mediated phosphorylation promotes pancreatic tumourigenesis. Cancer Lett 2021; 498:19-30. [PMID: 33148467 DOI: 10.1016/j.canlet.2020.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/24/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
The acyl-CoA thioesterase (ACOT) family catalyses the hydrolysis of acyl-CoA thioesters to their corresponding non-esterified fatty acid and coenzyme A (CoA). Increasing evidence suggests that cancer cells generally have altered lipid metabolism in different aspects. However, the roles of the ACOT family in cancer, especially in pancreatic ductal carcinoma (PDAC), are largely unknown. In the present study, we mined data to determine the clinical significance of all eleven ACOT genes among nine major solid tumour types from TCGA database and found that the expression of ACOT4 in PDAC was negatively correlated with patient survival, establishing ACOT4 as a potential biomarker of PDAC. Depletion of ACOT4 attenuated the proliferation and tumour formation of PDAC cells. Using mass spectrometry, HSPA1A was found to associate with ACOT4. Furthermore, we found that phosphorylation of ACOT4 at S392 by AKT decreased the binding of ACOT4 to HSPA1A, resulting in ACOT4 accumulation. The ACOT4 elevation promotes pancreatic tumourigenesis by producing excessive CoA to support tumour cell metabolism. Thus, our study expands the relationship between AKT signalling and lipid metabolism and establishes a functional role of ACOT4 in PDAC.
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Affiliation(s)
- Chenming Ni
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Kailian Zheng
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Yunshu Gao
- Department of Oncology, PLA General Hospital, Beijing, 100853, China
| | - Ying Chen
- Department of Pathology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Keqing Shi
- Precision Medical Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang Province, 325000, China
| | - Canrong Ni
- Department of Pathology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Gang Jin
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China.
| | - Guanzhen Yu
- Precision Medical Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang Province, 325000, China.
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23
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Lee KY, Dutta A. Chk1 promotes non-homologous end joining in G1 through direct phosphorylation of ASF1A. Cell Rep 2021; 34:108680. [PMID: 33503415 DOI: 10.1016/j.celrep.2020.108680] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/16/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
The cell-cycle phase is a major determinant of repair pathway choice at DNA double strand breaks, non-homologous end joining (NHEJ), or homologous recombination (HR). Chk1 responds to genotoxic stress in S/G2 phase, but here, we report a role of Chk1 in directly promoting NHEJ repair in G1 phase. ASF1A is a histone chaperone, but it promotes NHEJ through a pathway independent of its histone-chaperone activity. Chk1 activated by ataxia telangiectasia mutated (ATM) kinase on DNA breaks in G1 promotes NHEJ through direct phosphorylation of ASF1A at Ser-166. ASF1A phosphorylated at Ser-166 interacts with the repair protein MDC1 and thus enhances MDC1's interaction with ATM and the stable localization of ATM at DNA breaks. Chk1 deficiency suppresses all steps downstream of MDC1 following a DNA break in G1, namely histone ubiquitination, 53BP1 localization to the DNA break, and NHEJ. Thus, ASF1A phosphorylation by Chk1 is essential for DNA break repair by NHEJ in G1.
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Affiliation(s)
- Kyung Yong Lee
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA; Division of Cancer Biology, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408, South Korea
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.
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24
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Mognato M, Burdak-Rothkamm S, Rothkamm K. Interplay between DNA replication stress, chromatin dynamics and DNA-damage response for the maintenance of genome stability. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108346. [PMID: 34083038 DOI: 10.1016/j.mrrev.2020.108346] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
DNA replication stress is a major source of DNA damage, including double-stranded breaks that promote DNA damage response (DDR) signaling. Inefficient repair of such lesions can affect genome integrity. During DNA replication different factors act on chromatin remodeling in a coordinated way. While recent studies have highlighted individual molecular mechanisms of interaction, less is known about the orchestration of chromatin changes under replication stress. In this review we attempt to explore the complex relationship between DNA replication stress, DDR and genome integrity in mammalian cells, taking into account the role of chromatin disposition as an important modulator of DNA repair. Recent data on chromatin restoration and epigenetic re-establishment after DNA replication stress are reviewed.
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Affiliation(s)
| | - Susanne Burdak-Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
| | - Kai Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
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25
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Chen P, Zhang Z, Chen X. Overexpression of PKMYT1 Facilitates Tumor Development and Is Correlated with Poor Prognosis in Clear Cell Renal Cell Carcinoma. Med Sci Monit 2020; 26:e926755. [PMID: 33024069 PMCID: PMC7549326 DOI: 10.12659/msm.926755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Protein kinase membrane-associated tyrosine/threonine (PKMYT1) has been found in many tumors, but its association with clear cell renal cell carcinoma (ccRCC) remains unclear. MATERIAL AND METHODS PKMYT1 expression in ccRCC was examined in the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Tumor Immune Estimation Resource databases. The correlation between PKMYT1 expression and clinicopathological parameters was explored via the chi-square test. Receiver operating characteristic curves were used to estimate the diagnostic performance of PKMYT1. Kaplan-Meier curves, a Cox model, nomogram, time-dependent receiver operating characteristic curves, and decision curve analysis (DCA) were used to evaluate the prognostic value and clinical utility of PKMYT1. Genes coexpressed with PKMYT1 in ccRCC were identified based on TCGA, the gene expression profiling interactive, and cBioPortal. Gene Set Enrichment Analysis revealed biological pathways associated with PKMYT1 in ccRCC. RESULTS Weighted gene coexpression network analysis identified PKMYT1 as one of the genes most significantly correlated with progression of histological grade. PKMYT1 was significantly upregulated in ccRCC compared with normal tissue (P<0.001), with a trend toward differentiating between individuals with ccRCC and those who were healthy (area under the curve=0.942). High PKMYT1 expression was correlated with unsatisfactory survival (hazard ratio=1.67, P=0.001), indicating that it is a risk factor for ccRCC. A nomogram incorporating PKMYT1 level was created and showed a clinical net benefit. PKMYT1 was strongly positively correlated with the anti-silencing function of 1B histone chaperone (ASF1B) gene in ccRCC. CONCLUSIONS PKMYT1 is upregulated in ccRCC and its presence indicates poor prognosis, making it a potential therapeutic target for ccRCC.
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Affiliation(s)
- Peng Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China (mainland)
| | - Ziying Zhang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China (mainland).,Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China (mainland)
| | - Xiang Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China (mainland)
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26
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Francis NJ, Sihou D. Inheritance of Histone (H3/H4): A Binary Choice? Trends Biochem Sci 2020; 46:5-14. [PMID: 32917507 DOI: 10.1016/j.tibs.2020.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/09/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Histones carry information in the form of post-translational modifications (PTMs). For this information to be propagated through cell cycles, parental histones and their PTMs need to be maintained at the same genomic locations. Yet, during DNA replication, every nucleosome in the genome is disrupted to allow passage of the replisome. Recent data have identified histone chaperone activities that are intrinsic components of the replisome and implicate them in maintaining parental histones during DNA replication. We propose that structural and kinetic coordination between DNA replication and replisome-associated histone chaperone activities ensures positional inheritance of histones and their PTMs. When this coordination is perturbed, histones may instead be recycled to random genomic locations by alternative histone chaperones.
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Affiliation(s)
- Nicole J Francis
- Institut de Recherche Clinique de Montréal, 110 Avenue des Pins, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada; Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada.
| | - Djamouna Sihou
- Institut de Recherche Clinique de Montréal, 110 Avenue des Pins, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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27
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Deng K, Feng W, Liu X, Su X, Zuo E, Du S, Huang Y, Shi D, Lu F. Anti-silencing factor 1A is associated with genome stability maintenance of mouse preimplantation embryos†. Biol Reprod 2020; 102:817-827. [PMID: 31916576 DOI: 10.1093/biolre/ioaa001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/07/2019] [Accepted: 01/03/2020] [Indexed: 12/26/2022] Open
Abstract
Genome stability is critical for the normal development of preimplantation embryos, as DNA damages may result in mutation and even embryo lethality. Anti-silencing factor 1A (ASF1A) is a histone chaperone and enriched in the MII oocytes as a maternal factor, which may be associated with the maintenance of genome stability. Thus, this study was undertaken to explore the role of ASF1A in maintaining the genome stability of early mouse embryos. The ASF1A expressed in the preimplantation embryos and displayed a dynamic pattern throughout the early embryonic development. Inhibition of ASF1A expression decreased embryonic development and increased DNA damages. Overexpression of ASF1A improved the developmental potential and decreased DNA damages. When 293T cells that had been integrated with RGS-NHEJ were co-transfected with plasmids of pcDNA3.1-ASF1A, gRNA-NHEJ, and hCas9, less cells expressed eGFP, indicating that non-homologous end joining was reduced by ASF1A. When 293T cells were co-transfected with plasmids of HR-donor, gRNA-HR, hCas9, and pcDNA3.1-ASF1A, more cells expressed eGFP, indicating that homologous recombination (HR) was enhanced by ASF1A. These results indicate that ASF1A may be associated with the genome stability maintenance of early mouse embryos and this action may be mediated by promoting DNA damage repair through HR pathway.
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Affiliation(s)
- Kai Deng
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China and
| | - Wanyou Feng
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China and
| | - Xiaohua Liu
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China and
| | - Xiaoping Su
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China and
| | - Erwei Zuo
- Center for Animal Genomics, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shanshan Du
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China and
| | - Yongjun Huang
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China and
| | - Deshun Shi
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China and
| | - Fenghua Lu
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China and
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28
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Srivastava M, Chen Z, Zhang H, Tang M, Wang C, Jung SY, Chen J. Replisome Dynamics and Their Functional Relevance upon DNA Damage through the PCNA Interactome. Cell Rep 2019; 25:3869-3883.e4. [PMID: 30590055 PMCID: PMC6364303 DOI: 10.1016/j.celrep.2018.11.099] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/09/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic cells use copious measures to ensure accurate duplication of the genome. Various genotoxic agents pose threats to the ongoing replication fork that, if not efficiently dealt with, can result in replication fork collapse. It is unknown how replication fork is precisely controlled and regulated under different conditions. Here, we examined the complexity of replication fork composition upon DNA damage by using a PCNA-based proteomic screen to uncover known and unexplored players involved in replication and replication stress response. We used camptothecin or UV radiation, which lead to fork-blocking lesions, to establish a comprehensive proteomics map of the replisome under such replication stress conditions. We identified and examined two potential candidate proteins WIZ and SALL1 for their roles in DNA replication and replication stress response. In addition, our unbiased screen uncovered many prospective candidate proteins that help fill the knowledge gap in understanding chromosomal DNA replication and DNA repair.
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Affiliation(s)
- Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Yun Jung
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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29
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Segura-Bayona S, Stracker TH. The Tousled-like kinases regulate genome and epigenome stability: implications in development and disease. Cell Mol Life Sci 2019; 76:3827-3841. [PMID: 31302748 PMCID: PMC11105529 DOI: 10.1007/s00018-019-03208-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/05/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023]
Abstract
The Tousled-like kinases (TLKs) are an evolutionarily conserved family of serine-threonine kinases that have been implicated in DNA replication, DNA repair, transcription, chromatin structure, viral latency, cell cycle checkpoint control and chromosomal stability in various organisms. The functions of the TLKs appear to depend largely on their ability to regulate the H3/H4 histone chaperone ASF1, although numerous TLK substrates have been proposed. Over the last few years, a clearer picture of TLK function has emerged through the identification of new partners, the definition of specific roles in development and the elucidation of their structural and biochemical properties. In addition, the TLKs have been clearly linked to human disease; both TLK1 and TLK2 are frequently amplified in human cancers and TLK2 mutations have been identified in patients with neurodevelopmental disorders characterized by intellectual disability (ID), autism spectrum disorder (ASD) and microcephaly. A better understanding of the substrates, regulation and diverse roles of the TLKs is needed to understand their functions in neurodevelopment and determine if they are viable targets for cancer therapy. In this review, we will summarize current knowledge of TLK biology and its potential implications in development and disease.
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Affiliation(s)
- Sandra Segura-Bayona
- Department of Oncology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/Baldiri Reixac 10, 08028, Barcelona, Spain.
- The Francis Crick Institute, London, UK.
| | - Travis H Stracker
- Department of Oncology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/Baldiri Reixac 10, 08028, Barcelona, Spain.
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Zhang Y, Tao H, Huang SY. Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1. Int J Mol Sci 2019; 20:ijms20133325. [PMID: 31284555 PMCID: PMC6651421 DOI: 10.3390/ijms20133325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022] Open
Abstract
The recruitment and transference of proteins through protein-protein interactions is a general process involved in various biological functions in cells. Despite the importance of this general process, the dynamic mechanism of how proteins are recruited and transferred from one interacting partner to another remains unclear. In this study, we investigated the dynamic mechanisms of recruitment and translocation of histone chaperone CIA/ASF1 for nucleosome disassembly by exploring the conformational space and the free energy profile of unbound DBD(CCG1) and CIA/ASF1-bound DBD(CCG1) systems through extensive molecular dynamics simulations. It was found that there exists three metastable conformational states for DBD(CCG1), an unbound closed state, a CIA/ASF1-bound half-open state, and an open state. The free energy landscape shows that the closed state and the half-open state are separated by a high free energy barrier, while the half-open state and the open state are connected with a moderate free energy increase. The high free energy barrier between the closed and half-open states explains why DBD(CCG1) can recruit CIA/ASF1 and remain in the binding state during the transportation. In addition, the asymmetric binding of CIA/ASF1 on DBD(CCG1) allows DBD(CCG1) to adopt the open state by moving one of its two domains, such that the exposed domain of DBD(CCG1) is able to recognize the acetylated histone H4 tails. As such, CIA/ASF1 has a chance to translocate from DBD(CCG1) to histone, which is also facilitated by the moderate energy increase from the bound half-open state to the open state of DBD(CCG1). These findings suggest that the recruitment and transference of histone chaperone CIA/ASF1 is highly favored by its interaction with DBD(CCG1) via conformational selection and asymmetric binding, which may represent a general mechanism of similar biological processes.
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Affiliation(s)
- Yanjun Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huanyu Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China.
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31
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Shibata Y, Seki Y, Nishiwaki K. Maintenance of cell fates and regulation of the histone variant H3.3 by TLK kinase in Caenorhabditis elegans. Biol Open 2019; 8:bio.038448. [PMID: 30635266 PMCID: PMC6361200 DOI: 10.1242/bio.038448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cell-fate maintenance is important to preserve the variety of cell types that are essential for the formation and function of tissues. We previously showed that the acetylated histone-binding protein BET-1 maintains cell fate by recruiting the histone variant H2A.z. Here, we report that Caenorhabditis elegans TLK-1 and the histone H3 chaperone CAF1 prevent the accumulation of histone variant H3.3. In addition, TLK-1 and CAF1 maintain cell fate by repressing ectopic expression of transcription factors that induce cell-fate specification. Genetic analyses suggested that TLK-1 and BET-1 act in parallel pathways. In tlk-1 mutants, the loss of SIN-3, which promotes histone acetylation, suppressed a defect in cell-fate maintenance in a manner dependent on MYST family histone acetyltransferase MYS-2 and BET-1. sin-3 mutation also suppressed abnormal H3.3 incorporation. Thus, we propose a hypothesis that the regulation and interaction of histone variants play crucial roles in cell-fate maintenance through the regulation of selector genes. Summary: Histone H3 chaperone CAF1 maintains cell fate by repressing ectopic expression of genes for cell fate-specifying transcription factors. Accumulation of histone variant H3.3 correlates with defects in cell-fate maintenance.
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Affiliation(s)
- Yukimasa Shibata
- School of Science and Technology, Department of Bioscience, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Yoshiyuki Seki
- School of Science and Technology, Department of Bioscience, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Kiyoji Nishiwaki
- School of Science and Technology, Department of Bioscience, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
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32
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Abstract
We recently demonstrated that the circadian clock component CRY2 is an essential cofactor in the SCFFBXL3-mediated ubiquitination of c-MYC. Because our demonstration that CRY2 recruits phosphorylated substrates to SCFFBXL3 was unexpected, we investigated the scope of this role by searching for additional substrates of FBXL3 that require CRY1 or CRY2 as cofactors. Here, we describe an affinity purification mass spectrometry (APMS) screen through which we identified more than one hundred potential substrates of SCFFBXL3+CRY1/2, including the cell cycle regulated Tousled-like kinase, TLK2. Both CRY1 and CRY2 recruit TLK2 to SCFFBXL3, and TLK2 kinase activity is required for this interaction. Overexpression or genetic deletion of CRY1 and/or CRY2 decreases or enhances TLK2 protein abundance, respectively. These findings reinforce the idea that CRYs function as co-factors for SCFFBXL3, provide a resource of potential substrates, and establish a molecular connection between the circadian and cell cycle oscillators via CRY-modulated turnover of TLK2.
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Levings DC, Wang X, Kohlhase D, Bell DA, Slattery M. A distinct class of antioxidant response elements is consistently activated in tumors with NRF2 mutations. Redox Biol 2018; 19:235-249. [PMID: 30195190 PMCID: PMC6128101 DOI: 10.1016/j.redox.2018.07.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 12/17/2022] Open
Abstract
NRF2 is a redox-responsive transcription factor that regulates expression of cytoprotective genes via its interaction with DNA sequences known as antioxidant response elements (AREs). NRF2 activity is induced by oxidative stress, but oxidative stress is not the only context in which NRF2 can be activated. Mutations that disrupt the interaction between NRF2 and KEAP1, an inhibitor of NRF2, lead to NRF2 hyperactivation and promote oncogenesis. The mechanisms underlying NRF2's oncogenic properties remain unclear, but likely involve aberrant expression of select NRF2 target genes. We tested this possibility using an integrative genomics approach to get a precise view of the direct NRF2 target genes dysregulated in tumors with NRF2 hyperactivating mutations. This approach revealed a core set of 32 direct NRF2 targets that are consistently upregulated in NRF2 hyperactivated tumors. This set of NRF2 "cancer target genes" includes canonical redox-related NRF2 targets, as well as target genes that have not been previously linked to NRF2 activation. Importantly, NRF2-driven upregulation of this gene set is largely independent of the organ system where the tumor developed. One key distinguishing feature of these NRF2 cancer target genes is that they are regulated by high affinity AREs that fall within genomic regions possessing a ubiquitously permissive chromatin signature. This implies that these NRF2 cancer target genes are responsive to oncogenic NRF2 in most tissues because they lack the regulatory constraints that restrict expression of most other NRF2 target genes. This NRF2 cancer target gene set also serves as a reliable proxy for NRF2 activity, and high NRF2 activity is associated with significant decreases in survival in multiple cancer types. Overall, the pervasive upregulation of these NRF2 cancer targets across multiple cancers, and their association with negative outcomes, suggests that these will be central to dissecting the functional implications of NRF2 hyperactivation in several cancer contexts.
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Affiliation(s)
- Daniel C Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Xuting Wang
- Environmental Epigenomics and Disease Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Derek Kohlhase
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Douglas A Bell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA.
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Apta-Smith MJ, Hernandez-Fernaud JR, Bowman AJ. Evidence for the nuclear import of histones H3.1 and H4 as monomers. EMBO J 2018; 37:embj.201798714. [PMID: 30177573 PMCID: PMC6166134 DOI: 10.15252/embj.201798714] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 11/09/2022] Open
Abstract
Newly synthesised histones are thought to dimerise in the cytosol and undergo nuclear import in complex with histone chaperones. Here, we provide evidence that human H3.1 and H4 are imported into the nucleus as monomers. Using a tether-and-release system to study the import dynamics of newly synthesised histones, we find that cytosolic H3.1 and H4 can be maintained as stable monomeric units. Cytosolically tethered histones are bound to importin-alpha proteins (predominantly IPO4), but not to histone-specific chaperones NASP, ASF1a, RbAp46 (RBBP7) or HAT1, which reside in the nucleus in interphase cells. Release of monomeric histones from their cytosolic tether results in rapid nuclear translocation, IPO4 dissociation and incorporation into chromatin at sites of replication. Quantitative analysis of histones bound to individual chaperones reveals an excess of H3 specifically associated with sNASP, suggesting that NASP maintains a soluble, monomeric pool of H3 within the nucleus and may act as a nuclear receptor for newly imported histone. In summary, we propose that histones H3 and H4 are rapidly imported as monomeric units, forming heterodimers in the nucleus rather than the cytosol.
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Affiliation(s)
| | | | - Andrew James Bowman
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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35
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Lee SB, Segura-Bayona S, Villamor-Payà M, Saredi G, Todd MAM, Attolini CSO, Chang TY, Stracker TH, Groth A. Tousled-like kinases stabilize replication forks and show synthetic lethality with checkpoint and PARP inhibitors. SCIENCE ADVANCES 2018; 4:eaat4985. [PMID: 30101194 PMCID: PMC6082654 DOI: 10.1126/sciadv.aat4985] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 07/01/2018] [Indexed: 05/12/2023]
Abstract
DNA sequence and epigenetic information embedded in chromatin must be faithfully duplicated and transmitted to daughter cells during cell division. However, how chromatin assembly and DNA replication are integrated remains unclear. We examined the contribution of the Tousled-like kinases 1 and 2 (TLK1/TLK2) to chromatin assembly and maintenance of replication fork integrity. We show that TLK activity is required for DNA replication and replication-coupled nucleosome assembly and that lack of TLK activity leads to replication fork stalling and the accumulation of single-stranded DNA, a phenotype distinct from ASF1 depletion. Consistent with these results, sustained TLK depletion gives rise to replication-dependent DNA damage and p53-dependent cell cycle arrest in G1. We find that deficient replication-coupled de novo nucleosome assembly renders replication forks unstable and highly dependent on the ATR and CHK1 checkpoint kinases, as well as poly(adenosine 5'-diphosphate-ribose) polymerase (PARP) activity, to avoid collapse. Human cancer data revealed frequent up-regulation of TLK genes and an association with poor patient outcome in multiple types of cancer, and depletion of TLK activity leads to increased replication stress and DNA damage in a panel of cancer cells. Our results reveal a critical role for TLKs in chromatin replication and suppression of replication stress and identify a synergistic lethal relationship with checkpoint signaling and PARP that could be exploited in treatment of a broad range of cancers.
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Affiliation(s)
- Sung-Bau Lee
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Sandra Segura-Bayona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marina Villamor-Payà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Giulia Saredi
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Matthew A. M. Todd
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ting-Yu Chang
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Travis H. Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Corresponding author. (T.H.S.); (A.G.)
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Corresponding author. (T.H.S.); (A.G.)
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36
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Molecular basis of Tousled-Like Kinase 2 activation. Nat Commun 2018; 9:2535. [PMID: 29955062 PMCID: PMC6023931 DOI: 10.1038/s41467-018-04941-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 06/06/2018] [Indexed: 12/21/2022] Open
Abstract
Tousled-like kinases (TLKs) are required for genome stability and normal development in numerous organisms and have been implicated in breast cancer and intellectual disability. In humans, the similar TLK1 and TLK2 interact with each other and TLK activity enhances ASF1 histone binding and is inhibited by the DNA damage response, although the molecular mechanisms of TLK regulation remain unclear. Here we describe the crystal structure of the TLK2 kinase domain. We show that the coiled-coil domains mediate dimerization and are essential for activation through ordered autophosphorylation that promotes higher order oligomers that locally increase TLK2 activity. We show that TLK2 mutations involved in intellectual disability impair kinase activity, and the docking of several small-molecule inhibitors of TLK activity suggest that the crystal structure will be useful for guiding the rationale design of new inhibition strategies. Together our results provide insights into the structure and molecular regulation of the TLKs. The Tousled-like kinase (TLKs) family belongs to a distinct branch of Ser/Thr kinases that exhibit the highest levels of activity during DNA replication. Here the authors present the crystal structure of the kinase domain from human TLK2 and propose an activation model for TLK2 based on biochemical and phosphoproteomics experiments.
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37
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Reijnders MRF, Miller KA, Alvi M, Goos JAC, Lees MM, de Burca A, Henderson A, Kraus A, Mikat B, de Vries BBA, Isidor B, Kerr B, Marcelis C, Schluth-Bolard C, Deshpande C, Ruivenkamp CAL, Wieczorek D, Baralle D, Blair EM, Engels H, Lüdecke HJ, Eason J, Santen GWE, Clayton-Smith J, Chandler K, Tatton-Brown K, Payne K, Helbig K, Radtke K, Nugent KM, Cremer K, Strom TM, Bird LM, Sinnema M, Bitner-Glindzicz M, van Dooren MF, Alders M, Koopmans M, Brick L, Kozenko M, Harline ML, Klaassens M, Steinraths M, Cooper NS, Edery P, Yap P, Terhal PA, van der Spek PJ, Lakeman P, Taylor RL, Littlejohn RO, Pfundt R, Mercimek-Andrews S, Stegmann APA, Kant SG, McLean S, Joss S, Swagemakers SMA, Douzgou S, Wall SA, Küry S, Calpena E, Koelling N, McGowan SJ, Twigg SRF, Mathijssen IMJ, Nellaker C, Brunner HG, Wilkie AOM. De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder. Am J Hum Genet 2018; 102:1195-1203. [PMID: 29861108 PMCID: PMC5992133 DOI: 10.1016/j.ajhg.2018.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/26/2018] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.
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Affiliation(s)
- Margot R F Reijnders
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mohsan Alvi
- Visual Geometry Group, Department of Engineering Science, University of Oxford, Oxford OX1 2JD, UK
| | - Jacqueline A C Goos
- Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Melissa M Lees
- Department of Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Anna de Burca
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Alex Henderson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds LS7 4SA, UK
| | - Barbara Mikat
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147 Essen, Germany
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Bertrand Isidor
- CHU de Nantes, Service de Génétique Médicale, Nantes 44093 Cedex 1, France; INSERM, UMR-S 957, 1 Rue Gaston Veil, Nantes 44035, France
| | - Bronwyn Kerr
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK
| | - Carlo Marcelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Caroline Schluth-Bolard
- Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69500 Bron, France; INSERM U1028, CNRS UMR5292, UCB Lyon 1, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, 69500 Bron, France
| | - Charu Deshpande
- South East Thames Regional Genetics Service, Guy's Hospital, London SE1 9RT, UK
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147 Essen, Germany; Institute of Human Genetics, Heinrich-Heine-University, Medical Faculty, 40225 Düsseldorf, Germany
| | - Diana Baralle
- Human Development and Health, Duthie Building, University of Southampton, Southampton SO16 6YD, UK; Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton SO16 5YA, UK
| | - Edward M Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127 Bonn, Germany
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147 Essen, Germany; Institute of Human Genetics, Heinrich-Heine-University, Medical Faculty, 40225 Düsseldorf, Germany
| | - Jacqueline Eason
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Hucknall Road, Nottingham NG5 1PB, UK
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Jill Clayton-Smith
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK
| | - Kate Chandler
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK
| | - Katrina Tatton-Brown
- Southwest Thames Regional Genetics Centre, St George's University Hospitals NHS Foundation Trust, St George's University of London, London SW17 0RE, UK
| | - Katelyn Payne
- Riley Hospital for Children, Indianapolis, Indiana, IN 46202, USA
| | - Katherine Helbig
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Kelly Radtke
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Kimberly M Nugent
- Department of Pediatrics, Baylor College of Medicine, The Children's Hospital of San Antonio, San Antonio, TX 78207, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127 Bonn, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Lynne M Bird
- University of California, San Diego, Department of Pediatrics; Genetics and Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Margje Sinnema
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht 6229 ER, the Netherlands
| | - Maria Bitner-Glindzicz
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, PO Box 21455, 3001 AL Rotterdam, the Netherlands
| | - Marielle Alders
- Department of Clinical Genetics, Academic Medical Center, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Marije Koopmans
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Lauren Brick
- Division of Genetics, Department of Pediatrics, McMaster Children's Hospital, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Mariya Kozenko
- Division of Genetics, Department of Pediatrics, McMaster Children's Hospital, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Megan L Harline
- Department of Pediatrics, Baylor College of Medicine, The Children's Hospital of San Antonio, San Antonio, TX 78207, USA
| | - Merel Klaassens
- Department of Paediatrics, Maastricht University Medical Center, Maastricht 6229 ER, the Netherlands
| | - Michelle Steinraths
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V8Z 6R5, Canada
| | - Nicola S Cooper
- West Midlands Regional Clinical Genetics Unit, Birmingham Women's & Children's NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Patrick Edery
- Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69500 Bron, France; INSERM U1028, CNRS UMR5292, UCB Lyon 1, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, 69500 Bron, France
| | - Patrick Yap
- Genetic Health Service New Zealand, Auckland 1142, New Zealand; Victorian Clinical Genetic Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Auckland, Auckland 1142, New Zealand
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Peter J van der Spek
- Department of Pathology & Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Phillis Lakeman
- Department of Clinical Genetics, Academic Medical Center, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Rachel L Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK
| | - Rebecca O Littlejohn
- Department of Pediatrics, Baylor College of Medicine, The Children's Hospital of San Antonio, San Antonio, TX 78207, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Alexander P A Stegmann
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht 6229 ER, the Netherlands
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Scott McLean
- Department of Pediatrics, Baylor College of Medicine, The Children's Hospital of San Antonio, San Antonio, TX 78207, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shelagh Joss
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Sigrid M A Swagemakers
- Department of Pathology & Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK
| | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Sébastien Küry
- CHU de Nantes, Service de Génétique Médicale, 44093 Nantes Cedex 1, France
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Nils Koelling
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Christoffer Nellaker
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DS, UK; Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7FZ, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht 6229 ER, the Netherlands.
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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Sunavala-Dossabhoy G. Preserving salivary gland physiology against genotoxic damage - the Tousled way. Oral Dis 2018; 24:1390-1398. [PMID: 29383801 DOI: 10.1111/odi.12836] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 12/23/2022]
Abstract
Tousled and its homologs are evolutionarily conserved serine/threonine kinases present in plants and animals. Human Tousled-like kinases, TLK1 and TLK2, are implicated in chromatin assembly during DNA replication, chromosome segregation during mitosis, as well as in DNA damage response and repair. They share a high degree of sequence similarity, but have few non-redundant functions. Our laboratory has studied TLK1 and found that it increases the resistance of cells to ionizing radiation (IR) damage through expedited double-strand break (DSB) repair. DSBs are life-threatening lesions which when repaired restore DNA integrity and promote cell survival. A major focus in our laboratory is to dissect TLK1's role in DSB response and repair and study its usefulness in averting salivary gland hypofunction, a condition that invariably afflicts patients undergoing regional radiotherapy. The identification of anti-silencing factor 1 (ASF1), histone H3, and Rad9 as substrates of TLK1 links the protein to chromatin organization and DNA damage response and repair. However, recent findings of new interacting partners that include NEK1 suggest that TLK1 may play a broader role in DSB repair. This review provides a brief overview of the DNA damage response and DSB repair, and it highlights our current understanding of TLK1 in the process.
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Affiliation(s)
- G Sunavala-Dossabhoy
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
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Henriksson S, Groth P, Gustafsson N, Helleday T. Distinct mechanistic responses to replication fork stalling induced by either nucleotide or protein deprivation. Cell Cycle 2018; 17:568-579. [PMID: 28976232 DOI: 10.1080/15384101.2017.1387696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Incidents that slow or stall replication fork progression, collectively known as replication stress, represent a major source of spontaneous genomic instability. Here, we determine the requirement for global protein biosynthesis on DNA replication and associated downstream signaling. We study this response side by side with dNTP deprivation; one of the most commonly used means to investigate replication arrest and replicative stress. Our in vitro interrogations reveal that inhibition of translation by cycloheximide (CHX) rapidly impairs replication fork progression without decoupling helicase and polymerase activities or inducing DNA damage. In line with this, protein deprivation stress does not activate checkpoint signaling. In contrast to the direct link between insufficient dNTP pools and genome instability, our findings suggest that replication forks remain stable during short-term protein deficiency. We find that replication forks initially endure fluctuations in protein supply in order to efficiently resume DNA synthesis upon reversal of the induced protein deprivation stress. These results reveal distinct cellular responses to replication arrest induced by deprivation of either nucleotides or proteins.
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Affiliation(s)
- Sofia Henriksson
- a Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Petra Groth
- a Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Nina Gustafsson
- a Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Thomas Helleday
- a Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
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40
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Huang TH, Fowler F, Chen CC, Shen ZJ, Sleckman B, Tyler JK. The Histone Chaperones ASF1 and CAF-1 Promote MMS22L-TONSL-Mediated Rad51 Loading onto ssDNA during Homologous Recombination in Human Cells. Mol Cell 2018; 69:879-892.e5. [PMID: 29478807 DOI: 10.1016/j.molcel.2018.01.031] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 11/27/2017] [Accepted: 01/23/2018] [Indexed: 10/18/2022]
Abstract
The access-repair-restore model for the role of chromatin in DNA repair infers that chromatin is a mere obstacle to DNA repair. However, here we show that blocking chromatin assembly, via knockdown of the histone chaperones ASF1 or CAF-1 or a mutation that prevents ASF1A binding to histones, hinders Rad51 loading onto ssDNA during homologous recombination. This is a consequence of reduced recruitment of the Rad51 loader MMS22L-TONSL to ssDNA, resulting in persistent RPA foci, extensive DNA end resection, persistent activation of the ATR-Chk1 pathway, and cell cycle arrest. In agreement, histones occupy ssDNA during DNA repair in yeast. We also uncovered DNA-PKcs-dependent DNA damage-induced ASF1A phosphorylation, which enhances chromatin assembly, promoting MMS22L-TONSL recruitment and, hence, Rad51 loading. We propose that transient assembly of newly synthesized histones onto ssDNA serves to recruit MMS22L-TONSL to efficiently form the Rad51 nucleofilament for strand invasion, suggesting an active role of chromatin assembly in homologous recombination.
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Affiliation(s)
- Ting-Hsiang Huang
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Faith Fowler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Chin-Chuan Chen
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan
| | - Zih-Jie Shen
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Barry Sleckman
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Jessica K Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA.
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41
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Lee J, Kim MS, Park SH, Jang YK. Tousled-like kinase 1 is a negative regulator of core transcription factors in murine embryonic stem cells. Sci Rep 2018; 8:334. [PMID: 29321513 PMCID: PMC5762884 DOI: 10.1038/s41598-017-18628-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/13/2017] [Indexed: 11/19/2022] Open
Abstract
Although the differentiation of pluripotent cells in embryonic stem cells (ESCs) is often associated with protein kinase-mediated signaling pathways and Tousled-like kinase 1 (Tlk1) is required for development in several species, the role of Tlk1 in ESC function remains unclear. Here, we used mouse ESCs to study the function of Tlk1 in pluripotent cells. The knockdown (KD)-based Tlk1-deficient cells showed that Tlk1 is not essential for ESC self-renewal in an undifferentiated state. However, Tlk1-KD cells formed irregularly shaped embryoid bodies and induced resistance to differentiation cues, indicating their failure to differentiate into an embryoid body. Consistent with their failure to differentiate, Tlk1-KD cells failed to downregulate the expression of undifferentiated cell markers including Oct4, Nanog, and Sox2 during differentiation, suggesting a negative role of Tlk1. Interestingly, Tlk1 overexpression sufficiently downregulated the expression of core pluripotency factors possibly irrespective of its kinase activity, thereby leading to a partial loss of self-renewal ability even in an undifferentiated state. Moreover, Tlk1 overexpression caused severe growth defects and G2/M phase arrest as well as apoptosis. Collectively, our data suggest that Tlk1 negatively regulates the expression of pluripotency factors, thereby contributing to the scheduled differentiation of mouse ESCs.
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Affiliation(s)
- Jina Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.,Initiative for Biological Function and Systems, Yonsei University, Seoul, 03722, Republic of Korea
| | - Min Seong Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.,Initiative for Biological Function and Systems, Yonsei University, Seoul, 03722, Republic of Korea
| | - Su Hyung Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.,Initiative for Biological Function and Systems, Yonsei University, Seoul, 03722, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulsan, 689-798, Republic of Korea
| | - Yeun Kyu Jang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea. .,Initiative for Biological Function and Systems, Yonsei University, Seoul, 03722, Republic of Korea.
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42
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Tidwell TR, Søreide K, Hagland HR. Aging, Metabolism, and Cancer Development: from Peto's Paradox to the Warburg Effect. Aging Dis 2017; 8:662-676. [PMID: 28966808 PMCID: PMC5614328 DOI: 10.14336/ad.2017.0713] [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: 12/31/2016] [Accepted: 06/13/2017] [Indexed: 12/15/2022] Open
Abstract
Medical advances made over the last century have increased our lifespan, but age-related diseases are a fundamental health burden worldwide. Aging is therefore a major risk factor for cardiovascular disease, cancer, diabetes, obesity, and neurodegenerative diseases, all increasing in prevalence. However, huge inter-individual variations in aging and disease risk exist, which cannot be explained by chronological age, but rather physiological age decline initiated even at young age due to lifestyle. At the heart of this lies the metabolic system and how this is regulated in each individual. Metabolic turnover of food to energy leads to accumulation of co-factors, byproducts, and certain proteins, which all influence gene expression through epigenetic regulation. How these epigenetic markers accumulate over time is now being investigated as the possible link between aging and many diseases, such as cancer. The relationship between metabolism and cancer was described as early as the late 1950s by Dr. Otto Warburg, before the identification of DNA and much earlier than our knowledge of epigenetics. However, when the stepwise gene mutation theory of cancer was presented, Warburg's theories garnered little attention. Only in the last decade, with epigenetic discoveries, have Warburg's data on the metabolic shift in cancers been brought back to life. The stepwise gene mutation theory fails to explain why large animals with more cells, do not have a greater cancer incidence than humans, known as Peto's paradox. The resurgence of research into the Warburg effect has given us insight to what may explain Peto's paradox. In this review, we discuss these connections and how age-related changes in metabolism are tightly linked to cancer development, which is further affected by lifestyle choices modulating the risk of aging and cancer through epigenetic control.
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Affiliation(s)
- Tia R. Tidwell
- Department of Mathematics and Natural Sciences, Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
| | - Kjetil Søreide
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hanne R. Hagland
- Department of Mathematics and Natural Sciences, Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
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43
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Liu H, Dowdle JA, Khurshid S, Sullivan NJ, Bertos N, Rambani K, Mair M, Daniel P, Wheeler E, Tang X, Toth K, Lause M, Harrigan ME, Eiring K, Sullivan C, Sullivan MJ, Chang SW, Srivastava S, Conway JS, Kladney R, McElroy J, Bae S, Lu Y, Tofigh A, Saleh SMI, Fernandez SA, Parvin JD, Coppola V, Macrae ER, Majumder S, Shapiro CL, Yee LD, Ramaswamy B, Hallett M, Ostrowski MC, Park M, Chamberlin HM, Leone G. Discovery of Stromal Regulatory Networks that Suppress Ras-Sensitized Epithelial Cell Proliferation. Dev Cell 2017; 41:392-407.e6. [PMID: 28535374 DOI: 10.1016/j.devcel.2017.04.024] [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: 10/19/2016] [Revised: 03/20/2017] [Accepted: 04/26/2017] [Indexed: 01/09/2023]
Abstract
Mesodermal cells signal to neighboring epithelial cells to modulate their proliferation in both normal and disease states. We adapted a Caenorhabditis elegans organogenesis model to enable a genome-wide mesodermal-specific RNAi screen and discovered 39 factors in mesodermal cells that suppress the proliferation of adjacent Ras pathway-sensitized epithelial cells. These candidates encode components of protein complexes and signaling pathways that converge on the control of chromatin dynamics, cytoplasmic polyadenylation, and translation. Stromal fibroblast-specific deletion of mouse orthologs of several candidates resulted in the hyper-proliferation of mammary gland epithelium. Furthermore, a 33-gene signature of human orthologs was selectively enriched in the tumor stroma of breast cancer patients, and depletion of these factors from normal human breast fibroblasts increased proliferation of co-cultured breast cancer cells. This cross-species approach identified unanticipated regulatory networks in mesodermal cells with growth-suppressive function, exposing the conserved and selective nature of mesodermal-epithelial communication in development and cancer.
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Affiliation(s)
- Huayang Liu
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - James A Dowdle
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Safiya Khurshid
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Nicholas J Sullivan
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Nicholas Bertos
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, QC H3A 1A1, Canada; Department of Oncology, McGill University, Montreal, QC H3A 1A1, Canada
| | - Komal Rambani
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Markus Mair
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Piotr Daniel
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Esther Wheeler
- Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Xing Tang
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Kyle Toth
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Michael Lause
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Markus E Harrigan
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Karl Eiring
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Connor Sullivan
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Matthew J Sullivan
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Serena W Chang
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Siddhant Srivastava
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Joseph S Conway
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Raleigh Kladney
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Joseph McElroy
- Center for Biostatistics, Office of Health Sciences, McGill University, Montreal, QC H3A 1A1, Canada; Department of Biomedical Informatics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Sooin Bae
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Yuanzhi Lu
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Ali Tofigh
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, QC H3A 1A1, Canada; McGill Centre for Bioinformatics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Sadiq M I Saleh
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, QC H3A 1A1, Canada; McGill Centre for Bioinformatics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Soledad A Fernandez
- Center for Biostatistics, Office of Health Sciences, McGill University, Montreal, QC H3A 1A1, Canada; Department of Biomedical Informatics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Jeffrey D Parvin
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Biomedical Informatics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Vincenzo Coppola
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Erin R Macrae
- Division of Medical Oncology, Department of Internal Medicine, McGill University, Montreal, QC H3A 1A1, Canada
| | - Sarmila Majumder
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Charles L Shapiro
- Division of Medical Oncology, Department of Internal Medicine, McGill University, Montreal, QC H3A 1A1, Canada
| | - Lisa D Yee
- Department of Surgery, The Ohio State University, Columbus, OH 43210, USA
| | - Bhuvaneswari Ramaswamy
- Division of Medical Oncology, Department of Internal Medicine, McGill University, Montreal, QC H3A 1A1, Canada
| | - Michael Hallett
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, QC H3A 1A1, Canada; McGill Centre for Bioinformatics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Michael C Ostrowski
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada
| | - Morag Park
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, QC H3A 1A1, Canada; Department of Oncology, McGill University, Montreal, QC H3A 1A1, Canada
| | - Helen M Chamberlin
- Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
| | - Gustavo Leone
- Solid Tumor Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Department of Cancer Biology and Genetics, McGill University, Montreal, QC H3A 1A1, Canada; Hollings Cancer Center, Medical University of South Carolina, Hollings Cancer Center 124J, 86 Jonathan Lucas Street, Charleston, SC 29425, USA.
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Abstract
Proliferating cells rely on the so-called DNA replication checkpoint to ensure orderly completion of genome duplication, and its malfunction may lead to catastrophic genome disruption, including unscheduled firing of replication origins, stalling and collapse of replication forks, massive DNA breakage, and, ultimately, cell death. Despite many years of intensive research into the molecular underpinnings of the eukaryotic replication checkpoint, the mechanisms underlying the dismal consequences of its failure remain enigmatic. A recent development offers a unifying model in which the replication checkpoint guards against global exhaustion of rate-limiting replication regulators. Here we discuss how such a mechanism can prevent catastrophic genome disruption and suggest how to harness this knowledge to advance therapeutic strategies to eliminate cancer cells that inherently proliferate under increased DNA replication stress.
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Affiliation(s)
- Luis Toledo
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
| | - Kai John Neelsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
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45
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Differential requirements for Tousled-like kinases 1 and 2 in mammalian development. Cell Death Differ 2017; 24:1872-1885. [PMID: 28708136 DOI: 10.1038/cdd.2017.108] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 12/20/2022] Open
Abstract
The regulation of chromatin structure is critical for a wide range of essential cellular processes. The Tousled-like kinases, TLK1 and TLK2, regulate ASF1, a histone H3/H4 chaperone, and likely other substrates, and their activity has been implicated in transcription, DNA replication, DNA repair, RNA interference, cell cycle progression, viral latency, chromosome segregation and mitosis. However, little is known about the functions of TLK activity in vivo or the relative functions of the highly similar TLK1 and TLK2 in any cell type. To begin to address this, we have generated Tlk1- and Tlk2-deficient mice. We found that while TLK1 was dispensable for murine viability, TLK2 loss led to late embryonic lethality because of placental failure. TLK2 was required for normal trophoblast differentiation and the phosphorylation of ASF1 was reduced in placentas lacking TLK2. Conditional bypass of the placental phenotype allowed the generation of apparently healthy Tlk2-deficient mice, while only the depletion of both TLK1 and TLK2 led to extensive genomic instability, indicating that both activities contribute to genome maintenance. Our data identifies a specific role for TLK2 in placental function during mammalian development and suggests that TLK1 and TLK2 have largely redundant roles in genome maintenance.
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46
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Prado F, Maya D. Regulation of Replication Fork Advance and Stability by Nucleosome Assembly. Genes (Basel) 2017; 8:genes8020049. [PMID: 28125036 PMCID: PMC5333038 DOI: 10.3390/genes8020049] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/04/2017] [Accepted: 01/16/2017] [Indexed: 12/13/2022] Open
Abstract
The advance of replication forks to duplicate chromosomes in dividing cells requires the disassembly of nucleosomes ahead of the fork and the rapid assembly of parental and de novo histones at the newly synthesized strands behind the fork. Replication-coupled chromatin assembly provides a unique opportunity to regulate fork advance and stability. Through post-translational histone modifications and tightly regulated physical and genetic interactions between chromatin assembly factors and replisome components, chromatin assembly: (1) controls the rate of DNA synthesis and adjusts it to histone availability; (2) provides a mechanism to protect the integrity of the advancing fork; and (3) regulates the mechanisms of DNA damage tolerance in response to replication-blocking lesions. Uncoupling DNA synthesis from nucleosome assembly has deleterious effects on genome integrity and cell cycle progression and is linked to genetic diseases, cancer, and aging.
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Affiliation(s)
- Felix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), Spanish National Research Council (CSIC), Seville 41092, Spain.
| | - Douglas Maya
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), Spanish National Research Council (CSIC), Seville 41092, Spain.
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47
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Hammond CM, Strømme CB, Huang H, Patel DJ, Groth A. Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol 2017; 18:141-158. [PMID: 28053344 DOI: 10.1038/nrm.2016.159] [Citation(s) in RCA: 337] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The association of histones with specific chaperone complexes is important for their folding, oligomerization, post-translational modification, nuclear import, stability, assembly and genomic localization. In this way, the chaperoning of soluble histones is a key determinant of histone availability and fate, which affects all chromosomal processes, including gene expression, chromosome segregation and genome replication and repair. Here, we review the distinct structural and functional properties of the expanding network of histone chaperones. We emphasize how chaperones cooperate in the histone chaperone network and via co-chaperone complexes to match histone supply with demand, thereby promoting proper nucleosome assembly and maintaining epigenetic information by recycling modified histones evicted from chromatin.
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Affiliation(s)
- Colin M Hammond
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Caroline B Strømme
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Hongda Huang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
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48
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Alabert C, Jasencakova Z, Groth A. Chromatin Replication and Histone Dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:311-333. [PMID: 29357065 DOI: 10.1007/978-981-10-6955-0_15] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure to reassemble nucleosomes at replication forks blocks DNA replication progression in higher eukaryotes and leads to genomic instability, we further underline the importance of the mechanistic link between DNA replication and chromatin duplication.
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Affiliation(s)
- Constance Alabert
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zuzana Jasencakova
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark.
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49
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Yamaguchi N, Shibazaki M, Yamada C, Anzai E, Morii M, Nakayama Y, Kuga T, Hashimoto Y, Tomonaga T, Yamaguchi N. Tyrosine Phosphorylation of the Pioneer Transcription Factor FoxA1 Promotes Activation of Estrogen Signaling. J Cell Biochem 2016; 118:1453-1461. [DOI: 10.1002/jcb.25804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/21/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Noritaka Yamaguchi
- Laboratory of Molecular Cell BiologyGraduate School of Pharmaceutical SciencesChiba UniversityChiba260‐8675Japan
| | - Misato Shibazaki
- Laboratory of Molecular Cell BiologyGraduate School of Pharmaceutical SciencesChiba UniversityChiba260‐8675Japan
| | - Chiaki Yamada
- Laboratory of Molecular Cell BiologyGraduate School of Pharmaceutical SciencesChiba UniversityChiba260‐8675Japan
| | - Erina Anzai
- Laboratory of Molecular Cell BiologyGraduate School of Pharmaceutical SciencesChiba UniversityChiba260‐8675Japan
| | - Mariko Morii
- Laboratory of Molecular Cell BiologyGraduate School of Pharmaceutical SciencesChiba UniversityChiba260‐8675Japan
| | - Yuji Nakayama
- Department of Biochemistry and Molecular BiologyKyoto Pharmaceutical UniversityKyoto607‐8414Japan
| | - Takahisa Kuga
- Department of Biochemistry and Molecular BiologyKyoto Pharmaceutical UniversityKyoto607‐8414Japan
| | - Yuuki Hashimoto
- Laboratory of Proteome ResearchNational Institutes of Biomedical InnovationHealth and NutritionIbarakiOsaka567‐0085Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome ResearchNational Institutes of Biomedical InnovationHealth and NutritionIbarakiOsaka567‐0085Japan
| | - Naoto Yamaguchi
- Laboratory of Molecular Cell BiologyGraduate School of Pharmaceutical SciencesChiba UniversityChiba260‐8675Japan
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50
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Differential regulation of the histone chaperone HIRA during muscle cell differentiation by a phosphorylation switch. Exp Mol Med 2016; 48:e252. [PMID: 27515126 PMCID: PMC5007640 DOI: 10.1038/emm.2016.68] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 02/19/2016] [Accepted: 03/02/2016] [Indexed: 01/05/2023] Open
Abstract
Replication-independent incorporation of variant histone H3.3 has a profound impact on chromatin function and numerous cellular processes, including the differentiation of muscle cells. The histone chaperone HIRA and H3.3 have essential roles in MyoD regulation during myoblast differentiation. However, the precise mechanism that determines the onset of H3.3 deposition in response to differentiation signals is unclear. Here we show that HIRA is phosphorylated by Akt kinase, an important signaling modulator in muscle cells. By generating a phosphospecific antibody, we found that a significant amount of HIRA was phosphorylated in myoblasts. The phosphorylation level of HIRA and the occupancy of phosphorylated protein on muscle genes gradually decreased during cellular differentiation. Remarkably, the forced expression of the phosphomimic form of HIRA resulted in reduced H3.3 deposition and suppressed the activation of muscle genes in myotubes. Our data show that HIRA phosphorylation limits the expression of myogenic genes, while the dephosphorylation of HIRA is required for proficient H3.3 deposition and gene activation, demonstrating that the phosphorylation switch is exploited to modulate HIRA/H3.3-mediated muscle gene regulation during myogenesis.
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