1
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Nandy D, Shirude MB, S A, Devarajan A, Mukherjee A, Dutta D. Nuclear localization of APLF facilitates breast cancer metastasis. Biochim Biophys Acta Mol Basis Dis 2024; 1871:167537. [PMID: 39384105 DOI: 10.1016/j.bbadis.2024.167537] [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: 03/08/2024] [Revised: 10/02/2024] [Accepted: 10/03/2024] [Indexed: 10/11/2024]
Abstract
Most breast cancer deaths result from metastases. We previously reported that DNA repair factor and histone chaperone Aprataxin PNK-like Factor (APLF) is involved in EMT-associated metastasis of triple negative breast cancer (TNBC) cells. However, non-metastatic cells also expressed APLF, the implications of which in disease advancement remain uncertain. Here, we demonstrate that the metastatic prognosis of breast cancer cells may be determined by the cellular localization of APLF. Using TNBC patient samples and cell lines, we discovered that APLF was localized in the nucleus and cytoplasm, whereas other subtypes of breast cancer had cytosolic or perinuclear localization. To investigate metastatic properties in vitro and in vivo, we modeled APLF differential localization by stably producing APLF-tagged nuclear localization signal (NLS) in the luminal subtype MCF7 cells in the absence of putative APLF NLS. Nuclear APLF in non-metastatic MCF7 cells demonstrated pronounced migration, invasion and metastatic potential. We obtained the mechanistic insight from molecular studies that PARP1 could facilitate the transport of APLF from the cytosol to the nucleus, assisting in the metastasis of TNBC cells linked with EMT. Inhibition of PARP1 enzymatic activity with olaparib abrogated the nuclear expression of APLF with loss in expression of genes associated with EMT. Thus, our findings reveal that cellular localization of APLF may predict the risk of breast cancer to metastasize and hence could be exploited to determine the disease progression. We anticipate that the inhibition of cytosolic PARP1-APLF interaction may potentially aid in the prevention of breast cancer metastasis in TNBC patients.
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Affiliation(s)
- Debparna Nandy
- Rajiv Gandhi Centre for Biotechnology (RGCB), Regenerative Biology Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India; Manipal Academy of Higher Education, Manipal, Karnataka State 576104, India
| | - Mayur Balkrishna Shirude
- Rajiv Gandhi Centre for Biotechnology (RGCB), Regenerative Biology Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India; Manipal Academy of Higher Education, Manipal, Karnataka State 576104, India
| | - Archana S
- Rajiv Gandhi Centre for Biotechnology (RGCB), Animal Research Facility, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India
| | - Anjali Devarajan
- Rajiv Gandhi Centre for Biotechnology (RGCB), Regenerative Biology Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India
| | - Ananda Mukherjee
- Rajiv Gandhi Centre for Biotechnology (RGCB), Cancer Research Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India
| | - Debasree Dutta
- Rajiv Gandhi Centre for Biotechnology (RGCB), Regenerative Biology Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India.
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2
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Bayat L, Abbasi S, Balasuriya N, Schild-Poulter C. Critical residues in the Ku70 von Willebrand A domain mediate Ku interaction with the LigIV-XRCC4 complex in non-homologous end-joining. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119815. [PMID: 39151475 DOI: 10.1016/j.bbamcr.2024.119815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/02/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
The Ku heterodimer (Ku70/Ku80) is central to the non-homologous end-joining (NHEJ) pathway. Ku binds to the broken DNA ends and promotes the assembly of the DNA repair complex. The N-terminal Ku70 von Willebrand A (vWA) domain is known to mediate protein-protein interactions important for the repair process. In particular, the D192 and D195 residues within helix 5 of the Ku70 vWA domain were shown to be essential for NHEJ function, although the precise role of these residues was not identified. Here, we set up a miniTurbo screening system to identify Ku70 D192/D195 residue-specific interactors in a conditional, human Ku70-knockout cell line in response to DNA damage. Using fusion protein constructs of Ku70 wild-type and mutant (D192A/D195R) with miniTurbo, we identified a number of candidate proximal interactors in response to DNA damage treatment, including DNA Ligase IV (LigIV), a known and essential NHEJ complex member. Interestingly, LigIV was enriched in our wildtype screen but not the Ku70 D192A/D195R screen, suggesting its interaction is disrupted by the mutation. Validation experiments demonstrated that the DNA damage-induced interaction between Ku70 and LigIV was disrupted by the Ku70 D192A/D195R mutations. Our findings provide greater detail about the interaction surface between the Ku70 vWA domain and LigIV and offer strong evidence that the D192 and D195 residues are important for NHEJ completion through an interaction with LigIV. Altogether, this work reveals novel potential proximal interactors of Ku in response to DNA damage and identifies Ku70 D192/D195 residues as essential for LigIV interaction with Ku during NHEJ.
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Affiliation(s)
- Laila Bayat
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Nileeka Balasuriya
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada.
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3
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Wells SE, Caldecott KW. KBM-mediated interactions with KU80 promote cellular resistance to DNA replication stress in CHO cells. DNA Repair (Amst) 2024; 140:103710. [PMID: 38901287 DOI: 10.1016/j.dnarep.2024.103710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/17/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
The KU heterodimer (KU70/80) is rapidly recruited to DNA double-strand breaks (DSBs) to regulate their processing and repair. Previous work has revealed that the amino-terminal von Willebrand-like (vWA-like) domain in KU80 harbours a conserved hydrophobic pocket that interacts with a short peptide motif known as the Ku-binding motif (KBM). The KBM is present in a variety of DNA repair proteins such as APLF, CYREN, and Werner protein (WRN). Here, to investigate the importance of KBM-mediated protein-protein interactions for KU80 function, we employed KU80-deficient Chinese Hamster Ovary (Xrs-6) cells transfected with RFP-tagged wild-type human KU80 or KU80 harbouring a mutant vWA-like domain (KU80L68R). Surprisingly, while mutant RFP-KU80L68R largely or entirely restored NHEJ efficiency and radiation resistance in KU80-deficient Xrs-6 cells, it failed to restore cellular resistance to DNA replication stress induced by camptothecin (CPT) or hydroxyurea (HU). Moreover, KU80-deficient Xrs-6 cells expressing RFP-KU80L68R accumulated pan-nuclear γH2AX in an S/G2-phase-dependent manner following treatment with CPT or HU, suggesting that the binding of KU80 to one or more KBM-containing proteins is required for the processing and/or repair of DNA ends that arise during DNA replication stress. Consistent with this idea, depletion of WRN helicase/exonuclease recapitulated the CPT-induced γH2AX phenotype, and did so epistatically with mutation of the KU80 vWA-like domain. These data identify a role for the KBM-binding by KU80 in the response and resistance of CHO cells to arrested and/or collapsed DNA replication forks, and implicate the KBM-mediated interaction of KU80 with WRN as a critical effector of this role.
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Affiliation(s)
- Sophie E Wells
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
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4
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Wu CK, Shiu JL, Wu CL, Hung CF, Ho YC, Chen YT, Tung SY, Yeh CF, Shen CH, Liaw H, Su WP. APLF facilitates interstrand DNA crosslink repair and replication fork protection to confer cisplatin resistance. Nucleic Acids Res 2024; 52:5676-5697. [PMID: 38520407 PMCID: PMC11162786 DOI: 10.1093/nar/gkae211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Replication stress converts the stalled forks into reversed forks, which is an important protection mechanism to prevent fork degradation and collapse into poisonous DNA double-strand breaks (DSBs). Paradoxically, the mechanism also acts in cancer cells to contribute to chemoresistance against various DNA-damaging agents. PARP1 binds to and is activated by stalled forks to facilitate fork reversal. Aprataxin and polynucleotide kinase/phosphatase-like factor (APLF) binds to PARP1 through the poly(ADP-ribose) zinc finger (PBZ) domain and is known to be involved in non-homologous end joining (NHEJ). Here, we identify a novel function of APLF involved in interstrand DNA crosslink (ICL) repair and fork protection. We demonstrate that PARP1 activity facilitates the APLF recruitment to stalled forks, enabling the FANCD2 recruitment to stalled forks. The depletion of APLF sensitizes cells to cisplatin, impairs ICL repair, reduces the FANCD2 recruitment to stalled forks, and results in nascent DNA degradation by MRE11 nucleases. Additionally, cisplatin-resistant cancer cells show high levels of APLF and homologous recombination-related gene expression. The depletion of APLF sensitizes cells to cisplatin and results in fork instability. Our results reveal the novel function of APLF to facilitate ICL repair and fork protection, thereby contributing to cisplatin-resistant phenotypes of cancer cells.
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Affiliation(s)
- Cheng-Kuei Wu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
| | - Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Chao-Liang Wu
- Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Chi-Feng Hung
- Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Yen-Chih Ho
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Yen-Tzu Chen
- Department of Public Health & Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taiwan
| | - Sheng-Yung Tung
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Department of Urology, An Nan Hospital, China Medical University, Tainan, Taiwan
| | - Cheng-Fa Yeh
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Che-Hung Shen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Wen-Pin Su
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Departments of Oncology and Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan 701, Taiwan
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5
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Lee J, Bao X. Comparative Review on Cancer Pathology from Aberrant Histone Chaperone Activity. Int J Mol Sci 2024; 25:6403. [PMID: 38928110 PMCID: PMC11203986 DOI: 10.3390/ijms25126403] [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: 04/24/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Histone chaperones are integral to chromatin dynamics, facilitating the assembly and disassembly of nucleosomes, thereby playing a crucial role in regulating gene expression and maintaining genomic stability. Moreover, they prevent aberrant histone interactions prior to chromatin assembly. Disruption in histone chaperone function may result in genomic instability, which is implicated in pathogenesis. This review aims to elucidate the role of histone chaperones in cancer pathologies and explore their potential as therapeutic targets. Histone chaperones have been found to be dysregulated in various cancers, with alterations in expression levels, mutations, or aberrant interactions leading to tumorigenesis and cancer progression. In addition, this review intends to highlight the molecular mechanisms of interactions between histone chaperones and oncogenic factors, underscoring their roles in cancer cell survival and proliferation. The dysregulation of histone chaperones is significantly correlated with cancer development, establishing them as active contributors to cancer pathology and viable targets for therapeutic intervention. This review advocates for continued research into histone chaperone-targeted therapies, which hold potential for precision medicine in oncology. Future advancements in understanding chaperone functions and interactions are anticipated to lead to novel cancer treatments, enhancing patient care and outcomes.
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Affiliation(s)
| | - Xiucong Bao
- School of Biomedical Sciences, Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China;
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6
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Folkertsma R, Charbonnel N, Henttonen H, Heroldová M, Huitu O, Kotlík P, Manzo E, Paijmans JLA, Plantard O, Sándor AD, Hofreiter M, Eccard JA. Genomic signatures of climate adaptation in bank voles. Ecol Evol 2024; 14:e10886. [PMID: 38455148 PMCID: PMC10918726 DOI: 10.1002/ece3.10886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.
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Affiliation(s)
- Remco Folkertsma
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Comparative Cognition Unit, Messerli Research InstituteUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | - Marta Heroldová
- Department of Forest Ecology, FFWTMendel University in BrnoBrnoCzech Republic
| | - Otso Huitu
- Natural Resources Institute FinlandHelsinkiFinland
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and GeneticsCzech Academy of SciencesLiběchovCzech Republic
| | - Emiliano Manzo
- Fondazione Ethoikos, Convento dell'OsservanzaRadicondoliItaly
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Present address:
Evolutionary Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | | | - Attila D. Sándor
- HUN‐RENClimate Change: New Blood‐Sucking Parasites and Vector‐Borne Pathogens Research GroupBudapestHungary
- Department of Parasitology and ZoologyUniversity of Veterinary MedicineBudapestHungary
- Department of Parasitology and Parasitic DiseasesUniversity of Agricultural Sciences and Veterinary MedicineCluj‐NapocaRomania
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
| | - Jana A. Eccard
- Animal Ecology, Institute for Biochemistry and Biology, Faculty of ScienceBerlin‐Brandenburg Institute for Biodiversity ResearchUniversity of PotsdamPotsdamGermany
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7
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Loparo JJ. Holding it together: DNA end synapsis during non-homologous end joining. DNA Repair (Amst) 2023; 130:103553. [PMID: 37572577 PMCID: PMC10530278 DOI: 10.1016/j.dnarep.2023.103553] [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: 04/30/2023] [Revised: 08/04/2023] [Accepted: 08/06/2023] [Indexed: 08/14/2023]
Abstract
DNA double strand breaks (DSBs) are common lesions whose misrepair are drivers of oncogenic transformations. The non-homologous end joining (NHEJ) pathway repairs the majority of these breaks in vertebrates by directly ligating DNA ends back together. Upon formation of a DSB, a multiprotein complex is assembled on DNA ends which tethers them together within a synaptic complex. Synapsis is a critical step of the NHEJ pathway as loss of synapsis can result in mispairing of DNA ends and chromosome translocations. As DNA ends are commonly incompatible for ligation, the NHEJ machinery must also process ends to enable rejoining. This review describes how recent progress in single-molecule approaches and cryo-EM have advanced our molecular understanding of DNA end synapsis during NHEJ and how synapsis is coordinated with end processing to determine the fidelity of repair.
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Affiliation(s)
- Joseph J Loparo
- Dept. of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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8
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Bianchini RM, Kurz EU. The analysis of protein recruitment to laser microirradiation-induced DNA damage in live cells: Best practices for data analysis. DNA Repair (Amst) 2023; 129:103545. [PMID: 37524003 DOI: 10.1016/j.dnarep.2023.103545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
Laser microirradiation coupled with live-cell fluorescence microscopy is a powerful technique that has been used widely in studying the recruitment and retention of proteins at sites of DNA damage. Results obtained from this technique can be found in published works by both seasoned and infrequent users of microscopy. However, like many other microscopy-based techniques, the presentation of data from laser microirradiation experiments is inconsistent; papers report a wide assortment of analytic techniques, not all of which result in accurate and/or appropriate representation of the data. In addition to the varied methods of analysis, experimental and analytical details are commonly under-reported. Consequently, publications reporting data from laser microirradiation coupled with fluorescence microscopy experiments need to be carefully and critically assessed by readers. Here, we undertake a systematic investigation of commonly reported corrections used in the analysis of laser microirradiation data. We validate the critical need to correct data for photobleaching and we identify key experimental parameters that must be accounted for when presenting data from laser microirradiation experiments. Furthermore, we propose a straightforward, four-step analytical protocol that can readily be applied across platforms and that aims to improve the quality of data reporting in the DNA damage field.
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Affiliation(s)
- Ryan M Bianchini
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, and Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Ebba U Kurz
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, and Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
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9
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Ivanovska IL, Tobin MP, Bai T, Dooling LJ, Discher DE. Small lipid droplets are rigid enough to indent a nucleus, dilute the lamina, and cause rupture. J Cell Biol 2023; 222:e202208123. [PMID: 37212777 PMCID: PMC10202833 DOI: 10.1083/jcb.202208123] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 03/24/2023] [Accepted: 05/04/2023] [Indexed: 05/23/2023] Open
Abstract
The nucleus in many cell types is a stiff organelle, but fat-filled lipid droplets (FDs) in cytoplasm are seen to indent and displace the nucleus. FDs are phase-separated liquids with a poorly understood interfacial tension γ that determines how FDs interact with other organelles. Here, micron-sized FDs remain spherical as they indent peri-nuclear actomyosin and the nucleus, while causing local dilution of Lamin-B1 independent of Lamin-A,C and sometimes triggering nuclear rupture. Focal accumulation of the cytosolic DNA sensor cGAS at the rupture site is accompanied by sustained mislocalization of DNA repair factors to cytoplasm, increased DNA damage, and delayed cell cycle. Macrophages show FDs and engulfed rigid beads cause similar indentation dilution. Spherical shapes of small FDs indicate a high γ, which we measure for FDs mechanically isolated from fresh adipose tissue as ∼40 mN/m. This value is far higher than that of protein condensates, but typical of oils in water and sufficiently rigid to perturb cell structures including nuclei.
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Affiliation(s)
- Irena L. Ivanovska
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P. Tobin
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Tianyi Bai
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Lawrence J. Dooling
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Dennis E. Discher
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
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10
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Hardwick SW, Stavridi AK, Chirgadze DY, De Oliveira TM, Charbonnier JB, Ropars V, Meek K, Blundell TL, Chaplin AK. Cryo-EM structure of a DNA-PK trimer: higher order oligomerisation in NHEJ. Structure 2023; 31:895-902.e3. [PMID: 37311458 DOI: 10.1016/j.str.2023.05.013] [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: 02/07/2023] [Revised: 04/11/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023]
Abstract
The ability of humans to maintain the integrity of the genome is imperative for cellular survival. DNA double-strand breaks (DSBs) are considered the most critical type of DNA lesion, which can ultimately lead to diseases including cancer. Non-homologous end joining (NHEJ) is one of two core mechanisms utilized to repair DSBs. DNA-PK is a key component in this process and has recently been shown to form alternate long-range synaptic dimers. This has led to the proposal that these complexes can be formed before transitioning to a short-range synaptic complex. Here we present cryo-EM data representing an NHEJ supercomplex consisting of a trimer of DNA-PK in complex with XLF, XRCC4, and DNA Ligase IV. This trimer represents a complex of both long-range synaptic dimers. We discuss the potential role of the trimeric structure, and possible higher order oligomers, as structural intermediates in the NHEJ mechanism, or as functional DNA repair centers.
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Affiliation(s)
- Steven W Hardwick
- Cryo-EM Facility, Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK
| | - Antonia Kefala Stavridi
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK
| | - Dimitri Y Chirgadze
- Cryo-EM Facility, Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK
| | | | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), Institute Joliot, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK
| | - Amanda K Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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11
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Oh JM, Kim H. The effect of oral bacterial infection on DNA damage response in host cells. Am J Cancer Res 2023; 13:3157-3168. [PMID: 37559975 PMCID: PMC10408462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023] Open
Abstract
Maintaining and transferring intact genomes from one generation to another plays a pivotal role in all living organisms. DNA damage caused by numerous endogenous and exogenous factors must be adequately repaired, as unrepaired and accumulated DNA mutations can cause severe deleterious effects, such as cell death and cancer. To prevent adverse consequences, cells have established DNA damage response mechanisms that address different forms of DNA damage, including DNA double-strand breaks, mismatches, nucleotide excision, and base excision. Among several sources of exogenous DNA damage, bacterial infections cause inflammation in the host, generating reactive oxygen species (ROS) and causing oxidative DNA damage. Recent studies have revealed the importance of the oral microbiome in inflammation and several systemic host diseases. Dysbiosis of oral bacteria can induce chronic inflammation, which enhances ROS-induced DNA damage, and improperly repaired damage can lead to carcinogenesis. This review describes the various DNA repair pathways that are affected by chronic inflammation and the discovery of the DNA damage response induced by oral bacteria such as Porphyromonas gingivalis and Fusobacterium nucleatum.
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Affiliation(s)
- Jung-Min Oh
- Department of Oral Biochemistry, Dental and Life Science Institute, School of Dentistry, Pusan National UniversityYangsan 50612, Republic of Korea
- Department of Life Science in Dentistry, School of Dentistry, Pusan National UniversityYangsan 50612, Republic of Korea
| | - Hongtae Kim
- Department of Life Sciences, Ulsan National Institute of Science and Technology (UNIST)Ulsan 44919, Republic of Korea
- Center for Genomic Integrity Institute for Basic Science (IBS), UNISTUlsan 44919, Republic of Korea
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12
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Duma L, Ahel I. The function and regulation of ADP-ribosylation in the DNA damage response. Biochem Soc Trans 2023; 51:995-1008. [PMID: 37171085 PMCID: PMC10317172 DOI: 10.1042/bst20220749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
ADP-ribosylation is a post-translational modification involved in DNA damage response (DDR). In higher organisms it is synthesised by PARP 1-3, DNA strand break sensors. Recent advances have identified serine residues as the most common targets for ADP-ribosylation during DDR. To ADP-ribosylate serine, PARPs require an accessory factor, HPF1 which completes the catalytic domain. Through ADP-ribosylation, PARPs recruit a variety of factors to the break site and control their activities. However, the timely removal of ADP-ribosylation is also key for genome stability and is mostly performed by two hydrolases: PARG and ARH3. Here, we describe the key writers, readers and erasers of ADP-ribosylation and their contribution to the mounting of the DDR. We also discuss the use of PARP inhibitors in cancer therapy and the ways to tackle PARPi treatment resistance.
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Affiliation(s)
- Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
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13
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Smith R, Zentout S, Rother M, Bigot N, Chapuis C, Mihuț A, Zobel FF, Ahel I, van Attikum H, Timinszky G, Huet S. HPF1-dependent histone ADP-ribosylation triggers chromatin relaxation to promote the recruitment of repair factors at sites of DNA damage. Nat Struct Mol Biol 2023; 30:678-691. [PMID: 37106138 DOI: 10.1038/s41594-023-00977-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/28/2023] [Indexed: 04/29/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) activity is regulated by its co-factor histone poly(ADP-ribosylation) factor 1 (HPF1). The complex formed by HPF1 and PARP1 catalyzes ADP-ribosylation of serine residues of proteins near DNA breaks, mainly PARP1 and histones. However, the effect of HPF1 on DNA repair regulated by PARP1 remains unclear. Here, we show that HPF1 controls prolonged histone ADP-ribosylation in the vicinity of the DNA breaks by regulating both the number and length of ADP-ribose chains. Furthermore, we demonstrate that HPF1-dependent histone ADP-ribosylation triggers the rapid unfolding of chromatin, facilitating access to DNA at sites of damage. This process promotes the assembly of both the homologous recombination and non-homologous end joining repair machineries. Altogether, our data highlight the key roles played by the PARP1/HPF1 complex in regulating ADP-ribosylation signaling as well as the conformation of damaged chromatin at early stages of the DNA damage response.
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Affiliation(s)
- Rebecca Smith
- University of Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, Rennes, France.
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - Siham Zentout
- University of Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, Rennes, France
| | - Magdalena Rother
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nicolas Bigot
- University of Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, Rennes, France
| | - Catherine Chapuis
- University of Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, Rennes, France
| | - Alexandra Mihuț
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Gyula Timinszky
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
| | - Sébastien Huet
- University of Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, Rennes, France.
- Institut Universitaire de France, Paris, France.
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14
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De Bragança S, Aicart-Ramos C, Arribas-Bosacoma R, Rivera-Calzada A, Unfried JP, Prats-Mari L, Marin-Baquero M, Fortes P, Llorca O, Moreno-Herrero F. APLF and long non-coding RNA NIHCOLE promote stable DNA synapsis in non-homologous end joining. Cell Rep 2023; 42:111917. [PMID: 36640344 DOI: 10.1016/j.celrep.2022.111917] [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: 06/08/2022] [Revised: 10/26/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023] Open
Abstract
The synapsis of DNA ends is a critical step for the repair of double-strand breaks by non-homologous end joining (NHEJ). This is performed by a multicomponent protein complex assembled around Ku70-Ku80 heterodimers and regulated by accessory factors, including long non-coding RNAs, through poorly understood mechanisms. Here, we use magnetic tweezers to investigate the contributions of core NHEJ proteins and APLF and lncRNA NIHCOLE to DNA synapsis. APLF stabilizes DNA end bridging and, together with Ku70-Ku80, establishes a minimal complex that supports DNA synapsis for several minutes under piconewton forces. We find the C-terminal acidic region of APLF to be critical for bridging. NIHCOLE increases the dwell time of the synapses by Ku70-Ku80 and APLF. This effect is further enhanced by a small and structured RNA domain within NIHCOLE. We propose a model where Ku70-Ku80 can simultaneously bind DNA, APLF, and structured RNAs to promote the stable joining of DNA ends.
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Affiliation(s)
- Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Angel Rivera-Calzada
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Juan Pablo Unfried
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel; Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Laura Prats-Mari
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Mikel Marin-Baquero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain.
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain.
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15
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Löffler T, Krüger A, Zirak P, Winterhalder MJ, Müller AL, Fischbach A, Mangerich A, Zumbusch A. Influence of chain length and branching on poly(ADP-ribose)-protein interactions. Nucleic Acids Res 2023; 51:536-552. [PMID: 36625274 PMCID: PMC9881148 DOI: 10.1093/nar/gkac1235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/16/2022] [Accepted: 12/10/2022] [Indexed: 01/11/2023] Open
Abstract
Hundreds of proteins interact with poly(ADP-ribose) (PAR) via multiple PAR interaction motifs, thereby regulating their physico-chemical properties, sub-cellular localizations, enzymatic activities, or protein stability. Here, we present a targeted approach based on fluorescence correlation spectroscopy (FCS) to characterize potential structure-specific interactions of PAR molecules of defined chain length and branching with three prime PAR-binding proteins, the tumor suppressor protein p53, histone H1, and the histone chaperone APLF. Our study reveals complex and structure-specific PAR-protein interactions. Quantitative Kd values were determined and binding affinities for all three proteins were shown to be in the nanomolar range. We report PAR chain length dependent binding of p53 and H1, yet chain length independent binding of APLF. For all three PAR binders, we found a preference for linear over hyperbranched PAR. Importantly, protein- and PAR-structure-specific binding modes were revealed. Thus, while the H1-PAR interaction occurred largely on a bi-molecular 1:1 basis, p53-and potentially also APLF-can form complex multivalent PAR-protein structures. In conclusion, our study gives detailed and quantitative insight into PAR-protein interactions in a solution-based setting at near physiological buffer conditions. The results support the notion of protein and PAR-structure-specific binding modes that have evolved to fit the purpose of the respective biochemical functions and biological contexts.
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Affiliation(s)
| | | | - Peyman Zirak
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | | | - Anna-Lena Müller
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | - Arthur Fischbach
- Department of Biology, Universität Konstanz, Konstanz D-78457, Germany
| | - Aswin Mangerich
- To whom correspondence should be addressed. Tel: +49 33200 88 5301;
| | - Andreas Zumbusch
- Correspondence may also be addressed to Andreas Zumbusch. Tel: +49 7531 882027;
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16
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Pfeifer CR, Tobin MP, Cho S, Vashisth M, Dooling LJ, Vazquez LL, Ricci-De Lucca EG, Simon KT, Discher DE. Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate. Nucleus 2022; 13:129-143. [PMID: 35293271 PMCID: PMC8928808 DOI: 10.1080/19491034.2022.2045726] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Nuclear rupture has long been associated with deficits or defects in lamins, with recent results also indicating a role for actomyosin stress, but key physical determinants of rupture remain unclear. Here, lamin-B filaments stably interact with the nuclear membrane at sites of low Gaussian curvature yet dilute at high curvature to favor rupture, whereas lamin-A depletion requires high strain-rates. Live-cell imaging of lamin-B1 gene-edited cancer cells is complemented by fixed-cell imaging of rupture in: iPS-derived progeria patients cells, cells within beating chick embryo hearts, and cancer cells with multi-site rupture after migration through small pores. Data fit a model of stiff filaments that detach from a curved surface.Rupture is modestly suppressed by inhibiting myosin-II and by hypotonic stress, which slow the strain-rates. Lamin-A dilution and rupture probability indeed increase above a threshold rate of nuclear pulling. Curvature-sensing mechanisms of proteins at plasma membranes, including Piezo1, might thus apply at nuclear membranes.Summary statement: High nuclear curvature drives lamina dilution and nuclear envelope rupture even when myosin stress is inhibited. Stiff filaments generally dilute from sites of high Gaussian curvature, providing mathematical fits of experiments.
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Affiliation(s)
- Charlotte R. Pfeifer
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA,Graduate Group/Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P. Tobin
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA,Graduate Group/Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Sangkyun Cho
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Manasvita Vashisth
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Lawrence J. Dooling
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Lizeth Lopez Vazquez
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Emma G. Ricci-De Lucca
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Keiann T. Simon
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Dennis E. Discher
- Physical Sciences Oncology Center at Penn (PSOC@penn), University of Pennsylvania, Philadelphia, PA, USA,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA,Graduate Group/Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, USA,Graduate Group/Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA,CONTACT Dennis E. Discher Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA
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17
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Rivera-Calzada A, Arribas-Bosacoma R, Ruiz-Ramos A, Escudero-Bravo P, Boskovic J, Fernandez-Leiro R, Oliver AW, Pearl LH, Llorca O. Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus. Nat Commun 2022; 13:7062. [PMID: 36400800 PMCID: PMC9674614 DOI: 10.1038/s41467-022-34843-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
Detection of cytosolic DNA is a central element of the innate immunity system against viral infection. The Ku heterodimer, a component of the NHEJ pathway of DNA repair in the nucleus, functions as DNA sensor that detects dsDNA of viruses that replicate in the cytoplasm. Vaccinia virus expresses two proteins, C4 and C16, that inactivate DNA sensing and enhance virulence. The structural basis for this is unknown. Here we determine the structure of the C16 - Ku complex using cryoEM. Ku binds dsDNA by a preformed ring but C16 sterically blocks this access route, abrogating binding to a dsDNA end and its insertion into DNA-PK, thereby averting signalling into the downstream innate immunity system. C4 replicates these activities using a domain with 54% identity to C16. Our results reveal how vaccinia virus subverts the capacity of Ku to recognize viral DNA.
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Affiliation(s)
- Angel Rivera-Calzada
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW1E 6BT, UK
| | - Alba Ruiz-Ramos
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Paloma Escudero-Bravo
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Jasminka Boskovic
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Rafael Fernandez-Leiro
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW1E 6BT, UK.
| | - Oscar Llorca
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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18
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Zhang Y, Fang M, Li S, Xu H, Ren J, Tu L, Zuo B, Yao W, Liang G. BTApep-TAT peptide inhibits ADP-ribosylation of BORIS to induce DNA damage in cancer. Mol Cancer 2022; 21:158. [PMID: 35918747 PMCID: PMC9344678 DOI: 10.1186/s12943-022-01621-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brother of regulator of imprinted sites (BORIS) is expressed in most cancers and often associated with short survival and poor prognosis in patients. BORIS inhibits apoptosis and promotes proliferation of cancer cells. However, its mechanism of action has not been elucidated, and there is no known inhibitor of BORIS. METHODS A phage display library was used to find the BORIS inhibitory peptides and BTApep-TAT was identified. The RNA sequencing profile of BTApep-TAT-treated H1299 cells was compared with that of BORIS-knockdown cells. Antitumor activity of BTApep-TAT was evaluated in a non-small cell lung cancer (NSCLC) xenograft mouse model. BTApep-TAT was also used to investigate the post-translational modification (PTM) of BORIS and the role of BORIS in DNA damage repair. Site-directed mutants of BORIS were constructed and used for investigating PTM and the function of BORIS. RESULTS BTApep-TAT induced DNA damage in cancer cells and suppressed NSCLC xenograft tumor progression. Investigation of the mechanism of action of BTApep-TAT demonstrated that BORIS underwent ADP ribosylation upon double- or single-strand DNA damage. Substitution of five conserved glutamic acid (E) residues with alanine residues (A) between amino acids (AAs) 198 and 228 of BORIS reduced its ADP ribosylation. Inhibition of ADP ribosylation of BORIS by a site-specific mutation or by BTApep-TAT treatment blocked its interaction with Ku70 and impaired the function of BORIS in DNA damage repair. CONCLUSIONS The present study identified an inhibitor of BORIS, highlighted the importance of ADP ribosylation of BORIS, and revealed a novel function of BORIS in DNA damage repair. The present work provides a practical method for the future screening or optimization of drugs targeting BORIS.
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Affiliation(s)
- Yanmei Zhang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.
| | - Mengdie Fang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.,College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Shouye Li
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.,Zhejiang Eyoung Pharmaceutical Research and Development Center, Hangzhou, 311258, Zhejiang, China
| | - Hao Xu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Juan Ren
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Linglan Tu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Bowen Zuo
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Wanxin Yao
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Guang Liang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China. .,College of Pharmacy, Hangzhou Medical College, Hangzhou, 311300, Zhejiang, China.
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19
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Corbeski I, Guo X, Eckhardt BV, Fasci D, Wiegant W, Graewert MA, Vreeken K, Wienk H, Svergun DI, Heck AJR, van Attikum H, Boelens R, Sixma TK, Mattiroli F, van Ingen H. Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. SCIENCE ADVANCES 2022; 8:eabo0517. [PMID: 35895815 PMCID: PMC9328677 DOI: 10.1126/sciadv.abo0517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/10/2022] [Indexed: 05/26/2023]
Abstract
Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B. Here, we show that the acidic domain of DNA repair factor APLF (APLFAD) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLFAD-histone octamer complex shows that APLFAD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.
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Affiliation(s)
- Ivan Corbeski
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Xiaohu Guo
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Bruna V. Eckhardt
- Hubrecht Institute—KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Domenico Fasci
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Wouter Wiegant
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Melissa A. Graewert
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Kees Vreeken
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Titia K. Sixma
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute—KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
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20
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Hasan A, Rizvi SF, Parveen S, Mir SS. Molecular chaperones in DNA repair mechanisms: Role in genomic instability and proteostasis in cancer. Life Sci 2022; 306:120852. [DOI: 10.1016/j.lfs.2022.120852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/14/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023]
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21
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Ali A, Xiao W, Babar ME, Bi Y. Double-Stranded Break Repair in Mammalian Cells and Precise Genome Editing. Genes (Basel) 2022; 13:genes13050737. [PMID: 35627122 PMCID: PMC9142082 DOI: 10.3390/genes13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, double-strand breaks (DSBs) are repaired predominantly by error-prone non-homologous end joining (NHEJ), but less prevalently by error-free template-dependent homologous recombination (HR). DSB repair pathway selection is the bedrock for genome editing. NHEJ results in random mutations when repairing DSB, while HR induces high-fidelity sequence-specific variations, but with an undesirable low efficiency. In this review, we first discuss the latest insights into the action mode of NHEJ and HR in a panoramic view. We then propose the future direction of genome editing by virtue of these advancements. We suggest that by switching NHEJ to HR, full fidelity genome editing and robust gene knock-in could be enabled. We also envision that RNA molecules could be repurposed by RNA-templated DSB repair to mediate precise genetic editing.
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Affiliation(s)
- Akhtar Ali
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan
| | - Wei Xiao
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
| | - Masroor Ellahi Babar
- The University of Agriculture Dera Ismail Khan, Dera Ismail Khan 29220, Pakistan;
| | - Yanzhen Bi
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Correspondence: ; Tel.: +86-151-0714-8708
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22
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Species variations in XRCC1 recruitment strategies for FHA domain-containing proteins. DNA Repair (Amst) 2022; 110:103263. [PMID: 35026705 PMCID: PMC9282668 DOI: 10.1016/j.dnarep.2021.103263] [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: 07/26/2021] [Revised: 11/07/2021] [Accepted: 12/21/2021] [Indexed: 02/03/2023]
Abstract
DNA repair scaffolds XRCC1 and XRCC4 utilize a phosphopeptide FHA domain binding motif (FBM) of the form Y-x-x-pS-pT-D-E that supports recruitment of three identified FHA domain-containing DNA repair proteins: polynucleotide kinase/phosphatase (PNKP), aprataxin (APTX), and a third protein, APLF, that functions as a scaffold in support of non-homologous end joining (NHEJ). Mammalian dimeric XRCC4 is able to interact with two of these proteins at any given time, while monomeric XRCC1 binds only one. However, sequence analysis indicates that amphibian and teleost XRCC1 generally contain two FHA binding motifs. X1-FBM1, is similar to the single mammalian XRCC1 FBM and probably functions similarly. X1-FBM2, is more similar to mammalian XRCC4 FBM; it is located closer to the XRCC1 BRCT1 domain and probably is less discriminating among its three likely binding partners. Availability of an additional PNKP or APTX recruitment motif may alleviate the bottleneck that results from using a single FBM motif for recruitment of multiple repair factors. Alternatively, recruitment of APLF by X1-FBM2 may function to rescue a misdirected or unsuccessful SSB repair response by redirecting the damaged DNA to the NHEJ pathway, - a need that results from the ambiguity of the PARP1 signal regarding the nature of the damage. Evaluation of XRCC4 FBMs in acanthomorphs, which account for a majority of the reported teleost sequences, reveals the presence of an additional XRCC4-like paralog, distinct from other previously described members of the XRCC4 superfamily. The FBM is typically absent in acanthomorph XRCC4, but present in the XRCC4-like paralog. Modeling suggests that XRCC4 and its paralog may form homodimers or XRCC4-XRCC4-like heterodimers.
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23
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Oh JM, Myung K. Crosstalk between different DNA repair pathways for DNA double strand break repairs. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 873:503438. [PMID: 35094810 DOI: 10.1016/j.mrgentox.2021.503438] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/09/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022]
Abstract
DNA double strand breaks (DSBs) are the most threatening type of DNA lesions and must be repaired properly in order to inhibit severe diseases and cell death. There are four major repair pathways for DSBs: non-homologous end joining (NHEJ), homologous recombination (HR), single strand annealing (SSA) and alternative end joining (alt-EJ). Cells choose repair pathway depending on the cell cycle phase and the length of 3' end of the DNA when DSBs are generated. Blunt and short regions of the 5' or 3' overhang DNA are repaired by NHEJ, which uses direct ligation or limited resection processing of the broken DNA end. In contrast, HR, SSA and alt-EJ use the resected DNA generated by the MRN (MRE11-RAD50-NBS1) complex and C-terminal binding protein interacting protein (CtIP) activated during the S and G2 phases. Here, we review recent findings on each repair pathway and the choice of repair mechanism and highlight the role of mismatch repair (MMR) protein in HR.
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Affiliation(s)
- Jung-Min Oh
- Department of Oral Biochemistry, Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea.
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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24
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Singh JK, Smith R, Rother MB, de Groot AJL, Wiegant WW, Vreeken K, D’Augustin O, Kim RQ, Qian H, Krawczyk PM, González-Prieto R, Vertegaal ACO, Lamers M, Huet S, van Attikum H. Zinc finger protein ZNF384 is an adaptor of Ku to DNA during classical non-homologous end-joining. Nat Commun 2021; 12:6560. [PMID: 34772923 PMCID: PMC8589989 DOI: 10.1038/s41467-021-26691-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/19/2021] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are among the most deleterious types of DNA damage as they can lead to mutations and chromosomal rearrangements, which underlie cancer development. Classical non-homologous end-joining (cNHEJ) is the dominant pathway for DSB repair in human cells, involving the DNA-binding proteins XRCC6 (Ku70) and XRCC5 (Ku80). Other DNA-binding proteins such as Zinc Finger (ZnF) domain-containing proteins have also been implicated in DNA repair, but their role in cNHEJ remained elusive. Here we show that ZNF384, a member of the C2H2 family of ZnF proteins, binds DNA ends in vitro and is recruited to DSBs in vivo. ZNF384 recruitment requires the poly(ADP-ribosyl) polymerase 1 (PARP1)-dependent expansion of damaged chromatin, followed by binding of its C2H2 motifs to the exposed DNA. Moreover, ZNF384 interacts with Ku70/Ku80 via its N-terminus, thereby promoting Ku70/Ku80 assembly and the accrual of downstream cNHEJ factors, including APLF and XRCC4/LIG4, for efficient repair at DSBs. Altogether, our data suggest that ZNF384 acts as a 'Ku-adaptor' that binds damaged DNA and Ku70/Ku80 to facilitate the build-up of a cNHEJ repairosome, highlighting a role for ZNF384 in DSB repair and genome maintenance.
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Affiliation(s)
- Jenny Kaur Singh
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rebecca Smith
- grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, BIOSIT–UMS3480, F-35000 Rennes, France
| | - Magdalena B. Rother
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anton J. L. de Groot
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wouter W. Wiegant
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kees Vreeken
- grid.10419.3d0000000089452978Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ostiane D’Augustin
- grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, BIOSIT–UMS3480, F-35000 Rennes, France ,grid.457349.80000 0004 0623 0579Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, F-92265 Fontenay-aux-Roses, France
| | - Robbert Q. Kim
- grid.10419.3d0000000089452978Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Haibin Qian
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Przemek M. Krawczyk
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Román González-Prieto
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Alfred C. O. Vertegaal
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Meindert Lamers
- grid.16872.3a0000 0004 0435 165XDepartment of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sébastien Huet
- grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, BIOSIT–UMS3480, F-35000 Rennes, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, F-75000 Paris, France
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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25
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Sui H, Hao M, Chang W, Imamichi T. The Role of Ku70 as a Cytosolic DNA Sensor in Innate Immunity and Beyond. Front Cell Infect Microbiol 2021; 11:761983. [PMID: 34746031 PMCID: PMC8566972 DOI: 10.3389/fcimb.2021.761983] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/06/2021] [Indexed: 12/24/2022] Open
Abstract
Human Ku70 is a well-known endogenous nuclear protein involved in the non-homologous end joining pathway to repair double-stranded breaks in DNA. However, Ku70 has been studied in multiple contexts and grown into a multifunctional protein. In addition to the extensive functional study of Ku70 in DNA repair process, many studies have emphasized the role of Ku70 in various other cellular processes, including apoptosis, aging, and HIV replication. In this review, we focus on discussing the role of Ku70 in inducing interferons and proinflammatory cytokines as a cytosolic DNA sensor. We explored the unique structure of Ku70 binding with DNA; illustrated, with evidence, how Ku70, as a nuclear protein, responds to extracellular DNA stimulation; and summarized the mechanisms of the Ku70-involved innate immune response pathway. Finally, we discussed several new strategies to modulate Ku70-mediated innate immune response and highlighted some potential physiological insights based on the role of Ku70 in innate immunity.
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Affiliation(s)
- Hongyan Sui
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | | | | | - Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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26
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Unfried JP, Marín-Baquero M, Rivera-Calzada Á, Razquin N, Martín-Cuevas EM, de Bragança S, Aicart-Ramos C, McCoy C, Prats-Mari L, Arribas-Bosacoma R, Lee L, Caruso S, Zucman-Rossi J, Sangro B, Williams G, Moreno-Herrero F, Llorca O, Lees-Miller SP, Fortes P. Long Noncoding RNA NIHCOLE Promotes Ligation Efficiency of DNA Double-Strand Breaks in Hepatocellular Carcinoma. Cancer Res 2021; 81:4910-4925. [PMID: 34321241 PMCID: PMC8488005 DOI: 10.1158/0008-5472.can-21-0463] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/25/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) are emerging as key players in cancer as parts of poorly understood molecular mechanisms. Here, we investigated lncRNAs that play a role in hepatocellular carcinoma (HCC) and identified NIHCOLE, a novel lncRNA induced in HCC with oncogenic potential and a role in the ligation efficiency of DNA double-stranded breaks (DSB). NIHCOLE expression was associated with poor prognosis and survival of HCC patients. Depletion of NIHCOLE from HCC cells led to impaired proliferation and increased apoptosis. NIHCOLE deficiency led to accumulation of DNA damage due to a specific decrease in the activity of the nonhomologous end-joining (NHEJ) pathway of DSB repair. DNA damage induction in NIHCOLE-depleted cells further decreased HCC cell growth. NIHCOLE was associated with DSB markers and recruited several molecules of the Ku70/Ku80 heterodimer. Further, NIHCOLE putative structural domains supported stable multimeric complexes formed by several NHEJ factors including Ku70/80, APLF, XRCC4, and DNA ligase IV. NHEJ reconstitution assays showed that NIHCOLE promoted the ligation efficiency of blunt-ended DSBs. Collectively, these data show that NIHCOLE serves as a scaffold and facilitator of NHEJ machinery and confers an advantage to HCC cells, which could be exploited as a targetable vulnerability. SIGNIFICANCE: This study characterizes the role of lncRNA NIHCOLE in DNA repair and cellular fitness in HCC, thus implicating it as a therapeutic target.See related commentary by Barcena-Varela and Lujambio, p. 4899.
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MESH Headings
- Biomarkers, Tumor
- Carcinoma, Hepatocellular/diagnosis
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/mortality
- Cell Line, Tumor
- DNA Breaks, Double-Stranded
- DNA End-Joining Repair
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- High-Throughput Nucleotide Sequencing
- Humans
- Liver Neoplasms/diagnosis
- Liver Neoplasms/genetics
- Liver Neoplasms/mortality
- Models, Biological
- Nucleic Acid Conformation
- Nucleotide Motifs
- Prognosis
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
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Affiliation(s)
- Juan P Unfried
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain.
| | - Mikel Marín-Baquero
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Ángel Rivera-Calzada
- Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Nerea Razquin
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Eva M Martín-Cuevas
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sara de Bragança
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Christopher McCoy
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Laura Prats-Mari
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Functional Genomics of Solid Tumors laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Functional Genomics of Solid Tumors laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
| | - Bruno Sangro
- University of Navarra Clinic (CUN), Liver Unit, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain
| | - Gareth Williams
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Spanish National Centre for Biotechnology (CNB), Spanish National Research Council (CSIC), Madrid, Spain
| | - Oscar Llorca
- Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain.
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain
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27
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Guha S, Bhaumik SR. Transcription-coupled DNA double-strand break repair. DNA Repair (Amst) 2021; 109:103211. [PMID: 34883263 DOI: 10.1016/j.dnarep.2021.103211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/20/2022]
Abstract
The genomic DNA is constantly under attack by cellular and/or environmental factors. Fortunately, the cell is armed to safeguard its genome by various mechanisms such as nucleotide excision, base excision, mismatch and DNA double-strand break repairs. While these processes maintain the integrity of the genome throughout, DNA repair occurs preferentially faster at the transcriptionally active genes. Such transcription-coupled repair phenomenon plays important roles to maintain active genome integrity, failure of which would interfere with transcription, leading to an altered gene expression (and hence cellular pathologies/diseases). Among the various DNA damages, DNA double-strand breaks are quite toxic to the cells. If DNA double-strand break occurs at the active gene, it would interfere with transcription/gene expression, thus threatening cellular viability. Such DNA double-strand breaks are found to be repaired faster at the active gene in comparison to its inactive state or the inactive gene, thus supporting the existence of a new phenomenon of transcription-coupled DNA double-strand break repair. Here, we describe the advances of this repair process.
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Affiliation(s)
- Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA.
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28
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Liang S, Chaplin AK, Stavridi AK, Appleby R, Hnizda A, Blundell TL. Stages, scaffolds and strings in the spatial organisation of non-homologous end joining: Insights from X-ray diffraction and Cryo-EM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:60-73. [PMID: 33285184 PMCID: PMC8224183 DOI: 10.1016/j.pbiomolbio.2020.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/26/2020] [Indexed: 01/10/2023]
Abstract
Non-homologous end joining (NHEJ) is the preferred pathway for the repair of DNA double-strand breaks in humans. Here we describe three structural aspects of the repair pathway: stages, scaffolds and strings. We discuss the orchestration of DNA repair to guarantee robust and efficient NHEJ. We focus on structural studies over the past two decades, not only using X-ray diffraction, but also increasingly exploiting cryo-EM to investigate the macromolecular assemblies.
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Affiliation(s)
- Shikang Liang
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Antonia Kefala Stavridi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Robert Appleby
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Ales Hnizda
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK.
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29
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Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining. Essays Biochem 2021; 64:791-806. [PMID: 32579168 PMCID: PMC7588668 DOI: 10.1042/ebc20190092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Non-homologous end joining (NHEJ) is one of the two principal damage repair pathways for DNA double-strand breaks in cells. In this review, we give a brief overview of the system including a discussion of the effects of deregulation of NHEJ components in carcinogenesis and resistance to cancer therapy. We then discuss the relevance of targeting NHEJ components pharmacologically as a potential cancer therapy and review previous approaches to orthosteric regulation of NHEJ factors. Given the limited success of previous investigations to develop inhibitors against individual components, we give a brief discussion of the recent advances in computational and structural biology that allow us to explore different targets, with a particular focus on modulating protein-protein interaction interfaces. We illustrate this discussion with three examples showcasing some current approaches to developing protein-protein interaction inhibitors to modulate the assembly of NHEJ multiprotein complexes in space and time.
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30
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Hammel M, Tainer JA. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci 2021; 30:1735-1756. [PMID: 34056803 PMCID: PMC8376411 DOI: 10.1002/pro.4133] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIVBRCT–Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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31
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DNA double-strand break repair: Putting zinc fingers on the sore spot. Semin Cell Dev Biol 2021; 113:65-74. [DOI: 10.1016/j.semcdb.2020.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/22/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022]
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32
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Abbasi S, Parmar G, Kelly RD, Balasuriya N, Schild-Poulter C. The Ku complex: recent advances and emerging roles outside of non-homologous end-joining. Cell Mol Life Sci 2021; 78:4589-4613. [PMID: 33855626 PMCID: PMC11071882 DOI: 10.1007/s00018-021-03801-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022]
Abstract
Since its discovery in 1981, the Ku complex has been extensively studied under multiple cellular contexts, with most work focusing on Ku in terms of its essential role in non-homologous end-joining (NHEJ). In this process, Ku is well-known as the DNA-binding subunit for DNA-PK, which is central to the NHEJ repair process. However, in addition to the extensive study of Ku's role in DNA repair, Ku has also been implicated in various other cellular processes including transcription, the DNA damage response, DNA replication, telomere maintenance, and has since been studied in multiple contexts, growing into a multidisciplinary point of research across various fields. Some advances have been driven by clarification of Ku's structure, including the original Ku crystal structure and the more recent Ku-DNA-PKcs crystallography, cryogenic electron microscopy (cryoEM) studies, and the identification of various post-translational modifications. Here, we focus on the advances made in understanding the Ku heterodimer outside of non-homologous end-joining, and across a variety of model organisms. We explore unique structural and functional aspects, detail Ku expression, conservation, and essentiality in different species, discuss the evidence for its involvement in a diverse range of cellular functions, highlight Ku protein interactions and recent work concerning Ku-binding motifs, and finally, we summarize the clinical Ku-related research to date.
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Affiliation(s)
- Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Gursimran Parmar
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Rachel D Kelly
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Nileeka Balasuriya
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada.
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33
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London RE. XRCC1 - Strategies for coordinating and assembling a versatile DNA damage response. DNA Repair (Amst) 2021; 93:102917. [PMID: 33087283 DOI: 10.1016/j.dnarep.2020.102917] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
X-ray cross complementing protein 1 (XRCC1) is a DNA repair scaffold that supports base excision repair and single strand break repair, and is also a participant in other repair pathways. It also serves as an important co-transporter for several other repair proteins, including aprataxin and PNKP-like factor (APLF), and DNA Ligase 3α (LIG3). By combining highly specialized regions that help to organize specific repair functions with recruitment of additional enzymes whose contribution is dependent on the details of the damaged site, XRCC1 is able to handle an expanded range of problems that may arise as the repair progresses or in connection with other repair pathways with which it interfaces. This review discusses the interplay between these functions and considers some possible interactions that underlie its reported repair activities.
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Affiliation(s)
- Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, 111 T. W. Alexander Dr, NC, 27709, United States.
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Stinson BM, Loparo JJ. Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway. Annu Rev Biochem 2021; 90:137-164. [PMID: 33556282 DOI: 10.1146/annurev-biochem-080320-110356] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing.
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Affiliation(s)
- Benjamin M Stinson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; ,
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35
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Abstract
Adenosine diphosphate (ADP)-ribosylation is a unique post-translational modification that regulates many biological processes, such as DNA damage repair. During DNA repair, ADP-ribosylation needs to be reversed by ADP-ribosylhydrolases. A group of ADP-ribosylhydrolases have a catalytic domain, namely the macrodomain, which is conserved in evolution from prokaryotes to humans. Not all macrodomains remove ADP-ribosylation. One set of macrodomains loses enzymatic activity and only binds to ADP-ribose (ADPR). Here, we summarize the biological functions of these macrodomains in DNA damage repair and compare the structure of enzymatically active and inactive macrodomains. Moreover, small molecular inhibitors have been developed that target macrodomains to suppress DNA damage repair and tumor growth. Macrodomain proteins are also expressed in pathogens, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, these domains may not be directly involved in DNA damage repair in the hosts or pathogens. Instead, they play key roles in pathogen replication. Thus, by targeting macrodomains it may be possible to treat pathogen-induced diseases, such as coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Lily Yu
- Westridge School, Pasadena, California 91105, USA
| | - Xiuhua Liu
- Institute of Life Science and Green Development, College of Life Science, Hebei University, Baoding 071002, China.
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou 310024, China.
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Varghese PC, Rajam SM, Nandy D, Jory A, Mukherjee A, Dutta D. Histone chaperone APLF level dictates the implantation of mouse embryos. J Cell Sci 2021; 134:jcs.246900. [PMID: 33277378 DOI: 10.1242/jcs.246900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/25/2020] [Indexed: 11/20/2022] Open
Abstract
Our recent findings demonstrated that the histone chaperone and DNA repair factor aprataxin and PNK-like factor (APLF) could regulate epithelial to mesenchymal transition (EMT) during the reprogramming of murine fibroblasts and in breast cancer metastasis. Therefore, we investigated the function of APLF in EMT associated with mouse development. Here, we show that APLF is predominantly enhanced in trophectoderm (TE) and lineages derived from TE in pre- and post-implantation embryos. Downregulation of APLF induced the hatching of embryos in vitro, with a significant increase in Cdh1 and Cdx2 expression. Aplf short hairpin RNA-microinjected embryos failed to implant in vivo Rescue experiments neutralized the knockdown effects of APLF both in vitro and in vivo Reduced expression of Snai2 and Tead4, and the gain in Cdh1 and sFlt1 (also known as Flt1) level, marked the differentiation of APLF-knocked down trophoblast stem cells that might contribute towards the impaired implantation of embryos. Hence, our findings suggest a novel role for APLF during implantation and post-implantation development of mouse embryos. We anticipate that APLF might contribute to the establishment of maternal-fetal connection, as its fine balance is required to achieve implantation and thereby attain proper pregnancy.
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Affiliation(s)
- Pallavi Chinnu Varghese
- Rajiv Gandhi Centre for Biotechnology, Regenerative Biology Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India.,Department of Biotechnology, Manipal Academy of Higher Education, Manipal, Karnataka State 576104, India
| | - Sruthy Manuraj Rajam
- Rajiv Gandhi Centre for Biotechnology, Regenerative Biology Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India.,Department of Biotechnology, Manipal Academy of Higher Education, Manipal, Karnataka State 576104, India
| | - Debparna Nandy
- Rajiv Gandhi Centre for Biotechnology, Regenerative Biology Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India
| | - Aurelie Jory
- Mouse Genome Engineering Facility, National Centre for Biological Sciences, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Ananda Mukherjee
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India
| | - Debasree Dutta
- Rajiv Gandhi Centre for Biotechnology, Regenerative Biology Program, Thycaud PO, Poojappura, Thiruvananthapuram 695014, Kerala, India
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37
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Inhibitors of DNA double-strand break repair at the crossroads of cancer therapy and genome editing. Biochem Pharmacol 2020; 182:114195. [DOI: 10.1016/j.bcp.2020.114195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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Aberle L, Krüger A, Reber JM, Lippmann M, Hufnagel M, Schmalz M, Trussina IREA, Schlesiger S, Zubel T, Schütz K, Marx A, Hartwig A, Ferrando-May E, Bürkle A, Mangerich A. PARP1 catalytic variants reveal branching and chain length-specific functions of poly(ADP-ribose) in cellular physiology and stress response. Nucleic Acids Res 2020; 48:10015-10033. [PMID: 32667640 PMCID: PMC7544232 DOI: 10.1093/nar/gkaa590] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/24/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022] Open
Abstract
Poly(ADP-ribosyl)ation regulates numerous cellular processes like genome maintenance and cell death, thus providing protective functions but also contributing to several pathological conditions. Poly(ADP-ribose) (PAR) molecules exhibit a remarkable heterogeneity in chain lengths and branching frequencies, but the biological significance of this is basically unknown. To unravel structure-specific functions of PAR, we used PARP1 mutants producing PAR of different qualities, i.e. short and hypobranched (PARP1\G972R), short and moderately hyperbranched (PARP1\Y986S), or strongly hyperbranched PAR (PARP1\Y986H). By reconstituting HeLa PARP1 knockout cells, we demonstrate that PARP1\G972R negatively affects cellular endpoints, such as viability, cell cycle progression and genotoxic stress resistance. In contrast, PARP1\Y986S elicits only mild effects, suggesting that PAR branching compensates for short polymer length. Interestingly, PARP1\Y986H exhibits moderate beneficial effects on cell physiology. Furthermore, different PARP1 mutants have distinct effects on molecular processes, such as gene expression and protein localization dynamics of PARP1 itself, and of its downstream factor XRCC1. Finally, the biological relevance of PAR branching is emphasized by the fact that branching frequencies vary considerably during different phases of the DNA damage-induced PARylation reaction and between different mouse tissues. Taken together, this study reveals that PAR branching and chain length essentially affect cellular functions, which further supports the notion of a ‘PAR code’.
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Affiliation(s)
- Lisa Aberle
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Annika Krüger
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Julia M Reber
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michelle Lippmann
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Matthias Hufnagel
- Department of Food Chemistry and Toxicology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Michael Schmalz
- Department of Physics, University of Konstanz, 78457 Konstanz, Germany
| | | | - Sarah Schlesiger
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Tabea Zubel
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Karina Schütz
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Andrea Hartwig
- Department of Food Chemistry and Toxicology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | | | - Alexander Bürkle
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Aswin Mangerich
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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Thapar R, Wang JL, Hammel M, Ye R, Liang K, Sun C, Hnizda A, Liang S, Maw SS, Lee L, Villarreal H, Forrester I, Fang S, Tsai MS, Blundell TL, Davis AJ, Lin C, Lees-Miller SP, Strick TR, Tainer J. Mechanism of efficient double-strand break repair by a long non-coding RNA. Nucleic Acids Res 2020; 48:10953-10972. [PMID: 33045735 PMCID: PMC7641761 DOI: 10.1093/nar/gkaa784] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 12/28/2022] Open
Abstract
Mechanistic studies in DNA repair have focused on roles of multi-protein DNA complexes, so how long non-coding RNAs (lncRNAs) regulate DNA repair is less well understood. Yet, lncRNA LINP1 is over-expressed in multiple cancers and confers resistance to ionizing radiation and chemotherapeutic drugs. Here, we unveil structural and mechanistic insights into LINP1's ability to facilitate non-homologous end joining (NHEJ). We characterized LINP1 structure and flexibility and analyzed interactions with the NHEJ factor Ku70/Ku80 (Ku) and Ku complexes that direct NHEJ. LINP1 self-assembles into phase-separated condensates via RNA-RNA interactions that reorganize to form filamentous Ku-containing aggregates. Structured motifs in LINP1 bind Ku, promoting Ku multimerization and stabilization of the initial synaptic event for NHEJ. Significantly, LINP1 acts as an effective proxy for PAXX. Collective results reveal how lncRNA effectively replaces a DNA repair protein for efficient NHEJ with implications for development of resistance to cancer therapy.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing L Wang
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Ruiqiong Ye
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Alberta, T2N 4N1, Canada
| | - Ke Liang
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Chengcao Sun
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Ales Hnizda
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Shikang Liang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Su S Maw
- Biological Systems and Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Alberta, T2N 4N1, Canada
| | | | - Isaac Forrester
- CryoEM Core at Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shujuan Fang
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Alberta, T2N 4N1, Canada
| | - Miaw-Sheue Tsai
- Biological Systems and Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Alberta, T2N 4N1, Canada
| | - Terence R Strick
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005, France
- Programme “Equipe Labellisée’’, Ligue Nationale Contre le Cancer, Paris 75005, France
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Department of Cancer Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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40
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Rzeszutek I, Betlej G. The Role of Small Noncoding RNA in DNA Double-Strand Break Repair. Int J Mol Sci 2020; 21:ijms21218039. [PMID: 33126669 PMCID: PMC7663326 DOI: 10.3390/ijms21218039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 02/01/2023] Open
Abstract
DNA damage is a common phenomenon promoted through a variety of exogenous and endogenous factors. The DNA damage response (DDR) pathway involves a wide range of proteins, and as was indicated, small noncoding RNAs (sncRNAs). These are double-strand break-induced RNAs (diRNAs) and DNA damage response small RNA (DDRNA). Moreover, RNA binding proteins (RBPs) and RNA modifications have also been identified to modulate diRNA and DDRNA function in the DDR process. Several theories have been formulated regarding the synthesis and function of these sncRNAs during DNA repair; nevertheless, these pathways’ molecular details remain unclear. Here, we review the current knowledge regarding the mechanisms of diRNA and DDRNA biosynthesis and discuss the role of sncRNAs in maintaining genome stability.
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Affiliation(s)
- Iwona Rzeszutek
- Institute of Biology and Biotechnology, Department of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
- Correspondence: ; Tel.: +48-17-851-86-20; Fax: +48-17-851-87-64
| | - Gabriela Betlej
- Institute of Physical Culture Studies, College of Medical Sciences, University of Rzeszow, 35-310 Rzeszow, Poland;
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41
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Dong W, Li L, Teng X, Yang X, Si S, Chai J. End Processing Factor APLF Promotes NHEJ Efficiency and Contributes to TMZ- and Ionizing Radiation-Resistance in Glioblastoma Cells. Onco Targets Ther 2020; 13:10593-10605. [PMID: 33116637 PMCID: PMC7584509 DOI: 10.2147/ott.s254292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/02/2020] [Indexed: 11/23/2022] Open
Abstract
Purpose Glioblastoma (GBM) is the most commonly diagnosed primary brain tumor in adults. Despite a variety of advances in the understanding of GBM cancer biology during recent decades, very few of them were applied into treatment, and the survival rate of GBM patients has not been improved majorly due to the low chemosensitivity to temozolomide (TMZ) or low radiosensitivity. Therefore, it is urgent to elucidate mechanisms of TMZ- and IR-resistance and develop novel therapeutic strategies to improve GBM treatment. Methods TMZ- and IR-resistant cell lines were acquired by continuous exposing parental GBM cells to TMZ or IR for 3 months. Cell viability was determined by using Sulforhodamine B (SRB) assay. Protein and mRNA expression were examined by Western blotting assay and quantitative polymerase chain reaction (qPCR) assay, respectively. Homologous recombination (HR) and nonhomologous end joining (NHEJ) efficiency were measured by HR and NHEJ reporter assay. Cell apoptosis was determined by Caspase3/7 activity. Autophagy was analyzed using CYTO-ID® Autophagy detection kit. Tumor growth was examined by U87 xenograft mice model. Results DNA repair efficiency of non-homologous end joining (NHEJ) pathway is significantly increased in TMZ- and IR-resistant GBM cells. Importantly, APLF, which is one of the DNA end processing factors in NHEJ, is upregulated in TMZ- and IR-resistant GBM cells and patients. APLF deficiency significantly decreases NHEJ efficiency and improves cell sensitivity to TMZ and IR both in vitro and in vivo. Conclusion Our study provides evidence for APLF serving as a promising, novel target in GBM chemo- and radio-therapy.
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Affiliation(s)
- Wei Dong
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academic Sciences, Jinan, Shandong, People's Republic of China
| | - Lanlan Li
- Binzhou Medical University Hospital, Binzhou, Shandong, People's Republic of China
| | - Xuepeng Teng
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academic Sciences, Jinan, Shandong, People's Republic of China
| | - Xinhua Yang
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academic Sciences, Jinan, Shandong, People's Republic of China
| | - Shujing Si
- Department of Oncology, Gaoqing People's Hospital, Zibo, Shandong, People's Republic of China
| | - Jie Chai
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academic Sciences, Jinan, Shandong, People's Republic of China
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Modulation of DNA double-strand break repair as a strategy to improve precise genome editing. Oncogene 2020; 39:6393-6405. [PMID: 32884115 DOI: 10.1038/s41388-020-01445-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
In the present day, it is possible to incorporate targeted mutations or replace a gene using genome editing techniques such as customisable CRISPR/Cas9 system. Although induction of DNA double-strand breaks (DSBs) by genome editing tools can be repaired by both non-homologous end joining (NHEJ) and homologous recombination (HR), the skewness of the former pathway in human and other mammals normally result in imprecise repair. Scientists working at the crossroads of DNA repair and genome editing have devised new strategies for using a specific pathway to their advantage. Refinement in the efficiency of precise gene editing was witnessed upon downregulation of NHEJ by knockdown or using small molecule inhibitors on one hand, and upregulation of HR proteins and addition of HR stimulators, other hand. The exploitation of cell cycle phase differences together with appropriate donor DNA length/sequence and small molecules has provided further improvement in precise genome editing. The present article reviews the mechanisms of improving the efficiency of precise genome editing in several model organisms and in clinics.
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Aleksandrov R, Hristova R, Stoynov S, Gospodinov A. The Chromatin Response to Double-Strand DNA Breaks and Their Repair. Cells 2020; 9:cells9081853. [PMID: 32784607 PMCID: PMC7464352 DOI: 10.3390/cells9081853] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular DNA is constantly being damaged by numerous internal and external mutagenic factors. Probably the most severe type of insults DNA could suffer are the double-strand DNA breaks (DSBs). They sever both DNA strands and compromise genomic stability, causing deleterious chromosomal aberrations that are implicated in numerous maladies, including cancer. Not surprisingly, cells have evolved several DSB repair pathways encompassing hundreds of different DNA repair proteins to cope with this challenge. In eukaryotic cells, DSB repair is fulfilled in the immensely complex environment of the chromatin. The chromatin is not just a passive background that accommodates the multitude of DNA repair proteins, but it is a highly dynamic and active participant in the repair process. Chromatin alterations, such as changing patterns of histone modifications shaped by numerous histone-modifying enzymes and chromatin remodeling, are pivotal for proficient DSB repair. Dynamic chromatin changes ensure accessibility to the damaged region, recruit DNA repair proteins, and regulate their association and activity, contributing to DSB repair pathway choice and coordination. Given the paramount importance of DSB repair in tumorigenesis and cancer progression, DSB repair has turned into an attractive target for the development of novel anticancer therapies, some of which have already entered the clinic.
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44
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Structural biology of multicomponent assemblies in DNA double-strand-break repair through non-homologous end joining. Curr Opin Struct Biol 2020; 61:9-16. [DOI: 10.1016/j.sbi.2019.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/30/2019] [Indexed: 01/19/2023]
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45
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Radiation resistance in head and neck squamous cell carcinoma: dire need for an appropriate sensitizer. Oncogene 2020; 39:3638-3649. [PMID: 32157215 PMCID: PMC7190570 DOI: 10.1038/s41388-020-1250-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 01/11/2023]
Abstract
Radiation is a significant treatment for patients with head and neck cancer. Despite advances to improve treatment, many tumors acquire radiation resistance resulting in poor survival. Radiation kills cancer cells by inducing DNA double-strand breaks. Therefore, radiation resistance is enhanced by efficient repair of damaged DNA. Head and neck cancers overexpress EGFR and have a high frequency of p53 mutations, both of which enhance DNA repair. This review discusses the clinical criteria for radiation resistance in patients with head and neck cancer and summarizes how cancer cells evade radiation-mediated apoptosis by p53- and epidermal growth factor receptor (EGFR)-mediated DNA repair. In addition, we explore the role of cancer stem cells in promoting radiation resistance, and how the abscopal effect provides rationale for combination strategies with immunotherapy.
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Structural mechanism of DNA-end synapsis in the non-homologous end joining pathway for repairing double-strand breaks: bridge over troubled ends. Biochem Soc Trans 2020; 47:1609-1619. [PMID: 31829407 DOI: 10.1042/bst20180518] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022]
Abstract
Non-homologous end joining (NHEJ) is a major repair pathway for DNA double-strand breaks (DSBs), which is the most toxic DNA damage in cells. Unrepaired DSBs can cause genome instability, tumorigenesis or cell death. DNA end synapsis is the first and probably the most important step of the NHEJ pathway, aiming to bring two broken DNA ends close together and provide structural stability for end processing and ligation. This process is mediated through a group of NHEJ proteins forming higher-order complexes, to recognise and bridge two DNA ends. Spatial and temporal understanding of the structural mechanism of DNA-end synapsis has been largely advanced through recent structural and single-molecule studies of NHEJ proteins. This review focuses on core NHEJ proteins that mediate DNA end synapsis through their unique structures and interaction properties, as well as how they play roles as anchor and linker proteins during the process of 'bridge over troubled ends'.
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47
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Kim K, Min J, Kirby TW, Gabel SA, Pedersen LC, London RE. Ligand binding characteristics of the Ku80 von Willebrand domain. DNA Repair (Amst) 2020; 85:102739. [PMID: 31733588 PMCID: PMC7495496 DOI: 10.1016/j.dnarep.2019.102739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/18/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
The N-terminal von Willebrand domain of Ku80 supports interactions with a Ku binding motif (KBM) that has been identified in at least three other DNA repair proteins: the non-homologous end joining (NHEJ) scaffold APLF, the modulator of retrovirus infection, MRI, and the Werner syndrome protein (WRN). A second, more recently identified Ku binding motif present in XLF and several other proteins (KBMX) has also been reported to interact with this domain. The isolated Ku80 von Willebrand antigen domain (vWA) from Xenopus laevis has a sequence that is 60% identical with the human domain, is readily expressed and has been used to investigate these interactions. Structural characterization of the complexes formed with the KBM motifs in human APLF, MRI, and WRN identify a conserved binding site that is consistent with previously-reported mutational studies. In contrast with the KBM binding site, structural studies indicate that the KBMX site is occluded by a distorted helix. Fluorescence polarization and 19F NMR studies of a fluorinated XLF C-terminal peptide failed to indicate any interaction with the frog vWA. It was hypothesized that availability of this binding site is conditional, i.e., dependent on specific experimental conditions or other repair factors to make the site available for binding. Modulating the fraction of KBMX-accessible binding site mutationally demonstrated that the more open site is capable of binding the KBMXXLF motif peptide. It is suggested that the conditional nature of KBMX binding limits formation of non-productive complexes so that activation-dependent site availability can more optimally support advancing the synapsis process.
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Affiliation(s)
- Kyungmin Kim
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Jungki Min
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Thomas W Kirby
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Scott A Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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Pharmacological methods to transcriptionally modulate double-strand break DNA repair. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 354:187-213. [PMID: 32475473 DOI: 10.1016/bs.ircmb.2019.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is much interest in targeting DNA repair pathways for use in cancer therapy, as the effectiveness of many therapeutic agents relies on their ability to cause damage to DNA, and deficiencies in DSB repair pathways can make cells more sensitive to specific cancer therapies. For example, defects in the double-strand break (DSB) pathways, non-homologous end joining (NHEJ) and homology-directed repair (HDR), induce sensitivity to radiation therapy and poly(ADP)-ribose polymerase (PARP) inhibitors, respectively. However, traditional approaches to inhibit DNA repair through small molecule inhibitors have often been limited by toxicity and poor bioavailability. This review identifies several pharmacologic manipulations that modulate DSB repair by reducing expression of DNA repair factors. A number of pathways have been identified that modulate activity of NHEJ and HDR through this mechanism, including growth and hormonal receptor signaling pathways as well as epigenetic modifiers. We also discuss the effects of anti-angiogenic therapy on DSB repair. Preclinically, these pharmacological manipulations of DNA repair factor expression have been shown to increase sensitivity to specific cancer therapies, including ionizing radiation and PARP inhibitors. When applicable, relevant clinical trials are discussed and areas for future study are identified.
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Xia Y, Pfeifer CR, Zhu K, Irianto J, Liu D, Pannell K, Chen EJ, Dooling LJ, Tobin MP, Wang M, Ivanovska IL, Smith LR, Greenberg RA, Discher DE. Rescue of DNA damage after constricted migration reveals a mechano-regulated threshold for cell cycle. J Cell Biol 2019; 218:2545-2563. [PMID: 31239284 PMCID: PMC6683732 DOI: 10.1083/jcb.201811100] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/19/2019] [Accepted: 06/04/2019] [Indexed: 12/24/2022] Open
Abstract
Migration through 3D constrictions can cause nuclear rupture and mislocalization of nuclear proteins, but damage to DNA remains uncertain, as does any effect on cell cycle. Here, myosin II inhibition rescues rupture and partially rescues the DNA damage marker γH2AX, but an apparent block in cell cycle appears unaffected. Co-overexpression of multiple DNA repair factors or antioxidant inhibition of break formation also exert partial effects, independently of rupture. Combined treatments completely rescue cell cycle suppression by DNA damage, revealing a sigmoidal dependence of cell cycle on excess DNA damage. Migration through custom-etched pores yields the same damage threshold, with ∼4-µm pores causing intermediate levels of both damage and cell cycle suppression. High curvature imposed rapidly by pores or probes or else by small micronuclei consistently associates nuclear rupture with dilution of stiff lamin-B filaments, loss of repair factors, and entry from cytoplasm of chromatin-binding cGAS (cyclic GMP-AMP synthase). The cell cycle block caused by constricted migration is nonetheless reversible, with a potential for DNA misrepair and genome variation.
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Affiliation(s)
- Yuntao Xia
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Charlotte R. Pfeifer
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA,Department of Physics and Astronomy, Graduate Group, University of Pennsylvania, Philadelphia, PA
| | - Kuangzheng Zhu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Jerome Irianto
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Dazhen Liu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Kalia Pannell
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Emily J. Chen
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Lawrence J. Dooling
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Michael P. Tobin
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Mai Wang
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Irena L. Ivanovska
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Lucas R. Smith
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Roger A. Greenberg
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Dennis E. Discher
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA,Department of Physics and Astronomy, Graduate Group, University of Pennsylvania, Philadelphia, PA,Correspondence to D.E. Discher:
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