1
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Mamar H, Fajka-Boja R, Mórocz M, Jurado EP, Zentout S, Mihuţ A, Kopasz AG, Mérey M, Smith R, Sharma AB, Lakin ND, Bowman AJ, Haracska L, Huet S, Timinszky G. The loss of DNA polymerase epsilon accessory subunits POLE3-POLE4 leads to BRCA1-independent PARP inhibitor sensitivity. Nucleic Acids Res 2024:gkae439. [PMID: 38828775 DOI: 10.1093/nar/gkae439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024] Open
Abstract
The clinical success of PARP1/2 inhibitors (PARPi) prompts the expansion of their applicability beyond homologous recombination deficiency. Here, we demonstrate that the loss of the accessory subunits of DNA polymerase epsilon, POLE3 and POLE4, sensitizes cells to PARPi. We show that the sensitivity of POLE4 knockouts is not due to compromised response to DNA damage or homologous recombination deficiency. Instead, POLE4 loss affects replication speed leading to the accumulation of single-stranded DNA gaps behind replication forks upon PARPi treatment, due to impaired post-replicative repair. POLE4 knockouts elicit elevated replication stress signaling involving ATR and DNA-PK. We find POLE4 to act parallel to BRCA1 in inducing sensitivity to PARPi and counteracts acquired resistance associated with restoration of homologous recombination. Altogether, our findings establish POLE4 as a promising target to improve PARPi driven therapies and hamper acquired PARPi resistance.
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Affiliation(s)
- Hasan Mamar
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Biology, University of Szeged, 6720 Szeged, Hungary
| | - Roberta Fajka-Boja
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Department of Immunology, Albert Szent-Györgyi Medical School, Faculty of Science and Informatics, University of Szeged, 6720 Szeged, Hungary
| | - Mónika Mórocz
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
| | - Eva Pinto Jurado
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSITUMS 3480 Rennes, France
| | - Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSITUMS 3480 Rennes, France
| | - Alexandra Mihuţ
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Anna Georgina Kopasz
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Mihály Mérey
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSITUMS 3480 Rennes, France
| | | | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Andrew James Bowman
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, UK
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSITUMS 3480 Rennes, France
| | - Gyula Timinszky
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
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2
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Kanev PB, Varhoshkova S, Georgieva I, Lukarska M, Kirova D, Danovski G, Stoynov S, Aleksandrov R. A unified mechanism for PARP inhibitor-induced PARP1 chromatin retention at DNA damage sites in living cells. Cell Rep 2024; 43:114234. [PMID: 38758646 DOI: 10.1016/j.celrep.2024.114234] [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: 10/04/2023] [Revised: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) not only suppress PARP1 catalytic activity but also prolong its association to damaged chromatin. Here, through live-cell imaging, we quantify the alterations in PARP1 dynamics and activity elicited by seven PARPis over a wide range of concentrations to deliver a unified mechanism of PARPi-induced PARP1 chromatin retention. We find that gross PARP1 retention at DNA damage sites is jointly governed by catalytic inhibition and allosteric trapping, albeit in a strictly independent manner-catalytic inhibition causes multiple unproductive binding-dissociation cycles of PARP1, while allosteric trapping prolongs the lesion-bound state of PARP1 to greatly increase overall retention. Importantly, stronger PARP1 retention produces greater temporal shifts in downstream DNA repair events and superior cytotoxicity, highlighting PARP1 retention, a complex but precisely quantifiable characteristic of PARPis, as a valuable biomarker for PARPi efficacy. Our approach can be promptly repurposed for interrogating the properties of DNA-repair-targeting compounds beyond PARPis.
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Affiliation(s)
- Petar-Bogomil Kanev
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Sylvia Varhoshkova
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Irina Georgieva
- Transmembrane Signaling Laboratory, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Maria Lukarska
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dilyana Kirova
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Georgi Danovski
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Stoyno Stoynov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria.
| | - Radoslav Aleksandrov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria.
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3
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Szántó M, Yélamos J, Bai P. Specific and shared biological functions of PARP2 - is PARP2 really a lil' brother of PARP1? Expert Rev Mol Med 2024; 26:e13. [PMID: 38698556 PMCID: PMC11140550 DOI: 10.1017/erm.2024.14] [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: 11/28/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 05/05/2024]
Abstract
PARP2, that belongs to the family of ADP-ribosyl transferase enzymes (ART), is a discovery of the millennium, as it was identified in 1999. Although PARP2 was described initially as a DNA repair factor, it is now evident that PARP2 partakes in the regulation or execution of multiple biological processes as inflammation, carcinogenesis and cancer progression, metabolism or oxidative stress-related diseases. Hereby, we review the involvement of PARP2 in these processes with the aim of understanding which processes are specific for PARP2, but not for other members of the ART family. A better understanding of the specific functions of PARP2 in all of these biological processes is crucial for the development of new PARP-centred selective therapies.
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Affiliation(s)
- Magdolna Szántó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - José Yélamos
- Hospital del Mar Research Institute, Barcelona, Spain
| | - Péter Bai
- HUN-REN-UD Cell Biology and Signaling Research Group, Debrecen, 4032, Hungary
- MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, 4032, Hungary
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
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4
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McAvera RM, Morgan JJ, Herrero AB, Mills KI, Crawford LJ. TRIM33 loss in multiple myeloma is associated with genomic instability and sensitivity to PARP inhibitors. Sci Rep 2024; 14:8797. [PMID: 38627415 PMCID: PMC11021562 DOI: 10.1038/s41598-024-58828-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Deletions of chromosome 1p (del(1p)) are a recurrent genomic aberration associated with poor outcome in Multiple myeloma (MM.) TRIM33, an E3 ligase and transcriptional co-repressor, is located within a commonly deleted region at 1p13.2. TRIM33 is reported to play a role in the regulation of mitosis and PARP-dependent DNA damage response (DDR), both of which are important for maintenance of genome stability. Here, we demonstrate that MM patients with loss of TRIM33 exhibit increased chromosomal instability and poor outcome. Through knockdown studies, we show that TRIM33 loss induces a DDR defect, leading to accumulation of DNA double strand breaks (DSBs) and slower DNA repair kinetics, along with reduced efficiency of non-homologous end joining (NHEJ). Furthermore, TRIM33 loss results in dysregulated ubiquitination of ALC1, an important regulator of response to PARP inhibition. We show that TRIM33 knockdown sensitizes MM cells to the PARP inhibitor Olaparib, and this is synergistic with the standard of care therapy bortezomib, even in co-culture with bone marrow stromal cells (BMSCs). These findings suggest that TRIM33 loss contributes to the pathogenesis of high-risk MM and that this may be therapeutically exploited through the use of PARP inhibitors.
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Affiliation(s)
- Roisin M McAvera
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Jonathan J Morgan
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Ana B Herrero
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Ken I Mills
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Lisa J Crawford
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7BL, UK.
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5
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Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S. Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1. Nat Commun 2024; 15:1000. [PMID: 38307862 PMCID: PMC10837151 DOI: 10.1038/s41467-024-45237-8] [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: 03/09/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged as a cancer drug target, but how it is recruited to ADP-ribosylated nucleosomes to affect their positioning near DNA breaks is unknown. Here we find that PARP1/HPF1 preferentially initiates ADP-ribosylation on the histone H2B tail closest to the DNA break. To dissect the consequences of such asymmetry, we generate nucleosomes with a defined ADP-ribosylated H2B tail on one side only. The cryo-electron microscopy structure of ALC1 bound to such an asymmetric nucleosome indicates preferential engagement on one side. Using single-molecule FRET, we demonstrate that this asymmetric recruitment gives rise to directed sliding away from the DNA linker closest to the ADP-ribosylation site. Our data suggest a mechanism by which ALC1 slides nucleosomes away from a DNA break to render it more accessible to repair factors.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Guillaume Gaullier
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
- Department of Chemistry - Ångström, Uppsala University, 75120, Uppsala, Sweden
| | - Jugal Mohapatra
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Klaus Brackmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Mikhail Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Glen Liszczak
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden.
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6
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Longoria O, Beije N, de Bono JS. PARP inhibitors for prostate cancer. Semin Oncol 2024; 51:25-35. [PMID: 37783649 DOI: 10.1053/j.seminoncol.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors have transformed the treatment landscape for patients with metastatic castration-resistant prostate cancer (mCRPC) and alterations in DNA damage response genes. This has also led to widespread use of genomic testing in all patients with mCRPC. The current review will give an overview of (1) the current understanding of the interplay between DNA damage response and PARP enzymes; (2) the clinical landscape of PARP inhibitors, including the combination of PARP inhibitors with other agents such as androgen-receptor signaling agents; (3) biomarkers related to PARP inhibitor response and resistance; and (4) considerations for interpreting genomic testing results and treating patients with PARP inhibitors.
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Affiliation(s)
- Ossian Longoria
- The Institute of Cancer Research, London, United Kingdom; The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Nick Beije
- The Institute of Cancer Research, London, United Kingdom; The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Johann S de Bono
- The Institute of Cancer Research, London, United Kingdom; The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom.
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7
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Shen W, Lyu Q, Yi R, Sun Y, Zhang W, Wei T, Zhang Y, Shi J, Zhang J. HMGB1 promotes chemoresistance in small cell lung cancer by inducing PARP1-related nucleophagy. J Adv Res 2023:S2090-1232(23)00407-1. [PMID: 38159843 DOI: 10.1016/j.jare.2023.12.020] [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: 08/21/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
INTRODUCTION Small cell lung cancer (SCLC) is prone to chemoresistance, which is closely related to genome homeostasis-related processes, such as DNA damage and repair. Nucleophagy is the elimination of specific nuclear substances by cells themselves and is responsible for maintaining genome and chromosome stability. However, the roles of nucleophagy in tumour chemoresistance have not been investigated. OBJECTIVES The aim of this work was to elucidate the mechanism of chemoresistance in SCLC and reverse this chemoresistance. METHODS RNA-seq data from SCLC cohorts, chemosensitive SCLC cells and the corresponding chemoresistant cells were used to discover genes associated with chemoresistance and patient prognosis. In vitro and in vivo experiments were performed to verify the effect of high-mobility group box 1 (HMGB1) knockdown or overexpression on the chemotherapeutic response in SCLC. The regulatory effect of HMGB1 on nucleophagy was then investigated by coimmunoprecipitation (co-IP) and mass spectrometry (MS), and the underlying mechanism was explored using pharmacological inhibitors and mutant proteins. RESULTS HMGB1 is a factor indicating poor prognosis and promotes chemoresistance in SCLC. Mechanistically, HMGB1 significantly increases PARP1-LC3 binding to promote nucleophagy via PARP1 PARylation, which leads to PARP1 turnover from DNA lesions and chemoresistance. Furthermore, chemoresistance in SCLC can be attenuated by blockade of the PARP1-LC3 interaction or PARP1 inhibitor (PARPi) treatment. CONCLUSIONS HMGB1 can induce PARP1 self-modification, which promotes the interaction of PARP1 with LC3 to promote nucleophagy and thus chemoresistance in SCLC. HMGB1 could be a predictive biomarker for the PARPi response in patients with SCLC. Combining chemotherapy with PARPi treatment is an effective therapeutic strategy for overcoming SCLC chemoresistance.
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Affiliation(s)
- Weitao Shen
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Qiong Lyu
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Ruibin Yi
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yueqin Sun
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Wei Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Ting Wei
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yueming Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jian Shi
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong, People's Republic of China.
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China.
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8
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Rouleau-Turcotte É, Pascal JM. ADP-ribose contributions to genome stability and PARP enzyme trapping on sites of DNA damage; paradigm shifts for a coming-of-age modification. J Biol Chem 2023; 299:105397. [PMID: 37898399 PMCID: PMC10722394 DOI: 10.1016/j.jbc.2023.105397] [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: 08/04/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
ADP-ribose is a versatile modification that plays a critical role in diverse cellular processes. The addition of this modification is catalyzed by ADP-ribosyltransferases, among which notable poly(ADP-ribose) polymerase (PARP) enzymes are intimately involved in the maintenance of genome integrity. The role of ADP-ribose modifications during DNA damage repair is of significant interest for the proper development of PARP inhibitors targeted toward the treatment of diseases caused by genomic instability. More specifically, inhibitors promoting PARP persistence on DNA lesions, termed PARP "trapping," is considered a desirable characteristic. In this review, we discuss key classes of proteins involved in ADP-ribose signaling (writers, readers, and erasers) with a focus on those involved in the maintenance of genome integrity. An overview of factors that modulate PARP1 and PARP2 persistence at sites of DNA lesions is also discussed. Finally, we clarify aspects of the PARP trapping model in light of recent studies that characterize the kinetics of PARP1 and PARP2 recruitment at sites of lesions. These findings suggest that PARP trapping could be considered as the continuous recruitment of PARP molecules to sites of lesions, rather than the physical stalling of molecules. Recent studies and novel research tools have elevated the level of understanding of ADP-ribosylation, marking a coming-of-age for this interesting modification.
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Affiliation(s)
- Élise Rouleau-Turcotte
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada.
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9
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Bilkis R, Lake RJ, Cooper KL, Tomkinson A, Fan HY. The CSB chromatin remodeler regulates PARP1- and PARP2-mediated single-strand break repair at actively transcribed DNA regions. Nucleic Acids Res 2023; 51:7342-7356. [PMID: 37326017 PMCID: PMC10415129 DOI: 10.1093/nar/gkad515] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/03/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Efficient repair of oxidized DNA is critical for genome-integrity maintenance. Cockayne syndrome protein B (CSB) is an ATP-dependent chromatin remodeler that collaborates with Poly(ADP-ribose) polymerase I (PARP1) in the repair of oxidative DNA lesions. How these proteins integrate during DNA repair remains largely unknown. Here, using chromatin co-fractionation studies, we demonstrate that PARP1 and PARP2 promote recruitment of CSB to oxidatively-damaged DNA. CSB, in turn, contributes to the recruitment of XRCC1, and histone PARylation factor 1 (HPF1), and promotes histone PARylation. Using alkaline comet assays to monitor DNA repair, we found that CSB regulates single-strand break repair (SSBR) mediated by PARP1 and PARP2. Strikingly, CSB's function in SSBR is largely bypassed when transcription is inhibited, suggesting CSB-mediated SSBR occurs primarily at actively transcribed DNA regions. While PARP1 repairs SSBs at sites regardless of the transcription status, we found that PARP2 predominantly functions in actively transcribed DNA regions. Therefore, our study raises the hypothesis that SSBR is executed by different mechanisms based on the transcription status.
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Affiliation(s)
- Rabeya Bilkis
- Program in Cell and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Science Center, Albuquerque, NM 87131, USA
- Biomedical Sciences Graduate Program, University of New Mexico Health Science Center, Albuquerque, NM 87131, USA
| | - Robert J Lake
- Program in Cell and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Science Center, Albuquerque, NM 87131, USA
| | - Karen L Cooper
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Alan Tomkinson
- Program in Cell and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Science Center, Albuquerque, NM 87131, USA
| | - Hua-Ying Fan
- Program in Cell and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico Health Science Center, Albuquerque, NM 87131, USA
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10
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Awwad SW, Serrano-Benitez A, Thomas JC, Gupta V, Jackson SP. Revolutionizing DNA repair research and cancer therapy with CRISPR-Cas screens. Nat Rev Mol Cell Biol 2023; 24:477-494. [PMID: 36781955 DOI: 10.1038/s41580-022-00571-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/15/2023]
Abstract
All organisms possess molecular mechanisms that govern DNA repair and associated DNA damage response (DDR) processes. Owing to their relevance to human disease, most notably cancer, these mechanisms have been studied extensively, yet new DNA repair and/or DDR factors and functional interactions between them are still being uncovered. The emergence of CRISPR technologies and CRISPR-based genetic screens has enabled genome-scale analyses of gene-gene and gene-drug interactions, thereby providing new insights into cellular processes in distinct DDR-deficiency genetic backgrounds and conditions. In this Review, we discuss the mechanistic basis of CRISPR-Cas genetic screening approaches and describe how they have contributed to our understanding of DNA repair and DDR pathways. We discuss how DNA repair pathways are regulated, and identify and characterize crosstalk between them. We also highlight the impacts of CRISPR-based studies in identifying novel strategies for cancer therapy, and in understanding, overcoming and even exploiting cancer-drug resistance, for example in the contexts of PARP inhibition, homologous recombination deficiencies and/or replication stress. Lastly, we present the DDR CRISPR screen (DDRcs) portal , in which we have collected and reanalysed data from CRISPR screen studies and provide a tool for systematically exploring them.
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Affiliation(s)
- Samah W Awwad
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - John C Thomas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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11
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Krishnan A, Spegg V, Dettwiler S, Schraml P, Moch H, Dedes K, Varga Z, Altmeyer M. Analysis of the PARP1, ADP-Ribosylation, and TRIP12 Triad With Markers of Patient Outcome in Human Breast Cancer. Mod Pathol 2023; 36:100167. [PMID: 36990278 DOI: 10.1016/j.modpat.2023.100167] [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: 09/14/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
PARP inhibitors (PARPi) are increasingly used in breast cancer therapy, including high-grade triple-negative breast cancer (TNBC) treatment. Varying treatment responses and PARPi resistance with relapse currently pose limitations to the efficacy of PARPi therapy. The pathobiological reasons why individual patients respond differently to PARPi are poorly understood. In this study, we analyzed expression of PARP1, the main target of PARPi, in normal breast tissue, breast cancer, and its precursor lesions using human breast cancer tissue microarrays covering a total of 824 patients, including more than 100 TNBC cases. In parallel, we analyzed nuclear adenosine diphosphate (ADP)-ribosylation as a marker of PARP1 activity and TRIP12, an antagonist of PARPi-induced PARP1 trapping. Although we found PARP1 expression to be generally increased in invasive breast cancer, PARP1 protein levels and nuclear ADP-ribosylation were lower in higher tumor grade and TNBC samples than non-TNBCs. Cancers with low levels of PARP1 and low levels of nuclear ADP-ribosylation were associated with significantly reduced overall survival. This effect was even more pronounced in cases with high levels of TRIP12. These results indicate that PARP1-dependent DNA repair capacity may be compromised in aggressive breast cancers, potentially fueling enhanced accumulation of mutations. Moreover, the results revealed a subset of breast cancers with low PARP1, low nuclear ADP-ribosylation, and high TRIP12 levels, which may compromise their response to PARPi, suggesting a combination of markers for PARP1 abundance, enzymatic activity, and trapping capabilities might aid patient stratification for PARPi therapy.
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Affiliation(s)
- Aswini Krishnan
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Susanne Dettwiler
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Konstantin Dedes
- Department of Gynecology, University Hospital of Zurich, Zurich, Switzerland
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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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: 0] [Impact Index Per Article: 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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Dabin J, Mori M, Polo SE. The DNA damage response in the chromatin context: A coordinated process. Curr Opin Cell Biol 2023; 82:102176. [PMID: 37301060 DOI: 10.1016/j.ceb.2023.102176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023]
Abstract
In the cell nucleus, DNA damage signaling and repair machineries operate on a chromatin substrate, the integrity of which is critical for cell function and viability. Here, we review recent advances in deciphering the tight coordination between chromatin maintenance and the DNA damage response (DDR). We discuss how the DDR impacts chromatin marks, organization and mobility, and, in turn, how chromatin alterations actively contribute to the DDR, providing additional levels of regulation. We present our current knowledge of the molecular bases of these critical processes in physiological and pathological conditions, and also highlight open questions that emerge in this expanding field.
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Affiliation(s)
- Juliette Dabin
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Margherita Mori
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, 35 rue Hélène Brion, 75013 Paris, France.
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14
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Fleury H, MacEachern MK, Stiefel CM, Anand R, Sempeck C, Nebenfuehr B, Maurer-Alcalá K, Ball K, Proctor B, Belan O, Taylor E, Ortega R, Dodd B, Weatherly L, Dansoko D, Leung JW, Boulton SJ, Arnoult N. The APE2 nuclease is essential for DNA double-strand break repair by microhomology-mediated end joining. Mol Cell 2023; 83:1429-1445.e8. [PMID: 37044098 PMCID: PMC10164096 DOI: 10.1016/j.molcel.2023.03.017] [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: 07/21/2022] [Revised: 01/18/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023]
Abstract
Microhomology-mediated end joining (MMEJ) is an intrinsically mutagenic pathway of DNA double-strand break (DSB) repair essential for proliferation of homologous recombination (HR)-deficient tumors. Although targeting MMEJ has emerged as a powerful strategy to eliminate HR-deficient (HRD) cancers, this is limited by an incomplete understanding of the mechanism and factors required for MMEJ repair. Here, we identify the APE2 nuclease as an MMEJ effector. We show that loss of APE2 inhibits MMEJ at deprotected telomeres and at intra-chromosomal DSBs and is epistatic with Pol Theta for MMEJ activity. Mechanistically, we demonstrate that APE2 possesses intrinsic flap-cleaving activity, that its MMEJ function in cells depends on its nuclease activity, and further identify an uncharacterized domain required for its recruitment to DSBs. We conclude that this previously unappreciated role of APE2 in MMEJ contributes to the addiction of HRD cells to APE2, which could be exploited in the treatment of cancer.
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Affiliation(s)
- Hubert Fleury
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Myles K MacEachern
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Clara M Stiefel
- Department of Radiation Oncology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Roopesh Anand
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Colin Sempeck
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Benjamin Nebenfuehr
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Kelper Maurer-Alcalá
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Kerri Ball
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Bruce Proctor
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Ondrej Belan
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Erin Taylor
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Raquel Ortega
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Benjamin Dodd
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Laila Weatherly
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Djelika Dansoko
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Justin W Leung
- Department of Radiation Oncology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK; Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Nausica Arnoult
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, USA.
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15
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Groelly FJ, Fawkes M, Dagg RA, Blackford AN, Tarsounas M. Targeting DNA damage response pathways in cancer. Nat Rev Cancer 2023; 23:78-94. [PMID: 36471053 DOI: 10.1038/s41568-022-00535-5] [Citation(s) in RCA: 163] [Impact Index Per Article: 163.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Cells have evolved a complex network of biochemical pathways, collectively known as the DNA damage response (DDR), to prevent detrimental mutations from being passed on to their progeny. The DDR coordinates DNA repair with cell-cycle checkpoint activation and other global cellular responses. Genes encoding DDR factors are frequently mutated in cancer, causing genomic instability, an intrinsic feature of many tumours that underlies their ability to grow, metastasize and respond to treatments that inflict DNA damage (such as radiotherapy). One instance where we have greater insight into how genetic DDR abrogation impacts on therapy responses is in tumours with mutated BRCA1 or BRCA2. Due to compromised homologous recombination DNA repair, these tumours rely on alternative repair mechanisms and are susceptible to chemical inhibitors of poly(ADP-ribose) polymerase (PARP), which specifically kill homologous recombination-deficient cancer cells, and have become a paradigm for targeted cancer therapy. It is now clear that many other synthetic-lethal relationships exist between DDR genes. Crucially, some of these interactions could be exploited in the clinic to target tumours that become resistant to PARP inhibition. In this Review, we discuss state-of-the-art strategies for DDR inactivation using small-molecule inhibitors and highlight those compounds currently being evaluated in the clinic.
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Affiliation(s)
- Florian J Groelly
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Rebecca A Dagg
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.
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16
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Mahadevan J, Jha A, Rudolph J, Bowerman S, Narducci D, Hansen AS, Luger K. Dynamics of endogenous PARP1 and PARP2 during DNA damage revealed by live-cell single-molecule imaging. iScience 2022; 26:105779. [PMID: 36594010 PMCID: PMC9804145 DOI: 10.1016/j.isci.2022.105779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/16/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
PARP1 contributes to genome architecture and DNA damage repair through its dynamic association with chromatin. PARP1 and PARP2 (PARP1/2) recognize damaged DNA and recruit the DNA repair machinery. Using single-molecule microscopy in live cells, we monitored the movement of PARP1/2 on undamaged and damaged chromatin. We identify two classes of freely diffusing PARP1/2 and two classes of bound PARP1/2. The majority (>60%) of PARP1/2 diffuse freely in both undamaged and damaged nuclei and in the presence of inhibitors of PARP1/2 used for cancer therapy (PARPi). Laser-induced DNA damage results in a small fraction of slowly diffusing PARP1 and PARP2 to become transiently bound. Treatment of cells with PARPi in the presence of DNA damage causes subtle changes in the dynamics of bound PARP1/2, but not the high levels of PARP1/2 trapping seen previously. Our results imply that next-generation PARPi could specifically target the small fraction of DNA-bound PARP1/2.
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Affiliation(s)
- Jyothi Mahadevan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Asmita Jha
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Samuel Bowerman
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Domenic Narducci
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA,Corresponding author
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17
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Jackson LM, Moldovan GL. Mechanisms of PARP1 inhibitor resistance and their implications for cancer treatment. NAR Cancer 2022; 4:zcac042. [PMID: 36568963 PMCID: PMC9773381 DOI: 10.1093/narcan/zcac042] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The discovery of synthetic lethality as a result of the combined loss of PARP1 and BRCA has revolutionized the treatment of DNA repair-deficient cancers. With the development of PARP inhibitors, patients displaying germline or somatic mutations in BRCA1 or BRCA2 were presented with a novel therapeutic strategy. However, a large subset of patients do not respond to PARP inhibitors. Furthermore, many of those who do respond eventually acquire resistance. As such, combating de novo and acquired resistance to PARP inhibitors remains an obstacle in achieving durable responses in patients. In this review, we touch on some of the key mechanisms of PARP inhibitor resistance, including restoration of homologous recombination, replication fork stabilization and suppression of single-stranded DNA gap accumulation, as well as address novel approaches for overcoming PARP inhibitor resistance.
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Affiliation(s)
- Lindsey M Jackson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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18
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Alemasova EE, Lavrik OI. A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates. Nucleic Acids Res 2022; 50:10817-10838. [PMID: 36243979 DOI: 10.1093/nar/gkac866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/14/2022] [Accepted: 10/09/2022] [Indexed: 11/13/2022] Open
Abstract
Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids-DNA, RNA and poly(ADP-ribose) (PAR) play special roles in the process of condensate organization. These polymeric scaffolds provide multiple specific and nonspecific interactions during nucleation and 'development' of macromolecular assemblages. In this review, we focus on condensates formed with PAR. We discuss to what extent the literature supports the phase separation origin of these structures. Special attention is paid to similarities and differences between PAR and RNA in the process of dynamic restructuring of condensates during their functioning.
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Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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19
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Thada V, Greenberg RA. Unpaved roads: How the DNA damage response navigates endogenous genotoxins. DNA Repair (Amst) 2022; 118:103383. [PMID: 35939975 PMCID: PMC9703833 DOI: 10.1016/j.dnarep.2022.103383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 02/03/2023]
Abstract
Accurate DNA repair is essential for cellular and organismal homeostasis, and DNA repair defects result in genetic diseases and cancer predisposition. Several environmental factors, such as ultraviolet light, damage DNA, but many other molecules with DNA damaging potential are byproducts of normal cellular processes. In this review, we highlight some of the prominent sources of endogenous DNA damage as well as their mechanisms of repair, with a special focus on repair by the homologous recombination and Fanconi anemia pathways. We also discuss how modulating DNA damage caused by endogenous factors may augment current approaches used to treat BRCA-deficient cancers. Finally, we describe how synthetic lethal interactions may be exploited to exacerbate DNA repair deficiencies and cause selective toxicity in additional types of cancers.
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20
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Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
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Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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21
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Chu YY, Chen MK, Wei Y, Lee HH, Xia W, Wang YN, Yam C, Hsu JL, Wang HL, Chang WC, Yamaguchi H, Jiang Z, Liu C, Li CF, Nie L, Chan LC, Gao Y, Wang SC, Liu J, Westin SN, Lee S, Sood AK, Yang L, Hortobagyi GN, Yu D, Hung MC. Targeting the ALK-CDK9-Tyr19 kinase cascade sensitizes ovarian and breast tumors to PARP inhibition via destabilization of the P-TEFb complex. NATURE CANCER 2022; 3:1211-1227. [PMID: 36253486 PMCID: PMC9586872 DOI: 10.1038/s43018-022-00438-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/24/2022] [Indexed: 12/28/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors have demonstrated promising clinical activity in multiple cancers. However, resistance to PARP inhibitors remains a substantial clinical challenge. In the present study, we report that anaplastic lymphoma kinase (ALK) directly phosphorylates CDK9 at tyrosine-19 to promote homologous recombination (HR) repair and PARP inhibitor resistance. Phospho-CDK9-Tyr19 increases its kinase activity and nuclear localization to stabilize positive transcriptional elongation factor b and activate polymerase II-dependent transcription of HR-repair genes. Conversely, ALK inhibition increases ubiquitination and degradation of CDK9 by Skp2, an E3 ligase. Notably, combination of US Food and Drug Administration-approved ALK and PARP inhibitors markedly reduce tumor growth and improve survival of mice in PARP inhibitor-/platinum-resistant tumor xenograft models. Using human tumor biospecimens, we further demonstrate that phosphorylated ALK (p-ALK) expression is associated with resistance to PARP inhibitors and positively correlated with p-Tyr19-CDK9 expression. Together, our findings support a biomarker-driven, combinatorial treatment strategy involving ALK and PARP inhibitors to induce synthetic lethality in PARP inhibitor-/platinum-resistant tumors with high p-ALK-p-Tyr19-CDK9 expression.
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Affiliation(s)
- Yu-Yi Chu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mei-Kuang Chen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- UT Health Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yongkun Wei
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heng-Huan Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiya Xia
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Ying-Nai Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clinton Yam
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- UT Health Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer L Hsu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hung-Ling Wang
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Wei-Chao Chang
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Hirohito Yamaguchi
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Zhou Jiang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chunxiao Liu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ching-Fei Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lei Nie
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li-Chuan Chan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuan Gao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Jinsong Liu
- Department of Anatomic Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shannon N Westin
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanghoon Lee
- Department of Systems Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel N Hortobagyi
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dihua Yu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, Taiwan.
- Department of Biotechnology, Asia University, Taichung, Taiwan.
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22
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Tufan AB, Lazarow K, Kolesnichenko M, Sporbert A, von Kries JP, Scheidereit C. TSG101 associates with PARP1 and is essential for PARylation and DNA damage-induced NF-κB activation. EMBO J 2022; 41:e110372. [PMID: 36124865 DOI: 10.15252/embj.2021110372] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
In a genome-wide screening for components of the dsDNA-break-induced IKK-NF-κB pathway, we identified scores of regulators, including tumor susceptibility gene TSG101. TSG101 is essential for DNA damage-induced formation of cellular poly(ADP-ribose) (PAR). TSG101 binds to PARP1 and is required for PARP1 activation. This function of TSG101 is independent of its role in the ESCRT-I endosomal sorting complex. In the absence of TSG101, the PAR-dependent formation of a nuclear PARP1-IKKγ signalosome, which triggers IKK activation, is impaired. According to its requirement for PARP1 and NF-κB activation, TSG101-deficient cells are defective in DNA repair and apoptosis protection. Loss of TSG101 results in PARP1 trapping at damage sites and mimics the effect of pharmacological PARP inhibition. We also show that the loss of TSG101 in connection with inactivated tumor suppressors BRCA1/2 in breast cancer cells is lethal. Our results imply TSG101 as a therapeutic target to achieve synthetic lethality in cancer treatment.
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Affiliation(s)
- Ahmet Buğra Tufan
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Katina Lazarow
- Leibniz-Forschungsinstitut for Molecular Pharmacology (FMP), Berlin, Germany
| | - Marina Kolesnichenko
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anje Sporbert
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Advanced Light Microscopy Technology Platform, Berlin, Germany
| | | | - Claus Scheidereit
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
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23
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Bound NT, Vandenberg CJ, Kartikasari AER, Plebanski M, Scott CL. Improving PARP inhibitor efficacy in high-grade serous ovarian carcinoma: A focus on the immune system. Front Genet 2022; 13:886170. [PMID: 36159999 PMCID: PMC9505691 DOI: 10.3389/fgene.2022.886170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is a genomically unstable malignancy responsible for over 70% of all deaths due to ovarian cancer. With roughly 50% of all HGSOC harboring defects in the homologous recombination (HR) DNA repair pathway (e.g., BRCA1/2 mutations), the introduction of poly ADP-ribose polymerase inhibitors (PARPi) has dramatically improved outcomes for women with HR defective HGSOC. By blocking the repair of single-stranded DNA damage in cancer cells already lacking high-fidelity HR pathways, PARPi causes the accumulation of double-stranded DNA breaks, leading to cell death. Thus, this synthetic lethality results in PARPi selectively targeting cancer cells, resulting in impressive efficacy. Despite this, resistance to PARPi commonly develops through diverse mechanisms, such as the acquisition of secondary BRCA1/2 mutations. Perhaps less well documented is that PARPi can impact both the tumour microenvironment and the immune response, through upregulation of the stimulator of interferon genes (STING) pathway, upregulation of immune checkpoints such as PD-L1, and by stimulating the production of pro-inflammatory cytokines. Whilst targeted immunotherapies have not yet found their place in the clinic for HGSOC, the evidence above, as well as ongoing studies exploring the synergistic effects of PARPi with immune agents, including immune checkpoint inhibitors, suggests potential for targeting the immune response in HGSOC. Additionally, combining PARPi with epigenetic-modulating drugs may improve PARPi efficacy, by inducing a BRCA-defective phenotype to sensitise resistant cancer cells to PARPi. Finally, invigorating an immune response during PARPi therapy may engage anti-cancer immune responses that potentiate efficacy and mitigate the development of PARPi resistance. Here, we will review the emerging PARPi literature with a focus on PARPi effects on the immune response in HGSOC, as well as the potential of epigenetic combination therapies. We highlight the potential of transforming HGSOC from a lethal to a chronic disease and increasing the likelihood of cure.
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Affiliation(s)
- Nirashaa T. Bound
- Cancer Biology and Stem Cells, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Cancer Ageing and Vaccines (CAVA), Translational Immunology & Nanotechnology Research Program, School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Cassandra J. Vandenberg
- Cancer Biology and Stem Cells, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Apriliana E. R. Kartikasari
- Cancer Ageing and Vaccines (CAVA), Translational Immunology & Nanotechnology Research Program, School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Magdalena Plebanski
- Cancer Ageing and Vaccines (CAVA), Translational Immunology & Nanotechnology Research Program, School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Clare L. Scott
- Cancer Biology and Stem Cells, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
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24
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Blessing C, Apelt K, van den Heuvel D, Gonzalez-Leal C, Rother MB, van der Woude M, González-Prieto R, Yifrach A, Parnas A, Shah RG, Kuo TT, Boer DEC, Cai J, Kragten A, Kim HS, Schärer OD, Vertegaal ACO, Shah GM, Adar S, Lans H, van Attikum H, Ladurner AG, Luijsterburg MS. XPC-PARP complexes engage the chromatin remodeler ALC1 to catalyze global genome DNA damage repair. Nat Commun 2022; 13:4762. [PMID: 35963869 PMCID: PMC9376112 DOI: 10.1038/s41467-022-31820-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/29/2022] [Indexed: 11/24/2022] Open
Abstract
Cells employ global genome nucleotide excision repair (GGR) to eliminate a broad spectrum of DNA lesions, including those induced by UV light. The lesion-recognition factor XPC initiates repair of helix-destabilizing DNA lesions, but binds poorly to lesions such as CPDs that do not destabilize DNA. How difficult-to-repair lesions are detected in chromatin is unknown. Here, we identify the poly-(ADP-ribose) polymerases PARP1 and PARP2 as constitutive interactors of XPC. Their interaction results in the XPC-stimulated synthesis of poly-(ADP-ribose) (PAR) by PARP1 at UV lesions, which in turn enables the recruitment and activation of the PAR-regulated chromatin remodeler ALC1. PARP2, on the other hand, modulates the retention of ALC1 at DNA damage sites. Notably, ALC1 mediates chromatin expansion at UV-induced DNA lesions, leading to the timely clearing of CPD lesions. Thus, we reveal how chromatin containing difficult-to-repair DNA lesions is primed for repair, providing insight into mechanisms of chromatin plasticity during GGR. Cells employ global genome nucleotide excision repair to repair a broad spectrum of genomic DNA lesions. Here, the authors reveal how chromatin is primed for repair, providing insight into mechanisms of chromatin plasticity during DNA repair.
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Affiliation(s)
- Charlotte Blessing
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Claudia Gonzalez-Leal
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany
| | - Magdalena B Rother
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Genome Proteomics Laboratory, Andalusian Center For Molecular Biology and Regenerative Medicine (CABIMER), University of Seville, Seville, Spain.,Department of Cell Biology, University of Seville, Seville, Spain
| | - Adi Yifrach
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avital Parnas
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rashmi G Shah
- Laboratory for Skin Cancer Research, CHU-Q: Laval University Hospital Research Centre of Quebec (CHUL site), Quebec City, Canada
| | - Tia Tyrsett Kuo
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Jin Cai
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Girish M Shah
- Laboratory for Skin Cancer Research, CHU-Q: Laval University Hospital Research Centre of Quebec (CHUL site), Quebec City, Canada
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Andreas G Ladurner
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany. .,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany. .,Eisbach Bio GmbH, Planegg-Martinsried, Germany.
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
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25
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Revisiting PARP2 and PARP1 trapping through quantitative live-cell imaging. Biochem Soc Trans 2022; 50:1169-1177. [PMID: 35959996 DOI: 10.1042/bst20220366] [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: 06/21/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) and 2 (PARP2) are two DNA damage-induced poly (ADP-ribose) (PAR) polymerases in cells and are the targets of PARP inhibitors used for cancer therapy. Strand breaks recruit and activate PARP1 and 2, which rapidly generate PAR from NAD+. PAR promotes the recruitment of other repair factors, relaxes chromatin, and has a role in DNA repair, transcription regulation, and RNA biology. Four PARP1/2 dual inhibitors are currently used to treat BRCA-deficient breast, ovarian, prostate, and pancreatic cancers. In addition to blocking the enzymatic activity of PARP1 and 2, clinical PARP inhibitors extend the appearance of PARP1 and PARP2 on chromatin after damage, termed trapping. Loss of PARP1 confers resistance to PARP inhibitors, suggesting an essential role of trapping in cancer therapy. Yet, whether the persistent PARP1 and 2 foci at the DNA damage sites are caused by the retention of the same molecules or by the continual exchange of different molecules remains unknown. Here, we discuss recent results from quantitative live-cell imaging studies focusing on PARP1 and PARP2's distinct DNA substrate specificities and modes of recruitment and trapping with implications for cancer therapy and on-target toxicities of PARP inhibitors.
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26
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Ding X, Zhu Z, Lapek J, McMillan EA, Zhang A, Chung CY, Dubbury S, Lapira J, Firdaus S, Kang X, Gao J, Oyer J, Chionis J, Rollins RA, Li L, Niessen S, Bagrodia S, Zhang L, VanArsdale T. PARP1-SNAI2 transcription axis drives resistance to PARP inhibitor, Talazoparib. Sci Rep 2022; 12:12501. [PMID: 35864202 PMCID: PMC9304387 DOI: 10.1038/s41598-022-16623-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
The synthetic lethal association between BRCA deficiency and poly (ADP-ribose) polymerase (PARP) inhibition supports PARP inhibitor (PARPi) clinical efficacy in BRCA-mutated tumors. PARPis also demonstrate activity in non-BRCA mutated tumors presumably through induction of PARP1-DNA trapping. Despite pronounced clinical response, therapeutic resistance to PARPis inevitably develops. An abundance of knowledge has been built around resistance mechanisms in BRCA-mutated tumors, however, parallel understanding in non-BRCA mutated settings remains insufficient. In this study, we find a strong correlation between the epithelial-mesenchymal transition (EMT) signature and resistance to a clinical PARPi, Talazoparib, in non-BRCA mutated tumor cells. Genetic profiling demonstrates that SNAI2, a master EMT transcription factor, is transcriptionally induced by Talazoparib treatment or PARP1 depletion and this induction is partially responsible for the emerging resistance. Mechanistically, we find that the PARP1 protein directly binds to SNAI2 gene promoter and suppresses its transcription. Talazoparib treatment or PARP1 depletion lifts PARP1-mediated suppression and increases chromatin accessibility around SNAI2 promoters, thus driving SNAI2 transcription and drug resistance. We also find that depletion of the chromatin remodeler CHD1L suppresses SNAI2 expression and reverts acquired resistance to Talazoparib. The PARP1/CHD1L/SNAI2 transcription axis might be therapeutically targeted to re-sensitize Talazoparib in non-BRCA mutated tumors.
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Affiliation(s)
- Xia Ding
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.
| | - Zhou Zhu
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,AstraZeneca, Inc., Gaithersburg, MD, 20878, USA
| | - John Lapek
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Belharra Therapeutics, Inc., San Diego, CA, 92121, USA
| | - Elizabeth A McMillan
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Odyssey Therapeutics., San Diego, CA, 92121, USA
| | - Alexander Zhang
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Chi-Yeh Chung
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Sara Dubbury
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Bristol Myers Squibb., San Diego, CA, 92121, USA
| | - Jennifer Lapira
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Sarah Firdaus
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Xiaolin Kang
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Jingjin Gao
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Turning Point Therapeutics., San Diego, CA, 92121, USA
| | - Jon Oyer
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - John Chionis
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Genesis Therapeutics., San Diego, CA, 92121, USA
| | | | - Lianjie Li
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Sherry Niessen
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Belharra Therapeutics, Inc., San Diego, CA, 92121, USA
| | - Shubha Bagrodia
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Lianglin Zhang
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.
| | - Todd VanArsdale
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.
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27
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Longarini EJ, Matic I. The fast-growing business of Serine ADP-ribosylation. DNA Repair (Amst) 2022; 118:103382. [DOI: 10.1016/j.dnarep.2022.103382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022]
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28
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Onji H, Murai J. Reconsidering the mechanisms of action of PARP inhibitors based on clinical outcomes. Cancer Sci 2022; 113:2943-2951. [PMID: 35766436 PMCID: PMC9459283 DOI: 10.1111/cas.15477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/19/2022] [Accepted: 06/25/2022] [Indexed: 11/30/2022] Open
Abstract
PARP inhibitors (PARPis) were initially developed as DNA repair inhibitors that inhibit the catalytic activity of PARP1 and PARP2 and are expected to induce synthetic lethality in BRCA‐ or homologous recombination (HR)‐deficient tumors. However, the clinical indications for PARPis are not necessarily limited to BRCA mutations or HR deficiency; BRCA wild‐type and HR‐proficient cancers can also derive some benefit from PARPis. These facts are interpretable by an additional primary antitumor mechanism of PARPis named PARP trapping, resulting from the stabilization of PARP‐DNA complexes. Favorable response to platinum derivatives (cisplatin and carboplatin) in preceding treatment is used as a clinical biomarker for some PARPis, implying that sensitivity factors for platinum derivatives and PARPis are mainly common. Such common sensitivity factors include not only HR defects (HRD) but also additional factors. One of them is Schlafen 11 (SLFN11), a putative DNA/RNA helicase, that sensitizes cancer cells to a broad type of DNA‐damaging agents, including platinum and topoisomerase inhibitors. Mechanistically, SLFN11 induces a lethal replication block in response to replication stress (ie, DNA damage). As SLFN11 acts upon replication stress, trapping PARPis can activate SLFN11. Preclinical models show the importance of SLFN11 in PARPi sensitivity. However, the relevance of SLFN11 in PARPi response is less evident in clinical data compared with the significance of SLFN11 for platinum sensitivity. In this review, we consider the reasons for variable indications of PARPis resulting from clinical outcomes and review the mechanisms of action for PARPis as anticancer agents.
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Affiliation(s)
- Hiroshi Onji
- Department of Obstetrics and Gynecology, Ehime University Graduate School of Medicine, Japan.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
| | - Junko Murai
- Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
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29
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Lin X, Jiang W, Rudolph J, Lee BJ, Luger K, Zha S. PARP inhibitors trap PARP2 and alter the mode of recruitment of PARP2 at DNA damage sites. Nucleic Acids Res 2022; 50:3958-3973. [PMID: 35349716 PMCID: PMC9023293 DOI: 10.1093/nar/gkac188] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/24/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
Dual-inhibitors of PARP1 and PARP2 are promising anti-cancer drugs. In addition to blocking PARP1&2 enzymatic activity, PARP inhibitors also extend the lifetime of DNA damage-induced PARP1&2 foci, termed trapping. Trapping is important for the therapeutic effects of PARP inhibitors. Using live-cell imaging, we found that PARP inhibitors cause persistent PARP2 foci by switching the mode of PARP2 recruitment from a predominantly PARP1- and PAR-dependent rapid exchange to a WGR domain-mediated stalling of PARP2 on DNA. Specifically, PARP1-deletion markedly reduces but does not abolish PARP2 foci. The residual PARP2 foci in PARP1-deficient cells are DNA-dependent and abrogated by the R140A mutation in the WGR domain. Yet, PARP2-R140A forms normal foci in PARP1-proficient cells. In PARP1-deficient cells, PARP inhibitors - niraparib, talazoparib, and, to a lesser extent, olaparib - enhance PARP2 foci by preventing PARP2 exchange. This trapping of PARP2 is independent of auto-PARylation and is abolished by the R140A mutation in the WGR domain and the H415A mutation in the catalytic domain. Taken together, we found that PARP inhibitors trap PARP2 by physically stalling PARP2 on DNA via the WGR-DNA interaction while suppressing the PARP1- and PAR-dependent rapid exchange of PARP2.
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Affiliation(s)
- Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO80309, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
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30
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Huang D, Kraus WL. The expanding universe of PARP1-mediated molecular and therapeutic mechanisms. Mol Cell 2022; 82:2315-2334. [PMID: 35271815 DOI: 10.1016/j.molcel.2022.02.021] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022]
Abstract
ADP-ribosylation (ADPRylation) is a post-translational modification of proteins catalyzed by ADP-ribosyl transferase (ART) enzymes, including nuclear PARPs (e.g., PARP1 and PARP2). Historically, studies of ADPRylation and PARPs have focused on DNA damage responses in cancers, but more recent studies elucidate diverse roles in a broader array of biological processes. Here, we summarize the expanding array of molecular mechanisms underlying the biological functions of nuclear PARPs with a focus on PARP1, the founding member of the family. This includes roles in DNA repair, chromatin regulation, gene expression, ribosome biogenesis, and RNA biology. We also present new concepts in PARP1-dependent regulation, including PAR-dependent post-translational modifications, "ADPR spray," and PAR-mediated biomolecular condensate formation. Moreover, we review advances in the therapeutic mechanisms of PARP inhibitors (PARPi) as well as the progress on the mechanisms of PARPi resistance. Collectively, the recent progress in the field has yielded new insights into the expanding universe of PARP1-mediated molecular and therapeutic mechanisms in a variety of biological processes.
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Affiliation(s)
- Dan Huang
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China.
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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31
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Abstract
DNA repair and DNA damage signaling pathways are critical for the maintenance of genomic stability. Defects of DNA repair and damage signaling contribute to tumorigenesis, but also render cancer cells vulnerable to DNA damage and reliant on remaining repair and signaling activities. Here, we review the major classes of DNA repair and damage signaling defects in cancer, the genomic instability that they give rise to, and therapeutic strategies to exploit the resulting vulnerabilities. Furthermore, we discuss the impacts of DNA repair defects on both targeted therapy and immunotherapy, and highlight emerging principles for targeting DNA repair defects in cancer therapy.
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Affiliation(s)
- Jessica L Hopkins
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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32
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Hirota K, Ooka M, Shimizu N, Yamada K, Tsuda M, Ibrahim MA, Yamada S, Sasanuma H, Masutani M, Takeda S. XRCC1 counteracts PARP poisons, Olaparib and Talazoparib, and a clinical alkylating agent, Temozolomide, by promoting the removal of trapped PARP1 from broken DNA. Genes Cells 2022; 27:331-344. [PMID: 35194903 PMCID: PMC9310723 DOI: 10.1111/gtc.12929] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/30/2022]
Abstract
Base excision repair (BER) removes damaged bases by generating single‐strand breaks (SSBs), gap‐filling by DNA polymerase β (POLβ), and resealing SSBs. A base‐damaging agent, methyl methanesulfonate (MMS) is widely used to study BER. BER increases cellular tolerance to MMS, anti‐cancer base‐damaging drugs, temozolomide, carmustine, and lomustine, and to clinical poly(ADP ribose)polymerase (PARP) poisons, olaparib and talazoparib. The poisons stabilize PARP1/SSB complexes, inhibiting access of BER factors to SSBs. PARP1 and XRCC1 collaboratively promote SSB resealing by recruiting POLβ to SSBs, but XRCC1−/− cells are much more sensitive to MMS than PARP1−/− cells. We recently report that the PARP1 loss in XRCC1−/− cells restores their MMS tolerance and conclude that XPCC1 facilitates the release of PARP1 from SSBs by maintaining its autoPARylation. We here show that the PARP1 loss in XRCC1−/− cells also restores their tolerance to the three anti‐cancer base‐damaging drugs, although they and MMS induce different sets of base damage. We reveal the synthetic lethality of the XRCC1−/− mutation, but not POLβ−/−, with olaparib and talazoparib, indicating that XRCC1 is a unique BER factor in suppressing toxic PARP1/SSB complex and can suppress even when PARP1 catalysis is inhibited. In conclusion, XRCC1 suppresses the PARP1/SSB complex via PARP1 catalysis‐dependent and independent mechanisms.
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Affiliation(s)
- Kouji Hirota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan.,Department of Chemistry, Graduate school of Science, Tokyo Metropolitan University, Minami-Osawa, Hachioji- shi, Tokyo, Japan
| | - Masato Ooka
- Department of Chemistry, Graduate school of Science, Tokyo Metropolitan University, Minami-Osawa, Hachioji- shi, Tokyo, Japan
| | - Naoto Shimizu
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Kousei Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan.,Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Mahmoud Abdelghany Ibrahim
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Shintaro Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Mitsuko Masutani
- Department of Molecular and Genomic Biomedicine, CBMM, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shunichi Takeda
- Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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33
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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34
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Zhang C, Zhou B, Gu F, Liu H, Wu H, Yao F, Zheng H, Fu H, Chong W, Cai S, Huang M, Ma X, Guo Z, Li T, Deng W, Zheng M, Ji Q, Zhao Y, Ma Y, Wang QE, Tang TS, Guo C. Micropeptide PACMP inhibition elicits synthetic lethal effects by decreasing CtIP and poly(ADP-ribosyl)ation. Mol Cell 2022; 82:1297-1312.e8. [DOI: 10.1016/j.molcel.2022.01.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/19/2021] [Accepted: 01/24/2022] [Indexed: 12/19/2022]
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35
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Brustel J, Muramoto T, Fumimoto K, Ellins J, Pears CJ, Lakin ND. Linking DNA repair and cell cycle progression through serine ADP-ribosylation of histones. Nat Commun 2022; 13:185. [PMID: 35027540 PMCID: PMC8758696 DOI: 10.1038/s41467-021-27867-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 12/19/2021] [Indexed: 01/24/2023] Open
Abstract
Although serine ADP-ribosylation (Ser-ADPr) by Poly(ADP-ribose)-polymerases is a cornerstone of the DNA damage response, how this regulates DNA repair and genome stability is unknown. Here, we exploit the ability to manipulate histone genes in Dictyostelium to identify that ADPr of the histone variant H3b at S10 and S28 maintains genome stability by integrating double strand break (DSB) repair with mitotic entry. Given the critical requirement for mitotic H3S10/28 phosphorylation, we develop separation of function mutations that maintain S10 phosphorylation whilst disrupting ADPr. Mechanistically, this reveals a requirement for H3bS10/28 ADPr in non-homologous end-joining by recruiting Ku to DSBs. Moreover, this also identifies H3bS10/S28 ADPr is critical to prevent premature mitotic entry with unresolved DNA damage, thus maintaining genome stability. Together, these data demonstrate how serine ADPr of histones coordinates DNA repair with cell cycle progression to maintain genome stability.
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Affiliation(s)
- Julien Brustel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Tetsuya Muramoto
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Kazuki Fumimoto
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Jessica Ellins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Catherine J Pears
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK.
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36
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Batenburg NL, Mersaoui SY, Walker JR, Coulombe Y, Hammond-Martel I, Wurtele H, Masson JY, Zhu XD. Cockayne syndrome group B protein regulates fork restart, fork progression and MRE11-dependent fork degradation in BRCA1/2-deficient cells. Nucleic Acids Res 2021; 49:12836-12854. [PMID: 34871413 PMCID: PMC8682776 DOI: 10.1093/nar/gkab1173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 11/08/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
Cockayne syndrome group B (CSB) protein has been implicated in the repair of a variety of DNA lesions that induce replication stress. However, little is known about its role at stalled replication forks. Here, we report that CSB is recruited to stalled forks in a manner dependent upon its T1031 phosphorylation by CDK. While dispensable for MRE11 association with stalled forks in wild-type cells, CSB is required for further accumulation of MRE11 at stalled forks in BRCA1/2-deficient cells. CSB promotes MRE11-mediated fork degradation in BRCA1/2-deficient cells. CSB possesses an intrinsic ATP-dependent fork reversal activity in vitro, which is activated upon removal of its N-terminal region that is known to autoinhibit CSB’s ATPase domain. CSB functions similarly to fork reversal factors SMARCAL1, ZRANB3 and HLTF to regulate slowdown in fork progression upon exposure to replication stress, indicative of a role of CSB in fork reversal in vivo. Furthermore, CSB not only acts epistatically with MRE11 to facilitate fork restart but also promotes RAD52-mediated break-induced replication repair of double-strand breaks arising from cleavage of stalled forks by MUS81 in BRCA1/2-deficient cells. Loss of CSB exacerbates chemosensitivity in BRCA1/2-deficient cells, underscoring an important role of CSB in the treatment of cancer lacking functional BRCA1/2.
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Affiliation(s)
- Nicole L Batenburg
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sofiane Y Mersaoui
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Yan Coulombe
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Ian Hammond-Martel
- Centre de recherche, de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, Québec H1T 2M4, Canada
| | - Hugo Wurtele
- Centre de recherche, de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, Québec H1T 2M4, Canada.,Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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37
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Mohapatra J, Tashiro K, Beckner RL, Sierra J, Kilgore JA, Williams NS, Liszczak G. Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling. eLife 2021; 10:71502. [PMID: 34874266 PMCID: PMC8683085 DOI: 10.7554/elife.71502] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/20/2021] [Indexed: 12/27/2022] Open
Abstract
Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As the list of PARP1/2:HPF1 substrates continues to expand, there is a need for technologies to prepare mono- and poly-ADP-ribosylated proteins for biochemical interrogation. Here, we investigate the unique peptide ADPr activities catalyzed by PARP1 in the absence and presence of HPF1. We then exploit these activities to develop a method that facilitates installation of ADP-ribose polymers onto peptides with precise control over chain length and modification site. Importantly, the enzymatically mono- and poly-ADP-ribosylated peptides are fully compatible with protein ligation technologies. This chemoenzymatic protein synthesis strategy was employed to assemble a series of full-length, ADP-ribosylated histones and show that ADPr at histone H2B serine 6 or histone H3 serine 10 converts nucleosomes into robust substrates for the chromatin remodeler ALC1. We found ALC1 preferentially remodels 'activated' substrates within heterogeneous mononucleosome populations and asymmetrically ADP-ribosylated dinucleosome substrates, and that nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear extracts. Our study identifies a biochemical function for nucleosome serine ADPr and describes a new, highly modular approach to explore the impact that site-specific serine mono- and poly-ADPr have on protein function.
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Affiliation(s)
- Jugal Mohapatra
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Kyuto Tashiro
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Ryan L Beckner
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Jorge Sierra
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Jessica A Kilgore
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States.,Preclinical Pharmacology Core, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Noelle S Williams
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States.,Preclinical Pharmacology Core, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Glen Liszczak
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
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38
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Adam S, Rossi SE, Moatti N, De Marco Zompit M, Xue Y, Ng TF, Álvarez-Quilón A, Desjardins J, Bhaskaran V, Martino G, Setiaputra D, Noordermeer SM, Ohsumi TK, Hustedt N, Szilard RK, Chaudhary N, Munro M, Veloso A, Melo H, Yin SY, Papp R, Young JTF, Zinda M, Stucki M, Durocher D. The CIP2A-TOPBP1 axis safeguards chromosome stability and is a synthetic lethal target for BRCA-mutated cancer. NATURE CANCER 2021; 2:1357-1371. [PMID: 35121901 DOI: 10.1038/s43018-021-00266-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/10/2021] [Indexed: 05/26/2023]
Abstract
BRCA1/2-mutated cancer cells adapt to the genome instability caused by their deficiency in homologous recombination (HR). Identification of these adaptive mechanisms may provide therapeutic strategies to target tumors caused by the loss of these genes. In the present study, we report genome-scale CRISPR-Cas9 synthetic lethality screens in isogenic pairs of BRCA1- and BRCA2-deficient cells and identify CIP2A as an essential gene in BRCA1- and BRCA2-mutated cells. CIP2A is cytoplasmic in interphase but, in mitosis, accumulates at DNA lesions as part of a complex with TOPBP1, a multifunctional genome stability factor. Unlike PARP inhibition, CIP2A deficiency does not cause accumulation of replication-associated DNA lesions that require HR for their repair. In BRCA-deficient cells, the CIP2A-TOPBP1 complex prevents lethal mis-segregation of acentric chromosomes that arises from impaired DNA synthesis. Finally, physical disruption of the CIP2A-TOPBP1 complex is highly deleterious in BRCA-deficient tumors, indicating that CIP2A represents an attractive synthetic lethal therapeutic target for BRCA1- and BRCA2-mutated cancers.
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Affiliation(s)
- Salomé Adam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Silvia Emma Rossi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Nathalie Moatti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mara De Marco Zompit
- Department of Gynecology, University Hospital and University of Zurich, Schlieren, Switzerland
| | - Yibo Xue
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Timothy F Ng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alejandro Álvarez-Quilón
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Repare Therapeutics, St-Laurent, Quebec, Canada
| | | | | | | | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sylvie M Noordermeer
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Nicole Hustedt
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Lonza AG, Visp, Switzerland
| | - Rachel K Szilard
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Natasha Chaudhary
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Meagan Munro
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Henrique Melo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Robert Papp
- Repare Therapeutics, St-Laurent, Quebec, Canada
| | | | | | - Manuel Stucki
- Department of Gynecology, University Hospital and University of Zurich, Schlieren, Switzerland
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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39
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Fugger K, Hewitt G, West SC, Boulton SJ. Tackling PARP inhibitor resistance. Trends Cancer 2021; 7:1102-1118. [PMID: 34563478 DOI: 10.1016/j.trecan.2021.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022]
Abstract
Homologous recombination-deficient (HRD) tumours, including those harbouring mutations in the BRCA genes, are hypersensitive to treatment with inhibitors of poly(ADP-ribose) polymerase (PARPis). Despite high response rates, most HRD cancers ultimately develop resistance to PARPi treatment through reversion mutations or genetic/epigenetic alterations to DNA repair pathways. Counteracting these resistance pathways, thereby increasing the potency of PARPi therapy, represents a potential strategy to improve the treatment of HRD cancers. In this review, we discuss recent insights derived from genetic screens that have identified a number of novel genes that can be targeted to improve PARPi treatment of HRD cancers and may provide a means to overcome PARPi resistance.
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Affiliation(s)
- Kasper Fugger
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen C West
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Artios Pharma Ltd. B940, Babraham Research Campus, Cambridge, CB22 3FH, UK.
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40
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Palazzo L, Suskiewicz MJ, Ahel I. Serine ADP-ribosylation in DNA-damage response regulation. Curr Opin Genet Dev 2021; 71:106-113. [PMID: 34340015 DOI: 10.1016/j.gde.2021.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022]
Abstract
PARP1 and PARP2 govern the DNA-damage response by catalysing the reversible post-translational modification ADP-ribosylation. During the repair of DNA lesions, PARP1 and PARP2 combine with an accessory factor HPF1, which is required for the modification of target proteins on serine residues. Although the physiological role of individual ADP-ribosylation sites is still unclear, serine ADP-ribosylation at damage sites leads to the recruitment of chromatin remodellers and repair factors to ensure efficient DNA repair. ADP-ribosylation signalling is tightly controlled by the coordinated activities of (ADP-ribosyl)glycohydrolases PARG and ARH3 that, by reversing the modification, guarantee proper kinetics of DNA repair and cell cycle re-entry. The recent advances in the structural and mechanistic understanding of ADP-ribosylation provide new insights into human physiopathology and cancer therapy.
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Affiliation(s)
- Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, Via Tommaso de Amicis 95, 80145 Naples, Italy
| | - Marcin J Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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41
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Hayward SB, Ciccia A. Towards a CRISPeR understanding of homologous recombination with high-throughput functional genomics. Curr Opin Genet Dev 2021; 71:171-181. [PMID: 34583241 PMCID: PMC8671205 DOI: 10.1016/j.gde.2021.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-dependent genome editing enables the study of genes and mutations on a large scale. Here we review CRISPR-based functional genomics technologies that generate gene knockouts and single nucleotide variants (SNVs) and discuss how their use has provided new important insights into the function of homologous recombination (HR) genes. In particular, we highlight discoveries from CRISPR screens that have contributed to define the response to PARP inhibition in cells deficient for the HR genes BRCA1 and BRCA2, uncover genes whose loss causes synthetic lethality in combination with BRCA1/2 deficiency, and characterize the function of BRCA1/2 SNVs of uncertain clinical significance. Further use of these approaches, combined with next-generation CRISPR-based technologies, will aid to dissect the genetic network of the HR pathway, define the impact of HR mutations on cancer etiology and treatment, and develop novel targeted therapies for HR-deficient tumors.
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Affiliation(s)
- Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, United States.
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42
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Zhang X, Bai Y, Huang L, Liu S, Mo Y, Cheng W, Wang G, Cao Z, Chen X, Cui H, Qi L, Ma L, Liu M, Guan XY, Ma NF. CHD1L augments autophagy-mediated migration of hepatocellular carcinoma through targeting ZKSCAN3. Cell Death Dis 2021; 12:950. [PMID: 34654797 PMCID: PMC8520006 DOI: 10.1038/s41419-021-04254-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/25/2021] [Accepted: 10/04/2021] [Indexed: 01/18/2023]
Abstract
Autophagy is an important biological process in normal cells. However, how it affects tumor progression still remains poorly understood. Herein, we demonstrated that the oncogenic protein Chromodomain-helicase-DNA-binding-protein 1-like gene (CHD1L) might promote HCC cells migration and metastasis through autophagy. CHD1L could bind to the promotor region of Zinc finger with KRAB and SCAN domain 3 (ZKSCAN3), a pivotal autophagy suppressor, and inhibit its transcription. We established inducible CHD1L conditional knockout cell line (CHD1L-iKO cell) and found that the deletion of CHD1L significantly increased ZKSCAN3 expression both at mRNA and protein level. Deletion of CHD1L impaired the autophagic flux and migration of HCC cells, while specifically inhibiting ZKSCAN3 blocked these effects. Further exploration demonstrated that the enhanced tumor cell migration and metastasis induced by CHD1L was mediated through ZKSCAN3-induced autophagic degradation of Paxillin. In summary, we have characterized a previously unknown function of CHD1L in regulating tumor migration via ZKSCAN3-mediated autophagy in HCC. Further inhibition of CHD1L and its downstream autophagy signaling might shed new light on cancer therapeutics.
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MESH Headings
- Animals
- Autophagy
- Autophagy-Related Protein 5/metabolism
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/ultrastructure
- Cell Line, Tumor
- Cell Movement
- DNA Helicases/metabolism
- DNA-Binding Proteins/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Gene Knockdown Techniques
- Humans
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Liver Neoplasms/ultrastructure
- Mice, Inbred BALB C
- Mice, Nude
- Microtubule-Associated Proteins/metabolism
- Neoplasm Metastasis
- Paxillin/metabolism
- RNA, Small Interfering/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Mice
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Affiliation(s)
- Xiaofeng Zhang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yinshan Bai
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Li Huang
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shanshan Liu
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanxuan Mo
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Cheng
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Guangliang Wang
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhiming Cao
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaogang Chen
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huiqing Cui
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ling Qi
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong, China
| | - Lei Ma
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ming Liu
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Clinical Oncology, Center for Cancer Research, and State Key Laboratory for Liver Research, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ning-Fang Ma
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong, China.
- Guangzhou Municipal and Guangdong ProvincialKey Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China.
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China.
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43
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Saha LK, Murai Y, Saha S, Jo U, Tsuda M, Takeda S, Pommier Y. Replication-dependent cytotoxicity and Spartan-mediated repair of trapped PARP1-DNA complexes. Nucleic Acids Res 2021; 49:10493-10506. [PMID: 34551432 DOI: 10.1093/nar/gkab777] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
The antitumor activity of poly(ADP-ribose) polymerase inhibitors (PARPis) has been ascribed to PARP trapping, which consists in tight DNA-protein complexes. Here we demonstrate that the cytotoxicity of talazoparib and olaparib results from DNA replication. To elucidate the repair of PARP1-DNA complexes associated with replication in human TK6 and chicken DT40 lymphoblastoid cells, we explored the role of Spartan (SPRTN), a metalloprotease associated with DNA replication, which removes proteins forming DPCs. We find that SPRTN-deficient cells are hypersensitive to talazoparib and olaparib, but not to veliparib, a weak PARP trapper. SPRTN-deficient cells exhibit delayed clearance of trapped PARP1 and increased replication fork stalling upon talazoparib and olaparib treatment. We also show that SPRTN interacts with PARP1 and forms nuclear foci that colocalize with the replicative cell division cycle 45 protein (CDC45) in response to talazoparib. Additionally, SPRTN is deubiquitinated and epistatic with translesion synthesis (TLS) in response to talazoparib. Our results demonstrate that SPRTN is recruited to trapped PARP1 in S-phase to assist in the excision and replication bypass of PARP1-DNA complexes.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yasuhisa Murai
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Masataka Tsuda
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan.,Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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44
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Liu Q, Knobloch G, Voorneveld J, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Ladurner AG, Filippov DV. Chemical synthesis of linear ADP-ribose oligomers up to pentamer and their binding to the oncogenic helicase ALC1. Chem Sci 2021; 12:12468-12475. [PMID: 34603678 PMCID: PMC8480336 DOI: 10.1039/d1sc02340c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/12/2021] [Indexed: 11/21/2022] Open
Abstract
ADP-ribosylation is a pivotal post-translational modification that mediates various important cellular processes producing negatively charged biopolymer, poly (ADP-ribose), the functions of which need further elucidation. Toward this end, the availability of well-defined ADP-ribose (ADPr) oligomers in sufficient quantities is a necessity. In this work, we demonstrate the chemical synthesis of linear ADPr oligomers of defined, increasing length using a modified solid phase synthesis method. An advanced phosphoramidite building block temporarily protected with the base sensitive Fm-group was designed and implemented in the repeating pyrophosphate formation via a P(v)-P(iii) coupling procedure on Tentagel solid support. Linear ADPr oligomers up to a pentamer were successfully synthesized and their affinity for the poly-(ADP-ribose)-binding macrodomain of the human oncogenic helicase and chromatin remodeling enzyme ALC1 was determined. Our data reveal a length-dependent binding manner of the nucleic acid, with larger ADPr oligomers exhibiting higher binding enthalpies for ALC1, illustrating how the activity of this molecular machine is gated by PAR.
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Affiliation(s)
- Qiang Liu
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Gunnar Knobloch
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine LMU Munich 82152 Planegg-Martinsried Germany
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Nico J Meeuwenoord
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | | | - Andreas G Ladurner
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine LMU Munich 82152 Planegg-Martinsried Germany
- Eisbach Bio GmbH Am Klopferspitz 19, Planegg-Martinsried 82152 Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
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45
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Abstract
The SNF2 family ATPase Amplified in Liver Cancer 1 (ALC1) is the only chromatin remodeling enzyme with a poly(ADP-ribose) (PAR) binding macrodomain. ALC1 functions together with poly(ADP-ribose) polymerase PARP1 to remodel nucleosomes. Activation of ALC1 cryptic ATPase activity and the subsequent nucleosome remodeling requires binding of its macrodomain to PAR chains synthesized by PARP1 and NAD+ A key question is whether PARP1 has a role(s) in ALC1-dependent nucleosome remodeling beyond simply synthesizing the PAR chains needed to activate the ALC1 ATPase. Here, we identify PARP1 separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1. Investigation of these mutants has revealed multiple functions for PARP1 in ALC1-dependent nucleosome remodeling and provides insights into its multifaceted role in chromatin remodeling.
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46
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Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S. Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome. eLife 2021; 10:e71420. [PMID: 34486521 PMCID: PMC8463071 DOI: 10.7554/elife.71420] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/05/2021] [Indexed: 12/21/2022] Open
Abstract
The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and suggest that ALC1 preferentially slides nucleosomes away from DNA breaks.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Guillaume Gaullier
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Laura C Lehmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Klaus Brackmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Despoina Dimakou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Mario Halic
- Department of Structural Biology, St Jude Children's Research HospitalMemphisUnited States
| | | | | | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
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47
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Sinha S, Molla S, Kundu CN. PARP1-modulated chromatin remodeling is a new target for cancer treatment. Med Oncol 2021; 38:118. [PMID: 34432161 DOI: 10.1007/s12032-021-01570-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
Cancer progression requires certain tumorigenic mutations in genes encoding for different cellular and nuclear proteins. Altered expressions of these mutated genes are mediated by post-translational modifications and chromatin remodeling. Chromatin remodeling is mainly regulated by the chromatin remodeling enzyme complexes and histone modifications. Upon DNA damage, Poly-(ADP-ribose) Polymerase1 (PARP1) plays a very important role in the induction of chromatin modifications and activation of DNA repair pathways to repair the DNA lesion. It has been targeted to develop different anti-cancer therapeutic interventions and PARP inhibitors have been approved by the U.S. Food and Drug Administration (FDA) for clinical use. But it has been found that the cancer cells often develop resistance to these PARP inhibitors and chromatin remodeling helps in enhancing this process. Hence, it may be beneficial to target PARP1-mediated chromatin remodeling, which may allow to reverse the drug resistance. In the current review, we have discussed the role of chromatin remodeling in DNA repair, how PARP1 regulates modifications of chromatin dynamics, and the role of chromatin modifications in cancer. It has also been discussed how the PARP1-mediated chromatin remodeling can be targeted by PARP inhibitors alone or in combination with other chemotherapeutic agents to establish novel anti-cancer therapeutics. We have also considered the use of PARG inhibitors that may enhance the action of PARP inhibitors to target different types of cancers.
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Affiliation(s)
- Saptarshi Sinha
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Sefinew Molla
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Chanakya Nath Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India.
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48
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Simoneau A, Xiong R, Zou L. The trans cell cycle effects of PARP inhibitors underlie their selectivity toward BRCA1/2-deficient cells. Genes Dev 2021; 35:1271-1289. [PMID: 34385259 PMCID: PMC8415318 DOI: 10.1101/gad.348479.121] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/30/2021] [Indexed: 11/25/2022]
Abstract
In this study, Simoneau et al. investigated why PARPi is more effective than other DNA-damaging drugs when used to treat BRCA1/2-deficient tumors. They show that PARPi induces DSBs progressively through trans-cell-cycle ssDNA gaps, and BRCA1/2-deficient cells fail to slow down and repair DSBs over multiple cell cycles, explaining the unique efficacy of PARPi in BRCA1/2-deficient cells. PARP inhibitor (PARPi) is widely used to treat BRCA1/2-deficient tumors, but why PARPi is more effective than other DNA-damaging drugs is unclear. Here, we show that PARPi generates DNA double-strand breaks (DSBs) predominantly in a trans cell cycle manner. During the first S phase after PARPi exposure, PARPi induces single-stranded DNA (ssDNA) gaps behind DNA replication forks. By trapping PARP on DNA, PARPi prevents the completion of gap repair until the next S phase, leading to collisions of replication forks with ssDNA gaps and a surge of DSBs. In the second S phase, BRCA1/2-deficient cells are unable to suppress origin firing through ATR, resulting in continuous DNA synthesis and more DSBs. Furthermore, BRCA1/2-deficient cells cannot recruit RAD51 to repair collapsed forks. Thus, PARPi induces DSBs progressively through trans cell cycle ssDNA gaps, and BRCA1/2-deficient cells fail to slow down and repair DSBs over multiple cell cycles, explaining the unique efficacy of PARPi in BRCA1/2-deficient cells.
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Affiliation(s)
- Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Rosalinda Xiong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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49
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Thakar T, Moldovan GL. The emerging determinants of replication fork stability. Nucleic Acids Res 2021; 49:7224-7238. [PMID: 33978751 PMCID: PMC8287955 DOI: 10.1093/nar/gkab344] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/21/2022] Open
Abstract
A universal response to replication stress is replication fork reversal, where the nascent complementary DNA strands are annealed to form a protective four-way junction allowing forks to avert DNA damage while replication stress is resolved. However, reversed forks are in turn susceptible to nucleolytic digestion of the regressed nascent DNA arms and rely on dedicated mechanisms to protect their integrity. The most well studied fork protection mechanism involves the BRCA pathway and its ability to catalyze RAD51 nucleofilament formation on the reversed arms of stalled replication forks. Importantly, the inability to prevent the degradation of reversed forks has emerged as a hallmark of BRCA deficiency and underlies genome instability and chemosensitivity in BRCA-deficient cells. In the past decade, multiple factors underlying fork stability have been discovered. These factors either cooperate with the BRCA pathway, operate independently from it to augment fork stability in its absence, or act as enablers of fork degradation. In this review, we examine these novel determinants of fork stability, explore the emergent conceptual underpinnings underlying fork protection, as well as the impact of fork protection on cellular viability and cancer therapy.
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Affiliation(s)
- Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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50
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Thompson MK, Sobol RW, Prakash A. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair. BIOLOGY 2021; 10:530. [PMID: 34198612 PMCID: PMC8232306 DOI: 10.3390/biology10060530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.
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Affiliation(s)
- Marlo K. Thompson
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
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