201
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Ummarino S, Hausman C, Di Ruscio A. The PARP Way to Epigenetic Changes. Genes (Basel) 2021; 12:446. [PMID: 33804735 PMCID: PMC8003872 DOI: 10.3390/genes12030446] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022] Open
Abstract
ADP-ribosylation, is a reversible post-translational modification implicated in major biological functions. Poly ADP-ribose polymerases (PARP) are specialized enzymes that catalyze the addition of ADP ribose units from "nicotinamide adenine dinucleotide-donor molecules" to their target substrates. This reaction known as PARylation modulates essential cellular processes including DNA damage response, chromatin remodeling, DNA methylation and gene expression. Herein, we discuss emerging roles of PARP1 in chromatin remodeling and epigenetic regulation, focusing on its therapeutic implications for cancer treatment and beyond.
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Affiliation(s)
- Simone Ummarino
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
| | - Clinton Hausman
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
| | - Annalisa Di Ruscio
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
- Beth Israel Deaconess Medical Center, Cancer Research Institute, Boston, MA 02215, USA
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202
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Chan CY, Tan KV, Cornelissen B. PARP Inhibitors in Cancer Diagnosis and Therapy. Clin Cancer Res 2021; 27:1585-1594. [PMID: 33082213 DOI: 10.1158/1078-0432.ccr-20-2766] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/07/2020] [Accepted: 10/14/2020] [Indexed: 11/16/2022]
Abstract
Targeting of PARP enzymes has emerged as an effective therapeutic strategy to selectively target cancer cells with deficiencies in homologous recombination signaling. Currently used to treat BRCA-mutated cancers, PARP inhibitors (PARPi) have demonstrated improved outcome in various cancer types as single agents. Ongoing efforts have seen the exploitation of PARPi combination therapies, boosting patient responses as a result of drug synergisms. Despite great successes using PARPi therapy, selecting those patients who will benefit from single agent or combination therapy remains one of the major challenges. Numerous reports have demonstrated that the presence of a BRCA mutation does not always result in synthetic lethality with PARPi therapy in treatment-naïve tumors. Cancer cells can also develop resistance to PARPi therapy. Hence, combination therapy may significantly affect the treatment outcomes. In this review, we discuss the development and utilization of PARPi in different cancer types from preclinical models to clinical trials, provide a current overview of the potential uses of PARP imaging agents in cancer therapy, and discuss the use of radiolabeled PARPi as radionuclide therapies.
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Affiliation(s)
- Chung Ying Chan
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Kel Vin Tan
- Department of Diagnostic Radiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Bart Cornelissen
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom.
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203
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Rapid Detection and Signaling of DNA Damage by PARP-1. Trends Biochem Sci 2021; 46:744-757. [PMID: 33674152 DOI: 10.1016/j.tibs.2021.01.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/14/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
Poly(ADP-ribosyl) polymerase-1 (PARP-1) is an abundant ADP-ribosyl transferase that regulates various biological processes. PARP-1 is widely recognized as a first-line responder molecule in DNA damage response (DDR). Here, we review the full cycle of detecting DNA damage by PARP-1, PARP-1 activation upon DNA binding, and PARP-1 release from a DNA break. We also discuss the allosteric consequence upon binding of PARP inhibitors (PARPi) and the opportunity to tune its release from a DNA break. It is now possible to harness this new understanding to design novel PARPi for treating diseases where cell toxicity caused by PARP-1 'trapping' on DNA is either the desired consequence or entirely counterproductive.
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204
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Avoid the trap: Targeting PARP1 beyond human malignancy. Cell Chem Biol 2021; 28:456-462. [PMID: 33657415 DOI: 10.1016/j.chembiol.2021.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/22/2020] [Accepted: 02/03/2021] [Indexed: 01/24/2023]
Abstract
PARP1 is a poly(ADP-ribose) polymerase (PARP) enzyme that plays a critical role in regulating DNA damage response. The main enzymatic function of PARP1 is to catalyze a protein post-translational modification known as poly(ADP-ribosyl)ation (PARylation). Human cancers with homologous recombination deficiency are highly sensitive to PARP1 inhibitors. PARP1 is aberrantly activated in many non-oncological diseases, leading to the excessive NAD+ depletion and PAR formation, thus causing cell death and tissue damage. PARP1 deletion offers a profound protective effect in the relevant animal models. However, many of the current PARP1 inhibitors also induce PARP1 trapping, which drives subsequent DNA damage, innate immune response and cytotoxicity. This minireview provides an overview of the basic biology of PARP1 trapping, and its implications in disease. Furthermore, we also discuss the recent development of PARP1 PROTAC compounds, and their utility as "non-trapping" PARP1 degraders for the potential amelioration of non-oncological diseases driven by aberrant PARP1 activation.
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205
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Kutuzov MM, Belousova EA, Kurgina TA, Ukraintsev AA, Vasil’eva IA, Khodyreva SN, Lavrik OI. The contribution of PARP1, PARP2 and poly(ADP-ribosyl)ation to base excision repair in the nucleosomal context. Sci Rep 2021; 11:4849. [PMID: 33649352 PMCID: PMC7921663 DOI: 10.1038/s41598-021-84351-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
The regulation of repair processes including base excision repair (BER) in the presence of DNA damage is implemented by a cellular signal: poly(ADP-ribosyl)ation (PARylation), which is catalysed by PARP1 and PARP2. Despite ample studies, it is far from clear how BER is regulated by PARPs and how the roles are distributed between the PARPs. Here, we investigated the effects of PARP1, PARP2 and PARylation on activities of the main BER enzymes (APE1, DNA polymerase β [Polβ] and DNA ligase IIIα [LigIIIα]) in combination with BER scaffold protein XRCC1 in the nucleosomal context. We constructed nucleosome core particles with midward- or outward-oriented damage. It was concluded that in most cases, the presence of PARP1 leads to the suppression of the activities of APE1, Polβ and to a lesser extent LigIIIα. PARylation by PARP1 attenuated this effect to various degrees depending on the enzyme. PARP2 had an influence predominantly on the last stage of BER: DNA sealing. Nonetheless, PARylation by PARP2 led to Polβ inhibition and to significant stimulation of LigIIIα activities in a NAD+-dependent manner. On the basis of the obtained and literature data, we suggest a hypothetical model of the contribution of PARP1 and PARP2 to BER.
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Affiliation(s)
- M. M. Kutuzov
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - E. A. Belousova
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - T. A. Kurgina
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, Novosibirsk, Russia
| | - A. A. Ukraintsev
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - I. A. Vasil’eva
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - S. N. Khodyreva
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - O. I. Lavrik
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, Novosibirsk, Russia
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206
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Ogden TEH, Yang JC, Schimpl M, Easton LE, Underwood E, Rawlins P, McCauley M, Langelier MF, Pascal J, Embrey K, Neuhaus D. Dynamics of the HD regulatory subdomain of PARP-1; substrate access and allostery in PARP activation and inhibition. Nucleic Acids Res 2021; 49:2266-2288. [PMID: 33511412 PMCID: PMC7913765 DOI: 10.1093/nar/gkab020] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/17/2020] [Accepted: 01/08/2021] [Indexed: 01/08/2023] Open
Abstract
PARP-1 is a key early responder to DNA damage in eukaryotic cells. An allosteric mechanism links initial sensing of DNA single-strand breaks by PARP-1's F1 and F2 domains via a process of further domain assembly to activation of the catalytic domain (CAT); synthesis and attachment of poly(ADP-ribose) (PAR) chains to protein sidechains then signals for assembly of DNA repair components. A key component in transmission of the allosteric signal is the HD subdomain of CAT, which alone bridges between the assembled DNA-binding domains and the active site in the ART subdomain of CAT. Here we present a study of isolated CAT domain from human PARP-1, using NMR-based dynamics experiments to analyse WT apo-protein as well as a set of inhibitor complexes (with veliparib, olaparib, talazoparib and EB-47) and point mutants (L713F, L765A and L765F), together with new crystal structures of the free CAT domain and inhibitor complexes. Variations in both dynamics and structures amongst these species point to a model for full-length PARP-1 activation where first DNA binding and then substrate interaction successively destabilise the folded structure of the HD subdomain to the point where its steric blockade of the active site is released and PAR synthesis can proceed.
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Affiliation(s)
- Tom E H Ogden
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Laura E Easton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | - Michael M McCauley
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
| | | | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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207
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Genois MM, Gagné JP, Yasuhara T, Jackson J, Saxena S, Langelier MF, Ahel I, Bedford MT, Pascal JM, Vindigni A, Poirier GG, Zou L. CARM1 regulates replication fork speed and stress response by stimulating PARP1. Mol Cell 2021; 81:784-800.e8. [PMID: 33412112 PMCID: PMC7897296 DOI: 10.1016/j.molcel.2020.12.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/19/2020] [Accepted: 12/02/2020] [Indexed: 12/22/2022]
Abstract
DNA replication forks use multiple mechanisms to deal with replication stress, but how the choice of mechanisms is made is still poorly understood. Here, we show that CARM1 associates with replication forks and reduces fork speed independently of its methyltransferase activity. The speeding of replication forks in CARM1-deficient cells requires RECQ1, which resolves reversed forks, and RAD18, which promotes translesion synthesis. Loss of CARM1 reduces fork reversal and increases single-stranded DNA (ssDNA) gaps but allows cells to tolerate higher replication stress. Mechanistically, CARM1 interacts with PARP1 and promotes PARylation at replication forks. In vitro, CARM1 stimulates PARP1 activity by enhancing its DNA binding and acts jointly with HPF1 to activate PARP1. Thus, by stimulating PARP1, CARM1 slows replication forks and promotes the use of fork reversal in the stress response, revealing that CARM1 and PARP1 function as a regulatory module at forks to control fork speed and the choice of stress response mechanisms.
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Affiliation(s)
- Marie-Michelle Genois
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec City, QC G1V 0A6, Canada; CHU de Québec Research Center, CHUL Pavilion, Oncology Axis, Québec City, Québec G1V 4G2, Canada
| | - Takaaki Yasuhara
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec City, QC G1V 0A6, Canada; CHU de Québec Research Center, CHUL Pavilion, Oncology Axis, Québec City, Québec G1V 4G2, Canada
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
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208
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Rudolph J, Roberts G, Luger K. Histone Parylation factor 1 contributes to the inhibition of PARP1 by cancer drugs. Nat Commun 2021; 12:736. [PMID: 33531508 PMCID: PMC7854685 DOI: 10.1038/s41467-021-20998-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
Poly-(ADP-ribose) polymerase 1 and 2 (PARP1 and PARP2) are key enzymes in the DNA damage response. Four different inhibitors (PARPi) are currently in the clinic for treatment of ovarian and breast cancer. Recently, histone PARylation Factor 1 (HPF1) has been shown to play an essential role in the PARP1- and PARP2-dependent poly-(ADP-ribosylation) (PARylation) of histones, by forming a complex with both enzymes and altering their catalytic properties. Given the proximity of HPF1 to the inhibitor binding site both PARPs, we hypothesized that HPF1 may modulate the affinity of inhibitors toward PARP1 and/or PARP2. Here we demonstrate that HPF1 significantly increases the affinity for a PARP1 - DNA complex of some PARPi (i.e., olaparib), but not others (i.e., veliparib). This effect of HPF1 on the binding affinity of Olaparib also holds true for the more physiologically relevant PARP1 - nucleosome complex but does not extend to PARP2. Our results have important implications for the interpretation of PARP inhibition by current PARPi as well as for the design and analysis of the next generation of clinically relevant PARP inhibitors.
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Affiliation(s)
- Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Genevieve Roberts
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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209
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Control of replication stress and mitosis in colorectal cancer stem cells through the interplay of PARP1, MRE11 and RAD51. Cell Death Differ 2021; 28:2060-2082. [PMID: 33531658 PMCID: PMC8257675 DOI: 10.1038/s41418-020-00733-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/20/2020] [Accepted: 12/30/2020] [Indexed: 12/31/2022] Open
Abstract
Cancer stem cells (CSCs) are tumor subpopulations driving disease development, progression, relapse and therapy resistance, and their targeting ensures tumor eradication. CSCs display heterogeneous replication stress (RS), but the functionality/relevance of the RS response (RSR) centered on the ATR-CHK1 axis is debated. Here, we show that the RSR is efficient in primary CSCs from colorectal cancer (CRC-SCs), and describe unique roles for PARP1 and MRE11/RAD51. First, we demonstrated that PARP1 is upregulated in CRC-SCs resistant to several replication poisons and RSR inhibitors (RSRi). In these cells, PARP1 modulates replication fork speed resulting in low constitutive RS. Second, we showed that MRE11 and RAD51 cooperate in the genoprotection and mitosis execution of PARP1-upregulated CRC-SCs. These roles represent therapeutic vulnerabilities for CSCs. Indeed, PARP1i sensitized CRC-SCs to ATRi/CHK1i, inducing replication catastrophe, and prevented the development of resistance to CHK1i. Also, MRE11i + RAD51i selectively killed PARP1-upregulated CRC-SCs via mitotic catastrophe. These results provide the rationale for biomarker-driven clinical trials in CRC using distinct RSRi combinations.
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210
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Parsels LA, Engelke CG, Parsels J, Flanagan SA, Zhang Q, Tanska D, Wahl DR, Canman CE, Lawrence TS, Morgan MA. Combinatorial Efficacy of Olaparib with Radiation and ATR Inhibitor Requires PARP1 Protein in Homologous Recombination-Proficient Pancreatic Cancer. Mol Cancer Ther 2021; 20:263-273. [PMID: 33268569 PMCID: PMC7867626 DOI: 10.1158/1535-7163.mct-20-0365] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/06/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
PARP inhibitor monotherapy (olaparib) was recently FDA approved for the treatment of BRCA1/2-mutant, homologous recombination (HR) repair-deficient pancreatic cancer. Most pancreatic cancers, however, are HR proficient and thus resistant to PARP inhibitor monotherapy. We tested the hypothesis that combined therapy with radiation and ataxia telangiectasia and Rad3-related (ATR) inhibitor (AZD6738) would extend the therapeutic indication of olaparib to HR-proficient pancreatic cancers. We show that olaparib combined with AZD6738 significantly reduced radiation survival relative to either agent alone, regardless of HR status. Whereas catalytic inhibition of PARP with low concentrations of olaparib radiosensitized HR-deficient models, maximal sensitization in HR-proficient models required concentrations of olaparib that induce formation of PARP1-DNA complexes. Furthermore, CRISPR-Cas9-mediated PARP1 deletion failed to recapitulate the effects of olaparib on radiosensitivity and negated the combinatorial efficacy of olaparib and AZD6738 on radiosensitization, suggesting that PARP1-DNA complexes, rather than PARP catalytic inhibition, were responsible for radiosensitization. Mechanistically, therapeutic concentrations of olaparib in combination with radiation and AZD6738 increased DNA double-strand breaks. DNA fiber combing revealed that high concentrations of olaparib did not stall replication forks but instead accelerated replication fork progression in association with an ATR-mediated replication stress response that was antagonized by AZD6738. Finally, in HR-proficient tumor xenografts, the combination of olaparib, radiation, and AZD6738 significantly delayed tumor growth compared with all other treatments. These findings suggest that PARP1-DNA complexes are required for the therapeutic activity of olaparib combined with radiation and ATR inhibitor in HR-proficient pancreatic cancer and support the clinical development of this combination for tumors intrinsically resistant to PARP inhibitors.
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Affiliation(s)
- Leslie A Parsels
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Carl G Engelke
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joshua Parsels
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Sheryl A Flanagan
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Qiang Zhang
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Daria Tanska
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Daniel R Wahl
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Christine E Canman
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan.
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211
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Massively parallel assessment of human variants with base editor screens. Cell 2021; 184:1064-1080.e20. [PMID: 33606977 DOI: 10.1016/j.cell.2021.01.012] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/26/2022]
Abstract
Understanding the functional consequences of single-nucleotide variants is critical to uncovering the genetic underpinnings of diseases, but technologies to characterize variants are limiting. Here, we leverage CRISPR-Cas9 cytosine base editors in pooled screens to scalably assay variants at endogenous loci in mammalian cells. We benchmark the performance of base editors in positive and negative selection screens, identifying known loss-of-function mutations in BRCA1 and BRCA2 with high precision. To demonstrate the utility of base editor screens to probe small molecule-protein interactions, we screen against BH3 mimetics and PARP inhibitors, identifying point mutations that confer drug sensitivity or resistance. We also create a library of single guide RNAs (sgRNAs) predicted to generate 52,034 ClinVar variants in 3,584 genes and conduct screens in the presence of cellular stressors, identifying loss-of-function variants in numerous DNA damage repair genes. We anticipate that this screening approach will be broadly useful to readily and scalably functionalize genetic variants.
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212
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Janysek DC, Kim J, Duijf PHG, Dray E. Clinical use and mechanisms of resistance for PARP inhibitors in homologous recombination-deficient cancers. Transl Oncol 2021; 14:101012. [PMID: 33516088 PMCID: PMC7847957 DOI: 10.1016/j.tranon.2021.101012] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/14/2020] [Accepted: 12/31/2020] [Indexed: 12/11/2022] Open
Abstract
Cells are continuously subjected to DNA damaging agents. DNA damages are repaired by one of the many pathways guarding genomic integrity. When one or several DNA damage pathways are rendered inefficient, cells can accumulate mutations, which modify normal cellular pathways, favoring abnormal cell growth. This supports malignant transformation, which can occur when cells acquire resistance to cell cycle checkpoints, apoptosis, or growth inhibition signals. Mutations in genes involved in the repair of DNA double strand breaks (DSBs), such as BRCA1, BRCA2, or PALB2, significantly increase the risk of developing cancer of the breast, ovaries, pancreas, or prostate. Fortunately, the inability of these tumors to repair DNA breaks makes them sensitive to genotoxic chemotherapies, allowing for the development of therapies precisely tailored to individuals' genetic backgrounds. Unfortunately, as with many anti-cancer agents, drugs used to treat patients carrying a BRCA1 or BRCA2 mutation create a selective pressure, and over time tumors can become drug resistant. Here, we detail the cellular function of tumor suppressors essential in DNA damage repair pathways, present the mechanisms of action of inhibitors used to create synthetic lethality in BRCA carriers, and review the major molecular sources of drug resistance. Finally, we present examples of the many strategies being developed to circumvent drug resistance.
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Affiliation(s)
- Dawn C Janysek
- School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Jennifer Kim
- School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Pascal H G Duijf
- Queensland University of Technology, IHBI at the Translational Research Institute, Brisbane, QLD, Australia; Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia; University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Eloïse Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States; Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX, United States.
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213
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Kim DS, Camacho CV, Kraus WL. Alternate therapeutic pathways for PARP inhibitors and potential mechanisms of resistance. Exp Mol Med 2021; 53:42-51. [PMID: 33487630 PMCID: PMC8080675 DOI: 10.1038/s12276-021-00557-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/12/2020] [Indexed: 01/29/2023] Open
Abstract
Homologous recombination (HR) repair deficiency impairs the proper maintenance of genomic stability, thus rendering cancer cells vulnerable to loss or inhibition of DNA repair proteins, such as poly(ADP-ribose) polymerase-1 (PARP-1). Inhibitors of nuclear PARPs are effective therapeutics for a number of different types of cancers. Here we review key concepts and current progress on the therapeutic use of PARP inhibitors (PARPi). PARPi selectively induce synthetic lethality in cancer cells with homologous recombination deficiencies (HRDs), the most notable being cancer cells harboring mutations in the BRCA1 and BRCA2 genes. Recent clinical evidence, however, shows that PARPi can be effective as cancer therapeutics regardless of BRCA1/2 or HRD status, suggesting that a broader population of patients might benefit from PARPi therapy. Currently, four PARPi have been approved by the Food and Drug Administration (FDA) for the treatment of advanced ovarian and breast cancer with deleterious BRCA mutations. Although PARPi have been shown to improve progression-free survival, cancer cells inevitably develop resistance, which poses a significant obstacle to the prolonged use of PARP inhibitors. For example, somatic BRCA1/2 reversion mutations are often identified in patients with BRCA1/2-mutated cancers after treatment with platinum-based therapy, causing restoration of HR capacity and thus conferring PARPi resistance. Accordingly, PARPi have been studied in combination with other targeted therapies to overcome PARPi resistance, enhance PARPi efficacy, and sensitize tumors to PARP inhibition. Moreover, multiple clinical trials are now actively underway to evaluate novel combinations of PARPi with other anticancer therapies for the treatment of PARPi-resistant cancer. In this review, we highlight the mechanisms of action of PARP inhibitors with or without BRCA1/2 defects and provide an overview of the ongoing clinical trials of PARPi. We also review the current progress on PARPi-based combination strategies and PARP inhibitor resistance.
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Affiliation(s)
- Dae-Seok Kim
- grid.267313.20000 0000 9482 7121Laboratory 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 ,grid.267313.20000 0000 9482 7121Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Present Address: Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Cristel V. Camacho
- grid.267313.20000 0000 9482 7121Laboratory 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 ,grid.267313.20000 0000 9482 7121Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - W. Lee Kraus
- grid.267313.20000 0000 9482 7121Laboratory 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 ,grid.267313.20000 0000 9482 7121Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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214
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Moiani D, Link TM, Brosey CA, Katsonis P, Lichtarge O, Kim Y, Joachimiak A, Ma Z, Kim IK, Ahmed Z, Jones DE, Tsutakawa SE, Tainer JA. An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2. Methods Enzymol 2021; 661:407-431. [PMID: 34776222 PMCID: PMC8474023 DOI: 10.1016/bs.mie.2021.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present a Chemistry and Structure Screen Integrated Efficiently (CASSIE) approach (named for Greek prophet Cassandra) to design inhibitors for cancer biology and pathogenesis. CASSIE provides an effective path to target master keys to control the repair-replication interface for cancer cells and SARS CoV-2 pathogenesis as exemplified here by specific targeting of Poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribose glycohydrolase ARH3 macrodomains plus SARS CoV-2 nonstructural protein 3 (Nsp3) Macrodomain 1 (Mac1) and Nsp15 nuclease. As opposed to the classical massive effort employing libraries with large numbers of compounds against single proteins, we make inhibitor design for multiple targets efficient. Our compact, chemically diverse, 5000 compound Goldilocks (GL) library has an intermediate number of compounds sized between fragments and drugs with predicted favorable ADME (absorption, distribution, metabolism, and excretion) and toxicological profiles. Amalgamating our core GL library with an approved drug (AD) library, we employ a combined GLAD library virtual screen, enabling an effective and efficient design cycle of ranked computer docking, top hit biophysical and cell validations, and defined bound structures using human proteins or their avatars. As new drug design is increasingly pathway directed as well as molecular and mechanism based, our CASSIE approach facilitates testing multiple related targets by efficiently turning a set of interacting drug discovery problems into a tractable medicinal chemistry engineering problem of optimizing affinity and ADME properties based upon early co-crystal structures. Optimization efforts are made efficient by a computationally-focused iterative chemistry and structure screen. Thus, we herein describe and apply CASSIE to define prototypic, specific inhibitors for PARG vs distinct inhibitors for the related macrodomains of ARH3 and SARS CoV-2 Nsp3 plus the SARS CoV-2 Nsp15 RNA nuclease.
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Affiliation(s)
- Davide Moiani
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States,Department of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Todd M. Link
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States,Department of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chris A. Brosey
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States,Department of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Zhijun Ma
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Zamal Ahmed
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States,Department of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Darin E. Jones
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Susan E. Tsutakawa
- Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States,Corresponding authors:
| | - John A. Tainer
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States,Department of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States,Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States,Corresponding authors:
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215
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Blessing C, Mandemaker IK, Gonzalez-Leal C, Preisser J, Schomburg A, Ladurner AG. The Oncogenic Helicase ALC1 Regulates PARP Inhibitor Potency by Trapping PARP2 at DNA Breaks. Mol Cell 2020; 80:862-875.e6. [PMID: 33275888 DOI: 10.1016/j.molcel.2020.10.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/27/2020] [Accepted: 10/04/2020] [Indexed: 12/16/2022]
Abstract
The anti-tumor potency of poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) has been linked to trapping of PARP1 on damaged chromatin. However, little is known about their impact on PARP2, an isoform with overlapping functions at DNA lesions. Whether the release of PARP1/2 from DNA lesions is actively catalyzed by molecular machines is also not known. We found that PARPis robustly trap PARP2 and that the helicase ALC1 (CHD1L) is strictly required for PARP2 release. Catalytic inactivation of ALC1 quantitatively traps PARP2 but not PARP1. ALC1 manipulation impacts the response to single-strand DNA breaks through PARP2 trapping, potentiates PARPi-induced cancer cell killing, and mediates synthetic lethality upon BRCA deficiency. The chromatin remodeler ALC1 actively drives PARP2 turnover from DNA lesions, and PARP2 contributes to the cellular responses of PARPi. This suggests that disrupting the ATP-fueled remodeling forces of ALC1 might enable therapies that selectively target the DNA repair functions of PARPs in cancer.
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Affiliation(s)
- Charlotte Blessing
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School (IMPRS) for Molecular Life Sciences, 82152 Planegg-Martinsried, Germany
| | - Imke Karlijn Mandemaker
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Claudia Gonzalez-Leal
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School (IMPRS) for Molecular Life Sciences, 82152 Planegg-Martinsried, Germany
| | - Julia Preisser
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Adrian Schomburg
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; Eisbach Bio GmbH, Am Klopferspitz 19, 82152 Planegg-Martinsried, Germany
| | - Andreas Gerhard Ladurner
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; International Max Planck Research School (IMPRS) for Molecular Life Sciences, 82152 Planegg-Martinsried, Germany; Eisbach Bio GmbH, Am Klopferspitz 19, 82152 Planegg-Martinsried, Germany.
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216
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Rouleau-Turcotte É, Pascal JM. Bridging a DNA Break to Leave a Poly(ADP-Ribose) Mark on Chromatin. Mol Cell 2020; 80:560-561. [PMID: 33217315 DOI: 10.1016/j.molcel.2020.10.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bilokapic at al. (2020) capture PARP2 and its accessory factor HPF1 bridging a DNA break between two nucleosomes, providing a captivating view of the context in which PARP2/HPF1 employ ADP-ribose protein modification to coordinate DNA repair and alter chromatin structure.
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Affiliation(s)
- Élise Rouleau-Turcotte
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec H3T 1J4, Canada.
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217
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Shao Z, Lee BJ, Rouleau-Turcotte É, Langelier MF, Lin X, Estes VM, Pascal JM, Zha S. Clinical PARP inhibitors do not abrogate PARP1 exchange at DNA damage sites in vivo. Nucleic Acids Res 2020; 48:9694-9709. [PMID: 32890402 PMCID: PMC7515702 DOI: 10.1093/nar/gkaa718] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
DNA breaks recruit and activate PARP1/2, which deposit poly-ADP-ribose (PAR) to recruit XRCC1-Ligase3 and other repair factors to promote DNA repair. Clinical PARP inhibitors (PARPi) extend the lifetime of damage-induced PARP1/2 foci, referred to as ‘trapping’. To understand the molecular nature of ‘trapping’ in cells, we employed quantitative live-cell imaging and fluorescence recovery after photo-bleaching. Unexpectedly, we found that PARP1 exchanges rapidly at DNA damage sites even in the presence of clinical PARPi, suggesting the persistent foci are not caused by physical stalling. Loss of Xrcc1, a major downstream effector of PAR, also caused persistent PARP1 foci without affecting PARP1 exchange. Thus, we propose that the persistent PARP1 foci are formed by different PARP1 molecules that are continuously recruited to and exchanging at DNA lesions due to attenuated XRCC1-LIG3 recruitment and delayed DNA repair. Moreover, mutation analyses of the NAD+ interacting residues of PARP1 showed that PARP1 can be physically trapped at DNA damage sites, and identified H862 as a potential regulator for PARP1 exchange. PARP1-H862D, but not PARylation-deficient PARP1-E988K, formed stable PARP1 foci upon activation. Together, these findings uncovered the nature of persistent PARP1 foci and identified NAD+ interacting residues involved in the PARP1 exchange.
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Affiliation(s)
- Zhengping Shao
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York City, NY 10032, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York City, NY 10032, USA
| | - Élise Rouleau-Turcotte
- Université de Montréal, Biochemistry and Molecular Medicine, Montréal, Québec H3T 1J4, Canada
| | - Marie-France Langelier
- Université de Montréal, Biochemistry and Molecular Medicine, Montréal, Québec H3T 1J4, Canada
| | - Xiaohui Lin
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York City, NY 10032, USA
| | - Verna M Estes
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York City, NY 10032, USA
| | - John M Pascal
- Université de Montréal, Biochemistry and Molecular Medicine, Montréal, Québec H3T 1J4, Canada
| | - Shan Zha
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York City, NY 10032, USA.,Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of Pediatrics, College of Physicians & Surgeons, Columbia University, New York City, NY 10032, USA
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218
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Aberle L, Krüger A, Reber JM, Lippmann M, Hufnagel M, Schmalz M, Trussina IREA, Schlesiger S, Zubel T, Schütz K, Marx A, Hartwig A, Ferrando-May E, Bürkle A, Mangerich A. PARP1 catalytic variants reveal branching and chain length-specific functions of poly(ADP-ribose) in cellular physiology and stress response. Nucleic Acids Res 2020; 48:10015-10033. [PMID: 32667640 PMCID: PMC7544232 DOI: 10.1093/nar/gkaa590] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/24/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022] Open
Abstract
Poly(ADP-ribosyl)ation regulates numerous cellular processes like genome maintenance and cell death, thus providing protective functions but also contributing to several pathological conditions. Poly(ADP-ribose) (PAR) molecules exhibit a remarkable heterogeneity in chain lengths and branching frequencies, but the biological significance of this is basically unknown. To unravel structure-specific functions of PAR, we used PARP1 mutants producing PAR of different qualities, i.e. short and hypobranched (PARP1\G972R), short and moderately hyperbranched (PARP1\Y986S), or strongly hyperbranched PAR (PARP1\Y986H). By reconstituting HeLa PARP1 knockout cells, we demonstrate that PARP1\G972R negatively affects cellular endpoints, such as viability, cell cycle progression and genotoxic stress resistance. In contrast, PARP1\Y986S elicits only mild effects, suggesting that PAR branching compensates for short polymer length. Interestingly, PARP1\Y986H exhibits moderate beneficial effects on cell physiology. Furthermore, different PARP1 mutants have distinct effects on molecular processes, such as gene expression and protein localization dynamics of PARP1 itself, and of its downstream factor XRCC1. Finally, the biological relevance of PAR branching is emphasized by the fact that branching frequencies vary considerably during different phases of the DNA damage-induced PARylation reaction and between different mouse tissues. Taken together, this study reveals that PAR branching and chain length essentially affect cellular functions, which further supports the notion of a ‘PAR code’.
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Affiliation(s)
- Lisa Aberle
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Annika Krüger
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Julia M Reber
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michelle Lippmann
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Matthias Hufnagel
- Department of Food Chemistry and Toxicology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Michael Schmalz
- Department of Physics, University of Konstanz, 78457 Konstanz, Germany
| | | | - Sarah Schlesiger
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Tabea Zubel
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Karina Schütz
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Andrea Hartwig
- Department of Food Chemistry and Toxicology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | | | - Alexander Bürkle
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Aswin Mangerich
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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219
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Kühbacher U, Duxin JP. How to fix DNA-protein crosslinks. DNA Repair (Amst) 2020; 94:102924. [PMID: 32683310 PMCID: PMC7511601 DOI: 10.1016/j.dnarep.2020.102924] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/18/2022]
Abstract
Proteins that act on DNA, or are in close proximity to it, can become inadvertently crosslinked to DNA and form highly toxic lesions, known as DNA-protein crosslinks (DPCs). DPCs are generated by different chemotherapeutics, environmental or endogenous sources of crosslinking agents, or by lesions on DNA that stall the catalytic cycle of certain DNA processing enzymes. These bulky adducts impair processes on DNA such as DNA replication or transcription, and therefore pose a serious threat to genome integrity. The large diversity of DPCs suggests that there is more than one canonical mechanism to repair them. Indeed, many different enzymes have been shown to act on DPCs by either processing the protein, the DNA or the crosslink itself. In addition, the cell cycle stage or cell type are likely to dictate pathway choice. In recent years, a detailed understanding of DPC repair during S phase has started to emerge. Here, we review the current knowledge on the mechanisms of replication-coupled DPC repair, and describe and also speculate on possible pathways that remove DPCs outside of S phase. Moreover, we highlight a recent paradigm shifting finding that indicates that DPCs are not always detrimental, but can also play a protective role, preserving the genome from more deleterious forms of DNA damage.
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Affiliation(s)
- Ulrike Kühbacher
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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220
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Poly(ADP-ribose) Polymerase 1 (PARP1) restrains MyoD-dependent gene expression during muscle differentiation. Sci Rep 2020; 10:15086. [PMID: 32934320 PMCID: PMC7493885 DOI: 10.1038/s41598-020-72155-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
The myogenic factor MyoD regulates skeletal muscle differentiation by interacting with a variety of chromatin-modifying complexes. Although MyoD can induce and maintain chromatin accessibility at its target genes, its binding and trans-activation ability can be limited by some types of not fully characterized epigenetic constraints. In this work we analysed the role of PARP1 in regulating MyoD-dependent gene expression. PARP1 is a chromatin-associated enzyme, playing a well recognized role in DNA repair and that is implicated in transcriptional regulation. PARP1 affects gene expression through multiple mechanisms, often involving the Poly(ADP-ribosyl)ation of chromatin proteins. In line with PARP1 down-regulation during differentiation, we observed that PARP1 depletion boosts the up-regulation of MyoD targets, such as p57, myogenin, Mef2C and p21, while its re-expression reverts this effect. We also found that PARP1 interacts with some MyoD-binding regions and that its presence, independently of the enzymatic activity, interferes with MyoD recruitment and gene induction. We finally suggest a relationship between the binding of PARP1 and the loss of the activating histone modification H3K4me3 at MyoD-binding regions. This work highlights not only a novel player in the epigenetic control of myogenesis, but also a repressive and catalytic-independent mechanisms by which PARP1 regulates transcription.
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221
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Curtin NJ, Szabo C. Poly(ADP-ribose) polymerase inhibition: past, present and future. Nat Rev Drug Discov 2020; 19:711-736. [PMID: 32884152 DOI: 10.1038/s41573-020-0076-6] [Citation(s) in RCA: 340] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 12/11/2022]
Abstract
The process of poly(ADP-ribosyl)ation and the major enzyme that catalyses this reaction, poly(ADP-ribose) polymerase 1 (PARP1), were discovered more than 50 years ago. Since then, advances in our understanding of the roles of PARP1 in cellular processes such as DNA repair, gene transcription and cell death have allowed the investigation of therapeutic PARP inhibition for a variety of diseases - particularly cancers in which defects in DNA repair pathways make tumour cells highly sensitive to the inhibition of PARP activity. Efforts to identify and evaluate potent PARP inhibitors have so far led to the regulatory approval of four PARP inhibitors for the treatment of several types of cancer, and PARP inhibitors have also shown therapeutic potential in treating non-oncological diseases. This Review provides a timeline of PARP biology and medicinal chemistry, summarizes the pathophysiological processes in which PARP plays a role and highlights key opportunities and challenges in the field, such as counteracting PARP inhibitor resistance during cancer therapy and repurposing PARP inhibitors for the treatment of non-oncological diseases.
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Affiliation(s)
- Nicola J Curtin
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, University of Newcastle, Newcastle upon Tyne, UK.
| | - Csaba Szabo
- Chair of Pharmacology, Section of Science and Medicine, University of Fribourg, Fribourg, Switzerland.
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222
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Bilokapic S, Suskiewicz MJ, Ahel I, Halic M. Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin. Nature 2020; 585:609-613. [PMID: 32939087 PMCID: PMC7529888 DOI: 10.1038/s41586-020-2725-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023]
Abstract
Breaks in DNA strands recruit the protein PARP1 and its paralogue PARP2 to modify histones and other substrates through the addition of mono- and poly(ADP-ribose) (PAR)1-5. In the DNA damage responses, this post-translational modification occurs predominantly on serine residues6-8 and requires HPF1, an accessory factor that switches the amino acid specificity of PARP1 and PARP2 from aspartate or glutamate to serine9,10. Poly(ADP) ribosylation (PARylation) is important for subsequent chromatin decompaction and provides an anchor for the recruitment of downstream signalling and repair factors to the sites of DNA breaks2,11. Here, to understand the molecular mechanism by which PARP enzymes recognize DNA breaks within chromatin, we determined the cryo-electron-microscopic structure of human PARP2-HPF1 bound to a nucleosome. This showed that PARP2-HPF1 bridges two nucleosomes, with the broken DNA aligned in a position suitable for ligation, revealing the initial step in the repair of double-strand DNA breaks. The bridging induces structural changes in PARP2 that signal the recognition of a DNA break to the catalytic domain, which licenses HPF1 binding and PARP2 activation. Our data suggest that active PARP2 cycles through different conformational states to exchange NAD+ and substrate, which may enable PARP enzymes to act processively while bound to chromatin. The processes of PARP activation and the PARP catalytic cycle we describe can explain mechanisms of resistance to PARP inhibitors and will aid the development of better inhibitors as cancer treatments12-16.
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Affiliation(s)
- Silvija Bilokapic
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Mario Halic
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
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223
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Zhou P, Wang J, Mishail D, Wang CY. Recent advancements in PARP inhibitors-based targeted cancer therapy. PRECISION CLINICAL MEDICINE 2020; 3:187-201. [PMID: 32983586 PMCID: PMC7501589 DOI: 10.1093/pcmedi/pbaa030] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/11/2022] Open
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARPi) are a new class of agents with unparalleled clinical achievement for driving synthetic lethality in BRCA-deficient cancers. Recent FDA approval of PARPi has motivated clinical trials centered around the optimization of PARPi-associated therapies in a variety of BRCA-deficient cancers. This review highlights recent advancements in understanding the molecular mechanisms of PARP ‘trapping’ and synthetic lethality. Particular attention is placed on the potential extension of PARPi therapies from BRCA-deficient patients to populations with other homologous recombination-deficient backgrounds, and common characteristics of PARPi and non-homologous end-joining have been elucidated. The synergistic antitumor effect of combining PARPi with various immune checkpoint blockades has been explored to evaluate the potential of combination therapy in attaining greater therapeutic outcome. This has shed light onto the differing classifications of PARPi as well as the factors that result in altered PARPi activity. Lastly, acquired chemoresistance is a crucial issue for clinical application of PARPi. The molecular mechanisms underlying PARPi resistance and potential overcoming strategies are discussed.
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Affiliation(s)
- Ping Zhou
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Justin Wang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Daniel Mishail
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Cun-Yu Wang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
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224
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Kim C, Wang XD, Yu Y. PARP1 inhibitors trigger innate immunity via PARP1 trapping-induced DNA damage response. eLife 2020; 9:60637. [PMID: 32844745 PMCID: PMC7486119 DOI: 10.7554/elife.60637] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
It is being increasingly appreciated that the immunomodulatory functions of PARP1 inhibitors (PARPi) underlie their clinical activities in various BRCA-mutated tumors. PARPi possess both PARP1 inhibition and PARP1 trapping activities. The relative contribution of these two mechanisms toward PARPi-induced innate immune signaling, however, is poorly understood. We find that the presence of the PARP1 protein with uncompromised DNA-binding activities is required for PARPi-induced innate immune response. The activation of cGAS-STING signaling induced by various PARPi closely depends on their PARP1 trapping activities. Finally, we show that a small molecule PARP1 degrader blocks the enzymatic activity of PARP1 without eliciting PARP1 trapping or cGAS-STING activation. Our findings thus identify PARP1 trapping as a major contributor of the immunomodulatory functions of PARPi. Although PARPi-induced innate immunity is highly desirable in human malignancies, the ability of ‘non-trapping’ PARP1 degraders to avoid the activation of innate immune response could be useful in non-oncological diseases.
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Affiliation(s)
- Chiho Kim
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xu-Dong Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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225
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Human MYC G-quadruplex: From discovery to a cancer therapeutic target. Biochim Biophys Acta Rev Cancer 2020; 1874:188410. [PMID: 32827579 DOI: 10.1016/j.bbcan.2020.188410] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Overexpression of the MYC oncogene is a molecular hallmark of both cancer initiation and progression. Targeting MYC is a logical and effective cancer therapeutic strategy. A special DNA secondary structure, the G-quadruplex (G4), is formed within the nuclease hypersensitivity element III1 (NHE III1) region, located upstream of the MYC gene's P1 promoter that drives the majority of its transcription. Targeting such G4 structures has been a focus of anticancer therapies in recent decades. Thus, a comprehensive review of the MYC G4 structure and its role as a potential therapeutic target is timely. In this review, we first outline the discovery of the MYC G4 structure and evidence of its formation in vitro and in cells. Then, we describe the functional role of G4 in regulating MYC gene expression. We also summarize three types of MYC G4-interacting proteins that can promote, stabilize and unwind G4 structures. Finally, we discuss G4-binding molecules and the anticancer activities of G4-stabilizing ligands, including small molecular compounds and peptides, and assess their potential as novel anticancer therapeutics.
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Shao X, Pak S, Velagapudi UK, Gobbooru S, Kommaraju SS, Low WK, Subramaniam G, Pathak SK, Talele TT. Synthesis of 2,3-dihydrobenzo[b][1,4]dioxine-5-carboxamide and 3-oxo-3,4-dihydrobenzo[b][1,4]oxazine-8-carboxamide derivatives as PARP1 inhibitors. Bioorg Chem 2020; 102:104075. [PMID: 32777641 DOI: 10.1016/j.bioorg.2020.104075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/27/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1), a widely explored anticancer drug target, plays an important role in single-strand DNA break repair processes. High-throughput virtual screening (HTVS) of a Maybridge small molecule library using the PARP1-benzimidazole-4-carboxamide co-crystal structure and pharmacophore model led to the identification of eleven compounds. These compounds were evaluated using recombinant PARP1 enzyme assay that resulted in the acquisition of three PARP1 inhibitors: 3 (IC50 = 12 μM), 4 (IC50 = 5.8 μM), and 10 (IC50 = 0.88 μM). Compound 4 (2,3-dihydro-1,4-benzodioxine-5-carboxamide) was selected as a lead and was subjected to further chemical modifications, involving analogue synthesis and scaffold hopping. These efforts led to the identification of (Z)-2-(4-hydroxybenzylidene)-3-oxo-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-carboxamide (49, IC50 = 0.082 μM) as the most potent inhibitor of PARP1 from the series.
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Affiliation(s)
- Xuwei Shao
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Steven Pak
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Uday Kiran Velagapudi
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Shruthi Gobbooru
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Sai Shilpa Kommaraju
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Woon-Kai Low
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Gopal Subramaniam
- Chemistry and Biochemistry Department, Queens College of the City University of New York, 65-30 Kissena Blvd., Flushing, NY 11367, USA
| | - Sanjai Kumar Pathak
- Chemistry and Biochemistry Department, Queens College of the City University of New York, 65-30 Kissena Blvd., Flushing, NY 11367, USA; Chemistry Doctoral Program, Biochemistry Doctoral Program, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA.
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Aleksandrov R, Hristova R, Stoynov S, Gospodinov A. The Chromatin Response to Double-Strand DNA Breaks and Their Repair. Cells 2020; 9:cells9081853. [PMID: 32784607 PMCID: PMC7464352 DOI: 10.3390/cells9081853] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular DNA is constantly being damaged by numerous internal and external mutagenic factors. Probably the most severe type of insults DNA could suffer are the double-strand DNA breaks (DSBs). They sever both DNA strands and compromise genomic stability, causing deleterious chromosomal aberrations that are implicated in numerous maladies, including cancer. Not surprisingly, cells have evolved several DSB repair pathways encompassing hundreds of different DNA repair proteins to cope with this challenge. In eukaryotic cells, DSB repair is fulfilled in the immensely complex environment of the chromatin. The chromatin is not just a passive background that accommodates the multitude of DNA repair proteins, but it is a highly dynamic and active participant in the repair process. Chromatin alterations, such as changing patterns of histone modifications shaped by numerous histone-modifying enzymes and chromatin remodeling, are pivotal for proficient DSB repair. Dynamic chromatin changes ensure accessibility to the damaged region, recruit DNA repair proteins, and regulate their association and activity, contributing to DSB repair pathway choice and coordination. Given the paramount importance of DSB repair in tumorigenesis and cancer progression, DSB repair has turned into an attractive target for the development of novel anticancer therapies, some of which have already entered the clinic.
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Gomez MK, Illuzzi G, Colomer C, Churchman M, Hollis RL, O’Connor MJ, Gourley C, Leo E, Melton DW. Identifying and Overcoming Mechanisms of PARP Inhibitor Resistance in Homologous Recombination Repair-Deficient and Repair-Proficient High Grade Serous Ovarian Cancer Cells. Cancers (Basel) 2020; 12:cancers12061503. [PMID: 32526907 PMCID: PMC7353027 DOI: 10.3390/cancers12061503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/20/2022] Open
Abstract
High grade serous ovarian cancer (HGSOC) is a major cause of female cancer mortality. The approval of poly (ADP-ribose) polymerase (PARP) inhibitors for clinical use has greatly improved treatment options for patients with homologous recombination repair (HRR)-deficient HGSOC, although the development of PARP inhibitor resistance in some patients is revealing limitations to outcome. A proportion of patients with HRR-proficient cancers also benefit from PARP inhibitor therapy. Our aim is to compare mechanisms of resistance to the PARP inhibitor olaparib in these two main molecular categories of HGSOC and investigate a way to overcome resistance that we considered particularly suited to a cancer like HGSOC, where there is a very high incidence of TP53 gene mutation, making HGSOC cells heavily reliant on the G2 checkpoint for repair of DNA damage and survival. We identified alterations in multiple factors involved in resistance to PARP inhibition in both HRR-proficient and -deficient cancers. The most frequent change was a major reduction in levels of poly (ADP-ribose) glycohydrolase (PARG), which would be expected to preserve a residual PARP1-initiated DNA damage response to DNA single-strand breaks. Other changes seen would be expected to boost levels of HRR of DNA double-strand breaks. Growth of all olaparib-resistant clones isolated could be controlled by WEE1 kinase inhibitor AZD1775, which inactivates the G2 checkpoint. Our work suggests that use of the WEE1 kinase inhibitor could be a realistic therapeutic option for patients that develop resistance to olaparib.
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Affiliation(s)
- Miriam K. Gomez
- Nicola Murray Centre for Ovarian Cancer Research, Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (M.K.G.); (M.C.); (R.L.H.); (C.G.)
| | - Giuditta Illuzzi
- Early Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (G.I.); (C.C.); (M.J.O.); (E.L.)
| | - Carlota Colomer
- Early Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (G.I.); (C.C.); (M.J.O.); (E.L.)
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (M.K.G.); (M.C.); (R.L.H.); (C.G.)
| | - Robert L. Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (M.K.G.); (M.C.); (R.L.H.); (C.G.)
| | - Mark J. O’Connor
- Early Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (G.I.); (C.C.); (M.J.O.); (E.L.)
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (M.K.G.); (M.C.); (R.L.H.); (C.G.)
| | - Elisabetta Leo
- Early Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (G.I.); (C.C.); (M.J.O.); (E.L.)
| | - David W. Melton
- Nicola Murray Centre for Ovarian Cancer Research, Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (M.K.G.); (M.C.); (R.L.H.); (C.G.)
- Correspondence:
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Rudolph J, Mahadevan J, Luger K. Probing the Conformational Changes Associated with DNA Binding to PARP1. Biochemistry 2020; 59:2003-2011. [PMID: 32357296 PMCID: PMC12066077 DOI: 10.1021/acs.biochem.0c00256] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is an important first responder in the mechanism of DNA repair in eukaryotic cells. It is also a validated drug target, with four different PARP inhibitors (PARPi) approved for the treatment of BRCA-negative cancers. Despite past efforts, many aspects of PARPi are poorly understood, in particular their ability to trap PARP1 on chromatin and the relationships between their potencies, cellular toxicities, and trapping efficiencies. Because PARP trapping is widely believed to originate in allosteric coupling between DNA binding and the catalytic site, we further investigated the binding properties of PARP1 to a model for DNA with a double-strand break in the presence and absence of PARPi. Specifically, we have used sequential mixing stopped-flow spectroscopy to identify a slow conformational change that follows rapid DNA binding. Using a range of DNA concentrations and different mutants of PARP1 we demonstrate that this conformational change is one of the steps of the "monkey bar mechanism" that promotes DNA-dependent dissociation of DNA. This conformational change also corresponds to the previously identified conformational change associated with DNA-dependent activation of PARP1. Despite linking the conformational change associated with DNA binding and release to DNA activation, we find no evidence for PARPi perturbing this allosteric coupling.
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Affiliation(s)
- Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Jyothi Mahadevan
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
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230
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Abstract
Understanding anticancer drug binding to its target could improve drug discovery and efficacy
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Affiliation(s)
- Dea Slade
- Max Perutz Labs, University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
| | - Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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