1
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Gnanavelou R, Jayaraman M, Jeyaraman J, Girija KR. Computational design and structural insights into quinazoline-based lead molecules for targeting PARP10 in cancer therapy. J Mol Graph Model 2025; 137:109005. [PMID: 40101436 DOI: 10.1016/j.jmgm.2025.109005] [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: 01/30/2025] [Revised: 02/28/2025] [Accepted: 03/01/2025] [Indexed: 03/20/2025]
Abstract
Quinazoline scaffolds, a class of nitrogen-containing heterocyclic compounds, are considered a "privileged structure" in drug development due to their broad physiological activities and significant therapeutic potential. Many anti-breast cancer therapies are designed using this pharmacophore. Structural modifications such as halogen substitution and aromatic amino group insertion have been explored to improve the anticancer efficacy of quinazoline derivatives. Breast cancer continues to be the primary cause of cancer-related mortality among women, approximately 670,000 deaths globally in 2022, emphasizing the need for novel therapies. To combat multidrug resistance in breast cancer, new drug candidates targeting the Poly (ADP-ribose) polymerase (PARP) enzyme are being developed to improve chemotherapeutic efficacy and reduce toxicity. In this study, computational screening of 365 quinazoline derivatives was conducted to identify potential PARP inhibitors. Docking based screening identified three quinazoline scaffolds (RFAP77, RISA30, and RISAC) as top hits, demonstrating docking scores ranging from -8.41 to -9.31 kcal/mol and MM-GBSA binding free energy scores between -52.08 and -55.99 kcal/mol, compared to the reference approved inhibitor. ADMET analysis revealed favorable predicted drug-likeness profiles for the identified scaffolds. The structural stability of the docked PARP-ligand complexes was further investigated using molecular dynamics simulations (MDS). The computational simulations revealed significant conformational changes upon ligand binding, as evidenced by RMSD, RMSF, and hydrogen bond analyses. Essential dynamics analysis, including PCA-based FEL mapping, demonstrated energy minima profiles for all top docked PARP complexes. These computational findings highlight the potential of these scaffolds as promising candidates for further development as PARP inhibitors.
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Affiliation(s)
- Revathi Gnanavelou
- Department of Pharmaceutical Chemistry, College of Pharmacy, Mother Theresa Post Graduate and Research Institute of Health Sciences, (A Govt. of Puducherry Institution), Puducherry, 605 006, India
| | - Manikandan Jayaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Konda Reddy Girija
- Department of Pharmaceutical Chemistry, College of Pharmacy, Mother Theresa Post Graduate and Research Institute of Health Sciences, (A Govt. of Puducherry Institution), Puducherry, 605 006, India.
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2
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McFarland MR, Kulathu Y. Emerging tools and methods to study cell signalling mediated by branched ubiquitin chains. Biochem Soc Trans 2025:BST20253015. [PMID: 40380883 DOI: 10.1042/bst20253015] [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: 01/21/2025] [Accepted: 04/30/2025] [Indexed: 05/19/2025]
Abstract
Branched ubiquitin chains are complex molecular structures in which two or more ubiquitin moieties are attached to distinct lysine residues of a single ubiquitin molecule within a polyubiquitin chain. These bifurcated architectures significantly expand the signalling capacity of the ubiquitin system. Although branched chains constitute a substantial fraction of cellular polyubiquitin, their biological functions largely remain enigmatic due to their complex nature and the associated technical challenges of studying them. Recent technological innovations have enabled the identification of key molecular players and revealed essential roles for branched chains in diverse cellular processes. In this review, we discuss the bespoke strategies that have driven these discoveries, as well as the technologies needed to advance this rapidly evolving field.
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Affiliation(s)
- Matthew R McFarland
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, U.K
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, U.K
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3
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Huang C, Xiao H, Yang Y, Luo J, Lai Y, Liu S, Mao K, Chen J, Wang L. Adenosine diphosphate-ribosylation greatly affects proteins function: a focus on neurodegenerative diseases. Front Aging Neurosci 2025; 17:1575204. [PMID: 40370754 PMCID: PMC12075376 DOI: 10.3389/fnagi.2025.1575204] [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: 02/13/2025] [Accepted: 04/14/2025] [Indexed: 05/16/2025] Open
Abstract
Adenosine diphosphate-ribosylation (ADPRylation) is a reversible posttranslational modification that plays a crucial role in cellular homeostasis and disease development. ADPRylation is produced via nicotinamide adenine dinucleotide hydrolysis and modifies proteins via corresponding transferases, mainly poly(ADP-ribose) polymerases (PARPs), the inhibitors of which have been used in the clinical treatment of cancer. ADPRylation is involved in various physiological processes, including pathogen infection, inflammation, DNA repair, and neurological disorders. In neurodegenerative diseases (NDs), dysregulated ADPRylation contributes to protein aggregation, neuroinflammation, and metabolic disturbances, while targeted modulation shows therapeutic potential. ADPRylation differentially regulates neurodegenerative processes, and PARP inhibitors can reduce neuroinflammation, oxidative stress, and metabolic dysfunction. However, challenges such as poor blood-brain barrier penetration and cell type-specific responses limit clinical translation. This review summarizes recent findings on the role of ADPRylation and PARPs in NDs, highlighting their involvement in protein aggregation and cellular signaling. It emphasizes the importance of ADPRylation in neuronal cells and supports the development of precision therapies targeting this pathway to address current treatment challenges in NDs.
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Affiliation(s)
- Chaowen Huang
- Department of Respiratory Medicine, Jiangmen Central Hospital Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
| | - Huilin Xiao
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yang Yang
- Department of Rehabilitation, Affiliated Shenzhen Baoan Central Hospital Group of Guangdong Medical University, Shenzhen, China
| | - Jiankun Luo
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yixi Lai
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Shizhen Liu
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Kanmin Mao
- Hubei Key Laboratory of Food Nutrition and Safety and the Ministry of Education (MOE) Key Laboratory of Environment and Health, Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jialong Chen
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Liling Wang
- Department of Rehabilitation, Affiliated Shenzhen Baoan Central Hospital Group of Guangdong Medical University, Shenzhen, China
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4
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Straka J, Khatib JB, Pale L, Nicolae CM, Moldovan GL. CAF-1 promotes efficient PrimPol recruitment to nascent DNA for single-stranded DNA gap formation. Nucleic Acids Res 2024; 52:13865-13880. [PMID: 39558157 DOI: 10.1093/nar/gkae1068] [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: 09/18/2024] [Accepted: 10/22/2024] [Indexed: 11/20/2024] Open
Abstract
Suppression of single-stranded DNA (ssDNA) gap accumulation at replication forks has emerged as a potential determinant of chemosensitivity in homologous recombination (HR)-deficient tumors, as ssDNA gaps are transformed into cytotoxic double-stranded DNA breaks. We have previously shown that the histone chaperone CAF-1's nucleosome deposition function is vital to preventing degradation of stalled replication forks correlating with HR-deficient cells' response to genotoxic drugs. Here we report that the CAF-1-ASF1 pathway promotes ssDNA gap accumulation at replication forks in both wild-type and breast cancer (BRCA)-deficient backgrounds. We show that this is independent of CAF-1's nucleosome deposition function but instead may rely on its proper localization to replication forks. Moreover, we show that the efficient localization to nascent DNA of PrimPol, the enzyme responsible for repriming upon replication stress, is dependent on CAF-1. As PrimPol has been shown to be responsible for generating ssDNA gaps as a byproduct of its repriming function, CAF-1's role in its recruitment could directly impact ssDNA gap formation. We also show that chemoresistance observed in HR-deficient cells when CAF-1 or ASF1A are lost correlates with suppression of ssDNA gaps rather than protection of stalled replication forks. Overall, this work identifies an unexpected role of CAF-1 in regulating PrimPol recruitment and ssDNA gap generation.
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Affiliation(s)
- Joshua Straka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Jude B Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Lindsey Pale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- 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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5
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Morone B, Grimaldi G. PARP enzymes and mono-ADP-ribosylation: advancing the connection from interferon-signalling to cancer biology. Expert Rev Mol Med 2024; 26:e17. [PMID: 39189367 PMCID: PMC11440612 DOI: 10.1017/erm.2024.13] [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: 11/30/2023] [Revised: 03/05/2024] [Accepted: 03/20/2024] [Indexed: 08/28/2024]
Abstract
ADP-ribosyltransferases of the PARP family encompass a group of enzymes with variegated regulatory functions in cells, ranging from DNA damage repair to the control of cell-cycle progression and immune response. Over the years, this knowledge has led to the use of PARP1/2 inhibitors as mainstay pharmaceutical strategies for the treatment of ovarian, pancreatic, prostate and breast cancers, holding mutations in genes encoding for proteins involved in the DNA repair mechanisms (synthetic lethality). Meanwhile, the last decade has witnessed significant progress in comprehending cellular pathways regulated by mono-ADP-ribosylation, with a huge effort in the development of novel selective compounds to inhibit those PARPs endowed with mono-ADP-ribosylation activity. This review focuses on the progress achieved in the cancer field, delving into most recent findings regarding the role of a subset of enzymes - the interferon-stimulated PARPs - in cancer progression.
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Affiliation(s)
- Barbara Morone
- Institute for Endocrinology and Experimental Oncology, National Research Council, Via Pietro Castellino 111, Napoli, Italy
| | - Giovanna Grimaldi
- Institute for Endocrinology and Experimental Oncology, National Research Council, Via Pietro Castellino 111, Napoli, Italy
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6
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Waltho A, Popp O, Lenz C, Pluska L, Lambert M, Dötsch V, Mertins P, Sommer T. K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific ubiquitin interactors. Life Sci Alliance 2024; 7:e202402740. [PMID: 38803224 PMCID: PMC11109483 DOI: 10.26508/lsa.202402740] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
The ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different lengths, linkage types, and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying lengths, as well as homotypic and heterotypic branched chains of the two most abundant linkage types-lysine 48-linked (K48) and lysine 63-linked (K63) Ub. We identified some of the first K48/K63-linked branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4, and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50, and p97 adaptor FAF1. Crucially, we compared datasets collected using two common deubiquitinase inhibitors-chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.
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Affiliation(s)
- Anita Waltho
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Christopher Lenz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Lukas Pluska
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
| | - Mahil Lambert
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Volker Dötsch
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thomas Sommer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
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7
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Feijs-Žaja KLH, Ikenga NJ, Žaja R. Pathological and physiological roles of ADP-ribosylation: established functions and new insights. Biol Chem 2024:hsz-2024-0057. [PMID: 39066732 DOI: 10.1515/hsz-2024-0057] [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: 04/12/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
The posttranslational modification of proteins with poly(ADP-ribose) was discovered in the sixties. Since then, we have learned that the enzymes involved, the so-called poly(ADP-ribosyl)polymerases (PARPs), are transferases which use cofactor NAD+ to transfer ADP-ribose to their targets. Few PARPs are able to create poly(ADP-ribose), whereas the majority transfers a single ADP-ribose. In the last decade, hydrolases were discovered which reverse mono(ADP-ribosyl)ation, detection methods were developed and new substrates were defined, including nucleic acids. Despite the continued effort, relatively little is still known about the biological function of most PARPs. In this review, we summarise key functions of ADP-ribosylation and introduce emerging insights.
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Affiliation(s)
- Karla L H Feijs-Žaja
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Nonso J Ikenga
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Roko Žaja
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
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8
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Khatib JB, Dhoonmoon A, Moldovan GL, Nicolae CM. PARP10 promotes the repair of nascent strand DNA gaps through RAD18 mediated translesion synthesis. Nat Commun 2024; 15:6197. [PMID: 39043663 PMCID: PMC11266678 DOI: 10.1038/s41467-024-50429-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
Replication stress compromises genomic integrity. Fork blocking lesions such as those induced by cisplatin and other chemotherapeutic agents arrest replication forks. Repriming downstream of these lesions represents an important mechanism of replication restart, however the single stranded DNA (ssDNA) gaps left behind, unless efficiently filled, can serve as entry point for nucleases. Nascent strand gaps can be repaired by BRCA-mediated homology repair. Alternatively, gaps can also be filled by translesion synthesis (TLS) polymerases. How these events are regulated is still not clear. Here, we show that PARP10, a poorly-characterized mono-ADP-ribosyltransferase, is recruited to nascent strand gaps to promote their repair. PARP10 interacts with the ubiquitin ligase RAD18 and recruits it to these structures, resulting in the ubiquitination of the replication factor PCNA. PCNA ubiquitination, in turn, recruits the TLS polymerase REV1 for gap filling. We show that PARP10 recruitment to gaps and the subsequent REV1-mediated gap filling requires both the catalytic activity of PARP10, and its ability to interact with PCNA. We moreover show that PARP10 is hyperactive in BRCA-deficient cells, and its inactivation potentiates gap accumulations and cytotoxicity in these cells. Our work uncovers PARP10 as a regulator of ssDNA gap filling, which promotes genomic stability in BRCA-deficient cells.
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Affiliation(s)
- Jude B Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ashna Dhoonmoon
- 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
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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9
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Wu H, Lu A, Yuan J, Yu Y, Lv C, Lu J. Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms. Cell Death Discov 2024; 10:226. [PMID: 38734665 PMCID: PMC11088682 DOI: 10.1038/s41420-024-01994-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
The functional alterations of proteins and nucleic acids mainly rely on their modifications. ADP-ribosylation is a NAD+-dependent modification of proteins and, in some cases, of nucleic acids. This modification is broadly categorized as Mono(ADP-ribosyl)ation (MARylation) or poly(ADP-ribosyl)ation (PARylation). MARylation catalyzed by mono(ADP-ribosyl) transferases (MARTs) is more common in cells and the number of MARTs is much larger than poly(ADP-ribosyl) transferases. Unlike PARylation is well-characterized, research on MARylation is at the starting stage. However, growing evidence demonstrate the cellular functions of MARylation, supporting its potential roles in human health and diseases. In this review, we outlined MARylation-associated proteins including MARTs, the ADP-ribosyl hydrolyses and ADP-ribose binding domains. We summarized up-to-date findings about MARylation onto newly identified substrates including protein, DNA and RNA, and focused on the functions of these reactions in pathophysiological conditions as well as speculated the potential mechanisms. Furthermore, new strategies of MARylation detection and the current state of MARTs inhibitors were discussed. We also provided an outlook for future study, aiming to revealing the unknown biological properties of MARylation and its relevant mechanisms, and establish a novel therapeutic perspective in human diseases.
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Affiliation(s)
- Hao Wu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Anqi Lu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Jiuzhi Yuan
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yang Yu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Chongning Lv
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
- Liaoning Provincial Key Laboratory of TCM Resources Conservation and Development, Shenyang Pharmaceutical University, Shenyang, China
| | - Jincai Lu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China.
- Liaoning Provincial Key Laboratory of TCM Resources Conservation and Development, Shenyang Pharmaceutical University, Shenyang, China.
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10
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Ferrão Maciel-Fiuza M, Rengel BD, Wachholz GE, do Amaral Gomes J, de Oliveira MR, Kowalski TW, Roehe PM, Luiz Vianna FS, Schüler-Faccini L, Mayer FQ, Varela APM, Fraga LR. New candidate genes potentially involved in Zika virus teratogenesis. Comput Biol Med 2024; 173:108259. [PMID: 38522248 DOI: 10.1016/j.compbiomed.2024.108259] [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: 11/16/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Despite efforts to elucidate Zika virus (ZIKV) teratogenesis, still several issues remain unresolved, particularly on the molecular mechanisms behind the pathogenesis of Congenital Zika Syndrome (CZS). To answer this question, we used bioinformatics tools, animal experiments and human gene expression analysis to investigate genes related to brain development potentially involved in CZS. Searches in databases for genes related to brain development and CZS were performed, and a protein interaction network was created. The expression of these genes was analyzed in a CZS animal model and secondary gene expression analysis (DGE) was performed in human cells exposed to ZIKV. A total of 2610 genes were identified in the databases, of which 1013 were connected. By applying centrality statistics of the global network, 36 candidate genes were identified, which, after selection resulted in nine genes. Gene expression analysis revealed distinctive expression patterns for PRKDC, PCNA, ATM, SMC3 as well as for FGF8 and SHH in the CZS model. Furthermore, DGE analysis altered expression of ATM, PRKDC, PCNA. In conclusion, systems biology are helpful tools to identify candidate genes to be validated in vitro and in vivo. PRKDC, PCNA, ATM, SMC3, FGF8 and SHH have altered expression in ZIKV-induced brain malformations.
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Affiliation(s)
- Miriãn Ferrão Maciel-Fiuza
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Bruna Duarte Rengel
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Gabriela Elis Wachholz
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Julia do Amaral Gomes
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Maikel Rosa de Oliveira
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Teratogen Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - Paulo Michel Roehe
- Department of Microbiology, Immunology and Parasitology, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lavínia Schüler-Faccini
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Teratogen Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Fabiana Quoos Mayer
- Graduate Program in Molecular and Cellular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Paula Muterle Varela
- Graduate Program in Biosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.
| | - Lucas Rosa Fraga
- Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
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11
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Nusawardhana A, Pale LM, Nicolae CM, Moldovan GL. USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress. Nucleic Acids Res 2024; 52:2340-2354. [PMID: 38180818 PMCID: PMC10954467 DOI: 10.1093/nar/gkad1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
DNA replication stress-induced fork arrest represents a significant threat to genomic integrity. One major mechanism of replication restart involves repriming downstream of the arrested fork by PRIMPOL, leaving behind a single-stranded DNA (ssDNA) gap. Accumulation of nascent strand ssDNA gaps has emerged as a possible determinant of the cellular hypersensitivity to genotoxic agents in certain genetic backgrounds such as BRCA deficiency, but how gaps are converted into cytotoxic structures is still unclear. Here, we investigate the processing of PRIMPOL-dependent ssDNA gaps upon replication stress induced by hydroxyurea and cisplatin. We show that gaps generated in PRIMPOL-overexpressing cells are expanded in the 3'-5' direction by the MRE11 exonuclease, and in the 5'-3' direction by the EXO1 exonuclease. This bidirectional exonucleolytic gap expansion ultimately promotes their conversion into DSBs. We moreover identify the de-ubiquitinating enzyme USP1 as a critical regulator of PRIMPOL-generated ssDNA gaps. USP1 promotes gap accumulation during S-phase, and their expansion by the MRE11 and EXO1 nucleases. This activity of USP1 is linked to its role in de-ubiquitinating PCNA, suggesting that PCNA ubiquitination prevents gap accumulation during replication. Finally, we show that USP1 depletion suppresses DSB formation in PRIMPOL-overexpressing cells, highlighting an unexpected role for USP1 in promoting genomic instability under these conditions.
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Affiliation(s)
- Alexandra Nusawardhana
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Lindsey M Pale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- 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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12
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Khatib JB, Nicolae CM, Moldovan GL. Role of Translesion DNA Synthesis in the Metabolism of Replication-associated Nascent Strand Gaps. J Mol Biol 2024; 436:168275. [PMID: 37714300 PMCID: PMC10842951 DOI: 10.1016/j.jmb.2023.168275] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Translesion DNA synthesis (TLS) is a DNA damage tolerance pathway utilized by cells to overcome lesions encountered throughout DNA replication. During replication stress, cancer cells show increased dependency on TLS proteins for cellular survival and chemoresistance. TLS proteins have been described to be involved in various DNA repair pathways. One of the major emerging roles of TLS is single-stranded DNA (ssDNA) gap-filling, primarily after the repriming activity of PrimPol upon encountering a lesion. Conversely, suppression of ssDNA gap accumulation by TLS is considered to represent a mechanism for cancer cells to evade the toxicity of chemotherapeutic agents, specifically in BRCA-deficient cells. Thus, TLS inhibition is emerging as a potential treatment regimen for DNA repair-deficient tumors.
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Affiliation(s)
- Jude B Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA. https://twitter.com/JudeBKhatib
| | - Claudia M Nicolae
- 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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13
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Hale A, Dhoonmoon A, Straka J, Nicolae CM, Moldovan GL. Multi-step processing of replication stress-derived nascent strand DNA gaps by MRE11 and EXO1 nucleases. Nat Commun 2023; 14:6265. [PMID: 37805499 PMCID: PMC10560291 DOI: 10.1038/s41467-023-42011-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023] Open
Abstract
Accumulation of single stranded DNA (ssDNA) gaps in the nascent strand during DNA replication has been associated with cytotoxicity and hypersensitivity to genotoxic stress, particularly upon inactivation of the BRCA tumor suppressor pathway. However, how ssDNA gaps contribute to genotoxicity is not well understood. Here, we describe a multi-step nucleolytic processing of replication stress-induced ssDNA gaps which converts them into cytotoxic double stranded DNA breaks (DSBs). We show that ssDNA gaps are extended bidirectionally by MRE11 in the 3'-5' direction and by EXO1 in the 5'-3' direction, in a process which is suppressed by the BRCA pathway. Subsequently, the parental strand at the ssDNA gap is cleaved by the MRE11 endonuclease generating a double strand break. We also show that exposure to bisphenol A (BPA) and diethylhexyl phthalate (DEHP), which are widespread environmental contaminants due to their use in plastics manufacturing, causes nascent strand ssDNA gaps during replication. These gaps are processed through the same mechanism described above to generate DSBs. Our work sheds light on both the relevance of ssDNA gaps as major determinants of genomic instability, as well as the mechanism through which they are processed to generate genomic instability and cytotoxicity.
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Affiliation(s)
- Anastasia Hale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Joshua Straka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Claudia M Nicolae
- 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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14
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Suskiewicz MJ, Munnur D, Strømland Ø, Yang JC, Easton L, Chatrin C, Zhu K, Baretić D, Goffinont S, Schuller M, Wu WF, Elkins J, Ahel D, Sanyal S, Neuhaus D, Ahel I. Updated protein domain annotation of the PARP protein family sheds new light on biological function. Nucleic Acids Res 2023; 51:8217-8236. [PMID: 37326024 PMCID: PMC10450202 DOI: 10.1093/nar/gkad514] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023] Open
Abstract
AlphaFold2 and related computational tools have greatly aided studies of structural biology through their ability to accurately predict protein structures. In the present work, we explored AF2 structural models of the 17 canonical members of the human PARP protein family and supplemented this analysis with new experiments and an overview of recent published data. PARP proteins are typically involved in the modification of proteins and nucleic acids through mono or poly(ADP-ribosyl)ation, but this function can be modulated by the presence of various auxiliary protein domains. Our analysis provides a comprehensive view of the structured domains and long intrinsically disordered regions within human PARPs, offering a revised basis for understanding the function of these proteins. Among other functional insights, the study provides a model of PARP1 domain dynamics in the DNA-free and DNA-bound states and enhances the connection between ADP-ribosylation and RNA biology and between ADP-ribosylation and ubiquitin-like modifications by predicting putative RNA-binding domains and E2-related RWD domains in certain PARPs. In line with the bioinformatic analysis, we demonstrate for the first time PARP14's RNA-binding capability and RNA ADP-ribosylation activity in vitro. While our insights align with existing experimental data and are probably accurate, they need further validation through experiments.
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Affiliation(s)
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - 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
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Domagoj Baretić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Wing-Fung Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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15
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Nizi MG, Sarnari C, Tabarrini O. Privileged Scaffolds for Potent and Specific Inhibitors of Mono-ADP-Ribosylating PARPs. Molecules 2023; 28:5849. [PMID: 37570820 PMCID: PMC10420676 DOI: 10.3390/molecules28155849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
The identification of new targets to address unmet medical needs, better in a personalized way, is an urgent necessity. The introduction of PARP1 inhibitors into therapy, almost ten years ago, has represented a step forward this need being an innovate cancer treatment through a precision medicine approach. The PARP family consists of 17 members of which PARP1 that works by poly-ADP ribosylating the substrate is the sole enzyme so far exploited as therapeutic target. Most of the other members are mono-ADP-ribosylating (mono-ARTs) enzymes, and recent studies have deciphered their pathophysiological roles which appear to be very extensive with various potential therapeutic applications. In parallel, a handful of mono-ARTs inhibitors emerged that have been collected in a perspective on 2022. After that, additional very interesting compounds were identified highlighting the hot-topic nature of this research field and prompting an update. From the present review, where we have reported only mono-ARTs inhibitors endowed with the appropriate profile of pharmacological tools or drug candidate, four privileged scaffolds clearly stood out that constitute the basis for further drug discovery campaigns.
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Affiliation(s)
- Maria Giulia Nizi
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy;
| | | | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy;
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16
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Lovsund T, Mashayekhi F, Fitieh A, Stafford J, Ismail IH. Unravelling the Role of PARP1 in Homeostasis and Tumorigenesis: Implications for Anti-Cancer Therapies and Overcoming Resistance. Cells 2023; 12:1904. [PMID: 37508568 PMCID: PMC10378431 DOI: 10.3390/cells12141904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Detailing the connection between homeostatic functions of enzymatic families and eventual progression into tumorigenesis is crucial to our understanding of anti-cancer therapies. One key enzyme group involved in this process is the Poly (ADP-ribose) polymerase (PARP) family, responsible for an expansive number of cellular functions, featuring members well established as regulators of DNA repair, genomic stability and beyond. Several PARP inhibitors (PARPi) have been approved for clinical use in a range of cancers, with many more still in trials. Unfortunately, the occurrence of resistance to PARPi therapy is growing in prevalence and requires the introduction of novel counter-resistance mechanisms to maintain efficacy. In this review, we summarize the updated understanding of the vast homeostatic functions the PARP family mediates and pin the importance of PARPi therapies as anti-cancer agents while discussing resistance mechanisms and current up-and-coming counter-strategies for countering such resistance.
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Affiliation(s)
- Taylor Lovsund
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Amira Fitieh
- Department of Biophysics, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - James Stafford
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
- Department of Biophysics, Faculty of Science, Cairo University, Giza 12613, Egypt
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17
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Dhoonmoon A, Nicolae CM. Mono-ADP-ribosylation by PARP10 and PARP14 in genome stability. NAR Cancer 2023; 5:zcad009. [PMID: 36814782 PMCID: PMC9940457 DOI: 10.1093/narcan/zcad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
ADP-ribosylation is a post-translational modification involved in a variety of processes including DNA damage repair, transcriptional regulation, and cellular proliferation. Depending on the number of ADP moieties transferred to target proteins, ADP-ribosylation can be classified either as mono-ADP-ribosylation (MARylation) or poly-ADP-ribosylation (PARylation). This post-translational modification is catalyzed by enzymes known as ADP-ribosyltransferases (ARTs), which include the poly (ADP-ribose)-polymerase (PARP) superfamily of proteins. Certain members of the PARP family including PARP1 and PARP2 have been extensively studied and assessed as therapeutic targets. However, the other members of the PARP family of protein are not as well studied but have gained attention in recent years given findings suggesting their roles in an increasing number of cellular processes. Among these other members are PARP10 and PARP14, which have gradually emerged as key players in maintenance of genomic stability and carcinogenesis. PARP10 and PARP14 catalyze the transfer of a single ADP moiety to target proteins. Here, we summarize the current knowledge on MARylation in DNA repair and cancer, focusing on PARP10 and PARP14. We highlight the roles of PARP10 and PARP14 in cancer progression and response to chemotherapeutics and briefly discuss currently known PARP10 and PARP14 inhibitors.
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Affiliation(s)
- Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- 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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Murthy S, Nizi MG, Maksimainen MM, Massari S, Alaviuhkola J, Lippok BE, Vagaggini C, Sowa ST, Galera-Prat A, Ashok Y, Venkannagari H, Prunskaite-Hyyryläinen R, Dreassi E, Lüscher B, Korn P, Tabarrini O, Lehtiö L. [1,2,4]Triazolo[3,4- b]benzothiazole Scaffold as Versatile Nicotinamide Mimic Allowing Nanomolar Inhibition of Different PARP Enzymes. J Med Chem 2023; 66:1301-1320. [PMID: 36598465 PMCID: PMC9884089 DOI: 10.1021/acs.jmedchem.2c01460] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report [1,2,4]triazolo[3,4-b]benzothiazole (TBT) as a new inhibitor scaffold, which competes with nicotinamide in the binding pocket of human poly- and mono-ADP-ribosylating enzymes. The binding mode was studied through analogues and cocrystal structures with TNKS2, PARP2, PARP14, and PARP15. Based on the substitution pattern, we were able to identify 3-amino derivatives 21 (OUL243) and 27 (OUL232) as inhibitors of mono-ARTs PARP7, PARP10, PARP11, PARP12, PARP14, and PARP15 at nM potencies, with 27 being the most potent PARP10 inhibitor described to date (IC50 of 7.8 nM) and the first PARP12 inhibitor ever reported. On the contrary, hydroxy derivative 16 (OUL245) inhibits poly-ARTs with a selectivity toward PARP2. The scaffold does not possess inherent cell toxicity, and the inhibitors can enter cells and engage with the target protein. This, together with favorable ADME properties, demonstrates the potential of TBT scaffold for future drug development efforts toward selective inhibitors against specific enzymes.
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Affiliation(s)
- Sudarshan Murthy
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Maria Giulia Nizi
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy
| | - Mirko M. Maksimainen
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Serena Massari
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy
| | - Juho Alaviuhkola
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Barbara E. Lippok
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Chiara Vagaggini
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, SienaI-53100, Italy
| | - Sven T. Sowa
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Albert Galera-Prat
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Yashwanth Ashok
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Harikanth Venkannagari
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | | | - Elena Dreassi
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, SienaI-53100, Italy
| | - Bernhard Lüscher
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Patricia Korn
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Oriana Tabarrini
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy,
| | - Lari Lehtiö
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland,
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19
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Di Paola S, Matarese M, Barretta ML, Dathan N, Colanzi A, Corda D, Grimaldi G. PARP10 Mediates Mono-ADP-Ribosylation of Aurora-A Regulating G2/M Transition of the Cell Cycle. Cancers (Basel) 2022; 14:5210. [PMID: 36358629 PMCID: PMC9659153 DOI: 10.3390/cancers14215210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/11/2022] [Accepted: 10/22/2022] [Indexed: 08/13/2023] Open
Abstract
Intracellular mono-ADP-ribosyltransferases (mono-ARTs) catalyze the covalent attachment of a single ADP-ribose molecule to protein substrates, thus regulating their functions. PARP10 is a soluble mono-ART involved in the modulation of intracellular signaling, metabolism and apoptosis. PARP10 also participates in the regulation of the G1- and S-phase of the cell cycle. However, the role of this enzyme in G2/M progression is not defined. In this study, we found that genetic ablation, protein depletion and pharmacological inhibition of PARP10 cause a delay in the G2/M transition of the cell cycle. Moreover, we found that the mitotic kinase Aurora-A, a previously identified PARP10 substrate, is actively mono-ADP-ribosylated (MARylated) during G2/M transition in a PARP10-dependent manner. Notably, we showed that PARP10-mediated MARylation of Aurora-A enhances the activity of the kinase in vitro. Consistent with an impairment in the endogenous activity of Aurora-A, cells lacking PARP10 show a decreased localization of the kinase on the centrosomes and mitotic spindle during G2/M progression. Taken together, our data provide the first evidence of a direct role played by PARP10 in the progression of G2 and mitosis, an event that is strictly correlated to the endogenous MARylation of Aurora-A, thus proposing a novel mechanism for the modulation of Aurora-A kinase activity.
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Affiliation(s)
- Simone Di Paola
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Maria Matarese
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Maria Luisa Barretta
- National Research Council (CNR), Piazzale Aldo Moro, 700185 Rome, Italy
- Steril Farma Srl, Via L. Da Vinci 128, 80055 Portici, Italy
| | - Nina Dathan
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Antonino Colanzi
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Daniela Corda
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Giovanna Grimaldi
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
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20
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Khatib JB, Schleicher EM, Jackson LM, Dhoonmoon A, Moldovan GL, Nicolae CM. Complementary CRISPR genome-wide genetic screens in PARP10-knockout and overexpressing cells identify synthetic interactions for PARP10-mediated cellular survival. Oncotarget 2022; 13:1078-1091. [PMID: 36187556 PMCID: PMC9518689 DOI: 10.18632/oncotarget.28277] [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: 08/04/2022] [Accepted: 09/18/2022] [Indexed: 01/17/2023] Open
Abstract
PARP10 is a mono-ADP-ribosyltransferase with multiple cellular functions, including proliferation, apoptosis, metabolism and DNA repair. PARP10 is overexpressed in a significant proportion of tumors, particularly breast and ovarian cancers. Identifying genetic susceptibilities based on PARP10 expression levels is thus potentially relevant for finding new targets for precision oncology. Here, we performed a series of CRISPR genome-wide loss-of-function screens in isogenic control and PARP10-overexpressing or PARP10-knockout cell lines, to identify genetic determinants of PARP10-mediated cellular survival. We found that PARP10-overexpressing cells rely on multiple DNA repair genes for survival, including ATM, the master regulator of the DNA damage checkpoint. Moreover, we show that PARP10 impacts the recruitment of ATM to nascent DNA upon replication stress. Finally, we identify the CDK2-Cyclin E1 complex as essential for proliferation of PARP10-knockout cells. Our work identifies a network of functionally relevant PARP10 synthetic interactions, and reveals a set of factors which can potentially be targeted in personalized cancer therapy.
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Affiliation(s)
- Jude B Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,These authors contributed equally to this work
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,These authors contributed equally to this work
| | - Lindsey M Jackson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ashna Dhoonmoon
- 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
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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21
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Thakar T, Dhoonmoon A, Straka J, Schleicher EM, Nicolae CM, Moldovan GL. Lagging strand gap suppression connects BRCA-mediated fork protection to nucleosome assembly through PCNA-dependent CAF-1 recycling. Nat Commun 2022; 13:5323. [PMID: 36085347 PMCID: PMC9463168 DOI: 10.1038/s41467-022-33028-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The inability to protect stalled replication forks from nucleolytic degradation drives genome instability and underlies chemosensitivity in BRCA-deficient tumors. An emerging hallmark of BRCA-deficiency is the inability to suppress replication-associated single-stranded DNA (ssDNA) gaps. Here, we report that lagging strand ssDNA gaps interfere with the ASF1-CAF-1 nucleosome assembly pathway, and drive fork degradation in BRCA-deficient cells. We show that CAF-1 function at replication forks is lost in BRCA-deficient cells, due to defects in its recycling during replication stress. This CAF-1 recycling defect is caused by lagging strand gaps which preclude PCNA unloading, causing sequestration of PCNA-CAF-1 complexes on chromatin. Importantly, correcting PCNA unloading defects in BRCA-deficient cells restores CAF-1-dependent fork stability. We further show that the activation of a HIRA-dependent compensatory histone deposition pathway restores fork stability to BRCA-deficient cells. We thus define lagging strand gap suppression and nucleosome assembly as critical enablers of BRCA-mediated fork stability. Efficient DNA replication is crucial for genome stability. Here, Thakar et al. report that accumulation of lagging strand ssDNA gaps during replication interferes with nucleosome assembly and drives replication fork degradation in BRCA-deficient cells.
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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
| | - Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Joshua Straka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Claudia M Nicolae
- 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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22
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Dhoonmoon A, Nicolae CM, Moldovan GL. The KU-PARP14 axis differentially regulates DNA resection at stalled replication forks by MRE11 and EXO1. Nat Commun 2022; 13:5063. [PMID: 36030235 PMCID: PMC9420157 DOI: 10.1038/s41467-022-32756-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Suppression of nascent DNA degradation has emerged as an essential role of the BRCA pathway in genome protection. In BRCA-deficient cells, the MRE11 nuclease is responsible for both resection of reversed replication forks, and accumulation of single stranded DNA gaps behind forks. Here, we show that the mono-ADP-ribosyltransferase PARP14 is a critical co-factor of MRE11. PARP14 is recruited to nascent DNA upon replication stress in BRCA-deficient cells, and through its catalytic activity, mediates the engagement of MRE11. Loss or inhibition of PARP14 suppresses MRE11-mediated fork degradation and gap accumulation, and promotes genome stability and chemoresistance of BRCA-deficient cells. Moreover, we show that the KU complex binds reversed forks and protects them against EXO1-catalyzed degradation. KU recruits the PARP14-MRE11 complex, which initiates partial resection to release KU and allow long-range resection by EXO1. Our work identifies a multistep process of nascent DNA processing at stalled replication forks in BRCA-deficient cells. Protection of replication forks against nucleolytic degradation is crucial for genome stability. Here, Dhoonmoon et al identify PARP14 and the KU complex as essential regulators of fork degradation by MRE11 and EXO1 nucleases in BRCA-deficient cells.
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Affiliation(s)
- Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Claudia M Nicolae
- 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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23
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Li P, Lei Y, Qi J, Liu W, Yao K. Functional roles of ADP-ribosylation writers, readers and erasers. Front Cell Dev Biol 2022; 10:941356. [PMID: 36035988 PMCID: PMC9404506 DOI: 10.3389/fcell.2022.941356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
ADP-ribosylation is a reversible post-translational modification (PTM) tightly regulated by the dynamic interplay between its writers, readers and erasers. As an intricate and versatile PTM, ADP-ribosylation plays critical roles in various physiological and pathological processes. In this review, we discuss the major players involved in the ADP-ribosylation cycle, which may facilitate the investigation of the ADP-ribosylation function and contribute to the understanding and treatment of ADP-ribosylation associated disease.
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24
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Nizi MG, Maksimainen MM, Murthy S, Massari S, Alaviuhkola J, Lippok BE, Sowa ST, Galera-Prat A, Prunskaite-Hyyryläinen R, Lüscher B, Korn P, Lehtiö L, Tabarrini O. Potent 2,3-dihydrophthalazine-1,4-dione derivatives as dual inhibitors for mono-ADP-ribosyltransferases PARP10 and PARP15. Eur J Med Chem 2022; 237:114362. [DOI: 10.1016/j.ejmech.2022.114362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 02/07/2023]
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25
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Nizi M, Maksimainen MM, Lehtiö L, Tabarrini O. Medicinal Chemistry Perspective on Targeting Mono-ADP-Ribosylating PARPs with Small Molecules. J Med Chem 2022; 65:7532-7560. [PMID: 35608571 PMCID: PMC9189837 DOI: 10.1021/acs.jmedchem.2c00281] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Indexed: 12/13/2022]
Abstract
Major advances have recently defined functions for human mono-ADP-ribosylating PARP enzymes (mono-ARTs), also opening up potential applications for targeting them to treat diseases. Structural biology combined with medicinal chemistry has allowed the design of potent small molecule inhibitors which typically bind to the catalytic domain. Most of these inhibitors are at the early stages, but some have already a suitable profile to be used as chemical tools. One compound targeting PARP7 has even progressed to clinical trials. In this review, we collect inhibitors of mono-ARTs with a typical "H-Y-Φ" motif (Φ = hydrophobic residue) and focus on compounds that have been reported as active against one or a restricted number of enzymes. We discuss them from a medicinal chemistry point of view and include an analysis of the available crystal structures, allowing us to craft a pharmacophore model that lays the foundation for obtaining new potent and more specific inhibitors.
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Affiliation(s)
- Maria
Giulia Nizi
- Department
of Pharmaceutical Sciences, University of
Perugia, 06123 Perugia, Italy
| | - Mirko M. Maksimainen
- Faculty
of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 5400 Oulu, Finland
| | - Lari Lehtiö
- Faculty
of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 5400 Oulu, Finland
| | - Oriana Tabarrini
- Department
of Pharmaceutical Sciences, University of
Perugia, 06123 Perugia, Italy
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26
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Ruszkiewicz JA, Bürkle A, Mangerich A. Fueling genome maintenance: On the versatile roles of NAD + in preserving DNA integrity. J Biol Chem 2022; 298:102037. [PMID: 35595095 PMCID: PMC9194868 DOI: 10.1016/j.jbc.2022.102037] [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: 01/19/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 12/13/2022] Open
Abstract
NAD+ is a versatile biomolecule acting as a master regulator and substrate in various cellular processes, including redox regulation, metabolism, and various signaling pathways. In this article, we concisely and critically review the role of NAD+ in mechanisms promoting genome maintenance. Numerous NAD+-dependent reactions are involved in the preservation of genome stability, the cellular DNA damage response, and other pathways regulating nucleic acid metabolism, such as gene expression and cell proliferation pathways. Of note, NAD+ serves as a substrate to ADP-ribosyltransferases, sirtuins, and potentially also eukaryotic DNA ligases, all of which regulate various aspects of DNA integrity, damage repair, and gene expression. Finally, we critically analyze recent developments in the field as well as discuss challenges associated with therapeutic actions intended to raise NAD+ levels.
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Affiliation(s)
- Joanna A Ruszkiewicz
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Aswin Mangerich
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany.
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27
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Taayoshi F, Iraji A, Moazzam A, Soleimani M, Asadi M, Pedrood K, Akbari M, Salehabadi H, Larijani B, Adibpour N, Mahdavi M. Synthesis, molecular docking, and cytotoxicity of quinazolinone and dihydroquinazolinone derivatives as cytotoxic agents. BMC Chem 2022; 16:35. [PMID: 35585608 PMCID: PMC9118628 DOI: 10.1186/s13065-022-00825-x] [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: 01/27/2022] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cancer is the most cause of morbidity and mortality, and a major public health problem worldwide. In this context, two series of quinazolinone 5a–e and dihydroquinazolinone 10a–f compounds were designed, synthesized as cytotoxic agents. Methodology All derivatives (5a–e and 10a–f) were synthesized via straightforward pathways and elucidated by FTIR, 1H-NMR, CHNS elemental analysis, as well as the melting point. All the compounds were evaluated for their in vitro cytotoxicity effects using the MTT assay against two human cancer cell lines (MCF-7 and HCT-116) using doxorubicin as the standard drug. The test derivatives were additionally docked into the PARP10 active site using Gold software. Results and discussion Most of the synthesized compounds, especially 5a and 10f were found to be highly potent against both cell lines. Synthesized compounds demonstrated IC50 in the range of 4.87–205.9 μM against HCT-116 cell line and 14.70–98.45 μM against MCF-7 cell line compared with doxorubicin with IC50 values of 1.20 and 1.08 μM after 72 h, respectively, indicated the plausible activities of the synthesized compounds. Conclusion The compounds quinazolinone 5a–e and dihydroquinazolinone 10a–f showed potential activity against cancer cell lines which can lead to rational drug designing of the cytotoxic agents. Supplementary Information The online version contains supplementary material available at 10.1186/s13065-022-00825-x.
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Affiliation(s)
- Fahimeh Taayoshi
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Aida Iraji
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Central Research Laboratory, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Moazzam
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Science Hamadan, Hamedan, Iran
| | - Mehdi Asadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Keyvan Pedrood
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mosayeb Akbari
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hafezeh Salehabadi
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Adibpour
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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28
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Gan Y, Sha H, Zou R, Xu M, Zhang Y, Feng J, Wu J. Research Progress on Mono-ADP-Ribosyltransferases in Human Cell Biology. Front Cell Dev Biol 2022; 10:864101. [PMID: 35652091 PMCID: PMC9149570 DOI: 10.3389/fcell.2022.864101] [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: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is a well-established post-translational modification that is inherently connected to diverse processes, including DNA repair, transcription, and cell signaling. The crucial roles of mono-ADP-ribosyltransferases (mono-ARTs) in biological processes have been identified in recent years by the comprehensive use of genetic engineering, chemical genetics, and proteomics. This review provides an update on current methodological advances in the study of these modifiers. Furthermore, the review provides details on the function of mono ADP-ribosylation. Several mono-ARTs have been implicated in the development of cancer, and this review discusses the role and therapeutic potential of some mono-ARTs in cancer.
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Affiliation(s)
- Yujie Gan
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Huanhuan Sha
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Renrui Zou
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Miao Xu
- Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jifeng Feng
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
- *Correspondence: Jifeng Feng,
| | - Jianzhong Wu
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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Abstract
Post-translational modifications exist in different varieties to regulate diverse characteristics of their substrates, ultimately leading to maintenance of cell health. The enzymes of the intracellular poly(ADP-ribose) polymerase (PARP) family can transfer either a single ADP-ribose to targets, in a reaction called mono(ADP-ribosyl)ation or MARylation, or multiple to form chains of poly(ADP-ribose) or PAR. Traditionally thought to be attached to arginine or glutamate, recent data have added serine, tyrosine, histidine and others to the list of potential ADP-ribose acceptor amino acids. PARylation by PARP1 has been relatively well studied, whereas less is known about the other family members such as PARP7 and PARP10. ADP-ribosylation on arginine and serine is reversed by ARH1 and ARH3 respectively, whereas macrodomain-containing MACROD1, MACROD2 and TARG1 reverse modification of acidic residues. For the other amino acids, no hydrolases have been identified to date. For many PARPs, it is not clear yet what their endogenous targets are. Better understanding of their biochemical reactions is required to be able to determine their biological functions in future studies. In this review, we discuss the current knowledge of PARP specificity in vitro and in cells, as well as provide an outlook for future research.
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30
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Galera-Prat A, Alaviuhkola J, Alanen HI, Lehtiö L. Protein engineering approach to enhance activity assays of mono-ADP-ribosyltransferases through proximity. Protein Eng Des Sel 2022; 35:gzac006. [PMID: 36130221 PMCID: PMC9574550 DOI: 10.1093/protein/gzac006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Human mono-ADP-ribosylating PARP enzymes have been linked to several clinically relevant processes and many of these PARPs have been suggested as potential drug targets. Despite recent advances in the field, efforts to discover inhibitors have been hindered by the lack of tools to rapidly screen for high potency compounds and profile them against the different enzymes. We engineered mono-ART catalytic fragments to be incorporated into a cellulosome-based octavalent scaffold. Compared to the free enzymes, the scaffold-based system results in an improved activity for the tested PARPs due to improved solubility, stability and the proximity of the catalytic domains, altogether boosting their activity beyond 10-fold in the case of PARP12. This allows us to measure their activity using a homogeneous NAD+ conversion assay, facilitating its automation to lower the assay volume and costs. The approach will enable the discovery of more potent compounds due to increased assay sensitivity.
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Affiliation(s)
- Albert Galera-Prat
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Aapistie 7B, 90220 Oulu, University of Oulu, Finland
| | - Juho Alaviuhkola
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Aapistie 7B, 90220 Oulu, University of Oulu, Finland
| | - Heli I Alanen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Aapistie 7B, 90220 Oulu, University of Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Aapistie 7B, 90220 Oulu, University of Oulu, Finland
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31
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Ler AAL, Carty MP. DNA Damage Tolerance Pathways in Human Cells: A Potential Therapeutic Target. Front Oncol 2022; 11:822500. [PMID: 35198436 PMCID: PMC8859465 DOI: 10.3389/fonc.2021.822500] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 12/26/2022] Open
Abstract
DNA lesions arising from both exogenous and endogenous sources occur frequently in DNA. During DNA replication, the presence of unrepaired DNA damage in the template can arrest replication fork progression, leading to fork collapse, double-strand break formation, and to genome instability. To facilitate completion of replication and prevent the generation of strand breaks, DNA damage tolerance (DDT) pathways play a key role in allowing replication to proceed in the presence of lesions in the template. The two main DDT pathways are translesion synthesis (TLS), which involves the recruitment of specialized TLS polymerases to the site of replication arrest to bypass lesions, and homology-directed damage tolerance, which includes the template switching and fork reversal pathways. With some exceptions, lesion bypass by TLS polymerases is a source of mutagenesis, potentially contributing to the development of cancer. The capacity of TLS polymerases to bypass replication-blocking lesions induced by anti-cancer drugs such as cisplatin can also contribute to tumor chemoresistance. On the other hand, during homology-directed DDT the nascent sister strand is transiently utilised as a template for replication, allowing for error-free lesion bypass. Given the role of DNA damage tolerance pathways in replication, mutagenesis and chemoresistance, a more complete understanding of these pathways can provide avenues for therapeutic exploitation. A number of small molecule inhibitors of TLS polymerase activity have been identified that show synergy with conventional chemotherapeutic agents in killing cancer cells. In this review, we will summarize the major DDT pathways, explore the relationship between damage tolerance and carcinogenesis, and discuss the potential of targeting TLS polymerases as a therapeutic approach.
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Affiliation(s)
- Ashlynn Ai Li Ler
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
| | - Michael P. Carty
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
- DNA Damage Response Laboratory, Centre for Chromosome Biology, NUI Galway, Galway, Ireland
- *Correspondence: Michael P. Carty,
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32
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Richard IA, Burgess JT, O'Byrne KJ, Bolderson E. Beyond PARP1: The Potential of Other Members of the Poly (ADP-Ribose) Polymerase Family in DNA Repair and Cancer Therapeutics. Front Cell Dev Biol 2022; 9:801200. [PMID: 35096828 PMCID: PMC8795897 DOI: 10.3389/fcell.2021.801200] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/21/2021] [Indexed: 01/22/2023] Open
Abstract
The proteins within the Poly-ADP Ribose Polymerase (PARP) family encompass a diverse and integral set of cellular functions. PARP1 and PARP2 have been extensively studied for their roles in DNA repair and as targets for cancer therapeutics. Several PARP inhibitors (PARPi) have been approved for clinical use, however, while their efficacy is promising, tumours readily develop PARPi resistance. Many other members of the PARP protein family share catalytic domain homology with PARP1/2, however, these proteins are comparatively understudied, particularly in the context of DNA damage repair and tumourigenesis. This review explores the functions of PARP4,6-16 and discusses the current knowledge of the potential roles these proteins may play in DNA damage repair and as targets for cancer therapeutics.
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Affiliation(s)
- Iain A Richard
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Joshua T Burgess
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Kenneth J O'Byrne
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia.,Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
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33
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Jackson LM, Dhoonmoon A, Hale A, Dennis KA, Schleicher EM, Nicolae CM, Moldovan GL. Loss of MED12 activates the TGFβ pathway to promote chemoresistance and replication fork stability in BRCA-deficient cells. Nucleic Acids Res 2021; 49:12855-12869. [PMID: 34871431 PMCID: PMC8682781 DOI: 10.1093/nar/gkab1184] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding chemoresistance mechanisms in BRCA-deficient cells will allow for identification of biomarkers for predicting tumor response to therapy, as well as the design of novel therapeutic approaches targeting this chemoresistance. Here, we show that the protein MED12, a component of the Mediator transcription regulation complex, plays an unexpected role in regulating chemosensitivity in BRCA-deficient cells. We found that loss of MED12 confers resistance to cisplatin and PARP inhibitors in both BRCA1- and BRCA2-deficient cells, which is associated with restoration of both homologous recombination and replication fork stability. Surprisingly, MED12-controlled chemosensitivity does not involve a function of the Mediator complex, but instead reflects a distinct role of MED12 in suppression of the TGFβ pathway. Importantly, we show that ectopic activation of the TGFβ pathway is enough to overcome the fork protection and DNA repair defects of BRCA-mutant cells, resulting in chemoresistance. Our work identifies the MED12-TGFβ module as an important regulator of genomic stability and chemosensitivity in BRCA-deficient cells.
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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
| | - Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Anastasia Hale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Kady A Dennis
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- 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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Balasubramanian S, Hodkinson B, Schuster SJ, Fowler NH, Trotman J, Hess G, Cheson BD, Schaffer M, Sun S, Deshpande S, Vermeulen J, Salles G, Gopal AK. Identification of a genetic signature enriching for response to ibrutinib in relapsed/refractory follicular lymphoma in the DAWN phase 2 trial. Cancer Med 2021; 11:61-73. [PMID: 34791836 PMCID: PMC8704158 DOI: 10.1002/cam4.4422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 11/08/2022] Open
Abstract
Background The single‐arm DAWN trial (NCT01779791) of ibrutinib monotherapy in patients with relapsed/refractory follicular lymphoma (FL) showed an overall response rate (ORR) of 20.9% and a median response duration of 19.4 months. This biomarker analysis of the DAWN dataset sought to determine genetic classifiers for prediction of response to ibrutinib treatment. Methods Whole exome sequencing was performed on baseline tumor samples. Potential germline variants were excluded; a custom set of 1216 cancer‐related genes was examined. Responder‐ versus nonresponder‐associated variants were identified using Fisher's exact test. Classifiers with increasing numbers of genes were created using a greedy algorithm that repeatedly selected genes, adding the most nonresponders to the existing “predicted nonresponders” set and were evaluated with 10‐fold cross‐validation. Results Exome data were generated from 88 patient samples and 13,554 somatic mutation variants were inferred. Response data were available for 83 patients (17 responders, 66 nonresponders). Each sample showed 100 to >500 mutated genes, with greater variance across nonresponders. The overall variant pattern was consistent with previous FL studies; 75 genes had mutations in >10% of patients, including genes previously reported as associated with FL. Univariate analysis yielded responder‐associated genes FANCA, HISTH1B, ANXA6, BTG1, and PARP10, highlighting the importance of functions outside of B‐cell receptor signaling, including epigenetic processes, DNA damage repair, cell cycle/proliferation, and cell motility/invasiveness. While nonresponder‐associated genes included well‐known TP53 and CARD11, genetic classifiers developed using nonresponder‐associated genes included ATP6AP1, EP400, ARID1A, SOCS1, and TBL1XR1, suggesting resistance to ibrutinib may be related to broad biological functions connected to epigenetic modification, telomere maintenance, and cancer‐associated signaling pathways (mTOR, JAK/STAT, NF‐κB). Conclusion The results from univariate and genetic classifier analyses provide insights into genes associated with response or resistance to ibrutinib in FL and identify a classifier developed using nonresponder‐associated genes, which warrants further investigation. Trial registration: NCT01779791.
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Affiliation(s)
| | | | - Stephen J Schuster
- Lymphoma Program, Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nathan H Fowler
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Judith Trotman
- Haematology Department, Concord Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Georg Hess
- Department of Hematology/Oncology, Johannes Gutenberg-University, Mainz, Germany
| | - Bruce D Cheson
- Lombardi Comprehensive Cancer Center, Georgetown University Hospital, Washington, District of Columbia, USA
| | | | - Steven Sun
- Janssen Research & Development, Raritan, New Jersey, USA
| | | | | | - Gilles Salles
- Hospices Civils de Lyon, Université de Lyon, Pierre-Bénite Cedex, Lyon, France
| | - Ajay K Gopal
- Division of Medical Oncology, Department of Medicine, The University of Washington, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Lymphoma Program, Seattle Cancer Care Alliance, Seattle, Washington, USA
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35
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Chemical genetic methodologies for identifying protein substrates of PARPs. Trends Biochem Sci 2021; 47:390-402. [PMID: 34366182 DOI: 10.1016/j.tibs.2021.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/30/2021] [Accepted: 07/14/2021] [Indexed: 02/08/2023]
Abstract
Poly-ADP-ribose-polymerases (PARPs) are a family of 17 enzymes that regulate a diverse range of cellular processes in mammalian cells. PARPs catalyze the transfer of ADP-ribose from NAD+ to target molecules, most prominently amino acids on protein substrates, in a process known as ADP-ribosylation. Identifying the direct protein substrates of individual PARP family members is an essential first step for elucidating the mechanism by which PARPs regulate a particular pathway in cells. Two distinct chemical genetic (CG) strategies have been developed for identifying the direct protein substrates of individual PARP family members. In this review, we discuss the design principles behind these two strategies and how target identification has provided novel insight into the cellular function of individual PARPs and PARP-mediated ADP-ribosylation.
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36
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O'Connor MJ, Thakar T, Nicolae CM, Moldovan GL. PARP14 regulates cyclin D1 expression to promote cell-cycle progression. Oncogene 2021; 40:4872-4883. [PMID: 34158578 PMCID: PMC8384455 DOI: 10.1038/s41388-021-01881-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/09/2022]
Abstract
Cyclin D1 is an essential regulator of the G1-S cell-cycle transition and is overexpressed in many cancers. Expression of cyclin D1 is under tight cellular regulation that is controlled by many signaling pathways. Here we report that PARP14, a member of the poly(ADP-ribose) polymerase (PARP) family, is a regulator of cyclin D1 expression. Depletion of PARP14 leads to decreased cyclin D1 protein levels. In cells with a functional retinoblastoma (RB) protein pathway, this results in G1 cell-cycle arrest and reduced proliferation. Mechanistically, we found that PARP14 controls cyclin D1 mRNA levels. Using luciferase assays, we show that PARP14 specifically regulates cyclin D1 3'UTR mRNA stability. Finally, we also provide evidence that G1 arrest in PARP14-depleted cells is dependent on an intact p53-p21 pathway. Our work uncovers a new role for PARP14 in promoting cell-cycle progression through both cyclin D1 and the p53 pathway.
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Affiliation(s)
- Michael J O'Connor
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
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37
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Weixler L, Schäringer K, Momoh J, Lüscher B, Feijs KLH, Žaja R. ADP-ribosylation of RNA and DNA: from in vitro characterization to in vivo function. Nucleic Acids Res 2021; 49:3634-3650. [PMID: 33693930 PMCID: PMC8053099 DOI: 10.1093/nar/gkab136] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The functionality of DNA, RNA and proteins is altered dynamically in response to physiological and pathological cues, partly achieved by their modification. While the modification of proteins with ADP-ribose has been well studied, nucleic acids were only recently identified as substrates for ADP-ribosylation by mammalian enzymes. RNA and DNA can be ADP-ribosylated by specific ADP-ribosyltransferases such as PARP1-3, PARP10 and tRNA 2'-phosphotransferase (TRPT1). Evidence suggests that these enzymes display different preferences towards different oligonucleotides. These reactions are reversed by ADP-ribosylhydrolases of the macrodomain and ARH families, such as MACROD1, TARG1, PARG, ARH1 and ARH3. Most findings derive from in vitro experiments using recombinant components, leaving the relevance of this modification in cells unclear. In this Survey and Summary, we provide an overview of the enzymes that ADP-ribosylate nucleic acids, the reversing hydrolases, and the substrates' requirements. Drawing on data available for other organisms, such as pierisin1 from cabbage butterflies and the bacterial toxin-antitoxin system DarT-DarG, we discuss possible functions for nucleic acid ADP-ribosylation in mammals. Hypothesized roles for nucleic acid ADP-ribosylation include functions in DNA damage repair, in antiviral immunity or as non-conventional RNA cap. Lastly, we assess various methods potentially suitable for future studies of nucleic acid ADP-ribosylation.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Katja Schäringer
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
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38
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Poltronieri P, Celetti A, Palazzo L. Mono(ADP-ribosyl)ation Enzymes and NAD + Metabolism: A Focus on Diseases and Therapeutic Perspectives. Cells 2021; 10:128. [PMID: 33440786 PMCID: PMC7827148 DOI: 10.3390/cells10010128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Mono(ADP-ribose) transferases and mono(ADP-ribosyl)ating sirtuins use NAD+ to perform the mono(ADP-ribosyl)ation, a simple form of post-translational modification of proteins and, in some cases, of nucleic acids. The availability of NAD+ is a limiting step and an essential requisite for NAD+ consuming enzymes. The synthesis and degradation of NAD+, as well as the transport of its key intermediates among cell compartments, play a vital role in the maintenance of optimal NAD+ levels, which are essential for the regulation of NAD+-utilizing enzymes. In this review, we provide an overview of the current knowledge of NAD+ metabolism, highlighting the functional liaison with mono(ADP-ribosyl)ating enzymes, such as the well-known ARTD10 (also named PARP10), SIRT6, and SIRT7. To this aim, we discuss the link of these enzymes with NAD+ metabolism and chronic diseases, such as cancer, degenerative disorders and aging.
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Affiliation(s)
- Palmiro Poltronieri
- Institute of Sciences of Food Productions, National Research Council of Italy, via Monteroni 7, 73100 Lecce, Italy
| | - Angela Celetti
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, Via Tommaso de Amicis 95, 80145 Naples, Italy
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39
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Thapa K, Khan H, Sharma U, Grewal AK, Singh TG. Poly (ADP-ribose) polymerase-1 as a promising drug target for neurodegenerative diseases. Life Sci 2020; 267:118975. [PMID: 33387580 DOI: 10.1016/j.lfs.2020.118975] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/07/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023]
Abstract
AIMS Poly (ADP-ribose) polymerase- (PARP)-1 is predominantly triggered by DNA damage. Overexpression of PARP-1 is known for its association with the pathogenesis of several CNS disorders, such as Stroke, Parkinson's disease (PD), Alzheimer's disease (AD), Huntington (HD) and Amyotrophic lateral sclerosis (ALS). NAD+ depletion resulted PARP related cell death only happened when the trial used extreme high oxidization treatment. Inhibition of PARP1/2 may induce replication related cell death due to un-repaired DNA damage. This review has discussed PARP-1 modulated downstream pathways in neurodegeneration and various FDA approved PARP-1 inhibitors. MATERIALS AND METHODS A systematic literature review of PubMed, Medline, Bentham, Scopus and EMBASE (Elsevier) databases was carried out to understand the nature of the extensive work done on mechanistic role of Poly (ADP-ribose) polymerase and its inhibition in Neurodegenerative diseases. KEY FINDINGS Several researchers have put forward number of potential treatments, of which PARP-1 enzyme has been regarded as a potent target intended for the handling of neurodegenerative ailments. Targeting PARP using its chemical inhibitors in various neurodegenerative may have therapeutic outcomes by reducing neuronal death mediated by PARPi. Numerous PARP-1 inhibitors have been studied in neurodegenerative diseases but they haven't been clinically evaluated. SIGNIFICANCE In this review, the pathological role of PARP-1 in various neurodegenerative diseases has been discussed along with the therapeutic role of PARP-1 inhibitors in various neurodegenerative diseases.
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Affiliation(s)
- Komal Thapa
- Chitkara College of Pharmacy, Chitkara University, Punjab, India; Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
| | - Heena Khan
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Uma Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
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40
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Clements KE, Schleicher EM, Thakar T, Hale A, Dhoonmoon A, Tolman NJ, Sharma A, Liang X, Imamura Kawasawa Y, Nicolae CM, Wang HG, De S, Moldovan GL. Identification of regulators of poly-ADP-ribose polymerase inhibitor response through complementary CRISPR knockout and activation screens. Nat Commun 2020; 11:6118. [PMID: 33257658 PMCID: PMC7704667 DOI: 10.1038/s41467-020-19961-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 10/30/2020] [Indexed: 12/17/2022] Open
Abstract
Inhibitors of poly-ADP-ribose polymerase 1 (PARPi) are highly effective in killing cells deficient in homologous recombination (HR); thus, PARPi have been clinically utilized to successfully treat BRCA2-mutant tumors. However, positive response to PARPi is not universal, even among patients with HR-deficiency. Here, we present the results of genome-wide CRISPR knockout and activation screens which reveal genetic determinants of PARPi response in wildtype or BRCA2-knockout cells. Strikingly, we report that depletion of the ubiquitin ligase HUWE1, or the histone acetyltransferase KAT5, top hits from our screens, robustly reverses the PARPi sensitivity caused by BRCA2-deficiency. We identify distinct mechanisms of resistance, in which HUWE1 loss increases RAD51 levels to partially restore HR, whereas KAT5 depletion rewires double strand break repair by promoting 53BP1 binding to double-strand breaks. Our work provides a comprehensive set of putative biomarkers that advance understanding of PARPi response, and identifies novel pathways of PARPi resistance in BRCA2-deficient cells. Mutations in the homologous recombination proteins BRCA1 and BRCA2 can sensitize cells to treatment with inhibitors of poly-ADP-ribose polymerase 1 (PARPi), but resistance to the treatment can occur. Here the authors by genome-wide CRISPR knockout and activation screens reveal novel pathways of PARPi resistance in BRCA2-deficient cells.
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Affiliation(s)
- Kristen E Clements
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Anastasia Hale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Nathanial J Tolman
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Anchal Sharma
- Rutgers Cancer Institute of New Jersey, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Xinwen Liang
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Yuka Imamura Kawasawa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Hong-Gang Wang
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, 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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41
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Dual genome-wide CRISPR knockout and CRISPR activation screens identify mechanisms that regulate the resistance to multiple ATR inhibitors. PLoS Genet 2020; 16:e1009176. [PMID: 33137164 PMCID: PMC7660927 DOI: 10.1371/journal.pgen.1009176] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/12/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022] Open
Abstract
The ataxia telangiectasia and Rad3-related (ATR) protein kinase is a key regulator of the cellular response to DNA damage. Due to increased amount of replication stress, cancer cells heavily rely on ATR to complete DNA replication and cell cycle progression. Thus, ATR inhibition is an emerging target in cancer therapy, with multiple ATR inhibitors currently undergoing clinical trials. Here, we describe dual genome-wide CRISPR knockout and CRISPR activation screens employed to comprehensively identify genes that regulate the cellular resistance to ATR inhibitors. Specifically, we investigated two different ATR inhibitors, namely VE822 and AZD6738, in both HeLa and MCF10A cells. We identified and validated multiple genes that alter the resistance to ATR inhibitors. Importantly, we show that the mechanisms of resistance employed by these genes are varied, and include restoring DNA replication fork progression, and prevention of ATR inhibitor-induced apoptosis. In particular, we describe a role for MED12-mediated inhibition of the TGFβ signaling pathway in regulating replication fork stability and cellular survival upon ATR inhibition. Our dual genome-wide screen findings pave the way for personalized medicine by identifying potential biomarkers for ATR inhibitor resistance.
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42
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Conti BA, Smogorzewska A. Mechanisms of direct replication restart at stressed replisomes. DNA Repair (Amst) 2020; 95:102947. [PMID: 32853827 PMCID: PMC7669714 DOI: 10.1016/j.dnarep.2020.102947] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/09/2023]
Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA.
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43
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Sanderson DJ, Cohen MS. Mechanisms governing PARP expression, localization, and activity in cells. Crit Rev Biochem Mol Biol 2020; 55:541-554. [PMID: 32962438 DOI: 10.1080/10409238.2020.1818686] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Poly-(ADP)-ribose polymerases (PARPs) are a family of 17 enzymes in humans that have diverse roles in cell physiology including DNA damage repair, transcription, innate immunity, and regulation of signaling pathways. The modular domain architecture of PARPs gives rise to this functional diversity. PARPs catalyze the transfer of ADP-ribose from nicotinamide adenine dinucleotide (NAD+) to targets-proteins and poly-nucleic acids. This enigmatic post-translational modification comes in two varieties: the transfer of a single unit of ADP-ribose, known as mono-ADP-ribosylation (MARylation) or the transfer of multiple units of ADP-ribose, known as poly-ADP-ribosylation (PARylation). Emerging data shows that PARPs are regulated at multiple levels to control when and where PARP-mediated M/PARylation occurs in cells. In this review, we will discuss the latest knowledge regarding the regulation of PARPs in cells: from transcription and protein stability to subcellular localization and modulation of catalytic activity.
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Affiliation(s)
- Daniel J Sanderson
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
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44
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Lemke M, Ravenscroft H, Rueb NJ, Kireev D, Ferraris D, Franzini RM. Integrating DNA-encoded chemical libraries with virtual combinatorial library screening: Optimizing a PARP10 inhibitor. Bioorg Med Chem Lett 2020; 30:127464. [PMID: 32768646 DOI: 10.1016/j.bmcl.2020.127464] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 07/25/2020] [Accepted: 08/02/2020] [Indexed: 12/17/2022]
Abstract
Two critical steps in drug development are 1) the discovery of molecules that have the desired effects on a target, and 2) the optimization of such molecules into lead compounds with the required potency and pharmacokinetic properties for translation. DNA-encoded chemical libraries (DECLs) can nowadays yield hits with unprecedented ease, and lead-optimization is becoming the limiting step. Here we integrate DECL screening with structure-based computational methods to streamline the development of lead compounds. The presented workflow consists of enumerating a virtual combinatorial library (VCL) derived from a DECL screening hit and using computational binding prediction to identify molecules with enhanced properties relative to the original DECL hit. As proof-of-concept demonstration, we applied this approach to identify an inhibitor of PARP10 that is more potent and druglike than the original DECL screening hit.
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Affiliation(s)
- Mike Lemke
- Department of Chemistry, McDaniel College, 2 College Hill, Westminster, MD 21157, USA
| | - Hannah Ravenscroft
- Department of Chemistry, McDaniel College, 2 College Hill, Westminster, MD 21157, USA
| | - Nicole J Rueb
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT 84112, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Dana Ferraris
- Department of Chemistry, McDaniel College, 2 College Hill, Westminster, MD 21157, USA.
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT 84112, USA.
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45
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Ma X, Tang TS, Guo C. Regulation of translesion DNA synthesis in mammalian cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:680-692. [PMID: 31983077 DOI: 10.1002/em.22359] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/29/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
The genomes of all living cells are under endogenous and exogenous attacks every day, causing diverse genomic lesions. Most of the lesions can be timely repaired by multiple DNA repair pathways. However, some may persist during S-phase, block DNA replication, and challenge genome integrity. Eukaryotic cells have evolved DNA damage tolerance (DDT) to mitigate the lethal effects of arrested DNA replication without prior removal of the offending DNA damage. As one important mode of DDT, translesion DNA synthesis (TLS) utilizes multiple low-fidelity DNA polymerases to incorporate nucleotides opposite DNA lesions to maintain genome integrity. Three different mechanisms have been proposed to regulate the polymerase switching between high-fidelity DNA polymerases in the replicative machinery and one or more specialized enzymes. Additionally, it is known that proliferating cell nuclear antigen (PCNA) mono-ubiquitination is essential for optimal TLS. Given its error-prone property, TLS is closely associated with spontaneous and drug-induced mutations in cells, which can potentially lead to tumorigenesis and chemotherapy resistance. Therefore, TLS process must be tightly modulated to avoid unwanted mutagenesis. In this review, we will focus on polymerase switching and PCNA mono-ubiquitination, the two key events in TLS pathway in mammalian cells, and summarize current understandings of regulation of TLS process at the levels of protein-protein interactions, post-translational modifications as well as transcription and noncoding RNAs. Environ. Mol. Mutagen. 61:680-692, 2020. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiaolu Ma
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Caixia Guo
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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46
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Feijs KL, Cooper CD, Žaja R. The Controversial Roles of ADP-Ribosyl Hydrolases MACROD1, MACROD2 and TARG1 in Carcinogenesis. Cancers (Basel) 2020; 12:E604. [PMID: 32151005 PMCID: PMC7139919 DOI: 10.3390/cancers12030604] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/20/2020] [Accepted: 02/27/2020] [Indexed: 01/12/2023] Open
Abstract
Post-translational modifications (PTM) of proteins are crucial for fine-tuning a cell's response to both intracellular and extracellular cues. ADP-ribosylation is a PTM, which occurs in two flavours: modification of a target with multiple ADP-ribose moieties (poly(ADP-ribosyl)ation or PARylation) or with only one unit (MARylation), which are added by the different enzymes of the PARP family (also known as the ARTD family). PARylation has been relatively well-studied, particularly in the DNA damage response. This has resulted in the development of PARP inhibitors such as olaparib, which are increasingly employed in cancer chemotherapeutic approaches. Despite the fact that the majority of PARP enzymes catalyse MARylation, MARylation is not as well understood as PARylation. MARylation is a dynamic process: the enzymes reversing intracellular MARylation of acidic amino acids (MACROD1, MACROD2, and TARG1) were discovered in 2013. Since then, however, little information has been published about their physiological function. MACROD1, MACROD2, and TARG1 have a 'macrodomain' harbouring the catalytic site, but no other domains have been identified. Despite the lack of information regarding their cellular roles, there are a number of studies linking them to cancer. However, some of these publications oppose each other, some rely on poorly-characterised antibodies, or on aberrant localisation of overexpressed rather than native protein. In this review, we critically assess the available literature on a role for the hydrolases in cancer and find that, currently, there is limited evidence for a role for MACROD1, MACROD2, or TARG1 in tumorigenesis.
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Affiliation(s)
- Karla L.H. Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany;
| | - Christopher D.O. Cooper
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield West Yorkshire HD3 4AP, UK;
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany;
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47
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Abstract
Effective maintenance and stability of our genomes is essential for normal cell division, tissue homeostasis, and cellular and organismal fitness. The processes of chromosome replication and segregation require continual surveillance to insure fidelity. Accurate and efficient repair of DNA damage preserves genome integrity, which if lost can lead to multiple diseases, including cancer. Poly(ADP-ribose) a dynamic and reversible posttranslational modification and the enzymes that catalyze it (PARP1, PARP2, tankyrase 1, and tankyrase 2) function to maintain genome stability through diverse mechanisms. Here we review the role of these enzymes and the modification in genome repair, replication, and resolution in human cells.
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Affiliation(s)
- Kameron Azarm
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
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48
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Wu CF, Xiao M, Wang YL, Threadgill MD, Li M, Tang Y, Lin X, Yang L, Li QS, Li X. PARP10 Influences the Proliferation of Colorectal Carcinoma Cells, a Preliminary Study. Mol Biol 2020. [DOI: 10.1134/s0026893320020181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Higuchi F, Nagashima H, Ning J, Koerner MVA, Wakimoto H, Cahill DP. Restoration of Temozolomide Sensitivity by PARP Inhibitors in Mismatch Repair Deficient Glioblastoma is Independent of Base Excision Repair. Clin Cancer Res 2020; 26:1690-1699. [PMID: 31900275 DOI: 10.1158/1078-0432.ccr-19-2000] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/09/2019] [Accepted: 12/18/2019] [Indexed: 01/23/2023]
Abstract
PURPOSE Emergence of mismatch repair (MMR) deficiency is a frequent mechanism of acquired resistance to the alkylating chemotherapeutic temozolomide (TMZ) in gliomas. Poly(ADP-ribose) polymerase inhibitors (PARPi) have been shown to potentiate TMZ cytotoxicity in several cancer types, including gliomas. We tested whether PARP inhibition could re-sensitize MSH6-null MMR-deficient gliomas to TMZ, and assessed the role of the base excision repair (BER) DNA damage repair pathway in PARPi-mediated effects. EXPERIMENTAL DESIGN Isogenic pairs of MSH6 wild-type and MSH6-inactivated human glioblastoma (GBM) cells (including both IDH1/2 wild-type and IDH1 mutant), as well as MSH6-null cells derived from a patient with recurrent GBM were treated with TMZ, the PARPi veliparib or olaparib, and combination thereof. Efficacy of PARPi combined with TMZ was assessed in vivo. We used genetic and pharmacological approaches to dissect the contribution of BER. RESULTS While having no detectable effect in MSH6 wild-type GBMs, PARPi selectively restored TMZ sensitivity in MSH6-deficient GBM cells. This genotype-specific restoration of activity translated in vivo, where combination treatment of veliparib and TMZ showed potent suppression of tumor growth of MSH6-inactivated orthotopic xenografts, compared with TMZ monotherapy. Unlike PARPi, genetic and pharmacological blockage of BER pathway did not re-sensitize MSH6-inactivated GBM cells to TMZ. Similarly, CRISPR PARP1 knockout did not re-sensitize MSH6-inactivated GBM cells to TMZ. CONCLUSIONS PARPi restoration of TMZ chemosensitivity in MSH6-inactivated glioma represents a promising strategy to overcome acquired chemoresistance caused by MMR deficiency. Mechanistically, this PARPi-mediated synthetic phenotype was independent of BER blockage and was not recapitulated by loss of PARP1.
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Affiliation(s)
- Fumi Higuchi
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Neurosurgery, Dokkyo Medical University, Mibu, Tochigi, Japan
| | - Hiroaki Nagashima
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jianfang Ning
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Neurosurgery, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Mara V A Koerner
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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50
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Hoch NC, Polo LM. ADP-ribosylation: from molecular mechanisms to human disease. Genet Mol Biol 2019; 43:e20190075. [PMID: 31930280 PMCID: PMC7198025 DOI: 10.1590/1678-4685-gmb-2019-0075] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/04/2019] [Indexed: 12/23/2022] Open
Abstract
Post-translational modification of proteins by ADP-ribosylation, catalysed by
poly (ADP-ribose) polymerases (PARPs) using NAD+ as a substrate,
plays central roles in DNA damage signalling and repair, modulates a range of
cellular signalling cascades and initiates programmed cell death by parthanatos.
Here, we present mechanistic aspects of ADP-ribose modification, PARP activation
and the cellular functions of ADP-ribose signalling, and discuss how this
knowledge is uncovering therapeutic avenues for the treatment of increasingly
prevalent human diseases such as cancer, ischaemic damage and
neurodegeneration.
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Affiliation(s)
- Nicolas C Hoch
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luis M Polo
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK.,Institute of Histology and Embryology of Mendoza - CONICET, Mendoza, Argentina
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