1
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Bhandari SK, Wiest N, Sallmyr A, Du R, Tomkinson AE. Redundant but essential functions of PARP1 and PARP2 in DNA ligase I-independent DNA replication. Nucleic Acids Res 2024:gkae672. [PMID: 39106163 DOI: 10.1093/nar/gkae672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/09/2024] Open
Abstract
While DNA ligase I (LigI) joins most Okazaki fragments, a backup pathway involving poly(ADP-ribose) synthesis, XRCC1 and DNA ligase IIIα (LigIIIα) functions along with the LigI-dependent pathway and is also capable of supporting DNA replication in the absence of LigI. Here we have addressed for the first time the roles of PARP1 and PARP2 in this pathway using isogenic null derivatives of mouse CH12F3 cells. While single and double null mutants of the parental cell line and single mutants of LIG1 null cells were viable, loss of both PARP1 and PARP2 was synthetically lethal with LigI deficiency. Thus, PARP1 and PARP2 have a redundant essential role in LigI-deficient cells. Interestingly, higher levels of PARP2 but not PARP1 associated with newly synthesized DNA in the LIG1 null cells and there was a much higher increase in PARP2 chromatin retention in LIG1 null cells incubated with the PARP inhibitor olaparib with this effect occurring independently of PARP1. Together our results suggest that PARP2 plays a major role in specific cell types that are more dependent upon the backup pathway to complete DNA replication and that PARP2 retention at unligated Okazaki fragments likely contributes to the side effects of current clinical PARP inhibitors.
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Affiliation(s)
- Seema Khattri Bhandari
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Nathaniel Wiest
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Annahita Sallmyr
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Ruofei Du
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Alan E Tomkinson
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM 87131, USA
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2
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Jahan E, Mazumder T, Hasan T, Ahmed KS, Amanat M, Hossain H, Supty SJ, Liya IJ, Shuvo MSR, Daula AFMSU. Metabolomic Approach to Identify the Potential Metabolites from Alpinia malaccensis for Treating SARS-CoV-2 Infection. Biochem Genet 2024:10.1007/s10528-024-10869-4. [PMID: 38955878 DOI: 10.1007/s10528-024-10869-4] [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: 12/18/2023] [Accepted: 06/10/2024] [Indexed: 07/04/2024]
Abstract
The advent of the new coronavirus, leading to the SARS-CoV-2 pandemic, has presented a substantial worldwide health hazard since its inception in the latter part of 2019. The severity of the current pandemic is exacerbated by the occurrence of re-infection or co-infection with SARS-CoV-2. Hence, comprehending the molecular process underlying the pathophysiology of sepsis and discerning possible molecular targets for therapeutic intervention holds significant importance. For the first time, 31 metabolites were tentatively identified by GC-MS analysis from Alpinia malaccensis. On the other hand, five phenolic compounds were identified and quantified from the plant in HPLC-DAD analysis, including (-) epicatechin, rutin hydrate, rosmarinic acid, quercetin, and kaempferol. Nine GC-MS and five HPLC-identified metabolites had shown interactions with 45 and 30 COVID-19-associated human proteins, respectively. Among the proteins, PARP1, FN1, PRKCA, EGFR, ALDH2, AKR1C3, AHR, and IKBKB have been found as potential therapeutic targets to mitigate SARS-CoV-2 infection. KEGG pathway analysis also showed a strong association of FN1, EGFR, and IKBKB genes with SARS-CoV-2 viral replication and cytokine overexpression due to viral infection. Protein-protein interaction (PPI) analysis also showed that TP53, MMP9, FN1, EGFR, and NOS2 proteins are highly related to the genes involved in COVID-19 comorbidity. These proteins showed interaction with the plant phytoconstituents as well. As the study offers a robust network-based procedure for identifying biomolecules relevant to COVID-19 disease, A. malaccensis could be a good source of effective therapeutic agents against COVID-19 and related viral diseases.
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Affiliation(s)
- Esrat Jahan
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Tanoy Mazumder
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Tarek Hasan
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Khondoker Shahin Ahmed
- Chemical Research Division, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Muhammed Amanat
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Hemayet Hossain
- Chemical Research Division, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Sumaiya Jannat Supty
- Department of Soil, Water and Environment, University of Dhaka, Dhaka, Bangladesh
| | - Israt Jahan Liya
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Md Sadikur Rahman Shuvo
- Department of Microbiology, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh.
| | - A F M Shahid Ud Daula
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh.
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3
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Almohdar D, Murcia D, Tang Q, Ortiz A, Martinez E, Parwal T, Kamble P, Çağlayan M. Impact of DNA ligase 1 and IIIα interactions with APE1 and polβ on the efficiency of base excision repair pathway at the downstream steps. J Biol Chem 2024; 300:107355. [PMID: 38718860 PMCID: PMC11176775 DOI: 10.1016/j.jbc.2024.107355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/03/2024] Open
Abstract
Base excision repair (BER) requires a tight coordination between the repair enzymes through protein-protein interactions and involves gap filling by DNA polymerase (pol) β and subsequent nick sealing by DNA ligase (LIG) 1 or LIGIIIα at the downstream steps. Apurinic/apyrimidinic-endonuclease 1 (APE1), by its exonuclease activity, proofreads 3' mismatches incorporated by polβ during BER. We previously reported that the interruptions in the functional interplay between polβ and the BER ligases result in faulty repair events. Yet, how the protein interactions of LIG1 and LIGIIIα could affect the repair pathway coordination during nick sealing at the final steps remains unknown. Here, we demonstrate that LIGIIIα interacts more tightly with polβ and APE1 than LIG1, and the N-terminal noncatalytic region of LIG1 as well as the catalytic core and BRCT domain of LIGIIIα mediate interactions with both proteins. Our results demonstrated less efficient nick sealing of polβ nucleotide insertion products in the absence of LIGIIIα zinc-finger domain and LIG1 N-terminal region. Furthermore, we showed a coordination between APE1 and LIG1/LIGIIIα during the removal of 3' mismatches from the nick repair intermediate on which both BER ligases can seal noncanonical ends or gap repair intermediate leading to products of single deletion mutagenesis. Overall results demonstrate the importance of functional coordination from gap filling by polβ coupled to nick sealing by LIG1/LIGIIIα in the presence of proofreading by APE1, which is mainly governed by protein-protein interactions and protein-DNA intermediate communications, to maintain repair efficiency at the downstream steps of the BER pathway.
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Affiliation(s)
- Danah Almohdar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - David Murcia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Qun Tang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Abigail Ortiz
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Ernesto Martinez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Tanay Parwal
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Pradnya Kamble
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA.
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4
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Dehhaghi M, Heydari M, Panahi HKS, Lewin SR, Heng B, Brew BJ, Guillemin GJ. The roles of the kynurenine pathway in COVID-19 neuropathogenesis. Infection 2024:10.1007/s15010-024-02293-y. [PMID: 38802702 DOI: 10.1007/s15010-024-02293-y] [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: 03/07/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly contagious respiratory disease Corona Virus Disease 2019 (COVID-19) that may lead to various neurological and psychological disorders that can be acute, lasting days to weeks or months and possibly longer. The latter is known as long-COVID or more recently post-acute sequelae of COVID (PASC). During acute COVID-19 infection, a strong inflammatory response, known as the cytokine storm, occurs in some patients. The levels of interferon-γ (IFN-γ), interferon-β (IFN-β), interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) are particularly increased. These cytokines are known to activate the enzyme indoleamine 2,3-dioxygenase 1 (IDO-1), catalysing the first step of tryptophan (Trp) catabolism through the kynurenine pathway (KP) leading to the production of several neurotoxic and immunosuppressive metabolites. There is already data showing elevation in KP metabolites both acutely and in PASC, especially regarding cognitive impairment. Thus, it is likely that KP involvement is significant in SARS-CoV-2 pathogenesis especially neurologically.
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Affiliation(s)
- Mona Dehhaghi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mostafa Heydari
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Hamed Kazemi Shariat Panahi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The Alfred Hospital and Monash University, Melbourne, VIC, Australia
| | - Benjamin Heng
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Bruce J Brew
- Peter Duncan Neurosciences Unit, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia.
- Departments of Neurology and Immunology, St. Vincent's Hospital, Sydney, NSW, Australia.
- University of Notre Dame, Darlinghurst, Sydney, NSW, Australia.
| | - Gilles J Guillemin
- Peter Duncan Neurosciences Unit, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Institut Pertanian Bogor University, Bogor, Indonesia
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5
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Lin X, Leung KSK, Wolfe KF, Lee BJ, Zha S. XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594230. [PMID: 38798615 PMCID: PMC11118530 DOI: 10.1101/2024.05.14.594230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Poly-ADP-ribose polymerases 1 and 2 (PARP1 and PARP2) are crucial sensors of DNA-strand breaks and emerging cancer therapy targets. Once activated by DNA breaks, PARP1 and PARP2 generate poly-ADP-ribose (PAR) chains on themselves and other substrates to promote DNA single-strand break repair (SSBR). PARP1 can be activated by diverse DNA lesions, whereas PARP2 specifically recognizes 5' phosphorylated nicks. They can be activated independently and provide mutual backup in the absence of the other. However, whether PARP1 and PARP2 have synergistic functions in DNA damage response remains elusive. Here, we show that PARP1 and the PAR chains generated by PARP1 recruit PARP2 to the vicinity of DNA damage sites through the scaffold protein XRCC1. Using quantitative live-cell imaging, we found that loss of XRCC1 markedly reduces irradiation-induced PARP2 foci in PARP1-proficient cells. The central BRCT domain (BRCT1) of XRCC1 binds to the PAR chain, while the C-terminal BRCT domain (BRCT2) of XRCC1 interacts with the catalytic domain of PARP2, facilitating its localization near the breaks. Together, these findings unveil a new function of XRCC1 in augmenting PARP2 recruitment in response to PARP1 activation and explain why PARP1, but not PARP2, is aggregated and hyperactivated in XRCC1-deficient cells.
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Szántó M, Yélamos J, Bai P. Specific and shared biological functions of PARP2 - is PARP2 really a lil' brother of PARP1? Expert Rev Mol Med 2024; 26:e13. [PMID: 38698556 PMCID: PMC11140550 DOI: 10.1017/erm.2024.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 05/05/2024]
Abstract
PARP2, that belongs to the family of ADP-ribosyl transferase enzymes (ART), is a discovery of the millennium, as it was identified in 1999. Although PARP2 was described initially as a DNA repair factor, it is now evident that PARP2 partakes in the regulation or execution of multiple biological processes as inflammation, carcinogenesis and cancer progression, metabolism or oxidative stress-related diseases. Hereby, we review the involvement of PARP2 in these processes with the aim of understanding which processes are specific for PARP2, but not for other members of the ART family. A better understanding of the specific functions of PARP2 in all of these biological processes is crucial for the development of new PARP-centred selective therapies.
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Affiliation(s)
- Magdolna Szántó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - José Yélamos
- Hospital del Mar Research Institute, Barcelona, Spain
| | - Péter Bai
- HUN-REN-UD Cell Biology and Signaling Research Group, Debrecen, 4032, Hungary
- MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, 4032, Hungary
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
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7
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Muoio D, Laspata N, Dannenberg RL, Curry C, Darkoa-Larbi S, Hedglin M, Uttam S, Fouquerel E. PARP2 promotes Break Induced Replication-mediated telomere fragility in response to replication stress. Nat Commun 2024; 15:2857. [PMID: 38565848 PMCID: PMC10987537 DOI: 10.1038/s41467-024-47222-7] [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: 05/30/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
PARP2 is a DNA-dependent ADP-ribosyl transferase (ARTs) enzyme with Poly(ADP-ribosyl)ation activity that is triggered by DNA breaks. It plays a role in the Base Excision Repair pathway, where it has overlapping functions with PARP1. However, additional roles for PARP2 have emerged in the response of cells to replication stress. In this study, we demonstrate that PARP2 promotes replication stress-induced telomere fragility and prevents telomere loss following chronic induction of oxidative DNA lesions and BLM helicase depletion. Telomere fragility results from the activity of the break-induced replication pathway (BIR). During this process, PARP2 promotes DNA end resection, strand invasion and BIR-dependent mitotic DNA synthesis by orchestrating POLD3 recruitment and activity. Our study has identified a role for PARP2 in the response to replication stress. This finding may lead to the development of therapeutic approaches that target DNA-dependent ART enzymes, particularly in cancer cells with high levels of replication stress.
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Affiliation(s)
- Daniela Muoio
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA
| | - Natalie Laspata
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University park, State College, PA, 16802, USA
| | - Caroline Curry
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Simone Darkoa-Larbi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University park, State College, PA, 16802, USA
| | - Shikhar Uttam
- Department of Computational and Systems Biology, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA.
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8
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Mittra A, Coyne GHOS, Zlott J, Kummar S, Meehan R, Rubinstein L, Juwara L, Wilsker D, Ji J, Miller B, Navas T, Ferry-Galow KV, Voth AR, Chang TC, Jiwani S, Parchment RE, Doroshow JH, Chen AP. Pharmacodynamic effects of the PARP inhibitor talazoparib (MDV3800, BMN 673) in patients with BRCA-mutated advanced solid tumors. Cancer Chemother Pharmacol 2024; 93:177-189. [PMID: 38010394 PMCID: PMC10902014 DOI: 10.1007/s00280-023-04600-0] [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: 06/06/2023] [Accepted: 10/02/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE Talazoparib is an inhibitor of the poly (ADP-ribose) polymerase (PARP) family of enzymes and is FDA-approved for patients with (suspected) deleterious germline BRCA1/2-mutated, HER2‑negative, locally advanced or metastatic breast cancer. Because knowledge of the pharmacodynamic (PD) effects of talazoparib in patients has been limited to studies of PARP enzymatic activity (PARylation) in peripheral blood mononuclear cells, we developed a study to assess tumoral PD response to talazoparib treatment (NCT01989546). METHODS We administered single-agent talazoparib (1 mg/day) orally in 28-day cycles to adult patients with advanced solid tumors harboring (suspected) deleterious BRCA1 or BRCA2 mutations. The primary objective was to examine the PD effects of talazoparib; the secondary objective was to determine overall response rate (ORR). Tumor biopsies were mandatory at baseline and post-treatment on day 8 (optional at disease progression). Biopsies were analyzed for PARylation, DNA damage response (γH2AX), and epithelial‒mesenchymal transition. RESULTS Nine patients enrolled in this trial. Four of six patients (67%) evaluable for the primary PD endpoint exhibited a nuclear γH2AX response on day 8 of treatment, and five of six (83%) also exhibited strong suppression of PARylation. A transition towards a more mesenchymal phenotype was seen in 4 of 6 carcinoma patients, but this biological change did not affect γH2AX or PAR responses. The ORR was 55% with the five partial responses lasting a median of six cycles. CONCLUSION Intra-tumoral DNA damage response and inhibition of PARP enzymatic activity were confirmed in patients with advanced solid tumors harboring BRCA1/2 mutations after 8 days of talazoparib treatment.
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Affiliation(s)
- Arjun Mittra
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
- Division of Medical Oncology, The Ohio State University, Columbus, OH, 43210, USA
| | - Geraldine H O' Sullivan Coyne
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Jennifer Zlott
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Shivaani Kummar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Robert Meehan
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Lawrence Rubinstein
- Biometric Research Program, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Lamin Juwara
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Deborah Wilsker
- Clinical Pharmacodynamics Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jiuping Ji
- Clinical Pharmacodynamics Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brandon Miller
- Clinical Pharmacodynamics Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Tony Navas
- Clinical Pharmacodynamics Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, 10591, USA
| | - Katherine V Ferry-Galow
- Clinical Pharmacodynamics Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Andrea Regier Voth
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ting-Chia Chang
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Shahanawaz Jiwani
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ralph E Parchment
- Clinical Pharmacodynamics Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA.
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9
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Xu S, Wei J, Sun S, Zhang J, Chan TF, Li Y. SSBlazer: a genome-wide nucleotide-resolution model for predicting single-strand break sites. Genome Biol 2024; 25:46. [PMID: 38347618 PMCID: PMC10863285 DOI: 10.1186/s13059-024-03179-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Single-strand breaks are the major DNA damage in the genome and serve a crucial role in various biological processes. To reveal the significance of single-strand breaks, multiple sequencing-based single-strand break detection methods have been developed, which are costly and unfeasible for large-scale analysis. Hence, we propose SSBlazer, an explainable and scalable deep learning framework for single-strand break site prediction at the nucleotide level. SSBlazer is a lightweight model with robust generalization capabilities across various species and is capable of numerous unexplored SSB-related applications.
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Affiliation(s)
- Sheng Xu
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, 100871, Hong Kong SAR, China
- Research Institute of Intelligent Complex Systems, Fudan University, 220 Handan Rd, Shanghai, 200437, China
- Shanghai AI Lab, 422 Jingan Rd, 200041, Shanghai, China
| | - Junkang Wei
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, 100871, Hong Kong SAR, China.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA.
| | - Siqi Sun
- Research Institute of Intelligent Complex Systems, Fudan University, 220 Handan Rd, Shanghai, 200437, China
- Shanghai AI Lab, 422 Jingan Rd, 200041, Shanghai, China
| | - Jizhou Zhang
- School of Life Sciences, The Chinese University of Hong Kong, 100871, Hong Kong SAR, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, 100871, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, 100871, Hong Kong SAR, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, 100871, Hong Kong SAR, China
| | - Yu Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, 100871, Hong Kong SAR, China.
- The CUHK Shenzhen Research Institute, Hi-Tech Park, Nanshan, 518057, Shenzhen, China.
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10
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Zhang X, Zhao Q, Wang T, Long Q, Sun Y, Jiao L, Gullerova M. DNA damage response, a double-edged sword for vascular aging. Ageing Res Rev 2023; 92:102137. [PMID: 38007046 DOI: 10.1016/j.arr.2023.102137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/03/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Vascular aging is a major risk factor for age-related cardiovascular diseases, which have high rates of morbidity and mortality. It is characterized by changes in the blood vessels, such as macroscopically increased vascular diameter and intima-medial thickness, chronic inflammation, vascular calcification, arterial stiffening, and atherosclerosis. DNA damage and the subsequent various DNA damage response (DDR) pathways are important causative factors of vascular aging. Deficient DDR, which may result in the accumulation of unrepaired damaged DNA or mutations, can lead to vascular aging. On the other hand, over-activation of some DDR proteins, such as poly (ADP ribose) polymerase (PARP) and ataxia telangiectasia mutated (ATM), also can enhance the process of vascular aging, suggesting that DDR can have both positive and negative effects on vascular aging. Despite the evidence reviewed in this paper, the role of DDR in vascular aging and potential therapeutic targets remain poorly understood and require further investigation.
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Affiliation(s)
- Xiao Zhang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qing Zhao
- M.D. Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Tao Wang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qilin Long
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Yixin Sun
- First Hospital, Peking University, Beijing, China
| | - Liqun Jiao
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China; Department of Interventional Neuroradiology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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11
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Thakur A, Rana M, Ritika, Mathew J, Nepali S, Pan CH, Liou JP, Nepali K. Small molecule tractable PARP inhibitors: Scaffold construction approaches, mechanistic insights and structure activity relationship. Bioorg Chem 2023; 141:106893. [PMID: 37783100 DOI: 10.1016/j.bioorg.2023.106893] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
Diverse drug design strategies viz. molecular hybridization, substituent installation, scaffold hopping, isosteric replacement, high-throughput screening, induction and separation of chirality, structure modifications of phytoconstituents and use of structural templates have been exhaustively leveraged in the last decade to load the chemical toolbox of PARP inhibitors. Resultantly, numerous promising scaffolds have been pinpointed that in turn have led to the resuscitation of the credence to PARP inhibitors as cancer therapeutics. This review briefly presents the physiological functions of PARPs, the pharmacokinetics, and pharmacodynamics, and the interaction profiles of FDA-approved PARP inhibitors. Comprehensively covered is the section on the drug design strategies employed by drug discovery enthusiasts for furnishing PARP inhibitors. The impact of structural variations in the template of designed scaffolds on enzymatic and cellular activity (structure-activity relationship studies) has been discussed. The insights gained through the biological evaluation such as profiling of physicochemical properties andin vitroADME properties, PK assessments, and high-dose pharmacology are covered.
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Affiliation(s)
- Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Mandeep Rana
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Ritika
- College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Jacob Mathew
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Sanya Nepali
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Chun-Hsu Pan
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan.
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Chen H, Hu Y, Zhuang Z, Wang D, Ye Z, Jing J, Cheng X. Advancements and Obstacles of PARP Inhibitors in Gastric Cancer. Cancers (Basel) 2023; 15:5114. [PMID: 37958290 PMCID: PMC10647262 DOI: 10.3390/cancers15215114] [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: 09/17/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023] Open
Abstract
Gastric cancer (GC) is a common and aggressive cancer of the digestive system, exhibiting high aggressiveness and significant heterogeneity. Despite advancements in improving survival rates over the past few decades, GC continues to carry a worrisome prognosis and notable mortality. As a result, there is an urgent need for novel therapeutic approaches to address GC. Recent targeted sequencing studies have revealed frequent mutations in DNA damage repair (DDR) pathway genes in many GC patients. These mutations lead to an increased reliance on poly (adenosine diphosphate-ribose) polymerase (PARP) for DNA repair, making PARP inhibitors (PARPi) a promising treatment option for GC. This article presents a comprehensive overview of the rationale and development of PARPi, highlighting its progress and challenges in both preclinical and clinical research for treating GC.
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Affiliation(s)
- Hongjie Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; (H.C.); (Y.H.); (D.W.)
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Yangchan Hu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; (H.C.); (Y.H.); (D.W.)
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Zirui Zhuang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (UCAS), Hangzhou 310024, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dingyi Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; (H.C.); (Y.H.); (D.W.)
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Zu Ye
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
- Zhejiang Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Hangzhou 310022, China
| | - Ji Jing
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
- Zhejiang Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Hangzhou 310022, China
| | - Xiangdong Cheng
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
- Zhejiang Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Hangzhou 310022, China
- Zhejiang Provincial Research Center for Upper Gastrointestinal Tract Cancer, Zhejiang Cancer Hospital, Hangzhou 310022, China
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Maluchenko N, Saulina A, Geraskina O, Kotova E, Korovina A, Feofanov A, Studitsky V. Zinc-dependent Nucleosome Reorganization by PARP2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562808. [PMID: 37904948 PMCID: PMC10614866 DOI: 10.1101/2023.10.17.562808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Poly(ADP-ribose)polymerase 2 (PARP2) is a nuclear protein that acts as a DNA damage sensor; it recruits the repair enzymes to a DNA damage site and facilitates formation of the repair complex. Using single particle Förster resonance energy transfer microscopy and electrophoretic mobility shift assay (EMSA) we demonstrated that PARP2 forms complexes with a nucleosome containing different number of PARP2 molecules without altering conformation of nucleosomal DNA both in the presence and in the absence of Mg 2+ or Ca 2+ ions. In contrast, Zn 2+ ions directly interact with PARP2 inducing a local alteration of the secondary structure of the protein and PARP2-mediated, reversible structural reorganization of nucleosomal DNA. AutoPARylation activity of PARP2 is enhanced by Mg 2+ ions and modulated by Zn 2+ ions: suppressed or enhanced depending on the occupancy of two functionally different Zn 2+ binding sites. The data suggest that Zn 2+ /PARP2-induced nucleosome reorganization and transient changes in the concentration of the cations could modulate PARP2 activity and the DNA damage response. Significance Statement PARP2 recognizes and binds DNA damage sites, recruits the repair enzymes to these sites and facilitates formation of the repair complex. Zn 2+ -induced structural reorganization of nucleosomal DNA in the complex with PARP2, which is reported in the paper, could modulate the DNA damage response. The obtained data indicate the existence of specific binding sites of Mg 2+ and Zn 2+ ions in and/or near the catalytic domain of PARP2, which modulate strongly, differently and ion-specifically PARylation activity of PARP2, which is important for maintaining genome stability, adaptation of cells to stress, regulation of gene expression and antioxidant defense.
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Kamaletdinova T, Zong W, Urbánek P, Wang S, Sannai M, Grigaravičius P, Sun W, Fanaei-Kahrani Z, Mangerich A, Hottiger MO, Li T, Wang ZQ. Poly(ADP-Ribose) Polymerase-1 Lacking Enzymatic Activity Is Not Compatible with Mouse Development. Cells 2023; 12:2078. [PMID: 37626888 PMCID: PMC10453916 DOI: 10.3390/cells12162078] [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: 06/24/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP1) binds DNA lesions to catalyse poly(ADP-ribosyl)ation (PARylation) using NAD+ as a substrate. PARP1 plays multiple roles in cellular activities, including DNA repair, transcription, cell death, and chromatin remodelling. However, whether these functions are governed by the enzymatic activity or scaffolding function of PARP1 remains elusive. In this study, we inactivated in mice the enzymatic activity of PARP1 by truncating its C-terminus that is essential for ART catalysis (PARP1ΔC/ΔC, designated as PARP1-ΔC). The mutation caused embryonic lethality between embryonic day E8.5 and E13.5, in stark contrast to PARP1 complete knockout (PARP1-/-) mice, which are viable. Embryonic stem (ES) cell lines can be derived from PARP1ΔC/ΔC blastocysts, and these mutant ES cells can differentiate into all three germ layers, yet, with a high degree of cystic structures, indicating defects in epithelial cells. Intriguingly, PARP1-ΔC protein is expressed at very low levels compared to its full-length counterpart, suggesting a selective advantage for cell survival. Noticeably, PARP2 is particularly elevated and permanently present at the chromatin in PARP1-ΔC cells, indicating an engagement of PARP2 by non-enzymatic PARP1 protein at the chromatin. Surprisingly, the introduction of PARP1-ΔC mutation in adult mice did not impair their viability; yet, these mutant mice are hypersensitive to alkylating agents, similar to PARP1-/- mutant mice. Our study demonstrates that the catalytically inactive mutant of PARP1 causes the developmental block, plausibly involving PARP2 trapping.
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Affiliation(s)
- Tatiana Kamaletdinova
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
| | - Pavel Urbánek
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Sijia Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
| | - Mara Sannai
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Paulius Grigaravičius
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
| | - Zahra Fanaei-Kahrani
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Aswin Mangerich
- Molecular Toxicology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany;
- Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, 14469 Potsdam, Germany
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease, University of Zürich, 8057 Zürich, Switzerland;
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
| | - Zhao-Qi Wang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
- Faculty of Biological Sciences, Friedrich Schiller University of Jena, 07743 Jena, Germany
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15
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Antal D, Pór Á, Kovács I, Dull K, Póliska S, Ujlaki G, Demény MÁ, Szöllősi AG, Kiss B, Szegedi A, Bai P, Szántó M. PARP2 promotes inflammation in psoriasis by modulating estradiol biosynthesis in keratinocytes. J Mol Med (Berl) 2023; 101:987-999. [PMID: 37351597 PMCID: PMC10400701 DOI: 10.1007/s00109-023-02338-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/09/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
Poly(ADP-ribose) polymerase 2 (PARP2) alongside PARP1 are responsible for the bulk of cellular PARP activity, and they were first described as DNA repair factors. However, research in past decades implicated PARPs in biological functions as diverse as the regulation of cellular energetics, lipid homeostasis, cell death, and inflammation. PARP activation was described in Th2-mediated inflammatory processes, but studies focused on the role of PARP1, while we have little information on PARP2 in inflammatory regulation. In this study, we assessed the role of PARP2 in a Th17-mediated inflammatory skin condition, psoriasis. We found that PARP2 mRNA expression is increased in human psoriatic lesions. Therefore, we studied the functional consequence of decreased PARP2 expression in murine and cellular human models of psoriasis. We observed that the deletion of PARP2 attenuated the imiquimod-induced psoriasis-like dermatitis in mice. Silencing of PARP2 in human keratinocytes prevented their hyperproliferation, maintained their terminal differentiation, and reduced their production of inflammatory mediators after treatment with psoriasis-mimicking cytokines IL17A and TNFα. Underlying these observations, we found that aromatase was induced in the epidermis of PARP2 knock-out mice and in PARP2-deficient human keratinocytes, and the resulting higher estradiol production suppressed NF-κB activation, and hence, inflammation in keratinocytes. Steroidogenic alterations have previously been described in psoriasis, and we extend these observations by showing that aromatase expression is reduced in psoriatic lesions. Collectively, our data identify PARP2 as a modulator of estrogen biosynthesis by epidermal keratinocytes that may be relevant in Th17 type inflammation. KEY MESSAGES : PARP2 mRNA expression is increased in lesional skin of psoriasis patients. PARP2 deletion in mice attenuated IMQ-induced psoriasis-like dermatitis. NF-κB activation is suppressed in PARP2-deficient human keratinocytes. Higher estradiol in PARP2-deficient keratinocytes conveys anti-inflammatory effect.
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Affiliation(s)
- Dóra Antal
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Elettudomanyi Epulet, H-4032, Debrecen, Hungary
- The Hungarian Academy of Sciences, Center of Excellence, Budapest, Hungary
| | - Ágnes Pór
- Department of Pathology, Gyula Kenézy Campus, Clinical Centre, University of Debrecen, Debrecen, Hungary
| | - Ilona Kovács
- Department of Pathology, Gyula Kenézy Campus, Clinical Centre, University of Debrecen, Debrecen, Hungary
| | - Katalin Dull
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilárd Póliska
- Genomic Medicine and Bioinformatics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gyula Ujlaki
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Elettudomanyi Epulet, H-4032, Debrecen, Hungary
- The Hungarian Academy of Sciences, Center of Excellence, Budapest, Hungary
| | - Máté Ágoston Demény
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Elettudomanyi Epulet, H-4032, Debrecen, Hungary
- The Hungarian Academy of Sciences, Center of Excellence, Budapest, Hungary
| | - Attila Gábor Szöllősi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Borbála Kiss
- Department of Oncology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Andrea Szegedi
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- ELKH-DE Allergology Research Group, University of Debrecen, Debrecen, Hungary
| | - Péter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Elettudomanyi Epulet, H-4032, Debrecen, Hungary
- The Hungarian Academy of Sciences, Center of Excellence, Budapest, Hungary
- NKFIH-DE Lendület Laboratory of Cellular Metabolism, Debrecen, Hungary
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group ELKH, Debrecen, Hungary
| | - Magdolna Szántó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Elettudomanyi Epulet, H-4032, Debrecen, Hungary.
- The Hungarian Academy of Sciences, Center of Excellence, Budapest, Hungary.
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16
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Huang Y, Zheng D, Yang Q, Wu J, Tian H, Ji Z, Chen L, Cai J, Li Z, Chen Y. Global trends in BRCA-related breast cancer research from 2013 to 2022: A scientometric analysis. Front Oncol 2023; 13:1197168. [PMID: 37476378 PMCID: PMC10354558 DOI: 10.3389/fonc.2023.1197168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction Since the mid-2000s, breast cancer incidence among women has slowly increased at about 0.5% per year. In the last three decades, Breast Cancer Susceptibility Gene (BRCA) has been proven to be the crucial gene in encouraging the incidence and development of breast cancer. However, scientometric analysis on BRCA-related breast cancer is in shortage. Thus, to have a clear understanding of the current status and catch up with the hotspots, a scientometric analysis was conducted on specific academic publications collected from the Web of Science (WoS). Methods We searched the Web of Science Core Collection (WoSCC) to procure associated articles as our dataset. Bibliometric, CiteSpace, VOSviewer, and HistCite software were then applied to conduct visual analyses of countries, institutions, journals, authors, landmark articles, and keywords in this research field. Results A total of 7,266 articles and 1,310 review articles published between 2013 to 2022 were retrieved eventually. The annual output steadily rose year by year and peaked in 2021. The USA led the way in the number of published works, total citations, and collaboration. Breast Cancer Research and Treatment was the most favoured journal in this research field. Narod SA from the University of Toronto produced the most publications. At last, the most prominent keywords were "breast cancer" (n=1,778), "women" (n=1,369), "brca1" (n=1,276), "ovarian cancer" (n=1,259), "risk" (n=1,181), and "mutations" (n=929), which exposed the hotspots within the BRCA domain of breast cancer study. Conclusion The tendency in the BRCA research field over the past decade was presented by the scientometric analysis. The current research focus is the clinical trials of poly-adenosine diphosphate ribose polymerase inhibitors (PARPi) drugs and their resistance mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhiyang Li
- *Correspondence: Zhiyang Li, ; Yexi Chen,
| | - Yexi Chen
- *Correspondence: Zhiyang Li, ; Yexi Chen,
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Jankó L, Tóth E, Laczik M, Rauch B, Janka E, Bálint BL, Bai P. PARP2 poly(ADP-ribosyl)ates nuclear factor erythroid 2-related factor 2 (NRF2) affecting NRF2 subcellular localization. Sci Rep 2023; 13:7869. [PMID: 37188809 DOI: 10.1038/s41598-023-35076-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023] Open
Abstract
PARP2 is a member of the PARP enzyme family. Although, PARP2 plays role in DNA repair, it has regulatory roles in mitochondrial and lipid metabolism, it has pivotal role in bringing about the adverse effects of pharmacological PARP inhibitors. Previously, we showed that the ablation of PARP2 induces oxidative stress and, consequently, mitochondrial fragmentation. In attempt to identify the source of the reactive species we assessed the possible role of a central regulator of cellular antioxidant defense, nuclear factor erythroid 2-related factor 2 (NRF2). The silencing of PARP2 did not alter either the mRNA or the protein expression of NRF2, but changed its subcellular localization, decreasing the proportion of nuclear, active fraction of NRF2. Pharmacological inhibition of PARP2 partially restored the normal localization pattern of NRF2 and in line with that, we showed that NRF2 is PARylated that is absent in the cells in which PARP2 was silenced. Apparently, the PARylation of NRF2 by PARP2 has pivotal role in regulating the subcellular (nuclear) localization of NRF2. The silencing of PARP2 rearranged the expression of genes encoding proteins with antioxidant function, among these a subset of NRF2-dependent genes.
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Affiliation(s)
- Laura Jankó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary
| | - Emese Tóth
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary
| | - Miklós Laczik
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Boglárka Rauch
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary
| | - Eszter Janka
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Bálint L Bálint
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
- Department of Bioinformatics, Semmelweis University, Tűzoltó Utca 7-9., Budapest, 1094, Hungary
| | - Péter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary.
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary.
- MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, 4032, Hungary.
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary.
- MTA-DE Cell Biology and Signaling Research Group ELKH, Debrecen, Hungary.
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18
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Moliner L, Zhang B, Lamberti G, Ardizzoni A, Byers LA, Califano R. Novel therapeutic strategies for recurrent SCLC. Crit Rev Oncol Hematol 2023; 186:104017. [PMID: 37150311 DOI: 10.1016/j.critrevonc.2023.104017] [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: 12/01/2022] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023] Open
Abstract
Therapeutic options for patients with relapsed SCLC are limited, and the prognosis in this setting remains poor. While clinical outcomes for frontline treatment have modestly improved with the introduction of immunotherapy, treatment in the second-line setting persists almost unchanged. In this review, current treatment options and recent advances in molecular biology are described. Emerging therapeutic options in this setting and potential strategies to improve clinical outcomes of these patients are also addressed.
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Affiliation(s)
- Laura Moliner
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, M20 4BX, UK
| | - Bingnan Zhang
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Giuseppe Lamberti
- Department of Specialized, Experimental and Diagnostic Medicine, University of Bologna, Bologna, 40138, Italy
| | - Andrea Ardizzoni
- Department of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, 40138, Italy
| | - Lauren A Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Raffaele Califano
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, M20 4BX, UK; Division of Cancer Sciences, The University of Manchester, Manchester, M13 9NT, UK.
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Kaur J, Mojumdar A. A mechanistic overview of spinal cord injury, oxidative DNA damage repair and neuroprotective therapies. Int J Neurosci 2023; 133:307-321. [PMID: 33789065 DOI: 10.1080/00207454.2021.1912040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Despite substantial development in medical treatment strategies scientists are struggling to find a cure against spinal cord injury (SCI) which causes long term disability and paralysis. The prime rationale behind it is the enlargement of primary lesion due to an initial trauma to the spinal cord which spreads to the neighbouring spinal tissues It begins from the time of traumatic event happened and extends to hours and even days. It further causes series of biological and functional alterations such as inflammation, excitotoxicity and ischemia, and promotes secondary lesion to the cord which worsens the life of individuals affected by SCI. Oxidative DNA damage is a stern consequence of oxidative stress linked with secondary injury causes oxidative base alterations and strand breaks, which provokes cell death in neurons. It is implausible to stop primary damage however it is credible to halt the secondary lesion and improve the quality of the patient's life to some extent. Therefore it is crucial to understand the hidden perspectives of cell and molecular biology affecting the pathophysiology of SCI. Thus the focus of the review is to connect the missing links and shed light on the oxidative DNA damages and the functional repair mechanisms, as a consequence of the injury in neurons. The review will also probe the significance of neuroprotective strategies in the present scenario. HIGHLIGHTSSpinal cord injury, a pernicious condition, causes excitotoxicity and ischemia, ultimately leading to cell death.Oxidative DNA damage is a consequence of oxidative stress linked with secondary injury, provoking cell death in neurons.Base excision repair (BER) is one of the major repair pathways that plays a crucial role in repairing oxidative DNA damages.Neuroprotective therapies curbing SCI and boosting BER include the usage of pharmacological drugs and other approaches.
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Affiliation(s)
- Jaspreet Kaur
- Department of Neuroscience, University of Copenhagen, Copenhagen N, Denmark
| | - Aditya Mojumdar
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
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20
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Multi-Omics Profiling of Hypertrophic Cardiomyopathy Reveals Altered Mechanisms in Mitochondrial Dynamics and Excitation-Contraction Coupling. Int J Mol Sci 2023; 24:ijms24054724. [PMID: 36902152 PMCID: PMC10002553 DOI: 10.3390/ijms24054724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Hypertrophic cardiomyopathy is one of the most common inherited cardiomyopathies and a leading cause of sudden cardiac death in young adults. Despite profound insights into the genetics, there is imperfect correlation between mutation and clinical prognosis, suggesting complex molecular cascades driving pathogenesis. To investigate this, we performed an integrated quantitative multi-omics (proteomic, phosphoproteomic, and metabolomic) analysis to illuminate the early and direct consequences of mutations in myosin heavy chain in engineered human induced pluripotent stem-cell-derived cardiomyocytes relative to late-stage disease using patient myectomies. We captured hundreds of differential features, which map to distinct molecular mechanisms modulating mitochondrial homeostasis at the earliest stages of pathobiology, as well as stage-specific metabolic and excitation-coupling maladaptation. Collectively, this study fills in gaps from previous studies by expanding knowledge of the initial responses to mutations that protect cells against the early stress prior to contractile dysfunction and overt disease.
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21
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Plummer R. Evolution of the Development of PARP Inhibitors. Cancer Treat Res 2023; 186:1-11. [PMID: 37978127 DOI: 10.1007/978-3-031-30065-3_1] [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] [Indexed: 11/19/2023]
Abstract
PARP inhibitors first entered the clinic in 2003 in combination with DNA damaging agents in an attempt to overcome treatment resistance to established agents. A brief overview of ADP-ribosylator enzyme biology and the early preclinical development of the class is discussed, illustrating the multiple biological activities of these enzymes and potential wider clinical applicability. The chapter then documents those early years of clinical development and the evolution of the field and eventual registration of PARP inhibitors as active anticancer agents in their own right-in genetically vulnerable tumours.
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Affiliation(s)
- Ruth Plummer
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.
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22
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The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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23
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M A, Xavier J, A S F, Bisht P, Murti K, Ravichandiran V, Kumar N. Epigenetic basis for PARP mutagenesis in glioblastoma: A review. Eur J Pharmacol 2022; 938:175424. [PMID: 36442619 DOI: 10.1016/j.ejphar.2022.175424] [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: 10/10/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Several modifications in the glioblastoma genes are caused by epigenetic modifications, which are crucial in appropriate developmental processes such as self-renewal and destiny determination of neural stem cells. Poly (ADP-ribose)polymerase (PARP) is an essential cofactor involved in DNA repair as well as several other cellular functions such as transcription and chromatin shape modification. Inhibiting PARP has evolved for triggering cell damage in cancerous cells when paired with certain other anticancer drugs including temozolomide (TMZ). PARP1 is involved with in base excision repair (BER) pathway, however its functionality differs across types of tumours. Epigenomics as well as chromosomal statistics have contributed to the growth of main subgroups of glioma, which serve as foundation for the categorization of central nervous system (CNS) tumours as well as a unique classification based only on DNA methylation information, which demonstrates extraordinary diagnostic accuracy. Unfortunately, not all patients respond to PARP inhibitors (PARPi), and there is no way to anticipate who will and who will not. In this field, PARPi are one of the innovative medicines currently being explored. As a result, cancer cells that also have a homologous recombination defect become fatal synthetically. As well as preparing the tumour microenvironment for immunotherapy, PARPi may enhance the lethal effects of chemotherapy and radiotherapy. This article analyzes the justification and clinical evidence for PARPi in glioma to offer potential therapeutic approaches. Despite the effectiveness of these targeted drugs, researchers have looked into a number of resistance mechanisms as well as the growing usage of PARPi in clinical practice for the treatment of various malignancies.
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Affiliation(s)
- Anu M
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India
| | - Joyal Xavier
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India
| | - Fathima A S
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India
| | - Priya Bisht
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India
| | - Krishna Murti
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India
| | - V Ravichandiran
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India; Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India; Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India
| | - Nitesh Kumar
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur, Vaishali, Bihar, 844102, India.
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24
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Soni A, Lin X, Mladenov E, Mladenova V, Stuschke M, Iliakis G. BMN673 Is a PARP Inhibitor with Unique Radiosensitizing Properties: Mechanisms and Potential in Radiation Therapy. Cancers (Basel) 2022; 14:cancers14225619. [PMID: 36428712 PMCID: PMC9688666 DOI: 10.3390/cancers14225619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/17/2022] Open
Abstract
BMN673 is a relatively new PARP inhibitor (PARPi) that exhibits superior efficacy in vitro compared to olaparib and other clinically relevant PARPi. BMN673, similar to most clinical PARPi, inhibits the catalytic activities of PARP-1 and PARP-2 and shows impressive anticancer potential as monotherapy in several pre-clinical and clinical studies. Tumor resistance to PARPi poses a significant challenge in the clinic. Thus, combining PARPi with other treatment modalities, such as radiotherapy (RT), is being actively pursued to overcome such resistance. However, the modest to intermediate radiosensitization exerted by olaparib, rucaparib, and veliparib, limits the rationale and the scope of such combinations. The recently reported strong radiosensitizing potential of BMN673 forecasts a paradigm shift on this front. Evidence accumulates that BMN673 may radiosensitize via unique mechanisms causing profound shifts in the balance among DNA double-strand break (DSB) repair pathways. According to one of the emerging models, BMN673 strongly inhibits classical non-homologous end-joining (c-NHEJ) and increases reciprocally and profoundly DSB end-resection, enhancing error-prone DSB processing that robustly potentiates cell killing. In this review, we outline and summarize the work that helped to formulate this model of BMN673 action on DSB repair, analyze the causes of radiosensitization and discuss its potential as a radiosensitizer in the clinic. Finally, we highlight strategies for combining BMN673 with other inhibitors of DNA damage response for further improvements.
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Affiliation(s)
- Aashish Soni
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Xixi Lin
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Emil Mladenov
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Veronika Mladenova
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Martin Stuschke
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, German Cancer Research Center (DKFZ), 45147 Essen, Germany
| | - George Iliakis
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Correspondence: ; Tel.: +49-201-723-4152
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25
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Alemasova EE, Lavrik OI. Poly(ADP-ribose) in Condensates: The PARtnership of Phase Separation and Site-Specific Interactions. Int J Mol Sci 2022; 23:14075. [PMID: 36430551 PMCID: PMC9694962 DOI: 10.3390/ijms232214075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell faces certain challenges. In this review, we discuss a basic model of PS and the role of site-specific interactions and percolation in cellular PS-related events. Using a multivalent poly(ADP-ribose) molecule as an example, which has high PS-driving potential due to its structural features, we consider how site-specific interactions and network formation are involved in the formation of phase-separated cellular condensates.
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Affiliation(s)
- Elizaveta E. Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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26
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Tufan AB, Lazarow K, Kolesnichenko M, Sporbert A, von Kries JP, Scheidereit C. TSG101 associates with PARP1 and is essential for PARylation and DNA damage-induced NF-κB activation. EMBO J 2022; 41:e110372. [PMID: 36124865 DOI: 10.15252/embj.2021110372] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
In a genome-wide screening for components of the dsDNA-break-induced IKK-NF-κB pathway, we identified scores of regulators, including tumor susceptibility gene TSG101. TSG101 is essential for DNA damage-induced formation of cellular poly(ADP-ribose) (PAR). TSG101 binds to PARP1 and is required for PARP1 activation. This function of TSG101 is independent of its role in the ESCRT-I endosomal sorting complex. In the absence of TSG101, the PAR-dependent formation of a nuclear PARP1-IKKγ signalosome, which triggers IKK activation, is impaired. According to its requirement for PARP1 and NF-κB activation, TSG101-deficient cells are defective in DNA repair and apoptosis protection. Loss of TSG101 results in PARP1 trapping at damage sites and mimics the effect of pharmacological PARP inhibition. We also show that the loss of TSG101 in connection with inactivated tumor suppressors BRCA1/2 in breast cancer cells is lethal. Our results imply TSG101 as a therapeutic target to achieve synthetic lethality in cancer treatment.
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Affiliation(s)
- Ahmet Buğra Tufan
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Katina Lazarow
- Leibniz-Forschungsinstitut for Molecular Pharmacology (FMP), Berlin, Germany
| | - Marina Kolesnichenko
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anje Sporbert
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Advanced Light Microscopy Technology Platform, Berlin, Germany
| | | | - Claus Scheidereit
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
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27
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Nagy L, Rauch B, Szerafin T, Uray K, Tóth A, Bai P. Nicotinamide-riboside shifts the differentiation of human primary white adipocytes to beige adipocytes impacting substrate preference and uncoupling respiration through SIRT1 activation and mitochondria-derived reactive species production. Front Cell Dev Biol 2022; 10:979330. [PMID: 36072335 PMCID: PMC9441796 DOI: 10.3389/fcell.2022.979330] [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: 06/27/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Beige adipocytes play key roles in organismal energy and metabolic balance. In this study, we assessed whether the supplementation of human white adipocytes, differentiated from human adipose tissue-derived stem cells, with nicotinamide riboside (NR), a potent NAD + precursor, can shift differentiation to beige adipocytes (beiging). NR induced mitochondrial biogenesis and the expression of beige markers (TBX1 and UCP1) in white adipocytes demonstrating that NR can declutch beiging. NR did not induce PARP activity but supported SIRT1 induction, which plays a key role in beiging. NR induced etomoxir-resistant respiration, suggesting increases in the oxidation of carbohydrates, carbohydrate breakdown products, or amino acids. Furthermore, NR boosted oligomycin-resistant respiration corresponding to uncoupled respiration. Enhanced etomoxir and oligomycin-resistant respiration were dependent on mitochondrial reactive-species production. Taken together, NR supplementation can induce beiging and uncoupled respiration, which are beneficial for combatting metabolic diseases.
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Affiliation(s)
- Lilla Nagy
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Boglárka Rauch
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamás Szerafin
- Department of Cardiology and Heart Surgery, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Karen Uray
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Tóth
- Section of Clinical Physiology, Department of Cardiology and Heart Surgery, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group ELKH, Debrecen, Hungary
- Correspondence: Péter Bai,
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28
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Koczor CA, Haider AJ, Saville KM, Li J, Andrews JF, Beiser AV, Sobol RW. Live Cell Detection of Poly(ADP-Ribose) for Use in Genetic and Genotoxic Compound Screens. Cancers (Basel) 2022; 14:3676. [PMID: 35954352 PMCID: PMC9367489 DOI: 10.3390/cancers14153676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
Poly(ADP-ribose) (PAR) is a molecular scaffold that aids in the formation of DNA repair protein complexes. Tools to sensitively quantify PAR in live cells have been lacking. We recently described the LivePAR probe (EGFP fused to the RNF146-encoded WWE PAR binding domain) to measure PAR formation at sites of laser micro-irradiation in live cells. Here, we present two methods that expand on the use of LivePAR and its WWE domain. First, LivePAR enriches in the nucleus of cells following genotoxic challenge. Image quantitation can identify single-cell PAR formation following genotoxic stress at concentrations lower than PAR ELISA or PAR immunoblot, with greater sensitivity to genotoxic stress than CometChip. In a second approach, we used the RNF146-encoded WWE domain to develop a split luciferase probe for analysis in a 96-well plate assay. We then applied these PAR analysis tools to demonstrate their broad applicability. First, we show that both approaches can identify genetic modifications that alter PARylation levels, such as hyper-PARylation in BRCA2-deficient cancer cells. Second, we demonstrate the utility of the WWE split luciferase assay to characterize the cellular response of genotoxins, PARP inhibitors, and PARG inhibitors, thereby providing a screening method to identify PAR modulating compounds.
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Affiliation(s)
- Christopher A. Koczor
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Aaron J. Haider
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Kate M. Saville
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Jianfeng Li
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Joel F. Andrews
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Alison V. Beiser
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Robert W. Sobol
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
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29
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Danforth JM, Provencher L, Goodarzi AA. Chromatin and the Cellular Response to Particle Radiation-Induced Oxidative and Clustered DNA Damage. Front Cell Dev Biol 2022; 10:910440. [PMID: 35912116 PMCID: PMC9326100 DOI: 10.3389/fcell.2022.910440] [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] [Received: 04/01/2022] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Exposure to environmental ionizing radiation is prevalent, with greatest lifetime doses typically from high Linear Energy Transfer (high-LET) alpha particles via the radioactive decay of radon gas in indoor air. Particle radiation is highly genotoxic, inducing DNA damage including oxidative base lesions and DNA double strand breaks. Due to the ionization density of high-LET radiation, the consequent damage is highly clustered wherein ≥2 distinct DNA lesions occur within 1–2 helical turns of one another. These multiply-damaged sites are difficult for eukaryotic cells to resolve either quickly or accurately, resulting in the persistence of DNA damage and/or the accumulation of mutations at a greater rate per absorbed dose, relative to lower LET radiation types. The proximity of the same and different types of DNA lesions to one another is challenging for DNA repair processes, with diverse pathways often confounding or interplaying with one another in complex ways. In this context, understanding the state of the higher order chromatin compaction and arrangements is essential, as it influences the density of damage produced by high-LET radiation and regulates the recruitment and activity of DNA repair factors. This review will summarize the latest research exploring the processes by which clustered DNA damage sites are induced, detected, and repaired in the context of chromatin.
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30
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Bisht P, Kumar VU, Pandey R, Velayutham R, Kumar N. Role of PARP Inhibitors in Glioblastoma and Perceiving Challenges as Well as Strategies for Successful Clinical Development. Front Pharmacol 2022; 13:939570. [PMID: 35873570 PMCID: PMC9297740 DOI: 10.3389/fphar.2022.939570] [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: 05/09/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiform is the most aggressive primary type of brain tumor, representing 54% of all gliomas. The average life span for glioblastoma multiform is around 14-15 months instead of treatment. The current treatment for glioblastoma multiform includes surgical removal of the tumor followed by radiation therapy and temozolomide chemotherapy for 6.5 months, followed by another 6 months of maintenance therapy with temozolomide chemotherapy (5 days every month). However, resistance to temozolomide is frequently one of the limiting factors in effective treatment. Poly (ADP-ribose) polymerase (PARP) inhibitors have recently been investigated as sensitizing drugs to enhance temozolomide potency. However, clinical use of PARP inhibitors in glioblastoma multiform is difficult due to a number of factors such as limited blood-brain barrier penetration of PARP inhibitors, inducing resistance due to frequent use of PARP inhibitors, and overlapping hematologic toxicities of PARP inhibitors when co-administered with glioblastoma multiform standard treatment (radiation therapy and temozolomide). This review elucidates the role of PARP inhibitors in temozolomide resistance, multiple factors that make development of these PARP inhibitor drugs challenging, and the strategies such as the development of targeted drug therapies and combination therapy to combat the resistance of PARP inhibitors that can be adopted to overcome these challenges.
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Affiliation(s)
- Priya Bisht
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
| | - V. Udaya Kumar
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
| | - Ruchi Pandey
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
| | - Ravichandiran Velayutham
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
| | - Nitesh Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
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31
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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: 4.5] [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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32
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Manzo J, Puhalla S, Pahuja S, Ding F, Lin Y, Appleman L, Tawbi H, Stoller R, Lee JJ, Diergaarde B, Kiesel BF, Yu J, Tan AR, Belani CP, Chew H, Garcia AA, Morgan RJ, Wahner Hendrickson AE, Visscher DW, Hurley RM, Kaufmann SH, Swisher EM, Oesterreich S, Katz T, Ji J, Zhang Y, Parchment RE, Chen A, Duan W, Giranda V, Shepherd SP, Ivy SP, Chu E, Beumer JH. A phase 1 and pharmacodynamic study of chronically-dosed, single-agent veliparib (ABT-888) in patients with BRCA1- or BRCA2-mutated cancer or platinum-refractory ovarian or triple-negative breast cancer. Cancer Chemother Pharmacol 2022; 89:721-735. [PMID: 35435472 PMCID: PMC9116722 DOI: 10.1007/s00280-022-04430-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/27/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE BRCA1 or BRCA2 mutated cancers (BRCAmut) have intrinsic sensitivity to PARP inhibitors due to deficiency in homologous recombination-mediated DNA repair. There are similarities between BRCAmut and BRCAwt ovarian and basal-like breast cancers. This phase I study determined the recommended phase II dose (RP2D) and preliminary efficacy of the PARP inhibitor, veliparib (ABT-888), in these patients. PATIENTS AND METHODS Patients (n = 98) were dosed with veliparib 50-500 mg twice daily (BID). The BRCAmut cohort (n = 70) contained predominantly ovarian (53%) and breast (23%) cancers; the BRCAwt cohort (n = 28) consisted primarily of breast cancer (86%). The MTD, DLT, adverse events, PK, PD, and clinical response were assessed. RESULTS DLTs were grade 3 nausea/vomiting at 400 mg BID in a BRCAmut carrier, grade 2 seizure at 400 mg BID in a patient with BRCAwt cancer, and grade 2 seizure at 500 mg BID in a BRCAmut carrier. Common toxicities included nausea (65%), fatigue (45%), and lymphopenia (38%). Grade 3/4 toxicities were rare (highest lymphopenia at 15%). Overall response rate (ORR) was 23% (95% CI 13-35%) in BRCAmut overall, and 37% (95% CI 21-55%) at 400 mg BID and above. In BRCAwt, ORR was 8% (95% CI 1-26%), and clinical benefit rate was 16% (95% CI 4-36%), reflecting prolonged stable disease in some patients. PK was linear with dose and was correlated with response and nausea. CONCLUSIONS Continuous veliparib is safe and tolerable. The RP2D was 400 mg BID. There is evidence of clinical activity of veliparib in patients with BRCAmut and BRCAwt cancers.
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Affiliation(s)
- Julia Manzo
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Shannon Puhalla
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shalu Pahuja
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Fei Ding
- Biostatistics Facility, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Yan Lin
- Biostatistics Facility, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leonard Appleman
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hussein Tawbi
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ronald Stoller
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - James J Lee
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brenda Diergaarde
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian F Kiesel
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, Pittsburgh, PA, USA
| | - Jing Yu
- Department of Pathology, Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Antoinette R Tan
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Levine Cancer Institute, Charlotte, NC, USA
| | - Chandra P Belani
- Penn State Cancer Institute, Penn State College of Medicine, Hershey, PA, USA
| | - Helen Chew
- Division of Hematology/Oncology, Department of Medicine, University of California Davis, Sacramento, CA, USA
| | - Agustin A Garcia
- Department of Medicine, Louisiana State University, New Orleans, LA, USA
| | - Robert J Morgan
- Department of Molecular Pharmacology, City of Hope Beckman Research Institute, Duarte, CA, USA
| | | | - Daniel W Visscher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rachel M Hurley
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Scott H Kaufmann
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecologic, University of Washington, Seattle, WA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tiffany Katz
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jiuping Ji
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yiping Zhang
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ralph E Parchment
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Alice Chen
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Wenrui Duan
- Department of Human and Molecular Genetics, The Florida International University, Miami, FL, USA
| | | | | | - S Percy Ivy
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Edward Chu
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jan H Beumer
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy, Pittsburgh, PA, USA.
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Lin X, Jiang W, Rudolph J, Lee BJ, Luger K, Zha S. PARP inhibitors trap PARP2 and alter the mode of recruitment of PARP2 at DNA damage sites. Nucleic Acids Res 2022; 50:3958-3973. [PMID: 35349716 PMCID: PMC9023293 DOI: 10.1093/nar/gkac188] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/24/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
Dual-inhibitors of PARP1 and PARP2 are promising anti-cancer drugs. In addition to blocking PARP1&2 enzymatic activity, PARP inhibitors also extend the lifetime of DNA damage-induced PARP1&2 foci, termed trapping. Trapping is important for the therapeutic effects of PARP inhibitors. Using live-cell imaging, we found that PARP inhibitors cause persistent PARP2 foci by switching the mode of PARP2 recruitment from a predominantly PARP1- and PAR-dependent rapid exchange to a WGR domain-mediated stalling of PARP2 on DNA. Specifically, PARP1-deletion markedly reduces but does not abolish PARP2 foci. The residual PARP2 foci in PARP1-deficient cells are DNA-dependent and abrogated by the R140A mutation in the WGR domain. Yet, PARP2-R140A forms normal foci in PARP1-proficient cells. In PARP1-deficient cells, PARP inhibitors - niraparib, talazoparib, and, to a lesser extent, olaparib - enhance PARP2 foci by preventing PARP2 exchange. This trapping of PARP2 is independent of auto-PARylation and is abolished by the R140A mutation in the WGR domain and the H415A mutation in the catalytic domain. Taken together, we found that PARP inhibitors trap PARP2 by physically stalling PARP2 on DNA via the WGR-DNA interaction while suppressing the PARP1- and PAR-dependent rapid exchange of PARP2.
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Affiliation(s)
- Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO80309, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
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The PARP1 Inhibitor Niraparib Represses DNA Damage Repair and Synergizes with Temozolomide for Antimyeloma Effects. JOURNAL OF ONCOLOGY 2022; 2022:2800488. [PMID: 35422863 PMCID: PMC9005285 DOI: 10.1155/2022/2800488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/15/2022] [Accepted: 03/09/2022] [Indexed: 11/18/2022]
Abstract
Purpose Poly(ADP-ribose) polymerase 1 (PARP1) is necessary for single-strand break (SSB) repair by sensing DNA breaks and facilitating DNA repair through poly ADP-ribosylation of several DNA-binding and repair proteins. Inhibition of PARP1 results in collapsed DNA replication fork and double-strand breaks (DSBs). Accumulation of DSBs goes beyond the capacity of DNA repair response, ultimately resulting in cell death. This work is aimed at assessing the synergistic effects of the DNA-damaging agent temozolomide (TMZ) and the PARP inhibitor niraparib (Nira) in human multiple myeloma (MM) cells. Materials and Methods MM RPMI8226 and NCI-H929 cells were administered TMZ and/or Nira for 48 hours. CCK-8 was utilized for cell viability assessment. Cell proliferation and apoptosis were detected flow-cytometrically. Immunofluorescence was performed for detecting γH2A.X expression. Soft-agar colony formation assay was applied to evaluate the antiproliferative effect. The amounts of related proteins were obtained by immunoblot. The combination index was calculated with the CompuSyn software. A human plasmacytoma xenograft model was established to assess the anti-MM effects in vivo. The anti-MM activities of TMZ and/or Nira were evaluated by H&E staining, IHC, and the TUNEL assay. Results The results demonstrated that cotreatment with TMZ and Nira promoted DNA damage, cell cycle arrest, and apoptotic death in cultured cells but also reduced MM xenograft growth in nude mice, yielding highly synergistic effects. Immunoblot revealed that TMZ and Nira cotreatment markedly increased the expression of p-ATM, p-CHK2, RAD51, and γH2A.X, indicating the suppression of DNA damage response (DDR) and elevated DSB accumulation. Conclusion Inhibition of PARP1 sensitizes genotoxic agents and represents an important therapeutic approach for MM. These findings provide preliminary evidence for combining PARP1 inhibitors with TMZ for MM treatment.
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Abstract
PARP is an important target in the treatment of cancers, particularly in patients with breast, ovarian, or prostate cancer that have compromised homologous recombination repair (i.e., BRCA−/−). This review about inhibitors of PARP (PARPi) is for readers interested in the development of next-generation drugs for the treatment of cancer, providing insights into structure–activity relationships, in vitro vs. in vivo potency, PARP trapping, and synthetic lethality. Selective inhibitors of PARP1 and PARP2 (PARP1/2) are used to treat cancer patients with deficiencies in the repair of DNA via homologous recombination. Here we provide a perspective on the reported potencies of the most studied of these inhibitors (olaparib, talazoparib, niraparib, rucaparib, and veliparib) in vitro and in vivo and how these numbers relate to the known structures of these inhibitors bound to the active sites of PARP1 and PARP2. We suggest that the phenomenon of PARP trapping is primarily due to the inhibition of the catalytic activity of PARP1 and that the basis for the higher potency of talazoparib compared to the other inhibitors lies in its more extensive network of interactions with conserved residues in the active site. We also consider the potential role of the recently characterized protein “Histone PARylation Factor 1” (HPF1), which interacts with PARP1/2 to form a shared active site, for the design of the next generation of inhibitors of PARP1/2.
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Huang J, Ralph D, Boraldi F, Quaglino D, Uitto J, Li Q. Inhibition of the DNA Damage Response Attenuates Ectopic Calcification in Pseudoxanthoma Elasticum. J Invest Dermatol 2022; 142:2140-2148.e1. [PMID: 35143822 PMCID: PMC9329183 DOI: 10.1016/j.jid.2022.01.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
Abstract
Pseudoxanthoma elasticum (PXE) is a heritable ectopic calcification disorder with multi-organ clinical manifestations. The gene at default, ABCC6, encodes an efflux transporter, ABCC6, which is a new player regulating the homeostasis of inorganic pyrophosphate (PPi), a potent endogenous anti-calcification factor. Previous studies suggested that systemic PPi deficiency is the major, but not the exclusive, cause of ectopic calcification in PXE. In this study, we demonstrate that the DNA damage response (DDR) and poly(ADP-ribose) (PAR) pathways are involved locally in PXE at sites of ectopic calcification. Genetic inhibition of PARP1, the predominant PAR-producing enzyme, showed a 54% reduction of calcification in the muzzle skin in Abcc6-/-Parp1-/- mice, as compared to age-matched Abcc6-/-Parp1+/+ littermates. Subsequently, oral administration of minocycline, an inhibitor of DDR/PAR signaling, resulted in an 86% reduction of calcification in the muzzle skin of Abcc6-/- mice. Minocycline treatment also attenuated the DDR/PAR signaling and reduced calcification of dermal fibroblasts derived from PXE patients. The anti-calcification effect of DDR/PAR inhibition was not accompanied by alterations in plasma PPi concentrations. These results suggest that local DDR/PAR signaling in calcification-prone tissues contributes to PXE pathogenesis, and its inhibition might provide a promising treatment strategy for ectopic calcification in PXE, a currently intractable disease.
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Affiliation(s)
- Jianhe Huang
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA; PXE international Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Douglas Ralph
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA; PXE international Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, PA 19107, USA; Genetics, Genomics and Cancer Biology Ph.D. Program, Jefferson College of Life Sciences, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Federica Boraldi
- Department of Life Science, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Daniela Quaglino
- Department of Life Science, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Jouni Uitto
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA; PXE international Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Qiaoli Li
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA; PXE international Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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Yu J, Luo L, Hu T, Cui Y, Sun X, Gou W, Hou W, Li Y, Sun T. Structure-based design, synthesis, and evaluation of inhibitors with high selectivity for PARP-1 over PARP-2. Eur J Med Chem 2022; 227:113898. [PMID: 34656898 DOI: 10.1016/j.ejmech.2021.113898] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/31/2022]
Abstract
The poly (ADP-ribose) polymerase (PARP) inhibitors play a crucial role in cancer therapy. However, most approved PARP inhibitors have lower selectivity to PARP-1 than to PARP-2, so they will inevitably have side effects. Based on the different catalytic domains of PARP-1 and PARP-2, we developed a strategy to design and synthesize highly selective PARP-1 inhibitors. Compounds Y17, Y29, Y31 and Y49 showed excellent PARP-1 inhibition, and their IC50 values were 0.61, 0.66, 0.41 and 0.96 nM, respectively. Then, Y49 (PARP-1 IC50 = 0.96 nM, PARP-2 IC50 = 61.90 nM, selectivity PARP-2/PARP-1 = 64.5) was proved to be the most selective inhibitor of PARP-1. Compounds Y29 and Y49 showed stronger inhibitory effect on proliferation in BRCA1 mutant MX-1 cells than in other cancer cells. In the MDA-MB-436 xenotransplantation model, Y49 was well tolerated and showed remarkable single dose activity. The design strategy proposed in this paper is of far-reaching significance for the further construction of the next generation of selective PARP-1 inhibitors.
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Affiliation(s)
- Jiang Yu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang, 110016, China; Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Lingling Luo
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Tong Hu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang, 110016, China
| | - Yating Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Xiao Sun
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Wenfeng Gou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Wenbin Hou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China.
| | - Yiliang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China.
| | - Tiemin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang, 110016, China.
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Derby SJ, Chalmers AJ, Carruthers RD. Radiotherapy-Poly(ADP-ribose) Polymerase Inhibitor Combinations: Progress to Date. Semin Radiat Oncol 2022; 32:15-28. [PMID: 34861992 DOI: 10.1016/j.semradonc.2021.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Radiation resistance remains a huge clinical problem for cancer patients and oncologists in the 21st century. In recent years, the mammalian DNA damage response (DDR) has been extensively characterized and shown to play a key role in determining cellular survival following ionizing radiation exposure. Genomic instability due to altered DDR is a hallmark of cancer, with many tumors exhibiting abnormal DNA repair or lack of redundancy in DDR. Targeting the abnormal DDR phenotype of tumor cells could lead to substantial gains in radiotherapy efficacy, improving local control and survival for patients with cancers that are refractory to current therapies. Poly(ADP-ribose) polymerase inhibitors (PARPi) are the most clinically advanced DDR inhibitors under investigation as radiosensitisers. Preclinical evidence suggests that PARPi may provide tumor specific radiosensitisation in certain contexts. In addition to inhibition of DNA single strand break repair, PARPi may offer other benefits in combination treatment including radiosensitisation of hypoxic cells and targeting of alternative repair pathways such as microhomology mediated end joining which are increasingly recognized to be upregulated in cancer. Several early phase clinical trials of PARPi with radiation have completed or are in progress. Early reports have highlighted tumor specific challenges, with tolerability dependent upon anatomical location and use of concomitant systemic therapies; these challenges were largely predicted by preclinical data. This review discusses the role of PARP in the cellular response to ionizing radiation, summarizes preclinical studies of PARPi in combination with radiotherapy and explores current early phase clinical trials that are evaluating these combinations.
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Affiliation(s)
- Sarah J Derby
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland.
| | - Anthony J Chalmers
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland
| | - Ross D Carruthers
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland
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Zong C, Zhu T, He J, Huang R, Jia R, Shen J. PARP mediated DNA damage response, genomic stability and immune responses. Int J Cancer 2021; 150:1745-1759. [PMID: 34952967 DOI: 10.1002/ijc.33918] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 11/11/2022]
Abstract
Poly (ADP-ribose) polymerase (PARP) enzymes, especially PARP1, play important roles in the DNA damage response and in the maintenance of genome stability, which makes PARPis a classic synthetic lethal therapy for BRCA-deficient tumors. Conventional mechanisms suggest that PARPis exert their effects via catalytic inhibition and PARP-DNA trapping. Recently, PARP1 has been found to play a role in the immune modulation of tumors. The blockade of PARP1 is able to induce innate immunity through a series of molecular mechanisms, thus allowing the prediction of the feasibility of PARPis combined with immune agents in the treatment of tumors. PARPis combined with immunomodulators may have a stronger tumor suppressive effect on inhibiting tumor growth and blocking immune escape. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chunyan Zong
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Tianyu Zhu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jie He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
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PARP Inhibitors and Myeloid Neoplasms: A Double-Edged Sword. Cancers (Basel) 2021; 13:cancers13246385. [PMID: 34945003 PMCID: PMC8699275 DOI: 10.3390/cancers13246385] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Poly(ADP-ribose) polymerase (PARP) inhibitors, which are medications approved to treat various solid tumors, including breast, prostate, ovarian, and prostate cancers, are being examined in hematological malignancies. This review summarizes the potential role of PARP inhibitors in the treatment of myeloid diseases, particularly acute myeloid leukemia (AML). We review ongoing clinical studies investigating the safety and efficacy of PARP inhibitors in the treatment of AML, focusing on specific molecular and genetic AML subgroups that could be particularly sensitive to PARP inhibitor treatment. We also discuss reports describing an increased risk of treatment-related myeloid neoplasms in patients receiving PARP inhibitors for solid tumors. Abstract Despite recent discoveries and therapeutic advances in aggressive myeloid neoplasms, there remains a pressing need for improved therapies. For instance, in acute myeloid leukemia (AML), while most patients achieve a complete remission with conventional chemotherapy or the combination of a hypomethylating agent and venetoclax, de novo or acquired drug resistance often presents an insurmountable challenge, especially in older patients. Poly(ADP-ribose) polymerase (PARP) enzymes, PARP1 and PARP2, are involved in detecting DNA damage and repairing it through multiple pathways, including base excision repair, single-strand break repair, and double-strand break repair. In the context of AML, PARP inhibitors (PARPi) could potentially exploit the frequently dysfunctional DNA repair pathways that, similar to deficiencies in homologous recombination in BRCA-mutant disease, set the stage for cell killing. PARPi appear to be especially effective in AML with certain gene rearrangements and molecular characteristics (RUNX1-RUNX1T1 and PML-RARA fusions, FLT3- and IDH1-mutated). In addition, PARPi can enhance the efficacy of other agents, particularly alkylating agents, TOP1 poisons, and hypomethylating agents, that induce lesions ordinarily repaired via PARP1-dependent mechanisms. Conversely, emerging reports suggest that long-term treatment with PARPi for solid tumors is associated with an increased incidence of myelodysplastic syndrome (MDS) and AML. Here, we (i) review the pre-clinical and clinical data on the role of PARPi, specifically olaparib, talazoparib, and veliparib, in aggressive myeloid neoplasms and (ii) discuss the reported risk of MDS/AML with PARPi, especially as the indications for PARPi use expand to include patients with potentially curable cancer.
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Rudolph J, Muthurajan UM, Palacio M, Mahadevan J, Roberts G, Erbse AH, Dyer PN, Luger K. The BRCT domain of PARP1 binds intact DNA and mediates intrastrand transfer. Mol Cell 2021; 81:4994-5006.e5. [PMID: 34919819 PMCID: PMC8769213 DOI: 10.1016/j.molcel.2021.11.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/15/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022]
Abstract
PARP1 is a key player in the response to DNA damage and is the target of clinical inhibitors for the treatment of cancers. Binding of PARP1 to damaged DNA leads to activation wherein PARP1 uses NAD+ to add chains of poly(ADP-ribose) onto itself and other nuclear proteins. PARP1 also binds abundantly to intact DNA and chromatin, where it remains enzymatically inactive. We show that intact DNA makes contacts with the PARP1 BRCT domain, which was not previously recognized as a DNA-binding domain. This binding mode does not result in the concomitant reorganization and activation of the catalytic domain. We visualize the BRCT domain bound to nucleosomal DNA by cryogenic electron microscopy and identify a key motif conserved from ancestral BRCT domains for binding phosphates on DNA and phospho-peptides. Finally, we demonstrate that the DNA-binding properties of the BRCT domain contribute to the "monkey-bar mechanism" that mediates DNA transfer of PARP1.
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Affiliation(s)
- Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Uma M Muthurajan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Megan Palacio
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Jyothi Mahadevan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Genevieve Roberts
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Pamela N Dyer
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA.
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Poly(ADP-Ribose) Polymerase Inhibition in Small Cell Lung Cancer: A Review. Cancer J 2021; 27:476-481. [PMID: 34904810 DOI: 10.1097/ppo.0000000000000555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine malignancy with high and rapid relapse rates and poor outcomes. Treatment for SCLC has historically been limited by the lack of targetable driver genomic lesions, however recent developments in the underpinnings of genomic instability in SCLC and understanding of its transcriptional subtypes have led to increased interest in the use of poly(ADP-ribose) polymerase (PARP) inhibitors as a rationale therapy. Poly(ADP-ribose) polymerase inhibitors, historically designed to target BRCA1/2-mutated malignancies, capitalize on synthetic lethality in homologous recombination-deficient tumors. In this review, we outline the mechanistic rationale for the use of PARP inhibitors in treating SCLC and detail key clinical trials investigating their use in combination with chemotherapy and immunotherapy. We describe developments in the understanding of biomarkers for sensitivity to therapy and highlight further investigational directions for the use of PARP inhibitors in treating SCLC.
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Santos SS, Brunialti MKC, Soriano FG, Szabo C, Salomão R. Repurposing of Clinically Approved Poly-(ADP-Ribose) Polymerase Inhibitors for the Therapy of Sepsis. Shock 2021; 56:901-909. [PMID: 34115723 DOI: 10.1097/shk.0000000000001820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT Sepsis' pathogenesis involves multiple mechanisms that lead to a dysregulation of the host's response. Significant efforts have been made in search of interventions that can reverse this situation and increase patient survival. Poly (ADP-polymerase) (PARP) is a constitutive nuclear and mitochondrial enzyme, which functions as a co-activator and co-repressor of gene transcription, thus regulating the production of inflammatory mediators. Several studies have already demonstrated an overactivation of PARP1 in various human pathophysiological conditions and that its inhibition has benefits in regulating intracellular processes. The PARP inhibitor olaparib, originally developed for cancer therapy, paved the way for the expansion of its clinical use for nononcological indications. In this review we discuss sepsis as one of the possible indications for the use of olaparib and other clinically approved PARP inhibitors as modulators of the inflammatory response and cellular dysfunction. The benefit of olaparib and other clinically approved PARP inhibitors has already been demonstrated in several experimental models of human diseases, such as neurodegeneration and neuroinflammation, acute hepatitis, skeletal muscle disorders, aging and acute ischemic stroke, protecting, for example, from the deterioration of the blood-brain barrier, restoring the cellular levels of NAD+, improving mitochondrial function and biogenesis and, among other effects, reducing oxidative stress and pro-inflammatory mediators, such as TNF-α, IL1-β, IL-6, and VCAM1. These data demonstrated that repositioning of clinically approved PARP inhibitors may be effective in protecting against hemodynamic dysfunction, metabolic dysfunction, and multiple organ failure in patients with sepsis. Age and gender affect the response to PARP inhibitors, the mechanisms underlying the lack of many protective effects in females and aged animals should be further investigated and be cautiously considered in designing clinical trials.
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Affiliation(s)
- Sidnéia Sousa Santos
- Division of Infectious Diseasses, Paulista School of Medicine, Federal University of Sao Paulo, Brazil
| | | | - Francisco Garcia Soriano
- Laboratory of Medical Research, Faculty of Medicine of the University of São Paulo-USP, São Paulo, Brazil
| | - Csaba Szabo
- Chair of Pharmacology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Reinaldo Salomão
- Division of Infectious Diseasses, Paulista School of Medicine, Federal University of Sao Paulo, Brazil
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Zhou S, Zhu Q, Liu H, Jiang S, Zhang X, Peng C, Yang G, Li J, Cheng L, Zhong R, Zeng Q, Miao X, Lu Q. Associations of polycyclic aromatic hydrocarbons exposure and its interaction with XRCC1 genetic polymorphism with lung cancer: A case-control study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118077. [PMID: 34523522 DOI: 10.1016/j.envpol.2021.118077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
Humans are extensively exposed to polycyclic aromatic hydrocarbons (PAHs) daily via multiple pathways. Epidemiological studies have demonstrated that occupational exposure to PAHs increases the risk of lung cancer, but related studies in the general population are limited. Hence, we conducted a case-control study among the Chinese general population to investigate the associations between PAHs exposure and lung cancer risk and analyze the modifications of genetic polymorphisms in DNA repair genes. In this study, we enrolled 122 lung cancer cases and 244 healthy controls in Wuhan, China. Urinary PAHs metabolites were determined by gas chromatography-mass spectrometry, and rs25487 in X-ray repair cross-complementation 1 (XRCC1) gene was genotyped by the Agena Bioscience MassARRAY System. Then, multivariable logistic regression models were performed to estimate the potential associations. We found that urinary hydroxynaphthalene (OH-Nap), hydroxyphenanthrene (OH-Phe) and the sum of hydroxy PAHs (∑OH-PAHs) levels were significantly higher in lung cancer cases than those in controls. After adjusting for gender, age, BMI, smoking status, smoking pack-years, drinking status and family history, urinary ∑OH-Nap and ∑OH-Phe levels were positively associated with lung cancer risk, with dose-response relationships. Compared with those in the lowest tertiles, individuals in the highest tertiles of ∑OH-Nap and ∑OH-Phe had a 2.13-fold (95% CI: 1.10, 4.09) and 2.45-fold (95% CI: 1.23, 4.87) increased risk of lung cancer, respectively. Effects of gender, age, smoking status and smoking pack-years on the associations of PAHs exposure with lung cancer risk were shown in the subgroup analysis. Furthermore, associations of urinary ∑OH-Nap and ∑OH-PAHs levels with lung cancer risk were modified by XRCC1 rs25487 (Pinteraction ≤ 0.025), and were more pronounced in wild-types of rs25487. These findings suggest that environmental exposure to naphthalene and phenanthrene is associated with increased lung cancer risk, and polymorphism of XRCC1 rs25487 might modify the naphthalene exposure-related lung cancer effect.
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Affiliation(s)
- Shuang Zhou
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qiuqi Zhu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Huimin Liu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Shunli Jiang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China; Key Laboratory of Occupational Health and Environmental Medicine, Department of Public Health, Jining Medical University, 133 Hehua Road, Jining, Shandong, 272067, China
| | - Xu Zhang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Cheng Peng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Guanlin Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Road, Wuhan, Hubei, 430030, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Road, Wuhan, Hubei, 430030, China
| | - Rong Zhong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qiang Zeng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Xiaoping Miao
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qing Lu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China.
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Schützenhofer K, Rack JGM, Ahel I. The Making and Breaking of Serine-ADP-Ribosylation in the DNA Damage Response. Front Cell Dev Biol 2021; 9:745922. [PMID: 34869334 PMCID: PMC8634249 DOI: 10.3389/fcell.2021.745922] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022] Open
Abstract
ADP-ribosylation is a widespread posttranslational modification that is of particular therapeutic relevance due to its involvement in DNA repair. In response to DNA damage, PARP1 and 2 are the main enzymes that catalyze ADP-ribosylation at damage sites. Recently, serine was identified as the primary amino acid acceptor of the ADP-ribosyl moiety following DNA damage and appears to act as seed for chain elongation in this context. Serine-ADP-ribosylation strictly depends on HPF1, an auxiliary factor of PARP1/2, which facilitates this modification by completing the PARP1/2 active site. The signal is terminated by initial poly(ADP-ribose) chain degradation, primarily carried out by PARG, while another enzyme, (ADP-ribosyl)hydrolase 3 (ARH3), specifically cleaves the terminal seryl-ADP-ribosyl bond, thus completing the chain degradation initiated by PARG. This review summarizes recent findings in the field of serine-ADP-ribosylation, its mechanisms, possible functions and potential for therapeutic targeting through HPF1 and ARH3 inhibition.
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Affiliation(s)
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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Yang F, Chen J, Liu B, Gao G, Sebastian M, Jeter C, Shen J, Person MD, Bedford MT. SPINDOC binds PARP1 to facilitate PARylation. Nat Commun 2021; 12:6362. [PMID: 34737271 PMCID: PMC8568969 DOI: 10.1038/s41467-021-26588-y] [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: 02/28/2021] [Accepted: 09/30/2021] [Indexed: 11/12/2022] Open
Abstract
SPINDOC is tightly associated with the histone H3K4me3 effector protein SPIN1. To gain a better understanding of the biological roles of SPINDOC, we identified its interacting proteins. Unexpectedly, SPINDOC forms two mutually exclusive protein complexes, one with SPIN1 and the other with PARP1. Consistent with its ability to directly interact with PARP1, SPINDOC expression is induced by DNA damage, likely by KLF4, and recruited to DNA lesions with dynamics that follows PARP1. In SPINDOC knockout cells, the levels of PARylation are reduced, in both the absence and presence of DNA damage. The SPINDOC/PARP1 interaction promotes the clearance of PARP1 from damaged DNA, and also impacts the expression of known transcriptional targets of PARP1. To address the in vivo roles of SPINDOC in PARP1 regulation, we generate SPINDOC knockout mice, which are viable, but slightly smaller than their wildtype counterparts. The KO mice display reduced levels of PARylation and, like PARP1 KO mice, are hypersensitive to IR-induced DNA damage. The findings identify a SPIN1-independent role for SPINDOC in the regulation of PARP1-mediated PARylation and the DNA damage response. SPINDOC is known to interact with Spindlin1 (SPIN1), a histone code effector protein. Here, the authors show that SPINDOC is distributed between two distinct protein complexes, one comprising SPIN1 and the other one with PARP1. Their results suggest a role for SPINDOC in the regulation of PARP1- mediated PARylation and the DNA damage response.
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Affiliation(s)
- Fen Yang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Jianji Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.,Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Guozhen Gao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Manu Sebastian
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Collene Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Maria D Person
- Center for Biomedical Research Support The University of Texas at Austin, Austin, TX, 78712, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.
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Dual function of HPF1 in the modulation of PARP1 and PARP2 activities. Commun Biol 2021; 4:1259. [PMID: 34732825 PMCID: PMC8566583 DOI: 10.1038/s42003-021-02780-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/01/2021] [Indexed: 01/04/2023] Open
Abstract
Poly(ADP-ribosyl)ation catalyzed by poly(ADP-ribose) polymerases (PARPs) is one of the immediate cellular responses to DNA damage. The histone PARylation factor 1 (HPF1) discovered recently to form a joint active site with PARP1 and PARP2 was shown to limit the PARylation activity of PARPs and stimulate their NAD+-hydrolase activity. Here we demonstrate that HPF1 can stimulate the DNA-dependent and DNA-independent autoPARylation of PARP1 and PARP2 as well as the heteroPARylation of histones in the complex with nucleosome. The stimulatory action is detected in a defined range of HPF1 and NAD+ concentrations at which no HPF1-dependent enhancement in the hydrolytic NAD+ consumption occurs. PARP2, comparing with PARP1, is more efficiently stimulated by HPF1 in the autoPARylation reaction and is more active in the heteroPARylation of histones than in the automodification, suggesting a specific role of PARP2 in the ADP-ribosylation-dependent modulation of chromatin structure. Possible role of the dual function of HPF1 in the maintaining PARP activity is discussed. Kurgina et al. conduct in vitro characterization of the effect of HPF1 on the catalytic output of PARP1 and PARP2 under several experimental conditions. The authors report that the DNAdependent and DNA-independent autoPARylation of PARP1 and PARP2, as well as the heteroPARylation of histones in complex with the nucleosome are stimulated by HPF1 in a certain range of HPF1 and NAD + concentrations.
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Temporal dynamics of base excision/single-strand break repair protein complex assembly/disassembly are modulated by the PARP/NAD +/SIRT6 axis. Cell Rep 2021; 37:109917. [PMID: 34731617 PMCID: PMC8607749 DOI: 10.1016/j.celrep.2021.109917] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/03/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Assembly and disassembly of DNA repair protein complexes at DNA damage sites are essential for maintaining genomic integrity. Investigating factors coordinating assembly of the base excision repair (BER) proteins DNA polymerase β (Polβ) and XRCC1 to DNA lesion sites identifies a role for Polβ in regulating XRCC1 disassembly from DNA repair complexes and, conversely, demonstrates Polβ’s dependence on XRCC1 for complex assembly. LivePAR, a genetically encoded probe for live-cell imaging of poly(ADP-ribose) (PAR), reveals that Polβ and XRCC1 require PAR for repair-complex assembly, with PARP1 and PARP2 playing unique roles in complex dynamics. Further, BER complex assembly is modulated by attenuation/augmentation of NAD+ biosynthesis. Finally, SIRT6 does not modulate PARP1 or PARP2 activation but does regulate XRCC1 recruitment, leading to diminished Polβ abundance at sites of DNA damage. These findings highlight coordinated yet independent roles for PARP1, PARP2, and SIRT6 and their regulation by NAD+ bioavailability to facilitate BER. Koczor et al. use quantitative confocal microscopy to characterize DNA-damage-induced poly(ADP-ribose) (PAR) formation and assembly/disassembly kinetics in human cells. These studies highlight the coordinated yet independent roles for XRCC1, POLΒ, PARP1, PARP2, and SIRT6 (and regulation by NAD+) to facilitate BER/SSBR protein complex dynamics.
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Okunlola FO, Akawa OB, Soliman MES. Could the spanning of NAM-AD subsites by poly (ADP ribose) polymerase inhibitors potentiate their selective inhibitory activity in breast cancer treatment? Insight from biophysical computations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1994562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Felix O. Okunlola
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Oluwole B. Akawa
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E. S. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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50
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Hendriks IA, Buch-Larsen SC, Prokhorova E, Elsborg JD, Rebak AKLFS, Zhu K, Ahel D, Lukas C, Ahel I, Nielsen ML. The regulatory landscape of the human HPF1- and ARH3-dependent ADP-ribosylome. Nat Commun 2021; 12:5893. [PMID: 34625544 PMCID: PMC8501107 DOI: 10.1038/s41467-021-26172-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/21/2021] [Indexed: 11/08/2022] Open
Abstract
Despite the involvement of Poly(ADP-ribose) polymerase-1 (PARP1) in many important biological pathways, the target residues of PARP1-mediated ADP-ribosylation remain ambiguous. To explicate the ADP-ribosylation regulome, we analyze human cells depleted for key regulators of PARP1 activity, histone PARylation factor 1 (HPF1) and ADP-ribosylhydrolase 3 (ARH3). Using quantitative proteomics, we characterize 1,596 ADP-ribosylation sites, displaying up to 1000-fold regulation across the investigated knockout cells. We find that HPF1 and ARH3 inversely and homogenously regulate the serine ADP-ribosylome on a proteome-wide scale with consistent adherence to lysine-serine-motifs, suggesting that targeting is independent of HPF1 and ARH3. Notably, we do not detect an HPF1-dependent target residue switch from serine to glutamate/aspartate under the investigated conditions. Our data support the notion that serine ADP-ribosylation mainly exists as mono-ADP-ribosylation in cells, and reveal a remarkable degree of histone co-modification with serine ADP-ribosylation and other post-translational modifications.
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Affiliation(s)
- Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Sara C Buch-Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Jonas D Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Alexandra K L F S Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Claudia Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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