1
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Vekariya U, Minakhin L, Chandramouly G, Tyagi M, Kent T, Sullivan-Reed K, Atkins J, Ralph D, Nieborowska-Skorska M, Kukuyan AM, Tang HY, Pomerantz RT, Skorski T. PARG is essential for Polθ-mediated DNA end-joining by removing repressive poly-ADP-ribose marks. Nat Commun 2024; 15:5822. [PMID: 38987289 PMCID: PMC11236980 DOI: 10.1038/s41467-024-50158-7] [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: 08/29/2023] [Accepted: 06/27/2024] [Indexed: 07/12/2024] Open
Abstract
DNA polymerase theta (Polθ)-mediated end-joining (TMEJ) repairs DNA double-strand breaks and confers resistance to genotoxic agents. How Polθ is regulated at the molecular level to exert TMEJ remains poorly characterized. We find that Polθ interacts with and is PARylated by PARP1 in a HPF1-independent manner. PARP1 recruits Polθ to the vicinity of DNA damage via PARylation dependent liquid demixing, however, PARylated Polθ cannot perform TMEJ due to its inability to bind DNA. PARG-mediated de-PARylation of Polθ reactivates its DNA binding and end-joining activities. Consistent with this, PARG is essential for TMEJ and the temporal recruitment of PARG to DNA damage corresponds with TMEJ activation and dissipation of PARP1 and PAR. In conclusion, we show a two-step spatiotemporal mechanism of TMEJ regulation. First, PARP1 PARylates Polθ and facilitates its recruitment to DNA damage sites in an inactivated state. PARG subsequently activates TMEJ by removing repressive PAR marks on Polθ.
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Affiliation(s)
- Umeshkumar Vekariya
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Leonid Minakhin
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA, 19107, USA
| | - Gurushankar Chandramouly
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA, 19107, USA
| | - Mrityunjay Tyagi
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA, 19107, USA
| | - Tatiana Kent
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA, 19107, USA
| | - Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Jessica Atkins
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Douglas Ralph
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA, 19107, USA
| | - Margaret Nieborowska-Skorska
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Anna-Mariya Kukuyan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Richard T Pomerantz
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA, 19107, USA.
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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2
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Rajendra E, Grande D, Mason B, Di Marcantonio D, Armstrong L, Hewitt G, Elinati E, Galbiati A, Boulton SJ, Heald RA, Smith GCM, Robinson HMR. Quantitative, titratable and high-throughput reporter assays to measure DNA double strand break repair activity in cells. Nucleic Acids Res 2024; 52:1736-1752. [PMID: 38109306 PMCID: PMC10899754 DOI: 10.1093/nar/gkad1196] [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: 05/25/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
Repair of DNA damage is essential for the maintenance of genome stability and cell viability. DNA double strand breaks (DSBs) constitute a toxic class of DNA lesion and multiple cellular pathways exist to mediate their repair. Robust and titratable assays of cellular DSB repair (DSBR) are important to functionally interrogate the integrity and efficiency of these mechanisms in disease models as well as in response to genetic or pharmacological perturbations. Several variants of DSBR reporters are available, however these are often limited by throughput or restricted to specific cellular models. Here, we describe the generation and validation of a suite of extrachromosomal reporter assays that can efficiently measure the major DSBR pathways of homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single strand annealing (SSA). We demonstrate that these assays can be adapted to a high-throughput screening format and that they are sensitive to pharmacological modulation, thus providing mechanistic and quantitative insights into compound potency, selectivity, and on-target specificity. We propose that these reporter assays can serve as tools to dissect the interplay of DSBR pathway networks in cells and will have broad implications for studies of DSBR mechanisms in basic research and drug discovery.
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Affiliation(s)
- Eeson Rajendra
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Diego Grande
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Bethany Mason
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Lucy Armstrong
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Elias Elinati
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Simon J Boulton
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Robert A Heald
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Graeme C M Smith
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
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3
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Mehryar MM, Shi X, Li J, Wu Q. DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements. BMC Biol 2023; 21:288. [PMID: 38066536 PMCID: PMC10709867 DOI: 10.1186/s12915-023-01784-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Recent studies have shown that, owning to its cohesive cleavage, Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements or DNA-fragment editing are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. RESULTS Here we developed a customized computer program to take account of staggered or cohesive Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements or DNA-fragment editing, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system using HPRT1 and DCK as reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections or long deletions at junctions of chromosomal rearrangements. In addition, we found that knockdown of PolQ (encoding Polθ polymerase), which has a prominent role in theta-mediated end joining (TMEJ) or microhomology-mediated end joining (MMEJ), results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regard to their opposite dependencies on Polθ and Polλ (encoded by the PolL gene). Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5' overhangs of staggered Cas9 cleavage ends. CONCLUSIONS These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
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Affiliation(s)
- Mohammadreza M Mehryar
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Xin Shi
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- WLA Laboratories, Shanghai, 201203, China.
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4
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Chen ZJ, Xiao J, Chen HH. Identification of Key Genes Related to Immune Cells in Patients with COVID-19 Via Integrated Bioinformatics-Based Analysis. Biochem Genet 2023; 61:2650-2671. [PMID: 37222960 PMCID: PMC10206360 DOI: 10.1007/s10528-023-10400-1] [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] [Received: 01/07/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
COVID-19 has spread all over the world which poses a serious threat to social economic development and public health. Despite enormous progress has been made in the prevention and treatment of COVID-19, the specific mechanism and biomarker related to disease severity or prognosis have not been clarified yet. Our study intended to further explore the diagnostic markers of COVID-19 and their relationship with serum immunology by bioinformatics analysis. The datasets about COVID-19 were downloaded from the Gene Expression Omnibus (GEO) dataset. The differentially expressed genes (DEGs) were selected via the limma package. Then, weighted gene co-expression network analysis (WGCNA) was conducted to identify the critical module associated with the clinic status. The intersection DEGs were processed for further enrichment analysis. The final diagnostic genes for COVID-19 were selected and verified through special bioinformatics algorithms. There were significant DEGs between the normal and COVID-19 patients. These genes were mainly enriched in cell cycle, complement and coagulation cascade, extracellular matrix (ECM) receptor interaction, and the P53 signaling pathway. As much as 357 common intersected DEGs were selected in the end. These DEGs were enriched in organelle fission, mitotic cell cycle phase transition, DNA helicase activity, cell cycle, cellular senescence, and P53 signaling pathway. Our study also identified CDC25A, PDCD6, and YWAHE were potential diagnostic markers of COVID-19 with the AUC (area under curve), 0.958 (95% CI 0.920-0.988), 0.941(95% CI 0.892-0.980), and 0.929 (95% CI 0.880-0.971). Moreover, CDC25A, PDCD6, and YWAHE were correlated with plasma cells, macrophages M0, T cells CD4 memory resting, T cells CD8, dendritic cells, and NK cells. Our study discovered that CDC25A, PDCD6, and YWAHE can be used as diagnostic markers for COVID-19. Moreover, these biomarkers were also closely associated with immune cell infiltration, which plays a pivotal role in the diagnosis and progression of COVID-19.
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Affiliation(s)
- Zhao-Jun Chen
- Department of Infectious Disease, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Xiao
- Department of Cardiology, Wuhan Asia Heart General Hospital, Wuhan, China
| | - Hai-Hua Chen
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Research Center for Emergency and Resuscitation, Zhongnan Hospital of Wuhan University, Wuhan, China.
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5
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Vekariya U, Toma M, Nieborowska-Skorska M, Le BV, Caron MC, Kukuyan AM, Sullivan-Reed K, Podszywalow-Bartnicka P, Chitrala KN, Atkins J, Drzewiecka M, Feng W, Chan J, Chatla S, Golovine K, Jelinek J, Sliwinski T, Ghosh J, Matlawska-Wasowska K, Chandramouly G, Nejati R, Wasik M, Sykes SM, Piwocka K, Hadzijusufovic E, Valent P, Pomerantz RT, Morton G, Childers W, Zhao H, Paietta EM, Levine RL, Tallman MS, Fernandez HF, Litzow MR, Gupta GP, Masson JY, Skorski T. DNA polymerase θ protects leukemia cells from metabolically induced DNA damage. Blood 2023; 141:2372-2389. [PMID: 36580665 PMCID: PMC10273171 DOI: 10.1182/blood.2022018428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Leukemia cells accumulate DNA damage, but altered DNA repair mechanisms protect them from apoptosis. We showed here that formaldehyde generated by serine/1-carbon cycle metabolism contributed to the accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells, especially in driver clones harboring oncogenic tyrosine kinases (OTKs: FLT3(internal tandem duplication [ITD]), JAK2(V617F), BCR-ABL1). To counteract this effect, OTKs enhanced the expression of DNA polymerase theta (POLθ) via ERK1/2 serine/threonine kinase-dependent inhibition of c-CBL E3 ligase-mediated ubiquitination of POLθ and its proteasomal degradation. Overexpression of POLθ in OTK-positive cells resulted in the efficient repair of DPC-containing DNA double-strand breaks by POLθ-mediated end-joining. The transforming activities of OTKs and other leukemia-inducing oncogenes, especially of those causing the inhibition of BRCA1/2-mediated homologous recombination with and without concomitant inhibition of DNA-PK-dependent nonhomologous end-joining, was abrogated in Polq-/- murine bone marrow cells. Genetic and pharmacological targeting of POLθ polymerase and helicase activities revealed that both activities are promising targets in leukemia cells. Moreover, OTK inhibitors or DPC-inducing drug etoposide enhanced the antileukemia effect of POLθ inhibitor in vitro and in vivo. In conclusion, we demonstrated that POLθ plays an essential role in protecting leukemia cells from metabolically induced toxic DNA lesions triggered by formaldehyde, and it can be targeted to achieve a therapeutic effect.
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Affiliation(s)
- Umeshkumar Vekariya
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Monika Toma
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Margaret Nieborowska-Skorska
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Bac Viet Le
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Marie-Christine Caron
- CHU de Québec Research Centre (Oncology Division) and Laval University Cancer Research Center, Québec City, QC, Canada
| | - Anna-Mariya Kukuyan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Kumaraswamy N. Chitrala
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Jessica Atkins
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Malgorzata Drzewiecka
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Joe Chan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Srinivas Chatla
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Konstantin Golovine
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Gurushankar Chandramouly
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA
| | - Stephen M. Sykes
- Division of Hematology/Oncology, Department of Pediatrics, Washington University at St. Louis, St. Louis, MO
| | - Katarzyna Piwocka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Emir Hadzijusufovic
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
- Department for Companion Animals & Horses, Clinic for Internal Medicine and Infectious Diseases, University of Veterinary Medicine Vienna, Austria
| | - Peter Valent
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Richard T. Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - George Morton
- Moulder Center for Drug Discovery, Temple University School of Pharmacy, Philadelphia, PA
| | - Wayne Childers
- Moulder Center for Drug Discovery, Temple University School of Pharmacy, Philadelphia, PA
| | - Huaqing Zhao
- Department of Clinical Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Elisabeth M. Paietta
- Department of Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
| | - Ross L. Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin S. Tallman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hugo F. Fernandez
- Moffitt Malignant Hematology & Cellular Therapy at Memorial Healthcare System, Pembroke Pines, FL
| | - Mark R. Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Gaorav P. Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jean-Yves Masson
- CHU de Québec Research Centre (Oncology Division) and Laval University Cancer Research Center, Québec City, QC, Canada
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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6
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Pismataro MC, Astolfi A, Barreca ML, Pacetti M, Schenone S, Bandiera T, Carbone A, Massari S. Small Molecules Targeting DNA Polymerase Theta (POLθ) as Promising Synthetic Lethal Agents for Precision Cancer Therapy. J Med Chem 2023; 66:6498-6522. [PMID: 37134182 DOI: 10.1021/acs.jmedchem.2c02101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Synthetic lethality (SL) is an innovative strategy in targeted anticancer therapy that exploits tumor genetic vulnerabilities. This topic has come to the forefront in recent years, as witnessed by the increased number of publications since 2007. The first proof of concept for the effectiveness of SL was provided by the approval of poly(ADP-ribose)polymerase inhibitors, which exploit a SL interaction in BRCA-deficient cells, although their use is limited by resistance. Searching for additional SL interactions involving BRCA mutations, the DNA polymerase theta (POLθ) emerged as an exciting target. This review summarizes, for the first time, the POLθ polymerase and helicase inhibitors reported to date. Compounds are described focusing on chemical structure and biological activity. With the aim to enable further drug discovery efforts in interrogating POLθ as a target, we propose a plausible pharmacophore model for POLθ-pol inhibitors and provide a structural analysis of the known POLθ ligand binding sites.
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Affiliation(s)
- Maria Chiara Pismataro
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Martina Pacetti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Tiziano Bandiera
- D3 PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
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7
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Mayeur S, Lhermitte B, Gantzer J, Molitor A, Stemmelen T, Meyer S, Kolmer A, Kurtz JE, Bahram S, Carapito R. Genomic profiling of a metastatic anaplastic melanocytic neuroectodermal tumor arising from a mature thymic teratoma as part of a mediastinal germ cell tumor. Cold Spring Harb Mol Case Stud 2023; 9:mcs.a006257. [PMID: 37160315 DOI: 10.1101/mcs.a006257] [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: 11/17/2022] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
Following chemotherapy, a mediastinal germ cell tumor can lead to a mature teratoma that is composed of tissues derived from all three germ layers. Although teratoma is usually curable, in rare cases it can give rise to various somatic tumors and exceptionally it undergoes melanocytic neuroectodermal tumor (MNT) transformation, a process that is not well-described. We report a patient with a postchemotherapy thymic teratoma associated with an MNT component who, 10 years later, additionally presented a vertebral metastasis corresponding to an anaplastic MNT. Using exome sequencing of the mature teratoma, the MNT and its metastatic vertebral anaplastic MNT components, we identified 19 somatic mutations shared by at least two components. Six mutations were common to all three components, and three of them were located in the known cancer-related genes KRAS (p.E63K), TP53 (p.P222X), and POLQ (p.S447P). Gene set enrichment analysis revealed that the melanoma tumorigenesis pathway was enriched in mutated genes including the four major driver genes KRAS, TP53, ERBB4, and KDR, indicating that these genes may be involved in the development of the anaplastic MNT transformation of the teratoma. To our knowledge, this is the first molecular study realized on MNT. Understanding the clinicopathological and molecular characteristics of these tumors is essential to better understand their development and to improve therapeutics.
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Affiliation(s)
- Sylvain Mayeur
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, ITI TRANSPLANTEX NG, Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg 67091, France
- Department of Pathology, Strasbourg University Hospitals, Strasbourg 67200, France
| | - Benoit Lhermitte
- Department of Pathology, Strasbourg University Hospitals, Strasbourg 67200, France
| | - Justine Gantzer
- Pôle d'oncologie médico-chirurgicale et d'hématologie, ICANS-Europe, Strasbourg 67200, France
| | - Anne Molitor
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, ITI TRANSPLANTEX NG, Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg 67091, France
| | - Tristan Stemmelen
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, ITI TRANSPLANTEX NG, Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg 67091, France
| | - Sébastien Meyer
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, ITI TRANSPLANTEX NG, Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg 67091, France
| | - Aline Kolmer
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, ITI TRANSPLANTEX NG, Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg 67091, France
| | - Jean-Emmanuel Kurtz
- Pôle d'oncologie médico-chirurgicale et d'hématologie, ICANS-Europe, Strasbourg 67200, France
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, ITI TRANSPLANTEX NG, Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg 67091, France;
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg 67091, France
| | - Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, ITI TRANSPLANTEX NG, Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg 67091, France;
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg 67091, France
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8
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Multifaceted Nature of DNA Polymerase θ. Int J Mol Sci 2023; 24:ijms24043619. [PMID: 36835031 PMCID: PMC9962433 DOI: 10.3390/ijms24043619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
DNA polymerase θ belongs to the A family of DNA polymerases and plays a key role in DNA repair and damage tolerance, including double-strand break repair and DNA translesion synthesis. Pol θ is often overexpressed in cancer cells and promotes their resistance to chemotherapeutic agents. In this review, we discuss unique biochemical properties and structural features of Pol θ, its multiple roles in protection of genome stability and the potential of Pol θ as a target for cancer treatment.
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9
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Barszczewska-Pietraszek G, Drzewiecka M, Czarny P, Skorski T, Śliwiński T. Polθ Inhibition: An Anticancer Therapy for HR-Deficient Tumours. Int J Mol Sci 2022; 24:ijms24010319. [PMID: 36613762 PMCID: PMC9820168 DOI: 10.3390/ijms24010319] [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: 11/25/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
DNA polymerase theta (Polθ)-mediated end joining (TMEJ) is, along with homologous recombination (HR) and non-homologous end-joining (NHEJ), one of the most important mechanisms repairing potentially lethal DNA double-strand breaks (DSBs). Polθ is becoming a new target in cancer research because it demonstrates numerous synthetically lethal interactions with other DNA repair mechanisms, e.g., those involving PARP1, BRCA1/2, DNA-PK, ATR. Inhibition of Polθ could be achieved with different methods, such as RNA interference (RNAi), CRISPR/Cas9 technology, or using small molecule inhibitors. In the context of this topic, RNAi and CRISPR/Cas9 are still more often applied in the research itself rather than clinical usage, different than small molecule inhibitors. Several Polθ inhibitors have been already generated, and two of them, novobiocin (NVB) and ART812 derivative, are being tested in clinical trials against HR-deficient tumors. In this review, we describe the significance of Polθ and the Polθ-mediated TMEJ pathway. In addition, we summarize the current state of knowledge about Polθ inhibitors and emphasize the promising role of Polθ as a therapeutic target.
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Affiliation(s)
| | - Małgorzata Drzewiecka
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
| | - Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, 92-216 Lodz, Poland
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Tomasz Śliwiński
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
- Correspondence: ; Tel.: +48-42-635-44-86
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10
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Abstract
DNA polymerase θ (Pol θ) is a DNA repair enzyme widely conserved in animals and plants. Pol θ uses short DNA sequence homologies to initiate repair of double-strand breaks by theta-mediated end joining. The DNA polymerase domain of Pol θ is at the C terminus and is connected to an N-terminal DNA helicase-like domain by a central linker. Pol θ is crucial for maintenance of damaged genomes during development, protects DNA against extensive deletions, and limits loss of heterozygosity. The cost of using Pol θ for genome protection is that a few nucleotides are usually deleted or added at the repair site. Inactivation of Pol θ often enhances the sensitivity of cells to DNA strand-breaking chemicals and radiation. Since some homologous recombination-defective cancers depend on Pol θ for growth, inhibitors of Pol θ may be useful in treating such tumors.
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Affiliation(s)
- Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, Texas, USA;
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA;
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11
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Bubenik M, Mader P, Mochirian P, Vallée F, Clark J, Truchon JF, Perryman AL, Pau V, Kurinov I, Zahn KE, Leclaire ME, Papp R, Mathieu MC, Hamel M, Duffy NM, Godbout C, Casas-Selves M, Falgueyret JP, Baruah PS, Nicolas O, Stocco R, Poirier H, Martino G, Fortin AB, Roulston A, Chefson A, Dorich S, St-Onge M, Patel P, Pellerin C, Ciblat S, Pinter T, Barabé F, Bakkouri ME, Parikh P, Gervais C, Sfeir A, Mamane Y, Morris SJ, Black WC, Sicheri F, Gallant M. Identification of RP-6685, an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Polθ. J Med Chem 2022; 65:13198-13215. [PMID: 36126059 PMCID: PMC9942948 DOI: 10.1021/acs.jmedchem.2c00998] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerase theta (Polθ) is an attractive synthetic lethal target for drug discovery, predicted to be efficacious against breast and ovarian cancers harboring BRCA-mutant alleles. Here, we describe our hit-to-lead efforts in search of a selective inhibitor of human Polθ (encoded by POLQ). A high-throughput screening campaign of 350,000 compounds identified an 11 micromolar hit, giving rise to the N2-substituted fused pyrazolo series, which was validated by biophysical methods. Structure-based drug design efforts along with optimization of cellular potency and ADME ultimately led to the identification of RP-6685: a potent, selective, and orally bioavailable Polθ inhibitor that showed in vivo efficacy in an HCT116 BRCA2-/- mouse tumor xenograft model.
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Affiliation(s)
- Monica Bubenik
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Pavel Mader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
| | - Philippe Mochirian
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Fréderic Vallée
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Jillian Clark
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Jean-François Truchon
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Alexander L. Perryman
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Victor Pau
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, USA
| | - Karl E. Zahn
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Marie-Eve Leclaire
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Robert Papp
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Marie-Claude Mathieu
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Martine Hamel
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Nicole M. Duffy
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Claude Godbout
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Matias Casas-Selves
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Jean-Pierre Falgueyret
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Prasamit S. Baruah
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Olivier Nicolas
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Rino Stocco
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Hugo Poirier
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Giovanni Martino
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | | | - Anne Roulston
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Amandine Chefson
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Stéphane Dorich
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Miguel St-Onge
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Purvish Patel
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Charles Pellerin
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Stéphane Ciblat
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
- Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec, H4S 1Z9, Canada
| | - Thomas Pinter
- Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec, H4S 1Z9, Canada
| | - Francis Barabé
- Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec, H4S 1Z9, Canada
| | - Majida El Bakkouri
- Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec, H4S 1Z9, Canada
- National Research Council of Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
| | - Paranjay Parikh
- Piramal Pharma Ltd., Plot No. 18, Village Matoda, Taluka: Sanand, Ahmedabad-382213, Gujarat, India
| | - Christian Gervais
- National Research Council of Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, MSKCC, 430 E 67th Street, New York, NY 10065, USA
| | - Yael Mamane
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Stephen J. Morris
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - W. Cameron Black
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
| | - Michel Gallant
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
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12
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Liddiard K, Aston-Evans AN, Cleal K, Hendrickson E, Baird D. POLQ suppresses genome instability and alterations in DNA repeat tract lengths. NAR Cancer 2022; 4:zcac020. [PMID: 35774233 PMCID: PMC9241439 DOI: 10.1093/narcan/zcac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022] Open
Abstract
DNA polymerase theta (POLQ) is a principal component of the alternative non-homologous end-joining (ANHEJ) DNA repair pathway that ligates DNA double-strand breaks. Utilizing independent models of POLQ insufficiency during telomere-driven crisis, we found that POLQ - /- cells are resistant to crisis-induced growth deceleration despite sustaining inter-chromosomal telomere fusion frequencies equivalent to wild-type (WT) cells. We recorded longer telomeres in POLQ - / - than WT cells pre- and post-crisis, notwithstanding elevated total telomere erosion and fusion rates. POLQ - /- cells emerging from crisis exhibited reduced incidence of clonal gross chromosomal abnormalities in accordance with increased genetic heterogeneity. High-throughput sequencing of telomere fusion amplicons from POLQ-deficient cells revealed significantly raised frequencies of inter-chromosomal fusions with correspondingly depreciated intra-chromosomal recombinations. Long-range interactions culminating in telomere fusions with centromere alpha-satellite repeats, as well as expansions in HSAT2 and HSAT3 satellite and contractions in ribosomal DNA repeats, were detected in POLQ - / - cells. In conjunction with the expanded telomere lengths of POLQ - /- cells, these results indicate a hitherto unrealized capacity of POLQ for regulation of repeat arrays within the genome. Our findings uncover novel considerations for the efficacy of POLQ inhibitors in clinical cancer interventions, where potential genome destabilizing consequences could drive clonal evolution and resistant disease.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Alys N Aston-Evans
- Dementia Research Institute, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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13
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Bai W, Zhao B, Gu M, Dong J. Alternative end-joining in BCR gene rearrangements and translocations. Acta Biochim Biophys Sin (Shanghai) 2022; 54:782-795. [PMID: 35593472 PMCID: PMC9828324 DOI: 10.3724/abbs.2022051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) occur during antigen receptor gene recombination, namely V(D)J recombination in developing B lymphocytes and class switch recombination (CSR) in mature B cells. Repair of these DSBs by classical end-joining (c-NHEJ) enables the generation of diverse BCR repertoires for efficient humoral immunity. Deletion of or mutation in c-NHEJ genes in mice and humans confer various degrees of primary immune deficiency and predisposition to lymphoid malignancies that often harbor oncogenic chromosomal translocations. In the absence of c-NHEJ, alternative end-joining (A-EJ) catalyzes robust CSR and to a much lesser extent, V(D)J recombination, but the mechanisms of A-EJ are only poorly defined. In this review, we introduce recent advances in the understanding of A-EJ in the context of V(D)J recombination and CSR with emphases on DSB end processing, DNA polymerases and ligases, and discuss the implications of A-EJ to lymphoid development and chromosomal translocations.
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Affiliation(s)
- Wanyu Bai
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Bo Zhao
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Mingyu Gu
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Junchao Dong
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China,Correspondence address. Tel: +86-20-87330571; E-mail:
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