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Willman GH, Xu H, Zeigler TM, McIntosh MT, Bhaduri-McIntosh S. Polymerase theta is a synthetic lethal target for killing Epstein-Barr virus lymphomas. J Virol 2024; 98:e0057224. [PMID: 38860782 PMCID: PMC11265443 DOI: 10.1128/jvi.00572-24] [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: 04/02/2024] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
Treatment options for Epstein-Barr virus (EBV)-cancers are limited, underscoring the need for new therapeutic approaches. We have previously shown that EBV-transformed cells and cancers lack homologous recombination (HR) repair, a prominent error-free pathway that repairs double-stranded DNA breaks; instead, EBV-transformed cells demonstrate genome-wide scars of the error-prone microhomology-mediated end joining (MMEJ) repair pathway. This suggests that EBV-cancers are vulnerable to synthetic lethal therapeutic approaches that target MMEJ repair. Indeed, we have previously found that targeting PARP, an enzyme that contributes to MMEJ, results in the death of EBV-lymphoma cells. With the emergence of clinical resistance to PARP inhibitors and the recent discovery of inhibitors of Polymerase theta (POLθ), the polymerase essential for MMEJ, we investigated the role of POLθ in EBV-lymphoma cells. We report that EBV-transformed cell lines, EBV-lymphoma cell lines, and EBV-lymphomas in AIDS patients demonstrate greater abundance of POLθ, driven by the EBV protein EBNA1, compared to EBV-uninfected primary lymphocytes and EBV-negative lymphomas from AIDS patients (a group that also abundantly expresses POLθ). We also find POLθ enriched at cellular DNA replication forks and exposure to the POLθ inhibitor Novobiocin impedes replication fork progress, impairs MMEJ-mediated repair of DNA double-stranded breaks, and kills EBV-lymphoma cells. Notably, cell killing is not due to Novobiocin-induced activation of the lytic/replicative phase of EBV. These findings support a role for POLθ not just in DNA repair but also DNA replication and as a therapeutic target in EBV-lymphomas and potentially other EBV-cancers as EBNA1 is expressed in all EBV-cancers.IMPORTANCEEpstein-Barr virus (EBV) contributes to ~2% of the global cancer burden. With a recent estimate of >200,000 deaths a year, identifying molecular vulnerabilities will be key to the management of these frequently aggressive and treatment-resistant cancers. Building on our earlier work demonstrating reliance of EBV-cancers on microhomology-mediated end-joining repair, we now report that EBV lymphomas and transformed B cell lines abundantly express the MMEJ enzyme POLθ that likely protects cellular replication forks and repairs replication-related cellular DNA breaks. Importantly also, we show that a newly identified POLθ inhibitor kills EBV-cancer cells, revealing a novel strategy to block DNA replication and repair of these aggressive cancers.
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Affiliation(s)
- Griffin H. Willman
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Huanzhou Xu
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Travis M. Zeigler
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Michael T. McIntosh
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, Florida, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
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2
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Kanev PB, Varhoshkova S, Georgieva I, Lukarska M, Kirova D, Danovski G, Stoynov S, Aleksandrov R. A unified mechanism for PARP inhibitor-induced PARP1 chromatin retention at DNA damage sites in living cells. Cell Rep 2024; 43:114234. [PMID: 38758646 DOI: 10.1016/j.celrep.2024.114234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) not only suppress PARP1 catalytic activity but also prolong its association to damaged chromatin. Here, through live-cell imaging, we quantify the alterations in PARP1 dynamics and activity elicited by seven PARPis over a wide range of concentrations to deliver a unified mechanism of PARPi-induced PARP1 chromatin retention. We find that gross PARP1 retention at DNA damage sites is jointly governed by catalytic inhibition and allosteric trapping, albeit in a strictly independent manner-catalytic inhibition causes multiple unproductive binding-dissociation cycles of PARP1, while allosteric trapping prolongs the lesion-bound state of PARP1 to greatly increase overall retention. Importantly, stronger PARP1 retention produces greater temporal shifts in downstream DNA repair events and superior cytotoxicity, highlighting PARP1 retention, a complex but precisely quantifiable characteristic of PARPis, as a valuable biomarker for PARPi efficacy. Our approach can be promptly repurposed for interrogating the properties of DNA-repair-targeting compounds beyond PARPis.
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Affiliation(s)
- Petar-Bogomil Kanev
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Sylvia Varhoshkova
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Irina Georgieva
- Transmembrane Signaling Laboratory, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Maria Lukarska
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dilyana Kirova
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Georgi Danovski
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Stoyno Stoynov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria.
| | - Radoslav Aleksandrov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria.
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3
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Aleksakhina SN, Ivantsov AO, Imyanitov EN. Agnostic Administration of Targeted Anticancer Drugs: Looking for a Balance between Hype and Caution. Int J Mol Sci 2024; 25:4094. [PMID: 38612902 PMCID: PMC11012409 DOI: 10.3390/ijms25074094] [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: 02/18/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Many tumors have well-defined vulnerabilities, thus potentially allowing highly specific and effective treatment. There is a spectrum of actionable genetic alterations which are shared across various tumor types and, therefore, can be targeted by a given drug irrespective of tumor histology. Several agnostic drug-target matches have already been approved for clinical use, e.g., immune therapy for tumors with microsatellite instability (MSI) and/or high tumor mutation burden (TMB), NTRK1-3 and RET inhibitors for cancers carrying rearrangements in these kinases, and dabrafenib plus trametinib for BRAF V600E mutated malignancies. Multiple lines of evidence suggest that this histology-independent approach is also reasonable for tumors carrying ALK and ROS1 translocations, biallelic BRCA1/2 inactivation and/or homologous recombination deficiency (HRD), strong HER2 amplification/overexpression coupled with the absence of other MAPK pathway-activating mutations, etc. On the other hand, some well-known targets are not agnostic: for example, PD-L1 expression is predictive for the efficacy of PD-L1/PD1 inhibitors only in some but not all cancer types. Unfortunately, the individual probability of finding a druggable target in a given tumor is relatively low, even with the use of comprehensive next-generation sequencing (NGS) assays. Nevertheless, the rapidly growing utilization of NGS will significantly increase the number of patients with highly unusual or exceptionally rare tumor-target combinations. Clinical trials may provide only a framework for treatment attitudes, while the decisions for individual patients usually require case-by-case consideration of the probability of deriving benefit from agnostic versus standard therapy, drug availability, associated costs, and other circumstances. The existing format of data dissemination may not be optimal for agnostic cancer medicine, as conventional scientific journals are understandably biased towards the publication of positive findings and usually discourage the submission of case reports. Despite all the limitations and concerns, histology-independent drug-target matching is certainly feasible and, therefore, will be increasingly utilized in the future.
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Affiliation(s)
- Svetlana N. Aleksakhina
- Department of Tumor Growth Biology, N. N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
| | - Alexander O. Ivantsov
- Department of Tumor Growth Biology, N. N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
- Department of Medical Genetics, St. Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N. N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
- Department of Medical Genetics, St. Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
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4
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Harvey-Jones E, Raghunandan M, Robbez-Masson L, Magraner-Pardo L, Alaguthurai T, Yablonovitch A, Yen J, Xiao H, Brough R, Frankum J, Song F, Yeung J, Savy T, Gulati A, Alexander J, Kemp H, Starling C, Konde A, Marlow R, Cheang M, Proszek P, Hubank M, Cai M, Trendell J, Lu R, Liccardo R, Ravindran N, Llop-Guevara A, Rodriguez O, Balmana J, Lukashchuk N, Dorschner M, Drusbosky L, Roxanis I, Serra V, Haider S, Pettitt SJ, Lord CJ, Tutt ANJ. Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer. Ann Oncol 2024; 35:364-380. [PMID: 38244928 DOI: 10.1016/j.annonc.2024.01.003] [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] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but their existence and relative frequency in clinical disease are unclear, as is how to target resistance. PATIENTS AND METHODS Longitudinal mutation and methylation profiling of circulating tumour (ct)DNA was carried out in 47 patients with metastatic BRCA1-, BRCA2- or PALB2-mutant breast cancer treated with HRD-targeted therapy who developed progressive disease-18 patients had primary resistance and 29 exhibited response followed by resistance. ctDNA isolated at multiple time points in the patient treatment course (before, on-treatment and at progression) was sequenced using a novel >750-gene intron/exon targeted sequencing panel. Where available, matched tumour biopsies were whole exome and RNA sequenced and also used to assess nuclear RAD51. RESULTS BRCA1/2 reversion mutations were present in 60% of patients and were the most prevalent form of resistance. In 10 cases, reversions were detected in ctDNA before clinical progression. Two new reversion-based mechanisms were identified: (i) intragenic BRCA1/2 deletions with intronic breakpoints; and (ii) intragenic BRCA1/2 secondary mutations that formed novel splice acceptor sites, the latter being confirmed by in vitro minigene reporter assays. When seen before commencing subsequent treatment, reversions were associated with significantly shorter time to progression. Tumours with reversions retained HRD mutational signatures but had functional homologous recombination based on RAD51 status. Although less frequent than reversions, nonreversion mechanisms [loss-of-function (LoF) mutations in TP53BP1, RIF1 or PAXIP1] were evident in patients with acquired resistance and occasionally coexisted with reversions, challenging the notion that singular resistance mechanisms emerge in each patient. CONCLUSIONS These observations map the prevalence of candidate drivers of resistance across time in a clinical setting, information with implications for clinical management and trial design in HRD breast cancers.
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Affiliation(s)
- E Harvey-Jones
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK
| | - M Raghunandan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - L Robbez-Masson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - L Magraner-Pardo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - T Alaguthurai
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | | | - J Yen
- Guardant Health Inc., Redwood City, USA
| | - H Xiao
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Brough
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Frankum
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - F Song
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Yeung
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - T Savy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - A Gulati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Alexander
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - H Kemp
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - C Starling
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - A Konde
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - M Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - P Proszek
- Clinical Genomics, The Royal Marsden Hospital, London, UK
| | - M Hubank
- Clinical Genomics, The Royal Marsden Hospital, London, UK
| | - M Cai
- Guardant Health Inc., Redwood City, USA
| | - J Trendell
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - R Lu
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - R Liccardo
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - N Ravindran
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - O Rodriguez
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - J Balmana
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | | | - I Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - V Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - S Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S J Pettitt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - C J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - A N J Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK.
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5
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Cong K, MacGilvary N, Lee S, MacLeod SG, Calvo J, Peng M, Nedergaard Kousholt A, Day TA, Cantor SB. FANCJ promotes PARP1 activity during DNA replication that is essential in BRCA1 deficient cells. Nat Commun 2024; 15:2599. [PMID: 38521768 PMCID: PMC10960859 DOI: 10.1038/s41467-024-46824-5] [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: 09/27/2023] [Accepted: 03/07/2024] [Indexed: 03/25/2024] Open
Abstract
The effectiveness of poly (ADP-ribose) polymerase inhibitors (PARPi) in creating single-stranded DNA gaps and inducing sensitivity requires the FANCJ DNA helicase. Yet, how FANCJ relates to PARP1 inhibition or trapping, which contribute to PARPi toxicity, remains unclear. Here, we find PARPi effectiveness hinges on S-phase PARP1 activity, which is reduced in FANCJ deficient cells as G-quadruplexes sequester PARP1 and MSH2. Additionally, loss of the FANCJ-MLH1 interaction diminishes PARP1 activity; however, depleting MSH2 reinstates PARPi sensitivity and gaps. Indicating sequestered and trapped PARP1 are distinct, FANCJ loss increases PARPi resistance in cells susceptible to PARP1 trapping. However, with BRCA1 deficiency, the loss of FANCJ mirrors PARP1 loss or inhibition, with the detrimental commonality being loss of S-phase PARP1 activity. These insights underline the crucial role of PARP1 activity during DNA replication in BRCA1 deficient cells and emphasize the importance of understanding drug mechanisms for enhancing therapeutic response.
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Affiliation(s)
- Ke Cong
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Nathan MacGilvary
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Silviana Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Shannon G MacLeod
- Northeastern University Biology Department 360 Huntington Avenue, Mugar Life Science Building, Rm 220, Boston, MA, 02115-5005, USA
| | - Jennifer Calvo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Min Peng
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Arne Nedergaard Kousholt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX, Amsterdam, the Netherlands
| | - Tovah A Day
- Northeastern University Biology Department 360 Huntington Avenue, Mugar Life Science Building, Rm 220, Boston, MA, 02115-5005, USA
| | - Sharon B Cantor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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6
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Sturniolo I, Váróczy C, Regdon Z, Mázló A, Muzsai S, Bácsi A, Intili G, Hegedűs C, Boothby MR, Holechek J, Ferraris D, Schüler H, Virág L. PARP14 Contributes to the Development of the Tumor-Associated Macrophage Phenotype. Int J Mol Sci 2024; 25:3601. [PMID: 38612413 PMCID: PMC11011797 DOI: 10.3390/ijms25073601] [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: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Cancers reprogram macrophages (MΦs) to a tumor-growth-promoting TAM (tumor-associated MΦ) phenotype that is similar to the anti-inflammatory M2 phenotype. Poly(ADP-ribose) polymerase (PARP) enzymes regulate various aspects of MΦ biology, but their role in the development of TAM phenotype has not yet been investigated. Here, we show that the multispectral PARP inhibitor (PARPi) PJ34 and the PARP14 specific inhibitor MCD113 suppress the expression of M2 marker genes in IL-4-polarized primary murine MΦs, in THP-1 monocytic human MΦs, and in primary human monocyte-derived MΦs. MΦs isolated from PARP14 knockout mice showed a limited ability to differentiate to M2 cells. In a murine model of TAM polarization (4T1 breast carcinoma cell supernatant transfer to primary MΦs) and in a human TAM model (spheroids formed from JIMT-1 breast carcinoma cells and THP-1-MΦs), both PARPis and the PARP14 KO phenotype caused weaker TAM polarization. Increased JIMT-1 cell apoptosis in co-culture spheroids treated with PARPis suggested reduced functional TAM reprogramming. Protein profiling arrays identified lipocalin-2, macrophage migration inhibitory factor, and plasminogen activator inhibitor-1 as potential (ADP-ribosyl)ation-dependent mediators of TAM differentiation. Our data suggest that PARP14 inhibition might be a viable anticancer strategy with a potential to boost anticancer immune responses by reprogramming TAMs.
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Affiliation(s)
- Isotta Sturniolo
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (I.S.); (C.V.); (Z.R.); (C.H.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Csongor Váróczy
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (I.S.); (C.V.); (Z.R.); (C.H.)
- National Academy of Scientist Education, 4032 Debrecen, Hungary
| | - Zsolt Regdon
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (I.S.); (C.V.); (Z.R.); (C.H.)
| | - Anett Mázló
- Department of Immunology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.M.); (S.M.); (A.B.)
| | - Szabolcs Muzsai
- Department of Immunology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.M.); (S.M.); (A.B.)
- Gyula Petrányi Doctoral School of Clinical Immunology and Allergology, University of Debrecen, 4032 Debrecen, Hungary
| | - Attila Bácsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.M.); (S.M.); (A.B.)
- HUN-REN-DE Allergology Research Group, 4032 Debrecen, Hungary
| | - Giorgia Intili
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90133 Palermo, Italy;
| | - Csaba Hegedűs
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (I.S.); (C.V.); (Z.R.); (C.H.)
| | - Mark R. Boothby
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN 37235, USA;
| | | | - Dana Ferraris
- Department of Chemistry, McDaniel College, Westminster, MD 21157, USA;
| | - Herwig Schüler
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 22100 Lund, Sweden;
| | - László Virág
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (I.S.); (C.V.); (Z.R.); (C.H.)
- HUN-REN-DE Cell Biology and Signaling Research Group, 4032 Debrecen, Hungary
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7
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Anbil S, Reiss KA. Targeting BRCA and PALB2 in Pancreatic Cancer. Curr Treat Options Oncol 2024; 25:346-363. [PMID: 38311708 DOI: 10.1007/s11864-023-01174-0] [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] [Accepted: 12/22/2023] [Indexed: 02/06/2024]
Abstract
OPINION STATEMENT An important subgroup of pancreatic ductal adenocarcinomas (PDACs) harbor pathogenic variants in BRCA1, BRCA2, or PALB2. These tumors are exquisitely sensitive to platinum-based chemotherapy and patients may experience deep and durable responses to this treatment. PARP inhibitors offer potential respite from the cumulative toxicities of chemotherapy as they significantly extend progression-free survival compared to a chemotherapy holiday. Given the lack of proven survival benefit, the decision to use a maintenance PARP inhibitor rather than continue chemotherapy should be individualized. Interestingly, in both published clinical trials of maintenance PARP inhibitors, there is a striking range of interpatient benefit: Even in the platinum-sensitive setting, roughly 25% of tumors appear to be PARP inhibitor refractory (progressive disease within 2 months of starting treatment), 50% sustain moderate benefit (up to 2 years), and 25% are hyper-responsive (more than 2 years of benefit). This finding highlights the need to refine our understanding of which patients will respond to maintenance PARP inhibitors, both by being able to identify biallelic loss and by deepening our knowledge of resistance mechanisms and who develops them. Recent data supports that reversion mutations are common in PARP inhibitor refractory patients, but we have little understanding of the mechanisms that drive delayed resistance and long-term responses. Identifying which patients are more prone to certain mechanisms of resistance and tackling them with specific treatment strategies are areas of active investigation. Additionally, given that PARP inhibitors have limited overall efficacy for most patients, upfront combination strategies are an important future strategy.
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Affiliation(s)
- Sriram Anbil
- Abramson Cancer Center, 10th Floor Perelman Center South, The University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19121, USA
| | - Kim A Reiss
- Abramson Cancer Center, 10th Floor Perelman Center South, The University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19121, USA.
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8
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Cong K, MacGilvary N, Lee S, MacLeod SG, Calvo J, Peng M, Kousholt AN, Day T, Cantor SB. FANCJ promotes PARP1 activity during DNA replication that is essential in BRCA1 deficient cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574095. [PMID: 38260529 PMCID: PMC10802319 DOI: 10.1101/2024.01.04.574095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Single-stranded DNA gaps are postulated to be fundamental to the mechanism of anti-cancer drugs. Gaining insights into their induction could therefore be pivotal for advancing therapeutic strategies. For poly (ADP-ribose) polymerase inhibitors (PARPi) to be effective, the presence of FANCJ helicase is required. However, the relationship between FANCJ dependent gaps and PARP1 catalytic inhibition or trapping-both linked to PARPi toxicity in BRCA deficient cells-is yet to be elucidated. Here, we find that the efficacy of PARPi is contingent on S-phase PARP1 activity, which is compromised in FANCJ deficient cells because PARP1, along with MSH2, is "sequestered" by G-quadruplexes. PARP1's replication activity is also diminished in cells missing a FANCJ-MLH1 interaction, but in such cells, depleting MSH2 can release sequestered PARP1, restoring PARPi-induced gaps and sensitivity. Our observations indicate that sequestered and trapped PARP1 are different chromatin-bound forms, with FANCJ loss increasing PARPi resistance in cells susceptible to canonical PARP1 trapping. However, in BRCA1 null cells, the loss of FANCJ mirrors the effects of PARP1 loss or inhibition, with the common detrimental factor being the loss of PARP1 activity during DNA replication, not trapping. These insights underline the crucial role of PARP1 activity during DNA replication in BRCA deficient cells and emphasize the importance of understanding drug mechanisms for enhancing precision medicine.
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9
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Ryan CJ, Devakumar LPS, Pettitt SJ, Lord CJ. Complex synthetic lethality in cancer. Nat Genet 2023; 55:2039-2048. [PMID: 38036785 DOI: 10.1038/s41588-023-01557-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/04/2023] [Indexed: 12/02/2023]
Abstract
The concept of synthetic lethality has been widely applied to identify therapeutic targets in cancer, with varying degrees of success. The standard approach normally involves identifying genetic interactions between two genes, a driver and a target. In reality, however, most cancer synthetic lethal effects are likely complex and also polygenic, being influenced by the environment in addition to involving contributions from multiple genes. By acknowledging and delineating this complexity, we describe in this article how the success rate in cancer drug discovery and development could be improved.
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Affiliation(s)
- Colm J Ryan
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland.
| | - Lovely Paul Solomon Devakumar
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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Raseley K, Jinwala Z, Zhang D, Xiao M. Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM) Can Potentially Define the ALT Positivity of Cancer. Genes (Basel) 2023; 14:1278. [PMID: 37372458 DOI: 10.3390/genes14061278] [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: 05/02/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Telomeres play an essential role in protecting the ends of linear chromosomes and maintaining the integrity of the human genome. One of the key hallmarks of cancers is their replicative immortality. As many as 85-90% of cancers activate the expression of telomerase (TEL+) as the telomere maintenance mechanism (TMM), and 10-15% of cancers utilize the homology-dependent repair (HDR)-based Alternative Lengthening of Telomere (ALT+) pathway. Here, we performed statistical analysis of our previously reported telomere profiling results from Single Molecule Telomere Assay via Optical Mapping (SMTA-OM), which is capable of quantifying individual telomeres from single molecules across all chromosomes. By comparing the telomeric features from SMTA-OM in TEL+ and ALT+ cancer cells, we demonstrated that ALT+ cancer cells display certain unique telomeric profiles, including increased fusions/internal telomere-like sequence (ITS+), fusions/internal telomere-like sequence loss (ITS-), telomere-free ends (TFE), super-long telomeres, and telomere length heterogeneity, compared to TEL+ cancer cells. Therefore, we propose that ALT+ cancer cells can be differentiated from TEL+ cancer cells using the SMTA-OM readouts as biomarkers. In addition, we observed variations in SMTA-OM readouts between different ALT+ cell lines that may potentially be used as biomarkers for discerning subtypes of ALT+ cancer and monitoring the response to cancer therapy.
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Affiliation(s)
- Kaitlin Raseley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Zeal Jinwala
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
- Center for Cancer Research, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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Pillay N, Mariotti L, Zaleska M, Inian O, Jessop M, Hibbs S, Desfosses A, Hopkins PCR, Templeton CM, Beuron F, Morris EP, Guettler S. Structural basis of tankyrase activation by polymerization. Nature 2022; 612:162-169. [PMID: 36418402 PMCID: PMC9712121 DOI: 10.1038/s41586-022-05449-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/13/2022] [Indexed: 11/25/2022]
Abstract
The poly-ADP-ribosyltransferase tankyrase (TNKS, TNKS2) controls a wide range of disease-relevant cellular processes, including WNT-β-catenin signalling, telomere length maintenance, Hippo signalling, DNA damage repair and glucose homeostasis1,2. This has incentivized the development of tankyrase inhibitors. Notwithstanding, our knowledge of the mechanisms that control tankyrase activity has remained limited. Both catalytic and non-catalytic functions of tankyrase depend on its filamentous polymerization3-5. Here we report the cryo-electron microscopy reconstruction of a filament formed by a minimal active unit of tankyrase, comprising the polymerizing sterile alpha motif (SAM) domain and its adjacent catalytic domain. The SAM domain forms a novel antiparallel double helix, positioning the protruding catalytic domains for recurring head-to-head and tail-to-tail interactions. The head interactions are highly conserved among tankyrases and induce an allosteric switch in the active site within the catalytic domain to promote catalysis. Although the tail interactions have a limited effect on catalysis, they are essential to tankyrase function in WNT-β-catenin signalling. This work reveals a novel SAM domain polymerization mode, illustrates how supramolecular assembly controls catalytic and non-catalytic functions, provides important structural insights into the regulation of a non-DNA-dependent poly-ADP-ribosyltransferase and will guide future efforts to modulate tankyrase and decipher its contribution to disease mechanisms.
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Affiliation(s)
- Nisha Pillay
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Laura Mariotti
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Mariola Zaleska
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Oviya Inian
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Matthew Jessop
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sam Hibbs
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Ambroise Desfosses
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Paul C R Hopkins
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Catherine M Templeton
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK.
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK.
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12
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Role of Cockayne Syndrome Group B Protein in Replication Stress: Implications for Cancer Therapy. Int J Mol Sci 2022; 23:ijms231810212. [PMID: 36142121 PMCID: PMC9499456 DOI: 10.3390/ijms231810212] [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: 08/12/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 12/01/2022] Open
Abstract
A variety of endogenous and exogenous insults are capable of impeding replication fork progression, leading to replication stress. Several SNF2 fork remodelers have been shown to play critical roles in resolving this replication stress, utilizing different pathways dependent upon the nature of the DNA lesion, location on the DNA, and the stage of the cell cycle, to complete DNA replication in a manner preserving genetic integrity. Under certain conditions, however, the attempted repair may lead to additional genetic instability. Cockayne syndrome group B (CSB) protein, a SNF2 chromatin remodeler best known for its role in transcription-coupled nucleotide excision repair, has recently been shown to catalyze fork reversal, a pathway that can provide stability of stalled forks and allow resumption of DNA synthesis without chromosome breakage. Prolonged stalling of replication forks may collapse to give rise to DNA double-strand breaks, which are preferentially repaired by homology-directed recombination. CSB plays a role in repairing collapsed forks by promoting break-induced replication in S phase and early mitosis. In this review, we discuss roles of CSB in regulating the sources of replication stress, replication stress response, as well as the implications of CSB for cancer therapy.
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