1
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Prosz A, Duan H, Tisza V, Sahgal P, Topka S, Klus GT, Börcsök J, Sztupinszki Z, Hanlon T, Diossy M, Vizkeleti L, Stormoen DR, Csabai I, Pappot H, Vijai J, Offit K, Ried T, Sethi N, Mouw KW, Spisak S, Pathania S, Szallasi Z. Nucleotide excision repair deficiency is a targetable therapeutic vulnerability in clear cell renal cell carcinoma. Sci Rep 2023; 13:20567. [PMID: 37996508 PMCID: PMC10667362 DOI: 10.1038/s41598-023-47946-4] [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: 08/08/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
Due to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (ccRCC) has not benefitted from targeted synthetic lethality-based therapies. We investigated whether nucleotide excision repair (NER) deficiency is present in an identifiable subset of ccRCC cases that would render those tumors sensitive to therapy targeting this specific DNA repair pathway aberration. We used functional assays that detect UV-induced 6-4 pyrimidine-pyrimidone photoproducts to quantify NER deficiency in ccRCC cell lines. We also measured sensitivity to irofulven, an experimental cancer therapeutic agent that specifically targets cells with inactivated transcription-coupled nucleotide excision repair (TC-NER). In order to detect NER deficiency in clinical biopsies, we assessed whole exome sequencing data for the presence of an NER deficiency associated mutational signature previously identified in ERCC2 mutant bladder cancer. Functional assays showed NER deficiency in ccRCC cells. Some cell lines showed irofulven sensitivity at a concentration that is well tolerated by patients. Prostaglandin reductase 1 (PTGR1), which activates irofulven, was also associated with this sensitivity. Next generation sequencing data of the cell lines showed NER deficiency-associated mutational signatures. A significant subset of ccRCC patients had the same signature and high PTGR1 expression. ccRCC cell line-based analysis showed that NER deficiency is likely present in this cancer type. Approximately 10% of ccRCC patients in the TCGA cohort showed mutational signatures consistent with ERCC2 inactivation associated NER deficiency and also substantial levels of PTGR1 expression. These patients may be responsive to irofulven, a previously abandoned anticancer agent that has minimal activity in NER-proficient cells.
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Affiliation(s)
- Aurel Prosz
- Danish Cancer Institute, Copenhagen, Denmark
| | - Haohui Duan
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA, USA
- Department of Biology, University of Massachusetts, Boston, MA, USA
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pranshu Sahgal
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT), Harvard University, Cambridge, MA, USA
| | - Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gregory T Klus
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Judit Börcsök
- Danish Cancer Institute, Copenhagen, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Timothy Hanlon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miklos Diossy
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Dag Rune Stormoen
- Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, NY, USA
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nilay Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT), Harvard University, Cambridge, MA, USA
| | - Kent W Mouw
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Radiation Oncology, Brigham & Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sandor Spisak
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA, USA.
- Department of Biology, University of Massachusetts, Boston, MA, USA.
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary.
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Prosz A, Duan H, Tisza V, Sahgal P, Topka S, Klus GT, Börcsök J, Sztupinszki Z, Hanlon T, Diossy M, Vizkeleti L, Stormoen DR, Csabai I, Pappot H, Vijai J, Offit K, Ried T, Sethi N, Mouw KW, Spisak S, Pathania S, Szallasi Z. Nucleotide excision repair deficiency is a targetable therapeutic vulnerability in clear cell renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527498. [PMID: 36798363 PMCID: PMC9934582 DOI: 10.1101/2023.02.07.527498] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Purpose Due to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (ccRCC) has not benefitted from targeted synthetic lethality-based therapies. We investigated whether nucleotide excision repair (NER) deficiency is present in an identifiable subset of ccRCC cases that would render those tumors sensitive to therapy targeting this specific DNA repair pathway aberration. Experimental Design We used functional assays that detect UV-induced 6-4 pyrimidine-pyrimidone photoproducts to quantify NER deficiency in ccRCC cell lines. We also measured sensitivity to irofulven, an experimental cancer therapeutic agent that specifically targets cells with inactivated transcription-coupled nucleotide excision repair (TC-NER). In order to detect NER deficiency in clinical biopsies, we assessed whole exome sequencing data for the presence of an NER deficiency associated mutational signature previously identified in ERCC2 mutant bladder cancer. Results Functional assays showed NER deficiency in ccRCC cells. Irofulven sensitivity increased in some cell lines. Prostaglandin reductase 1 (PTGR1), which activates irofulven, was also associated with this sensitivity. Next generation sequencing data of the cell lines showed NER deficiency-associated mutational signatures. A significant subset of ccRCC patients had the same signature and high PTGR1 expression. Conclusions ccRCC cell line based analysis showed that NER deficiency is likely present in this cancer type. Approximately 10% of ccRCC patients in the TCGA cohort showed mutational signatures consistent with ERCC2 inactivation associated NER deficiency and also substantial levels of PTGR1 expression. These patients may be responsive to irofulven, a previously abandoned anticancer agent that has minimal activity in NER-proficient cells.
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Affiliation(s)
- Aurel Prosz
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Haohui Duan
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA
- Department of Biology, University of Massachusetts, Boston, MA
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Pranshu Sahgal
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gregory T Klus
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
| | - Timothy Hanlon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Miklos Diossy
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
| | - Laura Vizkeleti
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Dag Rune Stormoen
- Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Denmark
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Denmark
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York,New York
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York,New York
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nilay Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Kent W. Mouw
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Radiation Oncology, Brigham & Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Sandor Spisak
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA
- Department of Biology, University of Massachusetts, Boston, MA
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
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Casimir L, Zimmer S, Racine-Brassard F, Jacques PÉ, Maréchal A. The mutational impact of Illudin S on human cells. DNA Repair (Amst) 2023; 122:103433. [PMID: 36566616 DOI: 10.1016/j.dnarep.2022.103433] [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: 08/09/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Illudin S (ILS) is a fungal sesquiterpene secondary metabolite with potent genotoxic and cytotoxic properties. Early genetic studies and more recent genome-wide CRISPR screens showed that Illudin-induced lesions are preferentially repaired by transcription-coupled nucleotide excision repair (TC-NER) with some contribution from post-replication repair pathways. In line with these results, Irofulven, a semi-synthetic ILS analog was recently shown to be particularly effective on cell lines and patient-derived xenografts with impaired NER (e.g. ERCC2/3 mutations), raising hope that ILS-derived molecules may soon enter the clinic. Despite the therapeutic potential of ILS and its analogs, we still lack a global understanding of their mutagenic potential. Here, we characterize the mutational signatures associated with chronic exposure to ILS in human cells. ILS treatment rapidly stalls DNA replication and transcription, leading to the activation of the replication stress response and the accumulation of DNA damage. Novel single and double base substitution signatures as well as a characteristic indel signature indicate that ILS treatment preferentially alkylates purine residues and induces oxidative stress, confirming prior in vitro data. Many mutation contexts exhibit a strong transcriptional strand bias, highlighting the contribution of TC-NER to the repair of ILS lesions. Finally, collateral mutations are also observed in response to ILS, suggesting a contribution of translesion synthesis pathways to ILS tolerance. Accordingly, ILS treatment led to the rapid recruitment of the Y-family DNA polymerase kappa onto chromatin, supporting its preferential use for ILS lesion bypass. Altogether, our work provides the first global assessment of the genomic impact of ILS, demonstrating the contribution of multiple DNA repair pathways to ILS resistance and mutagenicity.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
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He J, Yu WW, Isaka M, Cox RJ, Liu JK, Feng T. Antroxazole A, an oxazole-containing chamigrane dimer from the fungus Antrodiella albocinnamomea with immunosuppressive activity. Org Biomol Chem 2022; 20:7278-7283. [PMID: 36043515 DOI: 10.1039/d2ob01443b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antroxazole A (1), a chamigrane type sesquiterpene dimer containing an oxazole moiety, has been characterized from cultures of the fungus Antrodiella albocinnamomea. The structure with absolute configuration was determined by extensive spectroscopic methods and single crystal X-ray diffraction. A plausible biosynthetic pathway for 1 was proposed. Compound 1 exhibits inhibition specifically against the LPS-induced proliferation of B lymphocyte cells with an IC50 value of 16.3 μM.
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Affiliation(s)
- Juan He
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minzu Road, Wuhan 430074, P.R. China.
| | - Wei-Wei Yu
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minzu Road, Wuhan 430074, P.R. China.
| | - Masahiko Isaka
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani 12120, Thailand
| | - Russell J Cox
- Institute for Organic Chemistry and Biomolekulares Wirkstoffzentrum (BMWZ), Schneiderberg 38, 30167 Hannover, Germany
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minzu Road, Wuhan 430074, P.R. China.
| | - Tao Feng
- School of Pharmaceutical Sciences, South-Central Minzu University, 182 Minzu Road, Wuhan 430074, P.R. China.
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Antitumor Effects of a New Retinoate of the Fungal Cytotoxin Illudin M in Brain Tumor Models. Int J Mol Sci 2022; 23:ijms23169056. [PMID: 36012321 PMCID: PMC9408991 DOI: 10.3390/ijms23169056] [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: 07/20/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
While the fungal metabolite illudin M (1) is indiscriminately cytotoxic in cancer and non-malignant cells, its retinoate 2 showed a greater selectivity for the former, especially in a cerebral context. Illudin M killed malignant glioma cells as well as primary neurons and astrocytes at similarly low concentrations and destroyed their microtubule and glial fibrillary acidic protein (GFAP) networks. In contrast, the ester 2 was distinctly more cytotoxic in highly dedifferentiated U87 glioma cells than in neurons, which were even stimulated to enhanced growth. This was also observed in co-cultures of neurons with U87 cells where conjugate 2 eventually killed them by induction of differentiation based on the activation of nuclear receptors, which bind to retinoid-responsive elements (RARE). Hence, illudin M retinoate 2 appears to be a promising drug candidate.
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Yang LY, Gong Q, Guo JQ, Li GL. Microbes as a production host to produce natural activecompounds from mushrooms: biosynthetic pathway elucidationand metabolic engineering. Chin J Nat Med 2021; 19:580-590. [PMID: 34419258 DOI: 10.1016/s1875-5364(21)60058-4] [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: 03/21/2021] [Indexed: 11/29/2022]
Abstract
Mushrooms are abundant in bioactive natural compounds. Due to strict growth conditions and long fermentation-time, microbe as a production host is an alternative and sustainable approach for the production of natural compounds. This review focuses on the biosynthetic pathways of mushroom originated natural compounds and microbes as the production host for the production of the above natural compounds.
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Affiliation(s)
- Li-Yang Yang
- School of Basic Medical Sciences, Shanxi University of Chinese Medicine, Jinzhong 030619, China
| | - Qiang Gong
- School of Basic Medical Sciences, Shanxi University of Chinese Medicine, Jinzhong 030619, China
| | - Jian-Quan Guo
- School of Public Health, Shanxi Medical University, Taiyuan 030001, China.
| | - Gui-Lan Li
- School of Basic Medical Sciences, Shanxi University of Chinese Medicine, Jinzhong 030619, China.
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Kathad U, Kulkarni A, McDermott JR, Wegner J, Carr P, Biyani N, Modali R, Richard JP, Sharma P, Bhatia K. A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications. BMC Bioinformatics 2021; 22:102. [PMID: 33653269 PMCID: PMC7923321 DOI: 10.1186/s12859-021-04040-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Non-targeted cytotoxics with anticancer activity are often developed through preclinical stages using response criteria observed in cell lines and xenografts. A panel of the NCI-60 cell lines is frequently the first line to define tumor types that are optimally responsive. Open data on the gene expression of the NCI-60 cell lines, provides a unique opportunity to add another dimension to the preclinical development of such drugs by interrogating correlations with gene expression patterns. Machine learning can be used to reduce the complexity of whole genome gene expression patterns to derive manageable signatures of response. Application of machine learning in early phases of preclinical development is likely to allow a better positioning and ultimate clinical success of molecules. LP-184 is a highly potent novel alkylating agent where the preclinical development is being guided by a dedicated machine learning-derived response signature. We show the feasibility and the accuracy of such a signature of response by accurately predicting the response to LP-184 validated using wet lab derived IC50s on a panel of cell lines. RESULTS We applied our proprietary RADR® platform to an NCI-60 discovery dataset encompassing LP-184 IC50s and publicly available gene expression data. We used multiple feature selection layers followed by the XGBoost regression model and reduced the complexity of 20,000 gene expression values to generate a 16-gene signature leading to the identification of a set of predictive candidate biomarkers which form an LP-184 response gene signature. We further validated this signature and predicted response to an additional panel of cell lines. Considering fold change differences and correlation between actual and predicted LP-184 IC50 values as validation performance measures, we obtained 86% accuracy at four-fold cut-off, and a strong (r = 0.70) and significant (p value 1.36e-06) correlation between actual and predicted LP-184 sensitivity. In agreement with the perceived mechanism of action of LP-184, PTGR1 emerged as the top weighted gene. CONCLUSION Integration of a machine learning-derived signature of response with in vitro assessment of LP-184 efficacy facilitated the derivation of manageable yet robust biomarkers which can be used to predict drug sensitivity with high accuracy and clinical value.
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Affiliation(s)
- Umesh Kathad
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA.
| | - Aditya Kulkarni
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | | | - Jordan Wegner
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Peter Carr
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Neha Biyani
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Rama Modali
- REPROCELL USA Inc., 9000 Virginia Manor Rd, Ste 207, Beltsville, MD, 20705, USA
| | | | - Panna Sharma
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Kishor Bhatia
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
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8
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Börcsök J, Sztupinszki Z, Bekele R, Gao SP, Diossy M, Samant AS, Dillon KM, Tisza V, Spisák S, Rusz O, Csabai I, Pappot H, Frazier ZJ, Konieczkowski DJ, Liu D, Vasani N, Rodrigues JA, Solit DB, Hoffman-Censits JH, Plimack ER, Rosenberg JE, Lazaro JB, Taplin ME, Iyer G, Brunak S, Lozsa R, Van Allen EM, Szüts D, Mouw KW, Szallasi Z. Identification of a Synthetic Lethal Relationship between Nucleotide Excision Repair Deficiency and Irofulven Sensitivity in Urothelial Cancer. Clin Cancer Res 2020; 27:2011-2022. [PMID: 33208343 DOI: 10.1158/1078-0432.ccr-20-3316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/16/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Cisplatin-based chemotherapy is a first-line treatment for muscle-invasive and metastatic urothelial cancer. Approximately 10% of bladder urothelial tumors have a somatic missense mutation in the nucleotide excision repair (NER) gene, ERCC2, which confers increased sensitivity to cisplatin-based chemotherapy. However, a significant subset of patients is ineligible to receive cisplatin-based therapy due to medical contraindications, and no NER-targeted approaches are available for platinum-ineligible or platinum-refractory ERCC2-mutant cases. EXPERIMENTAL DESIGN We used a series of NER-proficient and NER-deficient preclinical tumor models to test sensitivity to irofulven, an abandoned anticancer agent. In addition, we used available clinical and sequencing data from multiple urothelial tumor cohorts to develop and validate a composite mutational signature of ERCC2 deficiency and cisplatin sensitivity. RESULTS We identified a novel synthetic lethal relationship between tumor NER deficiency and sensitivity to irofulven. Irofulven specifically targets cells with inactivation of the transcription-coupled NER (TC-NER) pathway and leads to robust responses in vitro and in vivo, including in models with acquired cisplatin resistance, while having minimal effect on cells with intact NER. We also found that a composite mutational signature of ERCC2 deficiency was strongly associated with cisplatin response in patients and was also associated with cisplatin and irofulven sensitivity in preclinical models. CONCLUSIONS Tumor NER deficiency confers sensitivity to irofulven, a previously abandoned anticancer agent, with minimal activity in NER-proficient cells. A composite mutational signature of NER deficiency may be useful in identifying patients likely to respond to NER-targeting agents, including cisplatin and irofulven.See related commentary by Jiang and Greenberg, p. 1833.
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Affiliation(s)
- Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Raie Bekele
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Sizhi P Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Miklos Diossy
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Amruta S Samant
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kasia M Dillon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Zoë J Frazier
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David J Konieczkowski
- Department of Radiation Oncology, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Naresh Vasani
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Rodrigues
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Jean H Hoffman-Censits
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth R Plimack
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gopa Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Rita Lozsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Radiation Oncology, Brigham & Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
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9
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Wang M, Du JX, Hui-Xiang Y, Dai Q, Liu YP, He J, Wang Y, Li ZH, Feng T, Liu JK. Sesquiterpenoids from Cultures of the Basidiomycetes Irpex lacteus. JOURNAL OF NATURAL PRODUCTS 2020; 83:1524-1531. [PMID: 32315183 DOI: 10.1021/acs.jnatprod.9b01177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Eight previously undescribed sesquiterpenoids, tremutins A-H (1-8), together with three known ones (9-11), were isolated from cultures of the basidiomycetes Irpex lacteus. Structures of the new compounds together with absolute configurations were elucidated on the basis of extensive spectroscopic methods, as well as single-crystal X-ray diffractions and equivalent circulating density calculations. Compounds 1 and 2 possess an unusual 6/7-fused ring system that might be derived from a tremulane framework. Compounds 3-7 and 9-11 are tremulane sesquiterpenoids of which 4 and 5 are the first tremulane examples with a 1,2-epoxy moiety to be reported. Compounds 6, 7, 10, and 11 possess weak activities to several human cancer cell lines. Compound 8 shows a weak inhibitory effect on NO production with a half maximal inhibitory concentration (IC50) value of 22.7 μM. Compound 1 inhibits the lipopolysaccharide (LPS)-induced proliferation of B lymphocyte cells with an IC50 value of 22.4 μM, while 2 inhibits concanavalin A (Con A)-induced T cell proliferation and LPS-induced B lymphocyte cell proliferation with IC50 values of 16.7 and 13.6 μM, respectively.
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Affiliation(s)
- Meng Wang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
| | - Jiao-Xian Du
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
| | - Yang Hui-Xiang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
| | - Quan Dai
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
| | - Ya-Pei Liu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
| | - Juan He
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
| | - Yi Wang
- Bristol-Myers Squibb, Lawrenceville 08648, New Jersey, United States
| | - Zheng-Hui Li
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
| | - Tao Feng
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research, Leibniz University Hannover, Hannover 30167, Germany
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, People's Republic of China
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10
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Li W, He J, Feng T, Yang HX, Ai HL, Li ZH, Liu JK. Antroalbocin A, an Antibacterial Sesquiterpenoid from Higher Fungus Antrodiella albocinnamomea. Org Lett 2018; 20:8019-8021. [DOI: 10.1021/acs.orglett.8b03595] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei Li
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Juan He
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Tao Feng
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Hui-Xiang Yang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Hong-Lian Ai
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Zheng-Hui Li
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
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11
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Schobert R, Seibt S, Mahal K, Ahmad A, Biersack B, Effenberger-Neidnicht K, Padhye S, Sarkar FH, Mueller T. Cancer Selective Metallocenedicarboxylates of the Fungal Cytotoxin Illudin M. J Med Chem 2011; 54:6177-82. [DOI: 10.1021/jm200359n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rainer Schobert
- Organic Chemistry Laboratory, University Bayreuth, 95447 Bayreuth, Germany
| | - Sebastian Seibt
- Organic Chemistry Laboratory, University Bayreuth, 95447 Bayreuth, Germany
| | - Katharina Mahal
- Organic Chemistry Laboratory, University Bayreuth, 95447 Bayreuth, Germany
| | - Aamir Ahmad
- Department for Pathology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
| | - Bernhard Biersack
- Organic Chemistry Laboratory, University Bayreuth, 95447 Bayreuth, Germany
| | | | - Subhash Padhye
- Department for Pathology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
- Center for Drug Design and Molecular Medicine, Department of Environmental Sciences, University of Pune, Pune 411 007, India
| | - Fazlul H. Sarkar
- Department for Pathology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
| | - Thomas Mueller
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
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12
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Misiek M, Williams J, Schmich K, Hüttel W, Merfort I, Salomon CE, Aldrich CC, Hoffmeister D. Structure and cytotoxicity of arnamial and related fungal sesquiterpene aryl esters. JOURNAL OF NATURAL PRODUCTS 2009; 72:1888-1891. [PMID: 19795841 DOI: 10.1021/np900314p] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report on the structure elucidation of arnamial, a new Delta(2,4)-protoilludane everninate ester from the fungus Armillaria mellea, and on the apoptotic activity of arnamial as well as the cytotoxic activity of structurally related compounds on selected human cancer cells. Arnamial showed cytotoxicity against Jurkat T cells, MCF-7 breast adenocarcinoma, CCRF-CEM lymphoblastic leukemia, and HCT-116 colorectal carcinoma cells at IC50 = 3.9, 15.4, 8.9, and 10.7 microM, respectively, and the related aryl ester melledonal C showed cytotoxic activity against CCRF-CEM cells (IC50 = 14.75 microM). [1,2-13C2]Acetate feeding supports a polyketide origin of the orsellinic acid moiety of arnamial.
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Affiliation(s)
- Mathias Misiek
- Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
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13
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14
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Gignac GA, Morris MJ, Heller G, Schwartz LH, Scher HI. Assessing outcomes in prostate cancer clinical trials: a twenty-first century tower of Babel. Cancer 2008; 113:966-74. [PMID: 18661513 DOI: 10.1002/cncr.23719] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Because of the osseous distribution of prostate cancer metastases, progression is more readily identified than response in prostate cancer clinical trials. As a result, there is an increased focus on progression-free survival (PFS) as a phase 2 endpoint. PFS, however, is vulnerable to inter-study design variability. The authors sought to identify and quantify this variability and the resultant error in PFS across prostate cancer clinical trials. METHODS The authors reviewed phase 2 clinical trials of cytotoxic agents in castration-resistant metastatic prostate cancer over 5 years to evaluate the policies determining extent of disease and the definitions of disease progression. A simulation model was created to define the degree of error in estimating PFS in 3 hypothetical cohorts (median PFS of 12, 24, and 36 weeks) when the frequency of outcome assessments varies. RESULTS Imaging policies for trial entry were heterogeneous, as were the type, timing, and indications for outcome assessments. In the simulation, error in the reported PFS varied according to the interval between assessments. The difference between the detected and the true PFS could vary as much as 6.4 weeks per cycle, strictly resulting from the variability of assessment schedules tested. CONCLUSIONS Outcome assessment policies are highly variable in phase 2 studies of castration-resistant prostate cancer patients, despite published guidelines designed to standardize authentication of disease progression. The estimated error in PFS can exceed 6 weeks per cycle, exclusively because of variations in the assessment schedules. Comparisons of PFS times from different studies must be made with circumspection.
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Affiliation(s)
- Gretchen A Gignac
- Department of Medicine, Sidney Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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15
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Conjugates of the fungal cytotoxin illudin M with improved tumour specificity. Bioorg Med Chem 2008; 16:8592-7. [DOI: 10.1016/j.bmc.2008.08.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 07/31/2008] [Accepted: 08/04/2008] [Indexed: 11/18/2022]
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16
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Kelner MJ, McMorris TC, Rojas RJ, Estes LA, Suthipinijtham P. Synergy of irofulven in combination with other DNA damaging agents: synergistic interaction with altretamine, alkylating, and platinum-derived agents in the MV522 lung tumor model. Cancer Chemother Pharmacol 2008; 63:19-26. [DOI: 10.1007/s00280-008-0703-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
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17
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Kelner MJ, McMorris TC, Rojas RJ, Estes LA, Suthipinijtham P. Synergy of Irofulven in combination with various anti-metabolites, enzyme inhibitors, and miscellaneous agents in MV522 lung carcinoma cells: marked interaction with gemcitabine and 5-fluorouracil. Invest New Drugs 2008; 26:407-15. [PMID: 18227973 DOI: 10.1007/s10637-008-9113-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 01/09/2008] [Indexed: 11/24/2022]
Abstract
The novel agent Irofulven (HMAF, NSC 683863) has demonstrated significant antitumor activity against solid tumors in various xenograft models and human clinical trials. The antitumor potential of combining irofulven with 72 different anti-metabolite, enzyme inhibiting, and miscellaneous agents was investigated in this study. The human lung carcinoma MV522 cell line and its corresponding xenograft model were used to evaluate the activity of irofulven in combination with these different agents. Irofulven in combination with select anti-metabolites, notably cytidine or adenine-derived agents, displayed strong synergistic activity in both in vitro and in vivo studies. Agents demonstrating strong synergistic interaction with irofulven included gemcitabine, cyclocytidine, cytarabine, fludarabine phosphate, cladribine, and 5-fluorouracil. Other anti-metabolites, enzyme inhibitors, and a variety of miscellaneous agents failed to interact beneficially when administered in combination with irofulven. The therapeutic activity of irofulven is enhanced considerably when irofulven is combined with select anti-metabolite agents, and further clinical evaluation of these combinations is warranted. The synergistic interaction with these combinations may stem from a variety of actions including inhibition of the nucleotide excision repair (NER) pathway, topoisomerase I activity, and caspase-dependent and independent induction of apoptosis.
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Affiliation(s)
- Michael J Kelner
- Department of Pathology, University of California, San Diego, USA.
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18
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Neels JF, Gong J, Yu X, Sturla SJ. Quantitative correlation of drug bioactivation and deoxyadenosine alkylation by acylfulvene. Chem Res Toxicol 2007; 20:1513-9. [PMID: 17900171 DOI: 10.1021/tx7001756] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Acylfulvenes (AFs) are a class of antitumor agents that exert their cytotoxic effects by forming covalent adducts with biomolecules, including DNA and proteins; clinical trials are ongoing for (-)-(hydroxymethyl)AF. Recently, depurinating DNA adducts N3-AF-deoxyadenosine (dAdo) and N7-AF-deoxyguanosine (dGuo) were identified from reactions of the parent compound, AF, with calf thymus DNA in the presence of the reductase enzyme alkenal/one oxidoreductase (AOR) and cofactor NADPH. We report here the development of a structure-specific quantitative analytical method for evaluating levels of the major base adduct N3-AF-adenine (Ade), which results from depurination of N3-AF-dAdo, and its utilization to further probe the relationship between AOR-mediated bioactivation and adduct formation in a cell-free system. As an internal standard, the isotopomer N3-AF-Ade-d3 was synthesized, and electrospray-ionization mass spectrometry coupled with high-performance liquid chromatography (HPLC-ESI-MS/MS) was used to detect and quantitate the adduct. This method was validated and found to be accurate (R2>or=0.99) and precise (relative standard deviation 5.8-6.4%), with a limit of detection of 2 fmol. DNA samples, to which the stable-isotope-labeled internal standard was added, were subjected to neutral thermal hydrolysis yielding N3-AF-Ade. Adducts were isolated by a simple solid-liquid methanol extraction procedure, and adduct formation was examined in the presence of either high (1-3 micromol) or low (15 nmol) levels of DNA. Absolute amounts of N3-AF-Ade were measured in cell-free reaction mixtures containing varying levels of AOR as the only drug-activating enzyme. The increase in adduct formation (5-100 adducts per 10(5) DNA bases) over a range of enzyme concentrations (1-24 nM of AOR) showed saturation type behavior. This study reports a sensitive HPLC-ESI-MS/MS method for quantitation of the major DNA adduct induced by AF and illustrates a correlation between N3-AF-Ade formation and AOR-mediated enzymatic activation in a cell-free system, thus providing a template for further studies of drug toxicity in cells and in vivo.
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Affiliation(s)
- James F Neels
- Department of Medicinal Chemistry and The Cancer Center, University of Minnesota, Minneapolis 55455, USA
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19
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Alexandre J, Kahatt C, Bertheault-Cvitkovic F, Faivre S, Shibata S, Hilgers W, Goldwasser F, Lokiec F, Raymond E, Weems G, Shah A, MacDonald JR, Cvitkovic E. A phase I and pharmacokinetic study of irofulven and capecitabine administered every 2 weeks in patients with advanced solid tumors. Invest New Drugs 2007; 25:453-62. [PMID: 17628744 DOI: 10.1007/s10637-007-9071-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 06/18/2007] [Indexed: 12/27/2022]
Abstract
PURPOSE To determine the maximum tolerated dose (MTD), recommended dose, dose limiting toxicities (DLT), safety and pharmacokinetics of irofulven combined with capecitabine in advanced solid tumor patients. EXPERIMENTAL DESIGN Irofulven was given i.v. over 30 min on days 1 and 15 every 4 weeks; capecitabine was given orally twice daily, day 1 to 15. Dose levels (DL) were: irofulven (mg/kg)/capecitabine (mg/m2/day): DL1: 0.3/1,700; DL2: 0.4/1,700; DL3: 0.4/2,000; DL4: 0.5/2,000. RESULTS Between May 2002 and March 2004, 37 patients were treated and 36 evaluable for MTD. DLT occurred in 1/6 evaluable patients in DL1 (grade 3 thrombocytopenia); 1/6 in DL3 (grade 3 thrombocytopenia); 2/7 in DL4 (grade 3 febrile neutropenia, grade 3 thrombocytopenia). DL4 was defined as the MTD and DL3 was established as the recommended dose (RD). DLTs occurred in 1 of 14 additional patients treated at DL3. No treatment-related deaths or grade 4 non-hematological toxicity occurred, and grade 3 toxicities were infrequent. Antitumor activity was observed; two partial responses were noted in thyroid carcinoma (DL1, DL4); one unconfirmed partial response was observed in a patient with nasopharyngeal carcinoma, (DL3); 12 patients had disease stabilization >3 months; of eight patients with hormone refractory prostate cancer (HRPC), one patient had PSA normalization and four short-term stabilizations of PSA occurred. Capecitabine and irofulven pharmacokinetics results did not suggest drug-drug interactions. CONCLUSIONS Irofulven with capecitabine was adequately tolerated and evidence of antitumor activity was observed. The recommended dose is irofulven 0.4 mg/kg and capecitabine 2,000 mg/m2/day.
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Wang Y, Wiltshire T, Senft J, Wenger SL, Reed E, Wang W. Fanconi anemia D2 protein confers chemoresistance in response to the anticancer agent, irofulven. Mol Cancer Ther 2007; 5:3153-61. [PMID: 17172419 DOI: 10.1158/1535-7163.mct-06-0427] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Fanconi anemia-BRCA pathway of genes are frequently mutated or epigenetically repressed in human cancer. The proteins of this pathway play pivotal roles in DNA damage signaling and repair. Irofulven is one of a new class of anticancer agents that are analogues of mushroom-derived illudin toxins. Preclinical studies and clinical trials have shown that irofulven is effective against several tumor cell types. The exact nature of irofulven-induced DNA damage is not completely understood. Previously, we have shown that irofulven activates ATM and its targets, NBS1, SMC1, CHK2, and p53. In this study, we hypothesize that irofulven induces DNA double-strand breaks and FANCD2 may play an important role in modulating cellular responses and chemosensitivity in response to irofulven treatment. By using cells that are proficient or deficient for FANCD2, ATR, or ATM, we showed that irofulven induces FANCD2 monoubiquitination and nuclear foci formation. ATR is important in mediating irofulven-induced FANCD2 monoubiquitination. Furthermore, we showed that FANCD2 plays a critical role in maintaining chromosome integrity and modulating chemosensitivity in response to irofulven-induced DNA damage. Therefore, this study suggests that it might be clinically significant to target irofulven therapy to cancers defective for proteins of the Fanconi anemia-BRCA pathway.
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Affiliation(s)
- Yutian Wang
- Mary Babb Randolph Cancer Center, West Virginia University, 1835 Health Sciences South, P.O. Box 9300, Morgantown, WV 26506, USA.
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21
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Gong J, Vaidyanathan VG, Yu X, Kensler TW, Peterson LA, Sturla SJ. Depurinating acylfulvene-DNA adducts: characterizing cellular chemical reactions of a selective antitumor agent. J Am Chem Soc 2007; 129:2101-11. [PMID: 17256933 DOI: 10.1021/ja0665951] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acylfulvenes (AFs) are a class of semisynthetic agents with high toxicity toward certain tumor cells, and for one analogue, hydroxymethylacylfulvene (HMAF), clinical trials are in progress. DNA alkylation by AFs, mediated by bioreductive activation, is believed to contribute to cytotoxicity, but the structures and chemical properties of corresponding DNA adducts are unknown. This study provides the first structural characterization of AF-specific DNA adducts. In the presence of a reductive enzyme, alkenal/one oxidoreductase (AOR), AF selectively alkylates dAdo and dGuo in reactions with a monomeric nucleoside, as well as in reactions with naked or cellular DNA, with 3-alkyl-dAdo as the apparently most abundant AF-DNA adduct. Characterization of this adduct was facilitated by independent chemical synthesis of the corresponding 3-alkyl-Ade adduct. In addition, in naked or cellular DNA, evidence was obtained for the formation of an additional type of adduct resulting from direct conjugate addition of Ade to AF followed by hydrolytic cyclopropane ring-opening, indicating the potential for a competing reaction pathway involving direct DNA alkylation. The major AF-dAdo and AF-dGuo adducts are unstable under physiologically relevant conditions and depurinate to release an alkylated nucleobase in a process that has a half-life of 8.5 h for 3-alkyladenine and less than approximately 2 h for dGuo adducts. DNA alkylation further leads to single-stranded DNA cleavage, occurring exclusively at dGuo and dAdo sites, in a nonsequence-specific manner. In AF-treated cells that were transfected with either AOR or control vectors, the DNA adducts identified match those from in vitro studies. Moreover, a positive correlation was observed between DNA adduct levels and cell sensitivity to AF. The potential contributing roles of AOR-mediated bioactivation and adduct stability to the cytotoxicity of AF are discussed.
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Affiliation(s)
- Jiachang Gong
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, USA
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22
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Wiltshire T, Senft J, Wang Y, Konat GW, Wenger SL, Reed E, Wang W. BRCA1 contributes to cell cycle arrest and chemoresistance in response to the anticancer agent irofulven. Mol Pharmacol 2007; 71:1051-60. [PMID: 17229870 DOI: 10.1124/mol.106.029504] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Tumor suppressor gene BRCA1 is frequently mutated in familial breast and ovarian cancer. BRCA1 plays pivotal roles in maintaining genomic stability by interacting with numerous proteins in cell cycle control and DNA repair. Irofulven (6-hydroxymethylacylfulvene, HMAF, MGI 114, NSC 683863) is one of a new class of anticancer agents that are analogs of mushroom-derived illudin toxins. Preclinical studies and clinical trials have demonstrated that irofulven is effective against several tumor cell types. The exact nature of irofulven-induced DNA damage is not completely understood. We demonstrated previously that irofulven activates ATM and its targets, NBS1, SMC1, CHK2, and p53. In this study, we hypothesize that irofulven induces DNA double-strand breaks and that BRCA1 may affect chemosensitivity by controlling cell cycle checkpoints, DNA repair, and genomic stability in response to irofulven treatment. We observed that irofulven induces the formation of chromosome breaks and radials and the activation and foci formation of gamma-H2AX, BRCA1, and RAD51. We also provided evidence that irofulven induces the generation of DNA double-strand breaks. By using BRCA1-deficient or -proficient cells, we demonstrated that in response to irofulven, BRCA1 contributes to the control of S and G(2)/M cell cycle arrest and is critical for repairing DNA double-strand breaks and for RAD51-dependent homologous recombination. Furthermore, we found that BRCA1 deficiency results in increased chromosome damage and chemosensitivity after irofulven treatment.
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Affiliation(s)
- Timothy Wiltshire
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506-9300, USA
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23
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Wang Y, Wiltshire T, Senft J, Reed E, Wang W. Irofulven induces replication-dependent CHK2 activation related to p53 status. Biochem Pharmacol 2006; 73:469-80. [PMID: 17118344 PMCID: PMC1800887 DOI: 10.1016/j.bcp.2006.10.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 10/11/2006] [Accepted: 10/18/2006] [Indexed: 11/25/2022]
Abstract
CHK2 and p53 are frequently mutated in human cancers. CHK2 is known to phosphorylate and stabilize p53. CHK2 has also been implicated in DNA repair and apoptosis induction. However, whether p53 affects CHK2 activation and whether CHK2 activation modulates chemosensitivity are unclear. In this study, we found that in response to the DNA damage agent, irofulven, CHK2 activation, rather than its expression, is inversely correlated to p53 status. Irofulven inhibits DNA replication and induces chromosome aberrations (breaks and radials) and p53-dependent cell cycle arrest. Pretreatment of cells with the DNA polymerase inhibitor, aphidicolin, resulted in reduction of irofulven-induced CHK2 activation and foci formation, indicating that CHK2 activation by irofulven is replication-dependent. Furthermore, by using ovarian cancer cell lines expressing dominant-negative CHK2 and CHK2-knockout HCT116 cells, we found that CHK2 activation contributes to the control of S and G2/M cell cycle arrests, but not chemosensitivity to irofulven. Overall, this study demonstrates that in response to irofulven-induced DNA damage, the activation of CHK2 is dependent on DNA replication and related to p53 status. By controlling cell cycle arrest and DNA replication, p53 affects CHK2 activation. CHK2 activation contributes to cell cycle arrest, but not chemosensitivity.
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Affiliation(s)
- Yutian Wang
- Mary Babb Randolph Cancer Center; West Virginia University School of Medicine, Morgantown, WV 26506
| | - Timothy Wiltshire
- Department of Microbiology, Immunology and Cell Biology; West Virginia University School of Medicine, Morgantown, WV 26506
| | - Jamie Senft
- Mary Babb Randolph Cancer Center; West Virginia University School of Medicine, Morgantown, WV 26506
| | - Eddie Reed
- Mary Babb Randolph Cancer Center; West Virginia University School of Medicine, Morgantown, WV 26506
- Department of Microbiology, Immunology and Cell Biology; West Virginia University School of Medicine, Morgantown, WV 26506
| | - Weixin Wang
- Mary Babb Randolph Cancer Center; West Virginia University School of Medicine, Morgantown, WV 26506
- Department of Microbiology, Immunology and Cell Biology; West Virginia University School of Medicine, Morgantown, WV 26506
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Kralj A, Kehraus S, Krick A, Eguereva E, Kelter G, Maurer M, Wortmann A, Fiebig HH, König GM. Arugosins G and H: prenylated polyketides from the marine-derived fungus Emericellanidulans var. acristata. JOURNAL OF NATURAL PRODUCTS 2006; 69:995-1000. [PMID: 16872131 DOI: 10.1021/np050454f] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The fungus Emericella nidulans var. acristata was isolated as an endophyte from a Mediterranean green alga. Cultivation of this fungus yielded two new compounds, arugosins G (1) and H (2), together with the known metabolites 3-9. Arugosins (1-4) are benzophenone derivatives, biosynthetically related to the xanthones 5, 6, and 9. The indole alkaloid 7 displayed antitumor activity in a panel of 36 human tumor cell lines, exhibiting a mean IC(50) value of 5.5 microg/mL in an in vitro survival and proliferation assay. Furthermore, compounds 3 and 4 showed moderate antitumor activity toward individual tumor cell lines. None of compounds 1-8 exhibited any immunostimulatory activity assessed as the capacity to induce cytokines in PBMCs from healthy donors.
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Affiliation(s)
- Ana Kralj
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany, and Oncotest GmbH, Institute of Experimental Oncology, Am Flughafen 12-14, D-79108 Freiburg, Germany
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Yeo W, Boyer M, Chung HC, Ong SYK, Lim R, Zee B, Ma B, Lam KC, Mo FKF, Ng EKW, Ho R, Clarke S, Roh JK, Beale P, Rha SY, Jeung HC, Soo R, Goh BC, Chan ATC. Irofulven as first line therapy in recurrent or metastatic gastric cancer: a phase II multicenter study by the Cancer Therapeutics Research Group (CTRG). Cancer Chemother Pharmacol 2006; 59:295-300. [PMID: 16783579 DOI: 10.1007/s00280-006-0270-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 05/11/2006] [Indexed: 11/27/2022]
Abstract
BACKGROUND The purpose of this study was to evaluate the tolerability and efficacy of irofulven, a DNA interacting acylfulvene analog, as first line therapy for patients with recurrent or metastatic gastric cancer. PATIENTS AND METHODS Twenty-three patients with recurrent or metastatic gastric cancer received irofulven at a dose of 0.45 mg/kg administered intravenously over 30-min infusion (up to a maximum of 50 mg), on days 1 and 8, every 3 weeks. RESULTS The median number of cycles delivered per patient was 2 (range 1-6). Two patients (9%) had >or= 1-week delay in administration of subsequent cycle of chemotherapy. For the day 8 chemotherapy, dose reductions were required in seven patients (30%); dose omitting occurred in five patients (22%). Grade 3/4 anemia and neutropenia occurred in 22 and 17% of patients, respectively. There was no grade 4 thrombocytopenia and no neutropenic fever was observed. Of the 20 evaluable patients, there were no responses observed, 3 patients had stable disease after 2 cycles of treatment which was not confirmed by a further assessment. Median overall survival was 6.05 months (95% CI 4.55-9.39). CONCLUSIONS Irofulven was tolerated at the dose of 0.45 mg/kg on days 1 and 8, every 3 weeks but showed no evidence of antitumor activity in patients with advanced gastric cancer.
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Affiliation(s)
- W Yeo
- Comprehensive Cancer Trials Unit, Department of Clinical Oncology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong.
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Hilgers W, Faivre S, Chieze S, Alexandre J, Lokiec F, Goldwasser F, Raymond E, Kahatt C, Taamma A, Weems G, MacDonald JR, Misset JL, Cvitkovic E. A phase I and pharmacokinetic study of irofulven and cisplatin administered in a 30-min infusion every two weeks to patients with advanced solid tumors. Invest New Drugs 2006; 24:311-9. [PMID: 16683074 DOI: 10.1007/s10637-005-5055-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND To determine maximum tolerated dose (MTD), recommended dose, safety and pharmacokinetics of irofulven combined with cisplatin in advanced solid tumor patients. PATIENTS AND METHODS Cisplatin and irofulven were given sequentially i.v. over 30 min on day 1 and 15 every 4 weeks. Four dose levels (DL) were explored: irofulven (mg/kg)/cisplatin (mg/m2): DL1: 0.3/30; DL2: 0.4/30; DL3: 0.4/40; DL4: 0.5/40. Dose-limiting toxicity (DLT) included dosing omission and delay > 1 week. MTD was the DL with DLT in 2/2 or > or = 2/6 patients during cycle 1-2. RESULTS Between March 2002 and April 2003, 33 patients were treated. DLT occurred in 1/6 patients in DL1 (hypomagnesemia, hypocalcemia); 1/6 in DL2 (thrombocytopenia); 2 heavily pretreated patients out of 6 patients in DL3 (neutropenic infection, thrombocytopenia, stomatitis); 2/3 in DL4 (asthenia, blurred vision). Three DLT occurred in 12 additional patients treated at DL2. No toxic deaths occurred; grade 4 toxicity and grade 3 non-hematological toxicity were infrequent. Six patients reported grade 1-2 visual events. Antitumor activity was observed over a broad spectrum of tumor types in all DLs: 1 partial response in bulky sarcoma (DL1); 1 clinical response in endometrial carcinoma (DL1); 2 partial responses not confirmed due to discontinuation (ovarian DL2, renal DL4); 8 stabilizations > 3 months; PSA response: 3/9 prostate cancer patients. Irofulven showed rapid elimination and high interpatient variability. Platinum and irofulven pharmacokinetics did not suggest drug-drug interactions. CONCLUSION Irofulven with cisplatin was adequately tolerated and substantial evidence of antitumor activity was observed. The recommended dose is irofulven 0.4 mg/kg and cisplatin 30 mg/m2.
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