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Kulkarni A, Zhou J, Biyani N, Kathad U, Banerjee PP, Srivastava S, Prucsi Z, Solarczyk K, Bhatia K, Ewesuedo RB, Sharma P. LP-184, a Novel Acylfulvene Molecule, Exhibits Anticancer Activity against Diverse Solid Tumors with Homologous Recombination Deficiency. CANCER RESEARCH COMMUNICATIONS 2024; 4:1199-1210. [PMID: 38630886 PMCID: PMC11072798 DOI: 10.1158/2767-9764.crc-23-0554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/11/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Homologous recombination (HR)-related gene alterations are present in a significant subset of prostate, breast, ovarian, pancreatic, lung, and colon cancers rendering these tumors as potential responders to specific DNA damaging agents. A small molecule acylfulvene prodrug, LP-184, metabolizes to an active compound by the oxidoreductase activity of enzyme prostaglandin reductase 1 (PTGR1), which is frequently elevated in multiple solid tumor types. Prior work demonstrated that cancer cell lines deficient in a spectrum of DNA damage repair (DDR) pathway genes show increased susceptibility to LP-184. Here, we investigated the potential of LP-184 in targeting multiple tumors with impaired HR function and its mechanism of action as a DNA damaging agent. LP-184 induced elevated DNA double-strand breaks in HR deficient (HRD) cancer cells. Depletion of key HR components BRCA2 or ataxia telangiectasia mutated (ATM) in cancer cells conferred up to 12-fold increased sensitivity to the LP-184. LP-184 showed nanomolar potency in a diverse range of HRD cancer models, including prostate cancer organoids, leiomyosarcoma cell lines, and patient-derived tumor graft models of lung, pancreatic, and prostate cancers. LP-184 demonstrated complete, durable tumor regression in 10 patient-derived xenograft (PDX) models of HRD triple-negative breast cancer (TNBC) including those resistant to PARP inhibitors (PARPi). LP-184 further displayed strong synergy with PARPi in ovarian and prostate cancer cell lines as well as in TNBC PDX models. These preclinical findings illustrate the potential of LP-184 as a pan-HRD cancer therapeutic. Taken together, our results support continued clinical evaluation of LP-184 in a large subset of HRD solid tumors. SIGNIFICANCE New agents with activity against DDR-deficient solid tumors refractory to standard-of-care therapies are needed. We report multiple findings supporting the potential for LP-184, a novel alkylating agent with three FDA orphan drug designations, to fill this void clinically: strong nanomolar potency; sustained, durable regression of solid tumor xenografts; synthetic lethality with HR defects. LP-184 adult phase IA trial to assess safety in advanced solid tumors is ongoing.
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Affiliation(s)
| | | | | | | | - Partha P. Banerjee
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Shiv Srivastava
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
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Dichiara M, Cosentino G, Giordano G, Pasquinucci L, Marrazzo A, Costanzo G, Amata E. Designing drugs optimized for both blood-brain barrier permeation and intra-cerebral partition. Expert Opin Drug Discov 2024; 19:317-329. [PMID: 38145409 DOI: 10.1080/17460441.2023.2294118] [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: 10/08/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023]
Abstract
INTRODUCTION With the increasing incidence and prevalence of neurological disorders globally, there is a paramount need for new pharmacotherapies. BBB effectively protects the brain but raises a profound challenge to drug permeation, with less than 2% of most drugs reaching the CNS. AREAS COVERED This article reviews aspects of the most recent design strategies, providing insights into ideas and concepts in CNS drug discovery. An overview of the products available on the market is given and why clinical trials are continuously failing is discussed. EXPERT OPINION Among the available CNS drugs, small molecules account for most successful CNS therapeutics due to their ability to penetrate the BBB through passive or carrier-mediated mechanisms. The development of new CNS drugs is very difficult. To date, there is a lack of effective drugs for alleviating or even reversing the progression of brain diseases. Particularly, the use of artificial intelligence strategies, together with more appropriate animal models, may enable the design of molecules with appropriate permeation, to elicit a biological response from the neurotherapeutic target.
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Affiliation(s)
- Maria Dichiara
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Giuseppe Cosentino
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Giorgia Giordano
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Lorella Pasquinucci
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Agostino Marrazzo
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Giuliana Costanzo
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Emanuele Amata
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
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3
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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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Lal B, Kulkarni A, McDermott J, Rais R, Alt J, Wu Y, Lopez-Bertoni H, Sall S, Kathad U, Zhou J, Slusher BS, Bhatia K, Laterra J. Preclinical Efficacy of LP-184, a Tumor Site Activated Synthetic Lethal Therapeutic, in Glioblastoma. Clin Cancer Res 2023; 29:4209-4218. [PMID: 37494541 DOI: 10.1158/1078-0432.ccr-23-0673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/15/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Glioblastoma (GBM) is the most common brain malignancy with median survival <2 years. Standard-of-care temozolomide has marginal efficacy in approximately 70% of patients due to MGMT expression. LP-184 is an acylfulvene-derived prodrug activated by the oxidoreductase PTGR1 that alkylates at N3-adenine, not reported to be repaired by MGMT. This article examines LP-184 efficacy against preclinical GBM models and identifies molecular predictors of LP-184 efficacy in clinical GBM. EXPERIMENTAL DESIGN LP-184 effects on GBM cell viability and DNA damage were determined using cell lines, primary PDX-derived cells and patient-derived neurospheres. GBM cell sensitivities to LP-184 relative to temozolomide and MGMT expression were examined. Pharmacokinetics and CNS bioavailability were evaluated in mice with GBM xenografts. LP-184 effects on GBM xenograft growth and animal survival were determined. Machine learning, bioinformatic tools, and clinical databases identified molecular predictors of GBM cells and tumors to LP-184 responsiveness. RESULTS LP-184 inhibited viability of multiple GBM cell isolates including temozolomide-resistant and MGMT-expressing cells at IC50 = approximately 22-310 nmol/L. Pharmacokinetics showed favorable AUCbrain/plasma and AUCtumor/plasma ratios of 0.11 (brain Cmax = 839 nmol/L) and 0.2 (tumor Cmax = 2,530 nmol/L), respectively. LP-184 induced regression of GBM xenografts and prolonged survival of mice bearing orthotopic xenografts. Bioinformatic analyses identified PTGR1 elevation in clinical GBM subtypes and associated LP-184 sensitivity with EGFR signaling, low nucleotide excision repair (NER), and low ERCC3 expression. Spironolactone, which induces ERCC3 degradation, decreased LP-184 IC50 3 to 6 fold and enhanced GBM xenograft antitumor responses. CONCLUSIONS These results establish LP-184 as a promising chemotherapeutic for GBM with enhanced efficacy in intrinsic or spironolactone-induced TC-NER-deficient tumors.
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Affiliation(s)
- Bachchu Lal
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland
| | | | | | - Rana Rais
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Johns Hopkins Drug Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jesse Alt
- Johns Hopkins Drug Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ying Wu
- Johns Hopkins Drug Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sophie Sall
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland
| | | | | | - Barbara S Slusher
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Johns Hopkins Drug Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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5
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Restifo D, McDermott JR, Cvetkovic D, Santos TD, Ogier C, Surumbayeva A, Handorf EA, Schimke C, Ma C, Cai KQ, Olszanski AJ, Kathad U, Bhatia K, Sharma P, Kulkarni A, Astsaturov I. Conditional Dependency of LP-184 on Prostaglandin Reductase 1 is Synthetic Lethal in Pancreatic Cancers with DNA Damage Repair Deficiencies. Mol Cancer Ther 2023; 22:1182-1190. [PMID: 37552607 PMCID: PMC10592171 DOI: 10.1158/1535-7163.mct-22-0818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/22/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
The greater efficacy of DNA-damaging drugs for pancreatic adenocarcinoma (PDAC) relies on targeting cancer-specific vulnerabilities while sparing normal organs and tissues due to their inherent toxicities. We tested LP-184, a novel acylfulvene analog, for its activity in preclinical models of PDAC carrying mutations in the DNA damage repair (DDR) pathways. Cytotoxicity of LP-184 is solely dependent on prostaglandin reductase 1 (PTGR1), so that PTGR1 expression robustly correlates with LP-184 cytotoxicity in vitro and in vivo. Low-passage patient-derived PDAC xenografts with DDR deficiencies treated ex vivo are more sensitive to LP-184 compared with DDR-proficient tumors. Additional in vivo testing of PDAC xenografts for their sensitivity to LP-184 demonstrates marked tumor growth inhibition in models harboring pathogenic mutations in ATR, BRCA1, and BRCA2. Depletion of PTGR1, however, completely abrogates the antitumor effect of LP-184. Testing combinatorial strategies for LP-184 aimed at deregulation of nucleotide excision repair proteins ERCC3 and ERCC4 established synergy. Our results provide valuable biomarkers for clinical testing of LP-184 in a large subset of genetically defined characterized refractory carcinomas. High PTGR1 expression and deleterious DDR mutations are present in approximately one third of PDAC making these patients ideal candidates for clinical trials of LP-184.
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Affiliation(s)
- Diana Restifo
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | - Dusica Cvetkovic
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Troy Dos Santos
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Charline Ogier
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Aizhan Surumbayeva
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | | | - Charlie Ma
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Kathy Q. Cai
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Anthony J. Olszanski
- Department of Hematology and Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | | | | | | | - Igor Astsaturov
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Hematology and Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
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6
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Samarin J, Fabrowski P, Kurilov R, Nuskova H, Hummel-Eisenbeiss J, Pink H, Li N, Weru V, Alborzinia H, Yildiz U, Grob L, Taubert M, Czech M, Morgen M, Brandstädter C, Becker K, Mao L, Jayavelu AK, Goncalves A, Uhrig U, Seiler J, Lyu Y, Diederichs S, Klingmüller U, Muckenthaler M, Kopp-Schneider A, Teleman A, Miller AK, Gunkel N. Low level of antioxidant capacity biomarkers but not target overexpression predicts vulnerability to ROS-inducing drugs. Redox Biol 2023; 62:102639. [PMID: 36958250 PMCID: PMC10053401 DOI: 10.1016/j.redox.2023.102639] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
Despite a strong rationale for why cancer cells are susceptible to redox-targeting drugs, such drugs often face tumor resistance or dose-limiting toxicity in preclinical and clinical studies. An important reason is the lack of specific biomarkers to better select susceptible cancer entities and stratify patients. Using a large panel of lung cancer cell lines, we identified a set of "antioxidant-capacity" biomarkers (ACB), which were tightly repressed, partly by STAT3 and STAT5A/B in sensitive cells, rendering them susceptible to multiple redox-targeting and ferroptosis-inducing drugs. Contrary to expectation, constitutively low ACB expression was not associated with an increased steady state level of reactive oxygen species (ROS) but a high level of nitric oxide, which is required to sustain high replication rates. Using ACBs, we identified cancer entities with a high percentage of patients with favorable ACB expression pattern, making it likely that more responders to ROS-inducing drugs could be stratified for clinical trials.
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Affiliation(s)
- Jana Samarin
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Piotr Fabrowski
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roman Kurilov
- Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hana Nuskova
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hannelore Pink
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nan Li
- Somatic Evolution and Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vivienn Weru
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hamed Alborzinia
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Umut Yildiz
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura Grob
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Minerva Taubert
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marie Czech
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Morgen
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Brandstädter
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Lianghao Mao
- Proteomics and Cancer Cell Signaling Group, CCU Pediatric Leukemia, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ashok Kumar Jayavelu
- Proteomics and Cancer Cell Signaling Group, CCU Pediatric Leukemia, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angela Goncalves
- Somatic Evolution and Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrike Uhrig
- Chemical Biology Core Facility, EMBL, Heidelberg, Germany
| | - Jeanette Seiler
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yanhong Lyu
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Freiburg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Freiburg, Germany
| | - Ursula Klingmüller
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Martina Muckenthaler
- Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg, Heidelberg, Germany
| | | | - Aurelio Teleman
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aubry K Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Nikolas Gunkel
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany.
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7
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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: 0] [Impact Index Per Article: 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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