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Hoang MH, Skidmore ZL, Rindt H, Chu S, Fisk B, Foltz JA, Fronick C, Fulton R, Zhou M, Bivens NJ, Reinero CN, Fehniger TA, Griffith M, Bryan JN, Griffith OL. Single-cell T-cell receptor repertoire profiling in dogs. Commun Biol 2024; 7:484. [PMID: 38649520 PMCID: PMC11035579 DOI: 10.1038/s42003-024-06174-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Spontaneous cancers in companion dogs are robust models of human disease. Tracking tumor-specific immune responses in these models requires reagents to perform species-specific single cell T cell receptor sequencing (scTCRseq). scTCRseq and integration with scRNA data have not been demonstrated on companion dogs with cancer. Here, five healthy dogs, two dogs with T cell lymphoma and four dogs with melanoma are selected to demonstrate applicability of scTCRseq in a cancer immunotherapy setting. Single-cell suspensions of PBMCs or lymph node aspirates are profiled using scRNA and dog-specific scTCRseq primers. In total, 77,809 V(D)J-expressing cells are detected, with an average of 3498 (348 - 5,971) unique clonotypes identified per sample. In total, 29/34, 40/40, 22/22 and 9/9 known functional TRAV, TRAJ, TRBV and TRBJ gene segments are observed respectively. Pseudogene or otherwise defective gene segments are also detected supporting re-annotation of several as functional. Healthy dogs exhibit highly diverse repertoires, T cell lymphomas exhibit clonal repertoires, and vaccine-treated melanoma dogs are dominated by a small number of highly abundant clonotypes. scRNA libraries define large clusters of V(D)J-expressing CD8+ and CD4 + T cells. Dominant clonotypes observed in melanoma PBMCs are predominantly CD8 + T cells, with activated phenotypes, suggesting possible anti-tumor T cell populations.
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Affiliation(s)
- My H Hoang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Zachary L Skidmore
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Hans Rindt
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Shirley Chu
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Bryan Fisk
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Jennifer A Foltz
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Catrina Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Mingyi Zhou
- Genomics Technology Core, University of Missouri, Columbia, MO, USA
| | - Nathan J Bivens
- Genomics Technology Core, University of Missouri, Columbia, MO, USA
| | - Carol N Reinero
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
| | - Todd A Fehniger
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey N Bryan
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA.
| | - Obi L Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
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Khodair AI, El-Hallouty SM, Cagle-White B, Abdel Aziz MH, Hanafy MK, Mowafy S, Hamdy NM, Kassab SE. Camptothecin structure simplification elaborated new imidazo[2,1-b]quinazoline derivative as a human topoisomerase I inhibitor with efficacy against bone cancer cells and colon adenocarcinoma. Eur J Med Chem 2024; 265:116049. [PMID: 38185054 DOI: 10.1016/j.ejmech.2023.116049] [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: 10/03/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
Camptothecin is a pentacyclic natural alkaloid that inhibits the hTop1 enzyme involved in DNA transcription and cancer cell growth. Camptothecin structure pitfalls prompted us to design new congeners using a structure simplification strategy to reduce the ring extension number from pentacyclic to tetracyclic while maintaining potential stacking of the new compounds with the DNA base pairs at the Top1-mediated cleavage complex and aqueous solubility, as well as minimizing compound-liver toxicity. The principal axis of this study was the verification of hTop1 inhibiting activity as a possible mechanism of action and the elaboration of new simplified inhibitors with improved pharmacodynamic and pharmacokinetic profiling using three structure panels (A-C) of (isoquinolinoimidazoquinazoline), (imidazoquinazoline), and (imidazoisoquinoline), respectively. DNA relaxation assay identified five compounds as hTop1 inhibitors belonging to the imidazoisoquinolines 3a,b, the imidazoquinazolines 12, and the isoquinolinoimidazoquinazolines 7a,b. In an MTT cytotoxicity assay against different cancer cell lines, compound 12 was the most potent against HOS bone cancer cells (IC50 = 1.47 μM). At the same time, the other inhibitors had no detectable activity against any cancer cell type. Compound (12) demonstrated great penetrating power in the HOS cancer cells' 3D-multicellular tumor spheroid model. Bioinformatics research of the hTop1 gene revealed that the TP53 cell proliferative gene is in the network of hTop1. The finding is confirmed empirically using the gene expression assay that proved the increase in p53 expression. The impact of structure simplification on compound 12 profile, characterized by the absence of acute oral liver toxicity when compared to Doxorubicin as a standard inhibitor, the lethal dose measured on Swiss Albino female mice and reported at LD50 = 250 mg/kg, and therapeutic significance in reducing colon adenocarcinoma tumor volume by 75.36 % after five weeks of treatment with compound 12. The molecular docking solutions of the active CPT-based derivative 12 and the inactive congener 14 into the active site of hTop1 and the activity cliffing of such MMP directed us to recommend the addition of HBD and HBA variables to compound 12 imidazoquinazoline core scaffold to enhance the potency via hydrogen bond formation with the major groove amino acids (Asp533, Lys532) as well as maintaining the hydrogen bond with the minor groove amino acid Arg364.
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Affiliation(s)
- Ahmed I Khodair
- Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516, Kafrelsheikh, Egypt.
| | - Salwa M El-Hallouty
- Drug Bioassay-Cell Culture Laboratory, Department of Pharmacognosy, National Research Centre, Dokki, Giza 12622, Egypt
| | - Brittnee Cagle-White
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, TX 75799, USA
| | - May H Abdel Aziz
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, TX 75799, USA
| | - Mahmoud Kh Hanafy
- Drug Bioassay-Cell Culture Laboratory, Department of Pharmacognosy, National Research Centre, Dokki, Giza 12622, Egypt; Research Centre for Idling Brain Science, Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Science, University of Toyama, 930-0194, Japan
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Cairo, 11431, Egypt
| | - Nadia M Hamdy
- Biochemistry Dept., Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt.
| | - Shaymaa E Kassab
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt.
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Mertens RT, Gukathasan S, Arojojoye AS, Olelewe C, Awuah SG. Next Generation Gold Drugs and Probes: Chemistry and Biomedical Applications. Chem Rev 2023; 123:6612-6667. [PMID: 37071737 PMCID: PMC10317554 DOI: 10.1021/acs.chemrev.2c00649] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The gold drugs, gold sodium thiomalate (Myocrisin), aurothioglucose (Solganal), and the orally administered auranofin (Ridaura), are utilized in modern medicine for the treatment of inflammatory arthritis including rheumatoid and juvenile arthritis; however, new gold agents have been slow to enter the clinic. Repurposing of auranofin in different disease indications such as cancer, parasitic, and microbial infections in the clinic has provided impetus for the development of new gold complexes for biomedical applications based on unique mechanistic insights differentiated from auranofin. Various chemical methods for the preparation of physiologically stable gold complexes and associated mechanisms have been explored in biomedicine such as therapeutics or chemical probes. In this Review, we discuss the chemistry of next generation gold drugs, which encompasses oxidation states, geometry, ligands, coordination, and organometallic compounds for infectious diseases, cancer, inflammation, and as tools for chemical biology via gold-protein interactions. We will focus on the development of gold agents in biomedicine within the past decade. The Review provides readers with an accessible overview of the utility, development, and mechanism of action of gold-based small molecules to establish context and basis for the thriving resurgence of gold in medicine.
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Affiliation(s)
- R Tyler Mertens
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Sailajah Gukathasan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Adedamola S Arojojoye
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Chibuzor Olelewe
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Samuel G Awuah
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- University of Kentucky Markey Cancer Center, Lexington, Kentucky 40536, United States
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Beumer JH, Kennard BC, Holleran JL, Moore N, Zlott J, Miller BM, Kummar S, Chen A, Doroshow J, Park W, Gobburu J, Dunn A. Evaluating the indotecan-neutropenia relationship in patients with solid tumors by population pharmacokinetic modeling and sigmoidal E max regressions. Cancer Chemother Pharmacol 2023; 91:219-230. [PMID: 36813886 DOI: 10.1007/s00280-023-04509-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023]
Abstract
PURPOSE This study aimed at characterizing indotecan population pharmacokinetics and explore the indotecan-neutropenia relationship in patients with solid tumors. METHODS Population pharmacokinetics were assessed using nonlinear mixed-effects modeling of concentration data from two first-in-human phase 1 trials evaluating different dosing schedules of indotecan. Covariates were assessed in a stepwise manner. Final model qualification included bootstrap simulation, visual and quantitative predictive checks, and goodness-of-fit. A sigmoidal Emax model was developed to describe the relationship between average concentration and maximum percent neutrophil reduction. Simulations at fixed doses were conducted to determine the mean predicted decrease in neutrophil count for each schedule. RESULTS 518 concentrations from 41 patients supported a three-compartment pharmacokinetic model. Body weight and body surface area accounted for inter-individual variability of central/peripheral distribution volume and intercompartmental clearance, respectively. Estimated typical population values were CL 2.75 L/h, Q3 46.0 L/h, and V3 37.9 L. The estimated value of Q2 for a typical patient (BSA = 1.96 m2) was 17.3 L/h, while V1 and V2 for a typical patient (WT = 80 kg) was 33.9 L and 132 L. The final sigmoidal Emax model estimated that half-maximal ANC reduction occurs at an average concentration of 1416 µg/L and 1041 µg/L for the daily and weekly regimens, respectively. Simulations of the weekly regimen demonstrated lower percent reduction in ANC compared to the daily regimen at equivalent cumulative fixed doses. CONCLUSION The final PK model adequately describes indotecan population pharmacokinetics. Fixed dosing may be justified based on covariate analysis and the weekly dosing regimen may have a reduced neutropenic effect.
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Affiliation(s)
- Jan H Beumer
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Room G27E, Hillman Research Pavilion, 5117 Centre Avenue, Pittsburgh, PA, 15213-1863, USA.
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Benjamin C Kennard
- Center for Translational Medicine, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD, 21201, USA
| | - Julianne L Holleran
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Room G27E, Hillman Research Pavilion, 5117 Centre Avenue, Pittsburgh, PA, 15213-1863, USA
| | - Nancy Moore
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Jennifer Zlott
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Brian M Miller
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Room G27E, Hillman Research Pavilion, 5117 Centre Avenue, Pittsburgh, PA, 15213-1863, USA
| | - Shivaani Kummar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Alice Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - James Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Wansu Park
- Center for Translational Medicine, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD, 21201, USA
| | - Jogarao Gobburu
- Center for Translational Medicine, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD, 21201, USA
| | - Allison Dunn
- Center for Translational Medicine, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD, 21201, USA.
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Pinard CJ, Lagree A, Lu FI, Klein J, Oblak ML, Salgado R, Cardenas JCP, Brunetti B, Muscatello LV, Sarli G, Foschini MP, Hardas A, Castillo SP, AbdulJabbar K, Yuan Y, Moore DA, Tran WT. Comparative Evaluation of Tumor-Infiltrating Lymphocytes in Companion Animals: Immuno-Oncology as a Relevant Translational Model for Cancer Therapy. Cancers (Basel) 2022; 14:5008. [PMID: 36291791 PMCID: PMC9599753 DOI: 10.3390/cancers14205008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the important role of preclinical experiments to characterize tumor biology and molecular pathways, there are ongoing challenges to model the tumor microenvironment, specifically the dynamic interactions between tumor cells and immune infiltrates. Comprehensive models of host-tumor immune interactions will enhance the development of emerging treatment strategies, such as immunotherapies. Although in vitro and murine models are important for the early modelling of cancer and treatment-response mechanisms, comparative research studies involving veterinary oncology may bridge the translational pathway to human studies. The natural progression of several malignancies in animals exhibits similar pathogenesis to human cancers, and previous studies have shown a relevant and evaluable immune system. Veterinary oncologists working alongside oncologists and cancer researchers have the potential to advance discovery. Understanding the host-tumor-immune interactions can accelerate drug and biomarker discovery in a clinically relevant setting. This review presents discoveries in comparative immuno-oncology and implications to cancer therapy.
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Affiliation(s)
- Christopher J. Pinard
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
- Odette Cancer Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Radiogenomics Laboratory, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Andrew Lagree
- Odette Cancer Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Radiogenomics Laboratory, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Fang-I Lu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jonathan Klein
- Department of Radiation Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Michelle L. Oblak
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Department of Pathology, GZA-ZNA Hospitals, 2610 Antwerp, Belgium
| | | | - Barbara Brunetti
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy
| | - Luisa Vera Muscatello
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy
| | - Giuseppe Sarli
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy
| | - Maria Pia Foschini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40127 Bologna, Italy
| | - Alexandros Hardas
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | - Simon P. Castillo
- Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Khalid AbdulJabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK
| | - David A. Moore
- Department of Pathology, UCL Cancer Institute, London WC1E 6DD, UK
- University College Hospitals NHS Trust, London NW1 2PG, UK
| | - William T. Tran
- Odette Cancer Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Radiogenomics Laboratory, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON M5T 1P5, Canada
- Department of Radiation Oncology, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Temerty Centre for AI Research and Education in Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
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Chu S, Avery A, Yoshimoto J, Bryan JN. Genome wide exploration of the methylome in aggressive B-cell lymphoma in Golden Retrievers reveals a conserved hypermethylome. Epigenetics 2022; 17:2022-2038. [PMID: 35912844 PMCID: PMC9665123 DOI: 10.1080/15592294.2022.2105033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Few recurrent DNA mutations are seen in aggressive canine B cell lymphomas (cBCL), suggesting other frequent drivers. The methylated island recovery assay (MIRA-seq) or methylated CpG-binding domain sequencing (MBD-seq) was used to define the genome-wide methylation profiles in aggressive cBCL in Golden Retrievers to determine if cBCL can be better defined by epigenetic changes than by DNA mutations. DNA hypermethylation patterns were relatively homogenous within cBCL samples in Golden Retrievers, in different breeds and in geographical regions. Aberrant hypermethylation is thus suspected to be a central and early event in cBCL lymphomagenesis. Distinct subgroups within cBCL in Golden Retrievers were not identified with DNA methylation profiles. In comparison, the methylome profile of human DLBCL (hDLBCL) is relatively heterogeneous. Only moderate similarity between hDLBCL and cBCL was seen and cBCL likely cannot be accurately classified into the subtypes seen in hDLBCL. Genes with hypermethylated regions in the promoter-TSS-first exon of cBCL compared to normal B cells often also had additional hyper- and hypomethylated regions distributed throughout the gene suggesting non-randomized repeat targeting of key genes by epigenetic mechanisms. The prevalence of hypermethylation in transcription factor families in aggressive cBCL may represent a fundamental step in lymphomagenesis.
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Affiliation(s)
- Shirley Chu
- Department of Veterinary Medicine and Surgery, University of Missouri, 900 E. Campus Drive, Columbia, MO, USA
| | - Anne Avery
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Janna Yoshimoto
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jeffrey N Bryan
- Department of Veterinary Medicine and Surgery, University of Missouri, 900 E. Campus Drive, Columbia, MO, USA
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Martín-Encinas E, Selas A, Palacios F, Alonso C. The design and discovery of topoisomerase I inhibitors as anticancer therapies. Expert Opin Drug Discov 2022; 17:581-601. [PMID: 35321631 DOI: 10.1080/17460441.2022.2055545] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Cancer has been identified as one of the leading causes of death worldwide. The biological target of some anticancer agents is topoisomerase I, an enzyme involved in the relaxation of supercoiled DNA. The synthesis of new compounds with antiproliferative effect and behaving as topoisomerase I inhibitors has become an active field of research. Depending on their mechanism of inhibition, they can be classified as catalytic inhibitors or poisons. AREAS COVERED This review article summarizes the state of the art for the development of selective topoisomerase I inhibitors. Collected compounds showed inhibition of the enzyme, highlighting those approved for clinical use, the combination therapies developed, as well as related drawbacks and future focus. EXPERT OPINION Research related to topoisomerase I inhibitors in cancer therapy started with camptothecin (CPT). This compound was first selected as a good anticancer agent and then topoisomerase I was identified as its therapeutic target. Derivatives of CPT irinotecan, topotecan, and belotecan are the only clinically approved inhibitors. Currently, their limitations are being addressed by different stretegies. Future studies should focus not only on developing other active molecules but also on improving the bioavailability and pharmacokinetics of potent synthetic derivatives.
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Affiliation(s)
- Endika Martín-Encinas
- Departamento de Química Orgánica I - Centro de Investigación Lascaray, Facultad de Farmacia, Universidad del País Vasco, Paseo de la Universidad 7, 01006 Vitoria, Spain
| | - Asier Selas
- Departamento de Química Orgánica I - Centro de Investigación Lascaray, Facultad de Farmacia, Universidad del País Vasco, Paseo de la Universidad 7, 01006 Vitoria, Spain
| | - Francisco Palacios
- Departamento de Química Orgánica I - Centro de Investigación Lascaray, Facultad de Farmacia, Universidad del País Vasco, Paseo de la Universidad 7, 01006 Vitoria, Spain
| | - Concepción Alonso
- Departamento de Química Orgánica I - Centro de Investigación Lascaray, Facultad de Farmacia, Universidad del País Vasco, Paseo de la Universidad 7, 01006 Vitoria, Spain
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Cushman M. Design and Synthesis of Indenoisoquinolines Targeting Topoisomerase I and Other Biological Macromolecules for Cancer Chemotherapy. J Med Chem 2021; 64:17572-17600. [PMID: 34879200 DOI: 10.1021/acs.jmedchem.1c01491] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The discovery that certain indenoisoquinolines inhibit the religation reaction of DNA in the topoisomerase I-DNA-indenoisoquinoline ternary complex led to a structure-based drug design research program which resulted in three representatives that entered Phase I clinical trials in cancer patients at the National Cancer Institute. This has stimulated a great deal of interest in the design and execution of new synthetic pathways for indenoisoquinoline production. More recently, modulation of the substitution pattern and chemical nature of substituents on the indenoisoquinoline scaffold has resulted in a widening scope of additional biological targets, including RXR, PARP-1, MYC promoter G-quadruplex, topoisomerase II, estrogen receptor, VEGFR-2, HIF-1α, and tyrosyl DNA phosphodiesterases 1 and 2. Furthermore, convincing evidence has been advanced supporting the potential use of indenoisoquinolines for the treatment of diseases other than cancer. The rapidly expanding indenoisoquinoline knowledge base has provided a firm foundation for further advancements in indenoisoquinoline chemistry, pharmacology, and therapeutics.
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Affiliation(s)
- Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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9
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Coussy F, El-Botty R, Château-Joubert S, Dahmani A, Montaudon E, Leboucher S, Morisset L, Painsec P, Sourd L, Huguet L, Nemati F, Servely JL, Larcher T, Vacher S, Briaux A, Reyes C, La Rosa P, Lucotte G, Popova T, Foidart P, Sounni NE, Noel A, Decaudin D, Fuhrmann L, Salomon A, Reyal F, Mueller C, Ter Brugge P, Jonkers J, Poupon MF, Stern MH, Bièche I, Pommier Y, Marangoni E. BRCAness, SLFN11, and RB1 loss predict response to topoisomerase I inhibitors in triple-negative breast cancers. Sci Transl Med 2021; 12:12/531/eaax2625. [PMID: 32075943 DOI: 10.1126/scitranslmed.aax2625] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/17/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022]
Abstract
Topoisomerase I (TOP1) inhibitors trap TOP1 cleavage complexes resulting in DNA double-strand breaks (DSBs) during replication, which are repaired by homologous recombination (HR). Triple-negative breast cancer (TNBC) could be eligible for TOP1 inhibitors given the considerable proportion of tumors with a defect in HR-mediated repair (BRCAness). The TOP1 inhibitor irinotecan was tested in 40 patient-derived xenografts (PDXs) of TNBC. BRCAness was determined with a single-nucleotide polymorphism (SNP) assay, and expression of Schlafen family member 11 (SLFN11) and retinoblastoma transcriptional corepressor 1 (RB1) was evaluated by real-time polymerase chain reaction (RT-PCR) and immunohistochemistry analyses. In addition, the combination of irinotecan and the ataxia telangiectasia and Rad3-related protein (ATR) inhibitor VE-822 was tested in SLFN11-negative PDXs, and two clinical non-camptothecin TOP1 inhibitors (LMP400 and LMP776) were tested. Thirty-eight percent of the TNBC models responded to irinotecan. BRCAness combined with high SLFN11 expression and RB1 loss identified highly sensitive tumors, consistent with the notion that deficiencies in cell cycle checkpoints and DNA repair result in high sensitivity to TOP1 inhibitors. Treatment by the ATR inhibitor VE-822 increased sensitivity to irinotecan in SLFN11-negative PDXs and abolished irinotecan-induced phosphorylation of checkpoint kinase 1 (CHK1). LMP400 (indotecan) and LMP776 (indimitecan) showed high antitumor activity in BRCA1-mutated or BRCAness-positive PDXs. Last, low SLFN11 expression was associated with poor survival in 250 patients with TNBC treated with anthracycline-based chemotherapy. In conclusion, a substantial proportion of TNBC respond to irinotecan. BRCAness, high SLFN11 expression, and RB1 loss are highly predictive of response to irinotecan and the clinical indenoisoquinoline TOP1 inhibitors.
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Affiliation(s)
- Florence Coussy
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.,Medical Oncology Department, Institut Curie, PSL Research University, 75005 Paris, France.,Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Rania El-Botty
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | | | - Ahmed Dahmani
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Elodie Montaudon
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Sophie Leboucher
- Institut Curie, PSL Research University, UMR3306, 91405 Orsay, France
| | - Ludivine Morisset
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Pierre Painsec
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Laura Sourd
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Léa Huguet
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Fariba Nemati
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Jean-Luc Servely
- BioPôle Alfort, Ecole Nationale Vétérinaire d'Alfort, 94704 Maisons Alfort, France.,INRA, PHASE Department, 37380 Nouzilly, France
| | | | - Sophie Vacher
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Adrien Briaux
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Cécile Reyes
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Philippe La Rosa
- INSERM, U900, 75005 Paris, France.,Institut Curie, PSL Research University, 75005 Paris, France
| | - Georges Lucotte
- INSERM, U900, 75005 Paris, France.,Institut Curie, PSL Research University, 75005 Paris, France
| | - Tatiana Popova
- Institut Curie, PSL Research University, 75005 Paris, France.,INSERM U830, 75005 Paris, France
| | - Pierre Foidart
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Nor Eddine Sounni
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Agnès Noel
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Didier Decaudin
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.,Medical Oncology Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Laetitia Fuhrmann
- Department of Pathology, Institut Curie, PSL Research University, 75005 Paris, France
| | - Anne Salomon
- Department of Pathology, Institut Curie, PSL Research University, 75005 Paris, France
| | - Fabien Reyal
- Surgery Department, Institut Curie, PSL Research University, 75005 Paris, France.,U932, Immunity and Cancer, INSERM, Institut Curie, 75005 Paris, France
| | - Christopher Mueller
- Queen's Cancer Research Institute, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Petra Ter Brugge
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, 1066 CX, Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, 1066 CX, Netherlands
| | - Marie-France Poupon
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, 75005 Paris, France.,INSERM U830, 75005 Paris, France
| | - Ivan Bièche
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.
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10
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Gayle S, Aiello R, Leelatian N, Beckta JM, Bechtold J, Bourassa P, Csengery J, Maguire RJ, Marshall D, Sundaram RK, Van Doorn J, Jones K, Moore H, Lopresti-Morrow L, Paradis T, Tylaska L, Zhang Q, Visca H, Reshetnyak YK, Andreev OA, Engelman DM, Glazer PM, Bindra RS, Paralkar VM. Tumor-selective, antigen-independent delivery of a pH sensitive peptide-topoisomerase inhibitor conjugate suppresses tumor growth without systemic toxicity. NAR Cancer 2021; 3:zcab021. [PMID: 34316708 PMCID: PMC8210154 DOI: 10.1093/narcan/zcab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 05/03/2021] [Accepted: 05/19/2021] [Indexed: 02/04/2023] Open
Abstract
Topoisomerase inhibitors are potent DNA damaging agents which are widely used in oncology, and they demonstrate robust synergistic tumor cell killing in combination with DNA repair inhibitors, including poly(ADP)-ribose polymerase (PARP) inhibitors. However, their use has been severely limited by the inability to achieve a favorable therapeutic index due to severe systemic toxicities. Antibody-drug conjugates address this issue via antigen-dependent targeting and delivery of their payloads, but this approach requires specific antigens and yet still suffers from off-target toxicities. There is a high unmet need for a more universal tumor targeting technology to broaden the application of cytotoxic payloads. Acidification of the extracellular milieu arises from metabolic adaptions associated with the Warburg effect in cancer. Here we report the development of a pH-sensitive peptide-drug conjugate to deliver the topoisomerase inhibitor, exatecan, selectively to tumors in an antigen-independent manner. Using this approach, we demonstrate potent in vivo cytotoxicity, complete suppression of tumor growth across multiple human tumor models, and synergistic interactions with a PARP inhibitor. These data highlight the identification of a peptide-topoisomerase inhibitor conjugate for cancer therapy that provides a high therapeutic index, and is applicable to all types of human solid tumors in an antigen-independent manner.
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Affiliation(s)
| | | | - Nalin Leelatian
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jason M Beckta
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | | | | | | | | | - Ranjini K Sundaram
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jinny Van Doorn
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kelli Jones
- Cybrexa Therapeutics, New Haven, CT 06511, USA
| | | | | | | | | | - Qing Zhang
- Cybrexa Therapeutics, New Haven, CT 06511, USA
| | - Hannah Visca
- Physics Department, University of Rhode Island, Kingston, RI 02881, USA
| | - Yana K Reshetnyak
- Physics Department, University of Rhode Island, Kingston, RI 02881, USA
| | - Oleg A Andreev
- Physics Department, University of Rhode Island, Kingston, RI 02881, USA
| | - Donald M Engelman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ranjit S Bindra
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
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11
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Sloan SL, Renaldo KA, Long M, Chung JH, Courtney LE, Shilo K, Youssef Y, Schlotter S, Brown F, Klamer BG, Zhang X, Yilmaz AS, Ozer HG, Valli VE, Vaddi K, Scherle P, Alinari L, Kisseberth WC, Baiocchi RA. Validation of protein arginine methyltransferase 5 (PRMT5) as a candidate therapeutic target in the spontaneous canine model of non-Hodgkin lymphoma. PLoS One 2021; 16:e0250839. [PMID: 33989303 PMCID: PMC8121334 DOI: 10.1371/journal.pone.0250839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
Non-Hodgkin lymphoma (NHL) is a heterogeneous group of blood cancers arising in lymphoid tissues that commonly effects both humans and dogs. Protein arginine methyltransferase 5 (PRMT5), an enzyme that catalyzes the symmetric di-methylation of arginine residues, is frequently overexpressed and dysregulated in both human solid and hematologic malignancies. In human lymphoma, PRMT5 is a known driver of malignant transformation and oncogenesis, however, the expression and role of PRMT5 in canine lymphoma has not been explored. To explore canine lymphoma as a useful comparison to human lymphoma while validating PRMT5 as a rational therapeutic target in both, we characterized expression patterns of PRMT5 in canine lymphoma tissue microarrays, primary lymphoid biopsies, and canine lymphoma-derived cell lines. The inhibition of PRMT5 led to growth suppression and induction of apoptosis, while selectively decreasing global marks of symmetric dimethylarginine (SDMA) and histone H4 arginine 3 symmetric dimethylation. We performed ATAC-sequencing and gene expression microarrays with pathway enrichment analysis to characterize genome-wide changes in chromatin accessibility and whole-transcriptome changes in canine lymphoma cells lines upon PRMT5 inhibition. This work validates PRMT5 as a promising therapeutic target for canine lymphoma and supports the continued use of the spontaneously occurring canine lymphoma model for the preclinical development of PRMT5 inhibitors for the treatment of human NHL.
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Affiliation(s)
- Shelby L. Sloan
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Kyle A. Renaldo
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Mackenzie Long
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Ji-Hyun Chung
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Lindsay E. Courtney
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Konstantin Shilo
- Department of Pathology, The Ohio State University, Columbus, Ohio, United States of America
| | - Youssef Youssef
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Sarah Schlotter
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Fiona Brown
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Brett G. Klamer
- Department of Biomedical Informatics, Center for Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Xiaoli Zhang
- Department of Biomedical Informatics, Center for Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Ayse S. Yilmaz
- Department of Biomedical Informatics, Center for Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Hatice G. Ozer
- Department of Biomedical Informatics, Center for Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Victor E. Valli
- VDx Veterinary Diagnostics, Davis, California, United States of America
| | - Kris Vaddi
- Prelude Therapeutics, Wilmington, Delaware, United States of America
| | - Peggy Scherle
- Prelude Therapeutics, Wilmington, Delaware, United States of America
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - William C. Kisseberth
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (WCK); (RAB)
| | - Robert A. Baiocchi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (WCK); (RAB)
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12
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Selas A, Martin-Encinas E, Fuertes M, Masdeu C, Rubiales G, Palacios F, Alonso C. A patent review of topoisomerase I inhibitors (2016-present). Expert Opin Ther Pat 2021; 31:473-508. [PMID: 33475439 DOI: 10.1080/13543776.2021.1879051] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Topoisomerases are important targets for therapeutic improvement in the treatment of some diseases, including cancer. Inhibitors and poisons of topoisomerase I can limit the activity of this enzyme in its enzymatic cycle. This fact implies an anticancer effect of these drugs, since most cancer cells are characterized by both a higher activity of topoisomerase I and a higher replication rate compared to non-cancerous cells. Clinically approved inhibitors include camptothecin (CPT) and its derivatives. However, their limitations have encouraged different research groups to prepare new compounds, proof of which are the numerous research works and patents, some of them in the last five years. AREAS COVERED This review covers patent literature on topoisomerase I inhibitors and their application published between 2016-present. EXPERT OPINION The highest contribution toward patent development has been obtained from academics or small biotechnology companies. The most important fields of innovation include the preparation of prodrugs or inhibitors combined with other agents, as biocompatible polymers or antibodies. A promising development of topoisomerase I inhibitors is expected in the next years, directed to the treatment of diverse diseases, specifically toward different types of cancer and infectious diseases, among others.
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Affiliation(s)
- Asier Selas
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Endika Martin-Encinas
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Maria Fuertes
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Carme Masdeu
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Francisco Palacios
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Concepción Alonso
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
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13
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Abstract
Comparative oncology clinical trials play an important and growing role in cancer research and drug development efforts. These trials, typically conducted in companion (pet) dogs, allow assessment of novel anticancer agents and combination therapies in a veterinary clinical setting that supports serial biologic sample collections and exploration of dose, schedule and corresponding pharmacokinetic/pharmacodynamic relationships. Further, an intact immune system and natural co-evolution of tumour and microenvironment support exploration of novel immunotherapeutic strategies. Substantial improvements in our collective understanding of the molecular landscape of canine cancers have occurred in the past 10 years, facilitating translational research and supporting the inclusion of comparative studies in drug development. The value of the approach is demonstrated in various clinical trial settings, including single-agent or combination response rates, inhibition of metastatic progression and randomized comparison of multiple agents in a head-to-head fashion. Such comparative oncology studies have been purposefully included in the developmental plan for several US FDA-approved and up-and-coming anticancer drugs. Challenges for this field include keeping pace with technology and data dissemination/harmonization, improving annotation of the canine genome and immune system, and generation of canine-specific validated reagents to support integration of correlative biology within clinical trial efforts.
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Affiliation(s)
- Amy K LeBlanc
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Christina N Mazcko
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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14
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Marzi L, Sun Y, Huang SYN, James A, Difilippantonio S, Pommier Y. The Indenoisoquinoline LMP517: A Novel Antitumor Agent Targeting both TOP1 and TOP2. Mol Cancer Ther 2020; 19:1589-1597. [PMID: 32430490 PMCID: PMC7415565 DOI: 10.1158/1535-7163.mct-19-1064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/28/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022]
Abstract
The camptothecin derivatives topoisomerase I (TOP1) inhibitors, irinotecan and topotecan, are FDA approved for the treatment of colorectal, ovarian, lung and breast cancers. Because of the chemical instability of camptothecins, short plasma half-life, drug efflux by the multidrug-resistance ABC transporters, and the severe diarrhea produced by irinotecan, indenoisoquinoline TOP1 inhibitors (LMP400, LMP776, and LMP744), which overcome these limitations, have been developed and are in clinical development. Further modifications of the indenoisoquinolines led to the fluoroindenoisoquinolines, one of which, LMP517, is the focus of this study. LMP517 showed better antitumor activity than its parent compound LMP744 against H82 (small cell lung cancer) xenografts. Genetic analyses in DT40 cells showed a dual TOP1 and TOP2 signature with selectivity of LMP517 for DNA repair-deficient tyrosyl DNA phosphodiesterase 2 (TDP2)- and Ku70-knockout cells. RADAR assays revealed that LMP517, and to a lesser extent LMP744, induce TOP2 cleavage complexes (TOP2cc) in addition to TOP1ccs. Histone γH2AX detection showed that, unlike classical TOP1 inhibitors, LMP517 targets cells independently of their position in the cell cycle. Our study establishes LMP517 as a dual TOP1 and TOP2 inhibitor with therapeutic potential.
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Affiliation(s)
- Laetitia Marzi
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Shar-Yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Amy James
- Laboratory of Animal Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Simone Difilippantonio
- Laboratory of Animal Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
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15
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Venkataraman GR, Pineda AL, Bear Don’t Walk IV OJ, Zehnder AM, Ayyar S, Page RL, Bustamante CD, Rivas MA. FasTag: Automatic text classification of unstructured medical narratives. PLoS One 2020; 15:e0234647. [PMID: 32569327 PMCID: PMC7307763 DOI: 10.1371/journal.pone.0234647] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/30/2020] [Indexed: 02/07/2023] Open
Abstract
Unstructured clinical narratives are continuously being recorded as part of delivery of care in electronic health records, and dedicated tagging staff spend considerable effort manually assigning clinical codes for billing purposes. Despite these efforts, however, label availability and accuracy are both suboptimal. In this retrospective study, we aimed to automate the assignment of top-level International Classification of Diseases version 9 (ICD-9) codes to clinical records from human and veterinary data stores using minimal manual labor and feature curation. Automating top-level annotations could in turn enable rapid cohort identification, especially in a veterinary setting. To this end, we trained long short-term memory (LSTM) recurrent neural networks (RNNs) on 52,722 human and 89,591 veterinary records. We investigated the accuracy of both separate-domain and combined-domain models and probed model portability. We established relevant baseline classification performances by training Decision Trees (DT) and Random Forests (RF). We also investigated whether transforming the data using MetaMap Lite, a clinical natural language processing tool, affected classification performance. We showed that the LSTM-RNNs accurately classify veterinary and human text narratives into top-level categories with an average weighted macro F1 score of 0.74 and 0.68 respectively. In the "neoplasia" category, the model trained on veterinary data had a high validation accuracy in veterinary data and moderate accuracy in human data, with F1 scores of 0.91 and 0.70 respectively. Our LSTM method scored slightly higher than that of the DT and RF models. The use of LSTM-RNN models represents a scalable structure that could prove useful in cohort identification for comparative oncology studies. Digitization of human and veterinary health information will continue to be a reality, particularly in the form of unstructured narratives. Our approach is a step forward for these two domains to learn from and inform one another.
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Affiliation(s)
- Guhan Ram Venkataraman
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, United States of America
| | - Arturo Lopez Pineda
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, United States of America
| | - Oliver J. Bear Don’t Walk IV
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
| | | | - Sandeep Ayyar
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, United States of America
| | - Rodney L. Page
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States of America
| | - Carlos D. Bustamante
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, United States of America
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Manuel A. Rivas
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, United States of America
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16
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Lucroy MD, Suckow MA. Predictive modeling for cancer drug discovery using canine models. Expert Opin Drug Discov 2020; 15:731-738. [PMID: 32176534 DOI: 10.1080/17460441.2020.1739644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Rodent models of cancer lack many features associated with the disease in humans. Because dogs closely share an environment with humans, as well as comparable pathophysiology of cancer, they represent a powerful model with which to study novel approaches to cancer treatment. AREAS COVERED The authors summarize the weaknesses of rodent models of cancer and the ongoing need for better animal models with which to study potential therapeutic approaches. The homology of cancer in dogs and humans is described, along with examples specific to several common cancer types. EXPERT OPINION Laboratory mice and rats will continue to play a central role in cancer research; however, because of a variety of limitations, pet dogs with spontaneous cancer offer unique opportunities for research and should be included in the preclinical development of therapeutic compounds. Environmental homology between dogs and humans, along with biological and molecular similarities present circumstances that strengthen the translational rigor of studies conducted using canine patients. Progress will depend on a sufficient number of dogs to be diagnosed with cancer and available for use in studies; and essential to this will be the availability of enhanced resources for diagnosis of cancer in canine patients and reliable coordination between research scientists, veterinarians, and physicians.
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Affiliation(s)
- Michael D Lucroy
- Vice President, Oncology, Torigen Pharmaceuticals, Inc , Farmington, CT, USA
| | - Mark A Suckow
- Department of Biomedical Engineering, University of Kentucky , Lexington, KY, USA
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17
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Parissenti AM, Pritzker LB, Guo B, Narendrula R, Wang SX, Lin LL, Pei J, Skowronski K, Bienzle D, Woods JP, Pritzker KPH, Coomber BL. RNA disruption indicates CHOP therapy efficacy in canine lymphoma. BMC Vet Res 2019; 15:453. [PMID: 31842875 PMCID: PMC6916446 DOI: 10.1186/s12917-019-2189-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 11/25/2019] [Indexed: 01/21/2023] Open
Abstract
Background Assessment of the efficacy of a multi-agent chemotherapy protocol in which cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP) are administered in canine lymphoma is generally performed by physical measurement of lymph node diameter. However, no consistent correlation has been made with prognostic indicators and the length or absence of clinical remission based on lymph node size. RNA disruption measured mid-therapy has been correlated with increased disease-free survival in recent studies of human cancer and was assessed in this study of canine lymphoma patients. Fine needle aspirate samples were taken before treatment and at weeks 3, 6, and 11 of CHOP therapy. RNA was isolated from these samples and assessed using an Agilent Bioanalyzer. RNA disruption assay (RDA) analysis was performed on the data from the resulting electropherograms. Results An increased RNA disruption index (RDI) score was significantly associated with improved progression-free survival. Conclusions Predicting the risk of early relapse during chemotherapy could benefit veterinary patients by reducing ineffective treatment and could allow veterinary oncologists to switch earlier to a more effective drug regimen.
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Affiliation(s)
- Amadeo M Parissenti
- Departments of Biology, Chemistry and Biochemistry, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada. .,Rna Diagnostics, c/o Health Sciences North Research Institute, 2nd Floor North, 56 Walford Road, Sudbury, ON, P3E 2H3, Canada.
| | - Laura B Pritzker
- Rna Diagnostics, 21 St. Clair Avenue East, Suite 701, Toronto, ON, M4T 1L9, Canada
| | - Baoqing Guo
- Rna Diagnostics, c/o Health Sciences North Research Institute, 2nd Floor North, 56 Walford Road, Sudbury, ON, P3E 2H3, Canada
| | - Rashmi Narendrula
- Rna Diagnostics, c/o Health Sciences North Research Institute, 2nd Floor North, 56 Walford Road, Sudbury, ON, P3E 2H3, Canada
| | - Shirly Xiaohui Wang
- Rna Diagnostics, 21 St. Clair Avenue East, Suite 701, Toronto, ON, M4T 1L9, Canada
| | - Lin Laura Lin
- Rna Diagnostics, 21 St. Clair Avenue East, Suite 701, Toronto, ON, M4T 1L9, Canada
| | - Jingchun Pei
- Rna Diagnostics, 21 St. Clair Avenue East, Suite 701, Toronto, ON, M4T 1L9, Canada
| | - Karolina Skowronski
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Dorothee Bienzle
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - J Paul Woods
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Kenneth P H Pritzker
- Rna Diagnostics, 21 St. Clair Avenue East, Suite 701, Toronto, ON, M4T 1L9, Canada
| | - Brenda L Coomber
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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18
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Thamm DH. Canine Cancer: Strategies in Experimental Therapeutics. Front Oncol 2019; 9:1257. [PMID: 31803625 PMCID: PMC6873901 DOI: 10.3389/fonc.2019.01257] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022] Open
Abstract
Cancer is the most common cause of death in adult dogs. Many features of spontaneously developing tumors in pet dogs contribute to their potential utility as a human disease model. These include similar environmental exposures, similar clonal evolution as it applies to important factors such as immune avoidance, a favorable body size for imaging and serial biopsy, and a relatively contracted time course of disease progression, which makes evaluation of temporal endpoints such as progression free or overall survival feasible in a comparatively short time frame. These criteria have been leveraged to evaluate novel local therapies, demonstrate proof of tumor target inhibition or tumor localization, evaluate potential antimetastatic approaches, and assess the efficacy, safety and immune effects of a variety of immune-based therapeutics. Some of these canine proof of concept studies have been instrumental in informing subsequent human clinical trials. This review will cover key aspects of clinical trials in dogs with spontaneous neoplasia, with examples of how these studies have contributed to human cancer therapeutic development.
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Affiliation(s)
- Douglas H Thamm
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States.,University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, United States
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19
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Reguera RM, Álvarez-Velilla R, Domínguez-Asenjo B, Gutiérrez-Corbo C, Balaña-Fouce R, Cushman M, Pérez-Pertejo Y. Antiparasitic effect of synthetic aromathecins on Leishmania infantum. BMC Vet Res 2019; 15:405. [PMID: 31706354 PMCID: PMC6842543 DOI: 10.1186/s12917-019-2153-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022] Open
Abstract
Background Canine leishmaniasis is a zoonotic disease caused by Leishmania infantum, being the dogs one of the major reservoirs of human visceral leishmaniasis. DNA topology is a consolidated target for drug discovery. In this regard, topoisomerase IB – one of the enzymes controlling DNA topology – has been poisoned by hundreds of compounds that increase DNA fragility and cell death. Aromathecins are novel molecules with a multiheterocyclic ring scaffold that have higher stability than camptothecins. Results Aromathecins showed strong activity against both forms of L. infantum parasites, free-living promastigotes and intra-macrophagic amastigotes harbored in ex vivo splenic explant cultures obtained from infected BALB/c mice. However, they prevented the relaxation activity of leishmanial topoisomerase IB weakly, which suggests that the inhibition of topoisomerase IB partially explains the antileishmanial effect of these compounds. The effect of aromathecins was also studied against a strain resistant to camptothecin, and results suggested that the trafficking of these compounds is not through the ABCG6 transporter. Conclusions Aromathecins are promising novel compounds against canine leishmaniasis that can circumvent potential resistances based on drug efflux pumps.
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Affiliation(s)
- Rosa M Reguera
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n; 24071 León (SPAIN), León, Spain
| | - Raquel Álvarez-Velilla
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n; 24071 León (SPAIN), León, Spain
| | - Bárbara Domínguez-Asenjo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n; 24071 León (SPAIN), León, Spain
| | - Camino Gutiérrez-Corbo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n; 24071 León (SPAIN), León, Spain
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n; 24071 León (SPAIN), León, Spain
| | - Mark Cushman
- Department of Medicinal Chemistry, and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, Lafayette, Indiana, USA
| | - Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n; 24071 León (SPAIN), León, Spain.
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20
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Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. iScience 2019; 21:664-680. [PMID: 31733513 PMCID: PMC6889472 DOI: 10.1016/j.isci.2019.10.059] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 12/15/2022] Open
Abstract
Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and prefoldins are more evident than that at the mRNA level. The data are available in CellMiner (discover.nci.nih.gov/cellminercdb and discover.nci.nih.gov/cellminer), allowing casual users to test hypotheses and perform integrative, cross-database analyses of multi-omic drug response correlations for over 20,000 drugs. We demonstrate the value of proteome data in predicting drug response for over 240 clinically relevant chemotherapeutic and targeted therapies. In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses. High-quality NCI-60 proteotypes created using pressure cycling technology and SWATH-MS Proteotypes improve drug response prediction in multi-omics regression analysis ∼3000 measured proteins allow investigation into protein complex stoichiometry CellMinerCDB (discover.nci.nih.gov/cellminercdb) portal allows dataset exploration
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Affiliation(s)
- Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
| | - Augustin Luna
- cBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ching Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Zhicheng Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Wei Liu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Yaoting Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Huanhuan Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Michael P Menden
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany; Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Chao Xu
- Faculty of Software, Fujian Normal University, Fuzhou, China
| | - Laurence Calzone
- Institut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France
| | - Loredana Martignetti
- Institut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France
| | - Chiara Auwerx
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Marija Buljan
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Murat Iskar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ran Bi
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Jiangnan Zhang
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Huanhuan Zhang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Chenhuan Yu
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Qing Zhong
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; Cancer Data Science Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
| | | | - Uwe Schmitt
- Scientific IT Services, ETH Zurich, Zurich, Switzerland
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr., Atlanta, GA 30332, USA
| | - Qiushi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Peter J Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Mathew J Garnett
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kexin Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Julio Saez-Rodriguez
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chris Sander
- cBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
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21
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Marzi L, Szabova L, Gordon M, Weaver Ohler Z, Sharan SK, Beshiri ML, Etemadi M, Murai J, Kelly K, Pommier Y. The Indenoisoquinoline TOP1 Inhibitors Selectively Target Homologous Recombination-Deficient and Schlafen 11-Positive Cancer Cells and Synergize with Olaparib. Clin Cancer Res 2019; 25:6206-6216. [PMID: 31409613 PMCID: PMC6801079 DOI: 10.1158/1078-0432.ccr-19-0419] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Irinotecan and topotecan are used to treat a variety of different cancers. However, they have limitations, including chemical instability and severe side effects. To overcome these limitations, we developed the clinical indenoisoquinolines: LMP400 (indotecan), LMP776 (indimitecan), and LMP744. The purpose of the study is to build the molecular rationale for phase II clinical trials. EXPERIMENTAL DESIGN CellMinerCDB (http://discover.nci.nih.gov/cellminercdb) was used to mine the cancer cell lines genomic databases. The causality of Schlafen11 (SLFN11) was validated in isogenic cell lines. Because topoisomerase I (TOP1)-mediated replication DNA damage is repaired by homologous recombination (HR), we tested the "synthetic lethality" of HR-deficient (HRD) cells. Survival and cell-cycle alterations were performed after drug treatments in isogenic DT40, DLD1, and OVCAR cell lines with BRCA1, BRCA2, or PALB2 deficiencies and in organoids cultured from prostate cancer patient-derived xenografts with BRCA2 loss. We also used an ovarian orthotopic allograft model with BRCA1 loss to validate the efficacy of LMP400 and olaparib combination. RESULTS CellMinerCDB reveals that SLFN11, which kills cells undergoing replicative stress, is a dominant drug determinant to the clinical indenoisoquinolines. In addition, BRCA1-, BRCA2-, and PALB2-deficient cells were hypersensitive to the indenoisoquinolines. All 3 clinical indenoisoquinolines were also synergistic with olaparib, especially in the HRD cells. The synergy between LMP400 and olaparib was confirmed in the orthotopic allograft model harboring BRCA1 loss. CONCLUSIONS Our results provide a rationale for molecularly designed clinical trials with the indenoisoquinolines as single agents and in combination with PARP inhibitors in HRD cancers expressing SLFN11.
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Affiliation(s)
- Laetitia Marzi
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Ludmila Szabova
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, Maryland
| | - Melanie Gordon
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, Maryland
| | - Zoe Weaver Ohler
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, Maryland
| | - Shyam K Sharan
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, Maryland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland
| | - Michael L Beshiri
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Moudjib Etemadi
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Junko Murai
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
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22
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Abstract
DNA topoisomerases are enzymes that catalyze changes in the torsional and flexural strain of DNA molecules. Earlier studies implicated these enzymes in a variety of processes in both prokaryotes and eukaryotes, including DNA replication, transcription, recombination, and chromosome segregation. Studies performed over the past 3 years have provided new insight into the roles of various topoisomerases in maintaining eukaryotic chromosome structure and facilitating the decatenation of daughter chromosomes at cell division. In addition, recent studies have demonstrated that the incorporation of ribonucleotides into DNA results in trapping of topoisomerase I (TOP1)–DNA covalent complexes during aborted ribonucleotide removal. Importantly, such trapped TOP1–DNA covalent complexes, formed either during ribonucleotide removal or as a consequence of drug action, activate several repair processes, including processes involving the recently described nuclear proteases SPARTAN and GCNA-1. A variety of new TOP1 inhibitors and formulations, including antibody–drug conjugates and PEGylated complexes, exert their anticancer effects by also trapping these TOP1–DNA covalent complexes. Here we review recent developments and identify further questions raised by these new findings.
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Affiliation(s)
- Mary-Ann Bjornsti
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, 35294-0019, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacolgy & Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
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23
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Murai J, Thomas A, Miettinen M, Pommier Y. Schlafen 11 (SLFN11), a restriction factor for replicative stress induced by DNA-targeting anti-cancer therapies. Pharmacol Ther 2019; 201:94-102. [PMID: 31128155 PMCID: PMC6708787 DOI: 10.1016/j.pharmthera.2019.05.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022]
Abstract
Schlafen 11 (SLFN11) sensitizes cells to a broad range of anti-cancer drugs including platinum derivatives (cisplatin and carboplatin), inhibitors of topoisomerases (irinotecan, topotecan, doxorubicin, daunorubicin, mitoxantrone and etoposide), DNA synthesis inhibitors (gemcitabine, cytarabine, hydroxyurea and nucleoside analogues), and poly(ADPribose) polymerase (PARP) inhibitors (olaparib, rucaparib, niraparib and talazoparib). In spite of their different primary mechanisms of action, all these drugs damage DNA during S-phase, activate the intra-S-phase checkpoint and induce replication fork slowing and stalling with single-stranded DNA segments coated with replication protein A. Such situation with abnormal replication forks is known as replication stress. SLFN11 irreversibly blocks replication in cells under replication stress, explaining why SLFN11-positive cells are markedly more efficiently killed by DNA-targeting drugs than SLFN11-negative cells. SLFN11 is inactivated in ~50% of cancer cell lines and in a large fraction of tumors, and is linked with the native immune, interferon and T-cells responses, implying the translational relevance of measuring SLFN11 expression as a predictive biomarker of response and resistance in patients. SLFN11 is also a plausible epigenetic target for reactivation by inhibitors of histone deacetylases (HDAC), DNA methyltransferases (DNMT) and EZH2 histone methyltransferase and for combination of these epigenetic inhibitors with DNA-targeting drugs in cells lacking SLFN11 expression. In addition, resistance due to lack of SLFN11 expression in tumors is a potential indication for cell-cycle checkpoint inhibitors in combination with DNA-targeting therapies.
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Affiliation(s)
- Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Anish Thomas
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Markku Miettinen
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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24
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Thomas A, Pommier Y. Targeting Topoisomerase I in the Era of Precision Medicine. Clin Cancer Res 2019; 25:6581-6589. [PMID: 31227499 DOI: 10.1158/1078-0432.ccr-19-1089] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/06/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022]
Abstract
Irinotecan and topotecan have been widely used as anticancer drugs for the past 20 years. Because of their selectivity as topoisomerase I (TOP1) inhibitors that trap TOP1 cleavage complexes, camptothecins are also widely used to elucidate the DNA repair pathways associated with DNA-protein cross-links and replication stress. This review summarizes the basic molecular mechanisms of action of TOP1 inhibitors, their current use, and limitations as anticancer agents. We introduce new therapeutic strategies based on novel TOP1 inhibitor chemical scaffolds including the indenoisoquinolines LMP400 (indotecan), LMP776 (indimitecan), and LMP744, and on tumor-targeted delivery TOP1 inhibitors using liposome, PEGylation, and antibody-drug conjugates. We also address how tumor-specific determinants such as homologous recombination defects (HRD and BRCAness) and Schlafen 11 (SLFN11) expression can be used to guide clinical application of TOP1 inhibitors in combination with DNA damage response inhibitors including PARP, ATR, CHEK1, and ATM inhibitors.
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Affiliation(s)
- Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
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25
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Otake K, Yamada K, Miura K, Sasazawa Y, Miyazaki S, Niwa Y, Ogura A, Takao KI, Simizu S. Identification of topoisomerases as molecular targets of cytosporolide C and its analog. Bioorg Med Chem 2019; 27:3334-3338. [PMID: 31204230 DOI: 10.1016/j.bmc.2019.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 12/27/2022]
Abstract
Cytosporolide (Cytos) A-C, isolated from the fungus Cytospora sp., have anti-microbial activity, but their molecular targets in mammalian cells are unknown. We have previously reported the total synthesis of Cytos A by biomimetic hetero-Diels-Alder reaction. In this study, to examine the novel bioactivity of Cytos, we synthesized Cytos C and measured cell growth-inhibiting activities of 7 compounds, including Cytos A and C, in several human cancer cell lines. Among these compounds, Cytos C and tetradeoxycytosporolide A (TD-Cytos A), a model compound for the synthesis of Cytos A, had anti-proliferative effects on cancer cells, and TD-Cytos A exhibited stronger activity than Cytos C. In vitro topoisomerase-mediated DNA relaxing experiments showed that TD-Cytos A inhibited the activities of topoisomerase I and II, whereas Cytos C targeted only topoisomerase I. These data suggest that the anti-proliferative activities of Cytos correlate with the inhibition of topoisomerases and implicated TD-Cytos A as a novel anti-cancer drug that suppresses the activities of topoisomerase I and II.
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Affiliation(s)
- Keisuke Otake
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kana Yamada
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kazuki Miura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Yukiko Sasazawa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - So Miyazaki
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Yuki Niwa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Akihiro Ogura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Ken-Ichi Takao
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
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Maeda S, Murakami K, Inoue A, Yonezawa T, Matsuki N. CCR4 Blockade Depletes Regulatory T Cells and Prolongs Survival in a Canine Model of Bladder Cancer. Cancer Immunol Res 2019; 7:1175-1187. [DOI: 10.1158/2326-6066.cir-18-0751] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/16/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022]
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27
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Tang WL, Zhang Y, Hu DX, Yang H, Yu Q, Chen JW, Agama K, Pommier Y, An LK. Synthesis and biological evaluation of 5-aminoethyl benzophenanthridone derivatives as DNA topoisomerase IB inhibitors. Eur J Med Chem 2019; 178:81-92. [PMID: 31176097 DOI: 10.1016/j.ejmech.2019.05.074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 02/06/2023]
Abstract
DNA topoisomerase IB (TOP1) regulates DNA topological structure in many cellular metabolic processes and is a validated target for development of antitumor agents. Our previous study revealed that the benzophenanthridone scaffold is a novel chemotype for the discovery of TOP1 inhibitors. In this work, a series of novel 5-aminoethyl substituted benzophenanthridone derivatives have been synthesized and evaluated for TOP1 inhibition and cytotoxicity. Compound 12 exhibits the most potent TOP1 inhibition (+++) and cytotoxicity in human cancer cell lines with GI50 values at nanomolar concentration range. 12 induces the cellular TOP1cc formation and DNA damage, resulting in HCT116 cell apoptosis. The pharmacokinetics, acute toxicity and antitumor efficiency in vivo of 12 were also studied.
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Affiliation(s)
- Wen-Lin Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, 510006, China
| | - Yu Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - De-Xuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hui Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qian Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jian-Wen Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Keli Agama
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, 510006, China.
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Mochel JP, Ekker SC, Johannes CM, Jergens AE, Allenspach K, Bourgois-Mochel A, Knouse M, Benzekry S, Wierson W, LeBlanc AK, Kenderian SS. CAR T Cell Immunotherapy in Human and Veterinary Oncology: Changing the Odds Against Hematological Malignancies. AAPS JOURNAL 2019; 21:50. [PMID: 30963322 DOI: 10.1208/s12248-019-0322-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/17/2019] [Indexed: 01/14/2023]
Abstract
The advent of the genome editing era brings forth the promise of adoptive cell transfer using engineered chimeric antigen receptor (CAR) T cells for targeted cancer therapy. CAR T cell immunotherapy is probably one of the most encouraging developments for the treatment of hematological malignancies. In 2017, two CAR T cell therapies were approved by the US Food and Drug Administration: one for the treatment of pediatric acute lymphoblastic leukemia (ALL) and the other for adult patients with advanced lymphomas. However, despite significant progress in the area, CAR T cell therapy is still in its early days and faces significant challenges, including the complexity and costs associated with the technology. B cell lymphoma is the most common hematopoietic cancer in dogs, with an incidence approaching 0.1% and a total of 20-100 cases per 100,000 individuals. It is a widely accepted naturally occurring model for human non-Hodgkin's lymphoma. Current treatment is with combination chemotherapy protocols, which prolong life for less than a year in canines and are associated with severe dose-limiting side effects, such as gastrointestinal and bone marrow toxicity. To date, one canine study generated CAR T cells by transfection of mRNA for CAR domain expression. While this was shown to provide a transient anti-tumor activity, results were modest, indicating that stable, genomic integration of CAR modules is required in order to achieve lasting therapeutic benefit. This commentary summarizes the current state of knowledge on CAR T cell immunotherapy in human medicine and its potential applications in animal health, while discussing the potential of the canine model as a translational system for immuno-oncology research.
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Affiliation(s)
- Jonathan P Mochel
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA. .,Iowa State University College of Vet. Medicine, 2448 Lloyd, 1809 S Riverside Dr., Ames, Iowa, 50011-1250, USA.
| | - Stephen C Ekker
- Mayo Clinic Cancer Center Department of Biochemistry and Molecular Biology, Rochester, Minnesota, 55905, USA
| | - Chad M Johannes
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Albert E Jergens
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Karin Allenspach
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Agnes Bourgois-Mochel
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Michael Knouse
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Sebastien Benzekry
- Team MONC, Institut National de Recherche en Informatique et en Automatique, Bordeaux, France
| | - Wesley Wierson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Amy K LeBlanc
- Comparative Oncology Program, Center for Cancer Research National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Saad S Kenderian
- Department of Medicine, Mayo Clinic Division of Hematology, Rochester, Minnesota, 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, Minnesota, 55905, USA
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Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y. CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines. iScience 2018; 10:247-264. [PMID: 30553813 PMCID: PMC6302245 DOI: 10.1016/j.isci.2018.11.029] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/11/2018] [Accepted: 11/15/2018] [Indexed: 12/13/2022] Open
Abstract
CellMinerCDB provides a web-based resource (https://discover.nci.nih.gov/cellminercdb/) for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer cell line datasets (the NCI-60, NCI-SCLC, Sanger/MGH GDSC, and Broad CCLE/CTRP). CellMinerCDB enables data queries for genomics and gene regulatory network analyses, and exploration of pharmacogenomic determinants and drug signatures. It leverages overlaps of cell lines and drugs across databases to examine reproducibility and expand pathway analyses. We illustrate the value of CellMinerCDB for elucidating gene expression determinants, such as DNA methylation and copy number variations, and highlight complexities in assessing mutational burden. We demonstrate the value of CellMinerCDB in selecting drugs with reproducible activity, expand on the dominant role of SLFN11 for drug response, and present novel response determinants and genomic signatures for topoisomerase inhibitors and schweinfurthins. We also introduce LIX1L as a gene associated with mesenchymal signature and regulation of cellular migration and invasiveness.
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Affiliation(s)
- Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Augustin Luna
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA.
| | - Mihoko Yamade
- First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Lisa Loman
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Margot Sunshine
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; General Dynamics Information Technology Inc., 3211 Jermantown Road, Fairfax, VA 22030, USA
| | - Francesco Iorio
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Fabricio G Sousa
- Centro De Estudos Em Células Tronco, Terapia Celular E Genética Toxicológica, Programa De Pós-Graduação Em Farmácia, Universidade Federal De Mato Grosso Do Sul, Campo Grande, MS 79070-900, Brazil
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; General Dynamics Information Technology Inc., 3211 Jermantown Road, Fairfax, VA 22030, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Kurt W Kohn
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Mathew Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Pommier Y, Cushman M, Doroshow JH. Novel clinical indenoisoquinoline topoisomerase I inhibitors: a twist around the camptothecins. Oncotarget 2018; 9:37286-37288. [PMID: 30647868 PMCID: PMC6324668 DOI: 10.18632/oncotarget.26466] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 01/16/2023] Open
Affiliation(s)
- Yves Pommier
- Yves Pommier: Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Mark Cushman
- Yves Pommier: Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - James H Doroshow
- Yves Pommier: Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland, USA
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Zhang XR, Wang HW, Tang WL, Zhang Y, Yang H, Hu DX, Ravji A, Marchand C, Kiselev E, Ofori-Atta K, Agama K, Pommier Y, An LK. Discovery, Synthesis, and Evaluation of Oxynitidine Derivatives as Dual Inhibitors of DNA Topoisomerase IB (TOP1) and Tyrosyl-DNA Phosphodiesterase 1 (TDP1), and Potential Antitumor Agents. J Med Chem 2018; 61:9908-9930. [PMID: 30336023 DOI: 10.1021/acs.jmedchem.8b00639] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a recently discovered enzyme repairing DNA lesions resulting from stalled topoisomerase IB (TOP1)-DNA covalent complex. Inhibiting TDP1 in conjunction with TOP1 inhibitors can boost the action of the latter. Herein, we report the discovery of the natural product oxynitidine scaffold as a novel chemotype for the development of TOP1 and TDP1 inhibitors. Three kinds of analogues, benzophenanthridinone, dihydrobenzophenanthridine, and benzophenanthridine derivatives, were synthesized and evaluated for both TOP1 and TDP1 inhibition and cytotoxicity. Analogue 19a showed high TOP1 inhibition (+++) and induced the formation of cellular TOP1cc and DNA damage, resulting in cancer cells apoptosis at nanomolar concentration range. In vivo studies indicated that 19a exhibits antitumor efficiency in HCT116 xenograft model. 41a exhibited additional TDP1 inhibition with IC50 value of 7 μM and synergistic effect with camptothecin in MCF-7 cells. This work will facilitate future efforts for the discovery of natural product-based TOP1 and TDP1 inhibitors.
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Affiliation(s)
- Xiao-Ru Zhang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Hao-Wen Wang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Wen-Lin Tang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Yu Zhang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Hui Yang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - De-Xuan Hu
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Azhar Ravji
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Kwabena Ofori-Atta
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Lin-Kun An
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
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