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Ferrari AJ, Rawat P, Rendulich HS, Annapragada AV, Kinose Y, Zhang X, Devins K, Budina A, Scharpf RB, Mitchell MA, Tanyi JL, Morgan MA, Schwartz LE, Soong TR, Velculescu VE, Drapkin R. H2Bub1 loss is an early contributor to clear cell ovarian cancer progression. JCI Insight 2023; 8:e164995. [PMID: 37345659 PMCID: PMC10371241 DOI: 10.1172/jci.insight.164995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/04/2023] [Indexed: 06/23/2023] Open
Abstract
Epigenetic aberrations, including posttranslational modifications of core histones, are major contributors to cancer. Here, we define the status of histone H2B monoubiquitylation (H2Bub1) in clear cell ovarian carcinoma (CCOC), low-grade serous carcinoma, and endometrioid carcinomas. We report that clear cell carcinomas exhibited profound loss, with nearly all cases showing low or negative H2Bub1 expression. Moreover, we found that H2Bub1 loss occurred in endometriosis and atypical endometriosis, which are established precursors to CCOCs. To examine whether dysregulation of a specific E3 ligase contributes to the loss of H2Bub1, we explored expression of ring finger protein 40 (RNF40), ARID1A, and UBR7 in the same case cohort. Loss of RNF40 was significantly and profoundly correlated with loss of H2Bub1. Using genome-wide DNA methylation profiles of 230 patients with CCOC, we identified hypermethylation of RNF40 in CCOC as a likely mechanism underlying the loss of H2Bub1. Finally, we demonstrated that H2Bub1 depletion promoted cell proliferation and clonogenicity in an endometriosis cell line. Collectively, our results indicate that H2Bub1 plays a tumor-suppressive role in CCOCs and that its loss contributes to disease progression.
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Affiliation(s)
- Adam J. Ferrari
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
- Graduate Program in Cell and Molecular Biology; and
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Priyanka Rawat
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Hannah S. Rendulich
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Akshaya V. Annapragada
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yasuto Kinose
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Xiaoming Zhang
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle Devins
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Budina
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert B. Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marilyn A. Mitchell
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Janos L. Tanyi
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Mark A. Morgan
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
| | - Lauren E. Schwartz
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - T. Rinda Soong
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Victor E. Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology
- Graduate Program in Cell and Molecular Biology; and
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Yaari Z, Yang Y, Apfelbaum E, Cupo C, Settle AH, Cullen Q, Cai W, Roche KL, Levine DA, Fleisher M, Ramanathan L, Zheng M, Jagota A, Heller DA. A perception-based nanosensor platform to detect cancer biomarkers. Sci Adv 2021; 7:eabj0852. [PMID: 34797711 PMCID: PMC8604403 DOI: 10.1126/sciadv.abj0852] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/14/2021] [Indexed: 05/15/2023]
Abstract
Conventional molecular recognition elements, such as antibodies, present issues for developing biomolecular assays for use in certain technologies, such as implantable devices. Additionally, antibody development and use, especially for highly multiplexed applications, can be slow and costly. We developed a perception-based platform based on an optical nanosensor array that leverages machine learning algorithms to detect multiple protein biomarkers in biofluids. We demonstrated this platform in gynecologic cancers, often diagnosed at advanced stages, leading to low survival rates. We investigated the detection of protein biomarkers in uterine lavage samples, which are enriched with certain cancer markers compared to blood. We found that the method enables the simultaneous detection of multiple biomarkers in patient samples, with F1-scores of ~0.95 in uterine lavage samples from patients with cancer. This work demonstrates the potential of perception-based systems for the development of multiplexed sensors of disease biomarkers without the need for specific molecular recognition elements.
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Affiliation(s)
- Zvi Yaari
- Memorial Sloan Kettering Cancer Center, NY, New York 10065, USA
| | - Yoona Yang
- Lehigh University, Bethlehem, PA 18015, USA
| | - Elana Apfelbaum
- Memorial Sloan Kettering Cancer Center, NY, New York 10065, USA
| | - Christian Cupo
- Memorial Sloan Kettering Cancer Center, NY, New York 10065, USA
| | - Alex H. Settle
- Memorial Sloan Kettering Cancer Center, NY, New York 10065, USA
| | - Quinlan Cullen
- Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Winson Cai
- Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Kara Long Roche
- Memorial Sloan Kettering Cancer Center, NY, New York 10065, USA
| | | | - Martin Fleisher
- Memorial Sloan Kettering Cancer Center, NY, New York 10065, USA
| | | | - Ming Zheng
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | | | - Daniel A. Heller
- Memorial Sloan Kettering Cancer Center, NY, New York 10065, USA
- Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
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Podlesny B, Olszewska B, Yaari Z, Jena PV, Ghahramani G, Feiner R, Heller DA, Janas D. En route to single-step, two-phase purification of carbon nanotubes facilitated by high-throughput spectroscopy. Sci Rep 2021; 11:10618. [PMID: 34011997 PMCID: PMC8134628 DOI: 10.1038/s41598-021-89839-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022] Open
Abstract
Chirality purification of single-walled carbon nanotubes (SWCNTs) is desirable for applications in many fields, but general utility is currently hampered by low throughput. We discovered a method to obtain single-chirality SWCNT enrichment by the aqueous two-phase extraction (ATPE) method in a single step. To achieve appropriate resolution, a biphasic system of non-ionic tri-block copolymer surfactant is varied with an ionic surfactant. A nearly-monochiral fraction of SWCNTs can then be harvested from the top phase. We also found, via high-throughput, near-infrared excitation-emission photoluminescence spectroscopy, that the parameter space of ATPE can be mapped to probe the mechanics of the separation process. Finally, we found that optimized conditions can be used for sorting of SWCNTs wrapped with ssDNA as well. Elimination of the need for surfactant exchange and simplicity of the separation process make the approach promising for high-yield generation of purified single-chirality SWCNT preparations.
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Affiliation(s)
- Blazej Podlesny
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100, Gliwice, Poland
| | - Barbara Olszewska
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100, Gliwice, Poland
| | - Zvi Yaari
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Prakrit V Jena
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Gregory Ghahramani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Ron Feiner
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Daniel A Heller
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
| | - Dawid Janas
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100, Gliwice, Poland.
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Miller BF, Pisanic Ii TR, Margolin G, Petrykowska HM, Athamanolap P, Goncearenco A, Osei-Tutu A, Annunziata CM, Wang TH, Elnitski L. Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers. Clin Epigenetics 2020; 12:154. [PMID: 33081832 PMCID: PMC7574234 DOI: 10.1186/s13148-020-00939-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based cancer testing. Here, we describe development and validation of a methylation density binary classification method called EpiClass (available for download at https://github.com/Elnitskilab/EpiClass ) that can be used to predict and optimize the performance of methylation biomarkers, particularly in challenging, heterogeneous samples such as liquid biopsies. This approach is based upon leveraging statistical differences in single-molecule sample methylation density distributions to identify ideal thresholds for sample classification. RESULTS We developed and tested the classifier using reduced representation bisulfite sequencing (RRBS) data derived from ovarian carcinoma tissue DNA and controls. We used these data to perform in silico simulations using methylation density profiles from individual epiallelic copies of ZNF154, a genomic locus known to be recurrently methylated in numerous cancer types. From these profiles, we predicted the performance of the classifier in liquid biopsies for the detection of epithelial ovarian carcinomas (EOC). In silico analysis indicated that EpiClass could be leveraged to better identify cancer-positive liquid biopsy samples by implementing precise thresholds with respect to methylation density profiles derived from circulating cell-free DNA (cfDNA) analysis. These predictions were confirmed experimentally using DREAMing to perform digital methylation density analysis on a cohort of low volume (1-ml) plasma samples obtained from 26 EOC-positive and 41 cancer-free women. EpiClass performance was then validated in an independent cohort of 24 plasma specimens, derived from a longitudinal study of 8 EOC-positive women, and 12 plasma specimens derived from 12 healthy women, respectively, attaining a sensitivity/specificity of 91.7%/100.0%. Direct comparison of CA-125 measurements with EpiClass demonstrated that EpiClass was able to better identify EOC-positive women than standard CA-125 assessment. Finally, we used independent whole genome bisulfite sequencing (WGBS) datasets to demonstrate that EpiClass can also identify other cancer types as well or better than alternative methylation-based classifiers. CONCLUSIONS Our results indicate that assessment of intramolecular methylation density distributions calculated from cfDNA facilitates the use of methylation biomarkers for diagnostic applications. Furthermore, we demonstrated that EpiClass analysis of ZNF154 methylation was able to outperform CA-125 in the detection of etiologically diverse ovarian carcinomas, indicating broad utility of ZNF154 for use as a biomarker of ovarian cancer.
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Affiliation(s)
- Brendan F Miller
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas R Pisanic Ii
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Gennady Margolin
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hanna M Petrykowska
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander Goncearenco
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Akosua Osei-Tutu
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christina M Annunziata
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tza-Huei Wang
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Laura Elnitski
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Williams RM, Lee C, Galassi TV, Harvey JD, Leicher R, Sirenko M, Dorso MA, Shah J, Olvera N, Dao F, Levine DA, Heller DA. Noninvasive ovarian cancer biomarker detection via an optical nanosensor implant. Sci Adv 2018; 4:eaaq1090. [PMID: 29675469 PMCID: PMC5906074 DOI: 10.1126/sciadv.aaq1090] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/06/2018] [Indexed: 05/20/2023]
Abstract
Patients with high-grade serous ovarian carcinoma (HGSC) exhibit poor 5-year survival rates, which may be significantly improved by early-stage detection. The U.S. Food and Drug Administration-approved biomarkers for HGSC-CA-125 (cancer antigen 125) and HE4 (human epididymis protein 4)-do not generally appear at detectable levels in the serum until advanced stages of the disease. An implantable device placed proximal to disease sites, such as in or near the fallopian tube, ovary, uterine cavity, or peritoneal cavity, may constitute a feasible strategy to improve detection of HGSC. We engineered a prototype optical sensor composed of an antibody-functionalized carbon nanotube complex, which responds quantitatively to HE4 via modulation of the nanotube optical bandgap. The complexes measured HE4 with nanomolar sensitivity to differentiate disease from benign patient biofluids. The sensors were implanted into four models of ovarian cancer, within a semipermeable membrane, enabling the optical detection of HE4 within the live animals. We present the first in vivo optical nanosensor capable of noninvasive cancer biomarker detection in orthotopic models of disease.
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Affiliation(s)
| | - Christopher Lee
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Thomas V. Galassi
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Jackson D. Harvey
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Rachel Leicher
- Tri-Institutional Program in Chemical Biology, New York, NY 10065, USA
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Maria Sirenko
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Madeline A. Dorso
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Janki Shah
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Narciso Olvera
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
| | - Fanny Dao
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
| | - Douglas A. Levine
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
| | - Daniel A. Heller
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
- Corresponding author.
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6
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Yuan X, Yang M, Chen X, Zhang X, Sukhadia S, Musolino N, Bao H, Chen T, Xu C, Wang Q, Santoro S, Ricklin D, Hu J, Lin R, Yang W, Li Z, Qin W, Zhao A. Characterization of the first fully human anti-TEM1 scFv in models of solid tumor imaging and immunotoxin-based therapy. Cancer Immunol Immunother 2017; 66:367-378. [PMID: 27933426 PMCID: PMC11029759 DOI: 10.1007/s00262-016-1937-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/19/2016] [Indexed: 10/20/2022]
Abstract
Tumor endothelial marker 1 (TEM1) has been identified as a novel surface marker upregulated on the blood vessels and stroma in many solid tumors. We previously isolated a novel single-chain variable fragment (scFv) 78 against TEM1 from a yeast display scFv library. Here, we evaluated the potential applications of scFv78 as a tool for tumor molecular imaging, immunotoxin-based therapy and nanotherapy. Epitope mapping, three-dimensional structure docking and affinity measurements indicated that scFv78 could bind to both human and murine TEM1, with equivalent affinity, at a well-conserved conformational epitope. The rapid internalization of scFv78 and scFv78-labeled nanoparticles was triggered after specific TEM1 binding. The scFv78-saporin immunoconjugate also exerted dose-dependent cytotoxicity with high specificity to TEM1-positive cells in vitro. Finally, specific and sensitive tumor localization of scFv78 was confirmed with optical imaging in a tumor mouse model that has highly endogenous mTEM1 expression in the vasculature. Our data indicated that scFv78, the first fully human anti-TEM1 recombinant antibody, recognizes both human and mouse TEM1 and has unique and favorable features that are advantageous for the development of imaging probes or antibody-toxin conjugates for a large spectrum of human TEM1-positive solid tumors.
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Affiliation(s)
- Xiaopeng Yuan
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangdong, China
| | - Mingjuan Yang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiang Chen
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Xuhua Zhang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shrey Sukhadia
- Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA, USA
| | | | - Huijing Bao
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Tingtao Chen
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Chen Xu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Qirui Wang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen Santoro
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jia Hu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruihe Lin
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Yang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhijun Li
- Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA, USA
| | - Weijun Qin
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
| | - Aizhi Zhao
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
- University City Science Center, Room 544, 3624 Market Street, Philadelphia, PA, 19104, USA.
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