1
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Jaros RK, Fadason T, Cameron-Smith D, Golovina E, O'Sullivan JM. Comorbidity genetic risk and pathways impact SARS-CoV-2 infection outcomes. Sci Rep 2023; 13:9879. [PMID: 37336921 DOI: 10.1038/s41598-023-36900-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 06/12/2023] [Indexed: 06/21/2023] Open
Abstract
Understanding the genetic risk and mechanisms through which SARS-CoV-2 infection outcomes and comorbidities interact to impact acute and long-term sequelae is essential if we are to reduce the ongoing health burdens of the COVID-19 pandemic. Here we use a de novo protein diffusion network analysis coupled with tissue-specific gene regulatory networks, to examine putative mechanisms for associations between SARS-CoV-2 infection outcomes and comorbidities. Our approach identifies a shared genetic aetiology and molecular mechanisms for known and previously unknown comorbidities of SARS-CoV-2 infection outcomes. Additionally, genomic variants, genes and biological pathways that provide putative causal mechanisms connecting inherited risk factors for SARS-CoV-2 infection and coronary artery disease and Parkinson's disease are identified for the first time. Our findings provide an in depth understanding of genetic impacts on traits that collectively alter an individual's predisposition to acute and post-acute SARS-CoV-2 infection outcomes. The existence of complex inter-relationships between the comorbidities we identify raises the possibility of a much greater post-acute burden arising from SARS-CoV-2 infection if this genetic predisposition is realised.
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Affiliation(s)
- Rachel K Jaros
- The Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - Tayaza Fadason
- The Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1010, New Zealand
| | - David Cameron-Smith
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, 2308, Australia
| | - Evgeniia Golovina
- The Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - Justin M O'Sullivan
- The Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1010, New Zealand.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia.
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2
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Abstract
There is a large global unmet need for the development of countermeasures to combat hundreds of viruses known to cause human disease and for the establishment of a therapeutic portfolio for future pandemic preparedness. Most approved antiviral therapeutics target proteins encoded by a single virus, providing a narrow spectrum of coverage. This, combined with the slow pace and high cost of drug development, limits the scalability of this direct-acting antiviral (DAA) approach. Here, we summarize progress and challenges in the development of broad-spectrum antivirals that target either viral elements (proteins, genome structures, and lipid envelopes) or cellular proviral factors co-opted by multiple viruses via newly discovered compounds or repurposing of approved drugs. These strategies offer new means for developing therapeutics against both existing and emerging viral threats that complement DAAs.
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Affiliation(s)
- Marwah Karim
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
| | - Chieh-Wen Lo
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
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3
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Chiu W, Schepers J, Francken T, Vangeel L, Abbasi K, Jochmans D, De Jonghe S, Thibaut HJ, Thiel V, Neyts J, Laporte M, Leyssen P. Development of a robust and convenient dual-reporter high-throughput screening assay for SARS-CoV-2 antiviral drug discovery. Antiviral Res 2023; 210:105506. [PMID: 36565756 PMCID: PMC9767876 DOI: 10.1016/j.antiviral.2022.105506] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Massive efforts on both vaccine development and antiviral research were launched to combat the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We contributed, amongst others, by the development of a high-throughput screening (HTS) antiviral assay against SARS-CoV-2 using a fully automated, high-containment robot system. Here, we describe the development of this novel, convenient and phenotypic dual-reporter virus-cell-based high-content imaging assay using the A549+hACE2+TMPRSS2_mCherry reporter lung carcinoma cell line and an ancestral SARS-CoV-2_Wuhan_mNeonGreen reporter virus. Briefly, by means of clonal selection, a host cell subclone was selected that (i) efficiently supports replication of the reporter virus with high expression, upon infection, of the NeonGreen fluorescent reporter protein, (ii) that is not affected by virus-induced cytopathogenic effects and, (iii) that expresses a strong fluorescent mCherry signal in the nucleus. The selected clone matched these criteria with an infection rate on average of 75% with limited cell death. The average (R)Z'-factors of the assay plates were all >0.8, which indicates a robust assay suitable for HTS purposes. A selection of reference compounds that inhibits SARS-CoV-2 replication in vitro were used to validate this novel dual-reporter assay and confirms the data reported in the literature. This assay is a convenient and powerful tool for HTS of large compound libraries against SARS-CoV-2.
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Affiliation(s)
- Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Joost Schepers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Thibault Francken
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Kayvan Abbasi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Gaston Geenslaan 2, 3001, Leuven, Belgium
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Manon Laporte
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium.
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4
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Chen J, Na F. Organoid technology and applications in lung diseases: Models, mechanism research and therapy opportunities. Front Bioeng Biotechnol 2022; 10:1066869. [PMID: 36568297 PMCID: PMC9772457 DOI: 10.3389/fbioe.2022.1066869] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
The prevalency of lung disease has increased worldwide, especially in the aging population. It is essential to develop novel disease models, that are superior to traditional models. Organoids are three-dimensional (3D) in vitro structures that produce from self-organizing and differentiating stem cells, including pluripotent stem cells (PSCs) or adult stem cells (ASCs). They can recapitulate the in vivo cellular heterogeneity, genetic characteristics, structure, and functionality of original tissues. Drug responses of patient-derived organoids (PDOs) are consistent with that of patients, and show correlations with genetic alterations. Thus, organoids have proven to be valuable in studying the biology of disease, testing preclinical drugs and developing novel therapies. In recent years, organoids have been successfully applied in studies of a variety of lung diseases, such as lung cancer, influenza, cystic fibrosis, idiopathic pulmonary fibrosis, and the recent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. In this review, we provide an update on the generation of organoid models for these diseases and their applications in basic and translational research, highlighting these signs of progress in pathogenesis study, drug screening, personalized medicine and immunotherapy. We also discuss the current limitations and future perspectives in organoid models of lung diseases.
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5
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McAuley AJ, Jansen van Vuren P, Mohammed MU, Faheem, Goldie S, Riddell S, Gödde NJ, Styles IK, Bruce MP, Chahal S, Keating S, Blasdell KR, Tachedjian M, O'Brien CM, Singanallur NB, Viana JN, Vashi AV, Kirkpatrick CM, MacRaild CA, Shah RM, Vincan E, Athan E, Creek DJ, Trevaskis NL, Murugesan S, Kumar A, Vasan SS. Use of Human Lung Tissue Models for Screening of Drugs against SARS-CoV-2 Infection. Viruses 2022; 14. [PMID: 36366514 DOI: 10.3390/v14112417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
The repurposing of licenced drugs for use against COVID-19 is one of the most rapid ways to develop new and alternative therapeutic options to manage the ongoing pandemic. Given circa 7817 licenced compounds available from Compounds Australia that can be screened, this paper demonstrates the utility of commercially available ex vivo/3D airway and alveolar tissue models. These models are a closer representation of in vivo studies than in vitro models, but retain the benefits of rapid in vitro screening for drug efficacy. We demonstrate that several existing drugs appear to show anti-SARS-CoV-2 activity against both SARS-CoV-2 Delta and Omicron Variants of Concern in the airway model. In particular, fluvoxamine, as well as aprepitant, everolimus, and sirolimus, has virus reduction efficacy comparable to the current standard of care (remdesivir, molnupiravir, nirmatrelvir). Whilst these results are encouraging, further testing and efficacy studies are required before clinical use can be considered.
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6
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Affiliation(s)
- Jihoon Kim
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, Korea
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Korea
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands
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7
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Barbagallo D, Palermo CI, Barbagallo C, Battaglia R, Caponnetto A, Spina V, Ragusa M, Di Pietro C, Scalia G, Purrello M. Competing endogenous RNA network mediated by circ_3205 in SARS-CoV-2 infected cells. Cell Mol Life Sci 2022; 79:75. [PMID: 35039944 PMCID: PMC8763136 DOI: 10.1007/s00018-021-04119-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a new member of the Betacoronaviridae family, responsible for the recent pandemic outbreak of COVID-19. To start exploring the molecular events that follow host cell infection, we queried VirusCircBase and identified a circular RNA (circRNA) predicted to be synthesized by SARS-CoV-2, circ_3205, which we used to probe: (i) a training cohort comprised of two pools of cells from three nasopharyngeal swabs of SARS-CoV-2 infected (positive) or uninfected (negative, UCs) individuals; (ii) a validation cohort made up of 12 positive and 3 negative samples. The expression of circRNAs, miRNAs and miRNA targets was assayed through real-time PCR. CircRNA-miRNA interactions were predicted by TarpMiR, Analysis of Common Targets for circular RNAs (ACT), and STarMir tools. Enrichment of the biological processes and the list of predicted miRNA targets were retrieved from DIANA miRPath v3.0. Our results showed that the predicted SARS-CoV-2 circ_3205 was expressed only in positive samples and its amount positively correlated with that of SARS-CoV-2 Spike (S) mRNA and the viral load (r values = 0.80952 and 0.84867, Spearman's correlation test, respectively). Human (hsa) miR-298 was predicted to interact with circ_3205 by all three predictive tools. KCNMB4 and PRKCE were predicted as hsa-miR-298 targets. Interestingly, the function of both is correlated with blood coagulation and immune response. KCNMB4 and PRKCE mRNAs were upregulated in positive samples as compared to UCs (6 and 8.1-fold, p values = 0.049 and 0.02, Student's t test, respectively) and their expression positively correlated with that of circ_3205 (r values = 0.6 and 0.25, Spearman's correlation test, respectively). We propose that our results convincingly suggest that circ_3205 is a circRNA synthesized by SARS-CoV-2 upon host cell infection and that it may behave as a competitive endogenous RNA (ceRNA), sponging hsa-miR-298 and contributing to the upregulation of KCNMB4 and PRKCE mRNAs.
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Affiliation(s)
- Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy.
| | - Concetta Ilenia Palermo
- U.O.C. Laboratory Analysis Unit, A.O.U. Policlinico‑Vittorio Emanuele, 95123, Catania, Italy
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Vittoria Spina
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123, Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Guido Scalia
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123, Catania, Italy
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
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8
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White JM, Schiffer JT, Bender Ignacio RA, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ. Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses. mBio 2021; 12:e0334721. [PMID: 34933447 PMCID: PMC8689562 DOI: 10.1128/mbio.03347-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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] [Indexed: 12/15/2022] Open
Abstract
The world was unprepared for coronavirus disease 2019 (COVID-19) and remains ill-equipped for future pandemics. While unprecedented strides have been made developing vaccines and treatments for COVID-19, there remains a need for highly effective and widely available regimens for ambulatory use for novel coronaviruses and other viral pathogens. We posit that a priority is to develop pan-family drug cocktails to enhance potency, limit toxicity, and avoid drug resistance. We urge cocktail development for all viruses with pandemic potential both in the short term (<1 to 2 years) and longer term with pairs of drugs in advanced clinical testing or repurposed agents approved for other indications. While significant efforts were launched against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in vitro and in the clinic, many studies employed solo drugs and had disappointing results. Here, we review drug combination studies against SARS-CoV-2 and other viruses and introduce a model-driven approach to assess drug pairs with the highest likelihood of clinical efficacy. Where component agents lack sufficient potency, we advocate for synergistic combinations to achieve therapeutic levels. We also discuss issues that stymied therapeutic progress against COVID-19, including testing of agents with low likelihood of efficacy late in clinical disease and lack of focus on developing virologic surrogate endpoints. There is a need to expedite efficient clinical trials testing drug combinations that could be taken at home by recently infected individuals and exposed contacts as early as possible during the next pandemic, whether caused by a coronavirus or another viral pathogen. The approach herein represents a proactive plan for global viral pandemic preparedness.
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Affiliation(s)
- Judith M. White
- University of Virginia, Department of Cell Biology, Charlottesville, Virginia, USA
- University of Virginia, Department of Microbiology, Charlottesville, Virginia, USA
| | - Joshua T. Schiffer
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Rachel A. Bender Ignacio
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Shuang Xu
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute of Technology, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Stephen J. Polyak
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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9
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Kochat V, Raman AT, Landers SM, Tang M, Schulz J, Terranova C, Landry JP, Bhalla AD, Beird HC, Wu CC, Jiang Y, Mao X, Lazcano R, Gite S, Ingram DR, Yi M, Zhang J, Keung EZ, Scally CP, Roland CL, Hunt KK, Feig BW, Futreal PA, Hwu P, Wang WL, Lazar AJ, Slopis JM, Wilson-Robles H, Wiener DJ, McCutcheon IE, Wustefeld-Janssens B, Rai K, Torres KE. Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state. Acta Neuropathol 2021; 142:565-590. [PMID: 34283254 DOI: 10.1007/s00401-021-02341-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/09/2021] [Accepted: 06/22/2021] [Indexed: 02/03/2023]
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are soft tissue sarcomas that frequently harbor genetic alterations in polycomb repressor complex 2 (PRC2) components-SUZ12 and EED. Here, we show that PRC2 loss confers a dedifferentiated early neural-crest phenotype which is exclusive to PRC2-mutant MPNSTs and not a feature of neurofibromas. Neural crest phenotype in PRC2 mutant MPNSTs was validated via cross-species comparative analysis using spontaneous and transgenic MPNST models. Systematic chromatin state profiling of the MPNST cells showed extensive epigenomic reprogramming or chromatin states associated with PRC2 loss and identified gains of active enhancer states/super-enhancers on early neural crest regulators in PRC2-mutant conditions around genomic loci that harbored repressed/poised states in PRC2-WT MPNST cells. Consistently, inverse correlation between H3K27me3 loss and H3K27Ac gain was noted in MPNSTs. Epigenetic editing experiments established functional roles for enhancer gains on DLX5-a key regulator of neural crest phenotype. Consistently, blockade of enhancer activity by bromodomain inhibitors specifically suppressed this neural crest phenotype and tumor burden in PRC2-mutant PDXs. Together, these findings reveal accumulation of dedifferentiated neural crest like state in PRC2-mutant MPNSTs that can be targeted by enhancer blockade.
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Affiliation(s)
- Veena Kochat
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayush T Raman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sharon M Landers
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ming Tang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Schulz
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Terranova
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jace P Landry
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Louisiana State University School of Medicine, New Orleans, LA, USA
| | - Angela D Bhalla
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yingda Jiang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xizeng Mao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Swati Gite
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Min Yi
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily Z Keung
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher P Scally
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christina L Roland
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelly K Hunt
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barry W Feig
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology and Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Wei-Lien Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John M Slopis
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heather Wilson-Robles
- Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Dominique J Wiener
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Science, Texas A&M University, College Station, TX, USA
| | - Ian E McCutcheon
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brandan Wustefeld-Janssens
- Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Surgical Oncology, Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, USA
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.
| | - Keila E Torres
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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